Attributable lifestyle risks of fracture
Nick Tran
2024-07-27
Contribution of lifestyle risk factors to fracture risks
Study protocol
Aim: to quantify the contribution of lifestyle factors to the variability of the risk of (i) any fracture and (ii) hip fracture Design: - Data from all participants from MrOS/SOF with data on 1+ lifestyle factors (smoking, drinking, physcial activity, calcium use, protein use) - Although lifestyle factors are time varying, only factors at baseline are used (Need to be discussed) Analysis plan: - Sex- and fracture site-specific - Classification: + Smoking (Current vs. Never/past) + Drinking (High vs. No, Low, Moderate) - Might consider alternative of (High/Moderate vs. Low/No) + Physical activity (None/Low vs. Moderate/High) + Calcium uptake (No vs. Yes) + Protein (No vs. Yes) - Steps: + Cox’s model to quantify the contribution of each of these 5 lifestyle factors to fracture risk, on top of the Garvan fracture risk factors (age, BMD, falls and prior fractures) + Descriptive analysis to obtain the prevalence of each combination + Calculate Heuristic population attributable risk (PAR)
Data set-up
data = read.csv("C:\\Thach\\Research projects\\PAR for lifestyle factors\\SOF_MrOS_Nick_lifestyle_25jul24.csv")
head(data)## data ID Visit gender age race education weight height BMI no_falls
## 1 SOF 1 2 F 69 1:WHITE 9 67.3 150.5 29.71270 2
## 2 SOF 2 2 F 84 1:WHITE 10 68.4 151.8 29.68333 1
## 3 SOF 3 2 F 75 1:WHITE 12 72.7 151.0 31.88457 3
## 4 SOF 4 2 F 67 1:WHITE 12 60.6 155.1 25.19121 1
## 5 SOF 5 2 F 84 1:WHITE 17 44.7 157.0 18.13461 0
## 6 SOF 6 2 F 71 1:WHITE 15 84.1 161.6 32.20426 0
## fx50 physical hypertension copd parkinson cancer rheumatoid cvd renal
## 1 1 0 0 0 0 0 0 0 0
## 2 1 0 1 0 0 0 0 1 0
## 3 0 1 0 1 0 1 0 0 0
## 4 0 1 0 0 0 1 0 0 0
## 5 0 0 0 0 0 0 0 0 1
## 6 0 1 1 0 1 0 0 0 0
## depression diabetes MedYes DeathX fnbmd time2visit anyfx time2any hipfx
## 1 0 0 0 0 0.656 0 0 17.2238 0
## 2 0 2 0 1 0.585 0 0 6.5325 0
## 3 0 0 1 0 0.654 0 0 18.6366 0
## 4 0 0 1 0 0.842 0 0 19.7481 0
## 5 0 0 0 0 0.487 0 0 14.8720 0
## 6 0 0 0 0 0.851 0 0 19.6167 0
## time2hip death time2end Tscore Osteo smoke physical4 drink4
## 1 17.2238 0 17.223819 -1.68333333 Osteopenia Past No Low
## 2 6.5325 1 6.532512 -2.27500000 Osteopenia Never No No
## 3 18.6366 0 18.636550 -1.70000000 Osteopenia Past No Moderate
## 4 19.7481 0 19.748118 -0.13333333 Normal Never No No
## 5 14.8720 0 14.872005 -3.09166667 Osteoporosis Never No No
## 6 19.6167 0 19.616701 -0.05833333 Normal Never No No
## coffee4 calcium2 protein2
## 1 Low 1787 210
## 2 Low 6727 336
## 3 Moderate 5316 448
## 4 Moderate 8666 484
## 5 Moderate 5216 317
## 6 Moderate 1956 308Data management
library(tidyverse)## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.3 ✔ readr 2.1.4
## ✔ forcats 1.0.0 ✔ stringr 1.5.0
## ✔ ggplot2 3.4.3 ✔ tibble 3.2.1
## ✔ lubridate 1.9.3 ✔ tidyr 1.3.0
## ✔ purrr 1.0.2
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorsdata = data %>% mutate(race.n = case_when(race == "1:WHITE" ~ "1_White",
race == "2:AFRICAN AMERICAN" ~ "2_African",
race == "3:ASIAN" ~ "3_Asian",
race == "4:NATIVE HAWIIAN OR OTHER PACIFIC ISLANDER" | race == "5:AMERICAN INDIAN OR ALASKAN NATIVE" | race == "6:MULTI RACIAL" | race == "7:UNKNOWN" ~ "0_Other"))
data = data %>% mutate(age_bin = case_when(age < 75 ~ "1.Age< 75",
age >= 75 ~ "2.Age>= 75"))
data = data %>% mutate(bmd_bin = case_when(Tscore > -2.5 ~ "1.BMD> -2.5",
Tscore <= -2.5 ~ "2.BMD<= -2.5"))
data = data %>% mutate(fall_bin = case_when(no_falls == 0 ~ "1.No falls",
no_falls > 0 ~ "2.Falls 1+"))
data = data %>% mutate(fx50_bin = case_when(fx50 == 0 ~ "1.No fx",
fx50 > 0 ~ "2.Fx 1+"))
data = data %>% mutate(smoke_bin = case_when(smoke == "Never" | smoke == "Past" ~ "1.No/past smoking",
smoke == "Current" ~ "2.Current smoking"))
data = data %>% mutate(drink_bin = case_when(drink4 == "No" | drink4 == "Low" | drink4 == "Moderate" ~ "1.Less drinking",
drink4 == "High" ~ "2.Excessive drinking"))
data = data %>% mutate(activity_bin = case_when(physical4 == "Moderate" | physical4 == "High" ~ "1.Proactive",
physical4 == "No" | physical4 == "Low" ~ "2.Less active"))
data = data %>% mutate(calci_bin = case_when(calcium2 >= 1000 ~ "1.Sufficient Calcium",
calcium2 < 1000 ~ "2.Insufficient Calcium"))1. MEN
1.1 Descriptive analysis
men = subset(data, gender == "M")
library(table1)##
## Attaching package: 'table1'## The following objects are masked from 'package:base':
##
## units, units<-table1(~ age + as.factor(age_bin) + race + fnbmd + Tscore + as.factor(bmd_bin) + as.factor(no_falls) + as.factor(fall_bin) + as.factor(fx50) + as.factor(fx50_bin) + as.factor(smoke) + as.factor(smoke_bin) + drink4 + as.factor(drink_bin) + physical4 + as.factor(activity_bin) + calcium2 + as.factor(calci_bin) + protein2 + as.factor(education) + BMI + as.factor(cvd) + as.factor(hypertension) + as.factor(copd) + as.factor(diabetes) + as.factor(cancer) + as.factor(renal) + as.factor(parkinson) + as.factor(depression) + as.factor(rheumatoid) + as.factor(death) | anyfx, data = men, render.continuous = c(. = "Median [Q1, Q3]"))## Warning in table1.formula(~age + as.factor(age_bin) + race + fnbmd + Tscore + :
## Terms to the right of '|' in formula 'x' define table columns and are expected
## to be factors with meaningful labels.| 0 (N=4908) |
1 (N=1084) |
Overall (N=5992) |
|
|---|---|---|---|
| age | |||
| Median [Q1, Q3] | 73.0 [69.0, 78.0] | 74.0 [70.0, 78.0] | 73.0 [69.0, 78.0] |
| as.factor(age_bin) | |||
| 1.Age< 75 | 2909 (59.3%) | 567 (52.3%) | 3476 (58.0%) |
| 2.Age>= 75 | 1999 (40.7%) | 517 (47.7%) | 2516 (42.0%) |
| race | |||
| 1:WHITE | 4368 (89.0%) | 1016 (93.7%) | 5384 (89.9%) |
| 2:AFRICAN AMERICAN | 226 (4.6%) | 18 (1.7%) | 244 (4.1%) |
| 3:ASIAN | 166 (3.4%) | 26 (2.4%) | 192 (3.2%) |
| 4:NATIVE HAWIIAN OR OTHER PACIFIC ISLANDER | 6 (0.1%) | 1 (0.1%) | 7 (0.1%) |
| 5:AMERICAN INDIAN OR ALASKAN NATIVE | 6 (0.1%) | 1 (0.1%) | 7 (0.1%) |
| 6:MULTI RACIAL | 58 (1.2%) | 3 (0.3%) | 61 (1.0%) |
| 7:UNKNOWN | 78 (1.6%) | 19 (1.8%) | 97 (1.6%) |
| fnbmd | |||
| Median [Q1, Q3] | 0.783 [0.707, 0.870] | 0.728 [0.652, 0.812] | 0.774 [0.696, 0.860] |
| Tscore | |||
| Median [Q1, Q3] | -1.10 [-1.66, -0.466] | -1.50 [-2.06, -0.894] | -1.17 [-1.73, -0.539] |
| as.factor(bmd_bin) | |||
| 1.BMD> -2.5 | 4721 (96.2%) | 976 (90.0%) | 5697 (95.1%) |
| 2.BMD<= -2.5 | 187 (3.8%) | 108 (10.0%) | 295 (4.9%) |
| as.factor(no_falls) | |||
| 0 | 3924 (80.0%) | 801 (73.9%) | 4725 (78.9%) |
| 1 | 984 (20.0%) | 283 (26.1%) | 1267 (21.1%) |
| as.factor(fall_bin) | |||
| 1.No falls | 3924 (80.0%) | 801 (73.9%) | 4725 (78.9%) |
| 2.Falls 1+ | 984 (20.0%) | 283 (26.1%) | 1267 (21.1%) |
| as.factor(fx50) | |||
| 0 | 4141 (84.4%) | 820 (75.6%) | 4961 (82.8%) |
| 1 | 595 (12.1%) | 184 (17.0%) | 779 (13.0%) |
| 2 | 133 (2.7%) | 59 (5.4%) | 192 (3.2%) |
| 3 | 31 (0.6%) | 12 (1.1%) | 43 (0.7%) |
| 4 | 7 (0.1%) | 6 (0.6%) | 13 (0.2%) |
| 5 | 0 (0%) | 2 (0.2%) | 2 (0.0%) |
| 6 | 1 (0.0%) | 1 (0.1%) | 2 (0.0%) |
| as.factor(fx50_bin) | |||
| 1.No fx | 4141 (84.4%) | 820 (75.6%) | 4961 (82.8%) |
| 2.Fx 1+ | 767 (15.6%) | 264 (24.4%) | 1031 (17.2%) |
| as.factor(smoke) | |||
| Current | 162 (3.3%) | 44 (4.1%) | 206 (3.4%) |
| Never | 1837 (37.4%) | 412 (38.0%) | 2249 (37.5%) |
| Past | 2909 (59.3%) | 628 (57.9%) | 3537 (59.0%) |
| as.factor(smoke_bin) | |||
| 1.No/past smoking | 4746 (96.7%) | 1040 (95.9%) | 5786 (96.6%) |
| 2.Current smoking | 162 (3.3%) | 44 (4.1%) | 206 (3.4%) |
| drink4 | |||
| High | 1578 (32.2%) | 372 (34.3%) | 1950 (32.5%) |
| Low | 726 (14.8%) | 155 (14.3%) | 881 (14.7%) |
| Moderate | 393 (8.0%) | 70 (6.5%) | 463 (7.7%) |
| No | 2211 (45.0%) | 487 (44.9%) | 2698 (45.0%) |
| as.factor(drink_bin) | |||
| 1.Less drinking | 3330 (67.8%) | 712 (65.7%) | 4042 (67.5%) |
| 2.Excessive drinking | 1578 (32.2%) | 372 (34.3%) | 1950 (32.5%) |
| physical4 | |||
| High | 695 (14.2%) | 171 (15.8%) | 866 (14.5%) |
| Low | 1361 (27.7%) | 281 (25.9%) | 1642 (27.4%) |
| Moderate | 558 (11.4%) | 121 (11.2%) | 679 (11.3%) |
| No | 2294 (46.7%) | 511 (47.1%) | 2805 (46.8%) |
| as.factor(activity_bin) | |||
| 1.Proactive | 1253 (25.5%) | 292 (26.9%) | 1545 (25.8%) |
| 2.Less active | 3655 (74.5%) | 792 (73.1%) | 4447 (74.2%) |
| calcium2 | |||
| Median [Q1, Q3] | 730 [523, 991] | 720 [515, 993] | 728 [522, 991] |
| as.factor(calci_bin) | |||
| 1.Sufficient Calcium | 1194 (24.3%) | 264 (24.4%) | 1458 (24.3%) |
| 2.Insufficient Calcium | 3714 (75.7%) | 820 (75.6%) | 4534 (75.7%) |
| protein2 | |||
| Median [Q1, Q3] | 60.2 [45.8, 78.7] | 59.5 [45.2, 76.7] | 60.2 [45.7, 78.2] |
| as.factor(education) | |||
| 1 | 13 (0.3%) | 3 (0.3%) | 16 (0.3%) |
| 2 | 82 (1.7%) | 15 (1.4%) | 97 (1.6%) |
| 3 | 243 (5.0%) | 35 (3.2%) | 278 (4.6%) |
| 4 | 860 (17.5%) | 176 (16.2%) | 1036 (17.3%) |
| 5 | 1132 (23.1%) | 245 (22.6%) | 1377 (23.0%) |
| 6 | 874 (17.8%) | 220 (20.3%) | 1094 (18.3%) |
| 7 | 507 (10.3%) | 126 (11.6%) | 633 (10.6%) |
| 8 | 1197 (24.4%) | 264 (24.4%) | 1461 (24.4%) |
| BMI | |||
| Median [Q1, Q3] | 26.9 [24.9, 29.5] | 26.6 [24.4, 29.3] | 26.9 [24.8, 29.5] |
| Missing | 6 (0.1%) | 1 (0.1%) | 7 (0.1%) |
| as.factor(cvd) | |||
| 0 | 3889 (79.2%) | 852 (78.6%) | 4741 (79.1%) |
| 1 | 1019 (20.8%) | 232 (21.4%) | 1251 (20.9%) |
| as.factor(hypertension) | |||
| 0 | 2804 (57.1%) | 607 (56.0%) | 3411 (56.9%) |
| 1 | 2104 (42.9%) | 477 (44.0%) | 2581 (43.1%) |
| as.factor(copd) | |||
| 0 | 4393 (89.5%) | 959 (88.5%) | 5352 (89.3%) |
| 1 | 515 (10.5%) | 125 (11.5%) | 640 (10.7%) |
| as.factor(diabetes) | |||
| 0 | 4370 (89.0%) | 969 (89.4%) | 5339 (89.1%) |
| 1 | 538 (11.0%) | 115 (10.6%) | 653 (10.9%) |
| as.factor(cancer) | |||
| 0 | 4011 (81.7%) | 889 (82.0%) | 4900 (81.8%) |
| 1 | 897 (18.3%) | 195 (18.0%) | 1092 (18.2%) |
| as.factor(renal) | |||
| 0 | 2821 (57.5%) | 725 (66.9%) | 3546 (59.2%) |
| 1 | 436 (8.9%) | 117 (10.8%) | 553 (9.2%) |
| Missing | 1651 (33.6%) | 242 (22.3%) | 1893 (31.6%) |
| as.factor(parkinson) | |||
| 0 | 4253 (86.7%) | 950 (87.6%) | 5203 (86.8%) |
| 1 | 655 (13.3%) | 134 (12.4%) | 789 (13.2%) |
| as.factor(depression) | |||
| 0 | 3099 (63.1%) | 789 (72.8%) | 3888 (64.9%) |
| 1 | 158 (3.2%) | 53 (4.9%) | 211 (3.5%) |
| Missing | 1651 (33.6%) | 242 (22.3%) | 1893 (31.6%) |
| as.factor(rheumatoid) | |||
| 0 | 2573 (52.4%) | 574 (53.0%) | 3147 (52.5%) |
| 1 | 2335 (47.6%) | 510 (47.0%) | 2845 (47.5%) |
| as.factor(death) | |||
| 0 | 1990 (40.5%) | 391 (36.1%) | 2381 (39.7%) |
| 1 | 2918 (59.5%) | 693 (63.9%) | 3611 (60.3%) |
1.2 Smoking
1.2.1 Data management
men = men %>% mutate(group = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 32))
men = men %>% mutate(fu_anyfx = case_when(anyfx == 0 ~ time2end,
anyfx == 1 ~ time2any))
men = men %>% mutate(fu_hipfx = case_when(hipfx == 0 ~ time2end,
hipfx == 1 ~ time2hip))
men = men %>% mutate(protein_bin = case_when(protein2 >= 78.2 ~ "1.Sufficient protein",
protein2 < 78.2 ~ "2.Insufficient protein"))1.2.2 Prevalences
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + smoke_bin + drink_bin + activity_bin + as.factor(group) | anyfx, data = men, render.continuous = c(. = "Median [Q1, Q3]"))## Warning in table1.formula(~age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin
## + : Terms to the right of '|' in formula 'x' define table columns and are
## expected to be factors with meaningful labels.| 0 (N=4908) |
1 (N=1084) |
Overall (N=5992) |
|
|---|---|---|---|
| age | |||
| Median [Q1, Q3] | 73.0 [69.0, 78.0] | 74.0 [70.0, 78.0] | 73.0 [69.0, 78.0] |
| age_bin | |||
| 1.Age< 75 | 2909 (59.3%) | 567 (52.3%) | 3476 (58.0%) |
| 2.Age>= 75 | 1999 (40.7%) | 517 (47.7%) | 2516 (42.0%) |
| fnbmd | |||
| Median [Q1, Q3] | 0.783 [0.707, 0.870] | 0.728 [0.652, 0.812] | 0.774 [0.696, 0.860] |
| Tscore | |||
| Median [Q1, Q3] | -1.10 [-1.66, -0.466] | -1.50 [-2.06, -0.894] | -1.17 [-1.73, -0.539] |
| bmd_bin | |||
| 1.BMD> -2.5 | 4721 (96.2%) | 976 (90.0%) | 5697 (95.1%) |
| 2.BMD<= -2.5 | 187 (3.8%) | 108 (10.0%) | 295 (4.9%) |
| fall_bin | |||
| 1.No falls | 3924 (80.0%) | 801 (73.9%) | 4725 (78.9%) |
| 2.Falls 1+ | 984 (20.0%) | 283 (26.1%) | 1267 (21.1%) |
| fx50_bin | |||
| 1.No fx | 4141 (84.4%) | 820 (75.6%) | 4961 (82.8%) |
| 2.Fx 1+ | 767 (15.6%) | 264 (24.4%) | 1031 (17.2%) |
| smoke_bin | |||
| 1.No/past smoking | 4746 (96.7%) | 1040 (95.9%) | 5786 (96.6%) |
| 2.Current smoking | 162 (3.3%) | 44 (4.1%) | 206 (3.4%) |
| drink_bin | |||
| 1.Less drinking | 3330 (67.8%) | 712 (65.7%) | 4042 (67.5%) |
| 2.Excessive drinking | 1578 (32.2%) | 372 (34.3%) | 1950 (32.5%) |
| activity_bin | |||
| 1.Proactive | 1253 (25.5%) | 292 (26.9%) | 1545 (25.8%) |
| 2.Less active | 3655 (74.5%) | 792 (73.1%) | 4447 (74.2%) |
| as.factor(group) | |||
| 1 | 1956 (39.9%) | 302 (27.9%) | 2258 (37.7%) |
| 2 | 93 (1.9%) | 20 (1.8%) | 113 (1.9%) |
| 3 | 291 (5.9%) | 87 (8.0%) | 378 (6.3%) |
| 4 | 374 (7.6%) | 82 (7.6%) | 456 (7.6%) |
| 5 | 43 (0.9%) | 15 (1.4%) | 58 (1.0%) |
| 6 | 1200 (24.4%) | 249 (23.0%) | 1449 (24.2%) |
| 7 | 67 (1.4%) | 32 (3.0%) | 99 (1.7%) |
| 8 | 346 (7.0%) | 89 (8.2%) | 435 (7.3%) |
| 9 | 202 (4.1%) | 58 (5.4%) | 260 (4.3%) |
| 10 | 16 (0.3%) | 3 (0.3%) | 19 (0.3%) |
| 11 | 5 (0.1%) | 5 (0.5%) | 10 (0.2%) |
| 12 | 8 (0.2%) | 6 (0.6%) | 14 (0.2%) |
| 13 | 2 (0.0%) | 3 (0.3%) | 5 (0.1%) |
| 14 | 96 (2.0%) | 32 (3.0%) | 128 (2.1%) |
| 15 | 12 (0.2%) | 3 (0.3%) | 15 (0.3%) |
| 16 | 19 (0.4%) | 5 (0.5%) | 24 (0.4%) |
| 17 | 17 (0.3%) | 10 (0.9%) | 27 (0.5%) |
| 18 | 19 (0.4%) | 20 (1.8%) | 39 (0.7%) |
| 19 | 6 (0.1%) | 0 (0%) | 6 (0.1%) |
| 20 | 104 (2.1%) | 39 (3.6%) | 143 (2.4%) |
| 21 | 2 (0.0%) | 5 (0.5%) | 7 (0.1%) |
| 22 | 2 (0.0%) | 0 (0%) | 2 (0.0%) |
| 23 | 3 (0.1%) | 3 (0.3%) | 6 (0.1%) |
| 24 | 1 (0.0%) | 2 (0.2%) | 3 (0.1%) |
| 26 | 6 (0.1%) | 2 (0.2%) | 8 (0.1%) |
| 27 | 15 (0.3%) | 11 (1.0%) | 26 (0.4%) |
| 28 | 1 (0.0%) | 0 (0%) | 1 (0.0%) |
| 29 | 0 (0%) | 1 (0.1%) | 1 (0.0%) |
| 30 | 2 (0.0%) | 0 (0%) | 2 (0.0%) |
1.2.3 Association for any fracture
library(survival)
smoke.age.m = coxph(Surv(fu_anyfx, anyfx) ~ age + smoke_bin, data = men)
summary(smoke.age.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ age + smoke_bin, data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age 0.074427 1.077267 0.005392 13.802 < 2e-16 ***
## smoke_bin2.Current smoking 0.577183 1.781014 0.155247 3.718 0.000201 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age 1.077 0.9283 1.066 1.089
## smoke_bin2.Current smoking 1.781 0.5615 1.314 2.414
##
## Concordance= 0.617 (se = 0.009 )
## Likelihood ratio test= 185.6 on 2 df, p=<2e-16
## Wald test = 194.3 on 2 df, p=<2e-16
## Score (logrank) test = 198.2 on 2 df, p=<2e-16all.m = coxph(Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin, data = men)
summary(all.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin, data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.61650 1.85244 0.06317 9.759 < 2e-16 ***
## bmd_bin2.BMD<= -2.5 0.94617 2.57582 0.10295 9.191 < 2e-16 ***
## fall_bin2.Falls 1+ 0.33488 1.39777 0.06980 4.798 1.61e-06 ***
## fx50_bin2.Fx 1+ 0.47693 1.61112 0.07144 6.676 2.45e-11 ***
## smoke_bin2.Current smoking 0.51805 1.67875 0.15511 3.340 0.000838 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.852 0.5398 1.637 2.097
## bmd_bin2.BMD<= -2.5 2.576 0.3882 2.105 3.152
## fall_bin2.Falls 1+ 1.398 0.7154 1.219 1.603
## fx50_bin2.Fx 1+ 1.611 0.6207 1.401 1.853
## smoke_bin2.Current smoking 1.679 0.5957 1.239 2.275
##
## Concordance= 0.636 (se = 0.009 )
## Likelihood ratio test= 266.2 on 5 df, p=<2e-16
## Wald test = 306.6 on 5 df, p=<2e-16
## Score (logrank) test = 326.5 on 5 df, p=<2e-16options(digits = 8)
smoke.m = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(group), data = men)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 18,21,26,28 ; coefficient may be infinite.summary(smoke.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(group), data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 5.0352e-01 1.6545e+00 2.3097e-01 2.1801 0.0292529 *
## as.factor(group)3 5.8961e-01 1.8033e+00 1.2169e-01 4.8451 1.265e-06 ***
## as.factor(group)4 3.5916e-01 1.4321e+00 1.2454e-01 2.8839 0.0039279 **
## as.factor(group)5 7.9696e-01 2.2188e+00 2.6457e-01 3.0123 0.0025930 **
## as.factor(group)6 6.6358e-01 1.9417e+00 8.6417e-02 7.6788 1.606e-14 ***
## as.factor(group)7 1.5168e+00 4.5574e+00 1.8647e-01 8.1339 4.158e-16 ***
## as.factor(group)8 9.6142e-01 2.6154e+00 1.2141e-01 7.9189 2.397e-15 ***
## as.factor(group)9 1.0016e+00 2.7225e+00 1.4393e-01 6.9584 3.441e-12 ***
## as.factor(group)10 7.8152e-01 2.1848e+00 5.8046e-01 1.3464 0.1781787
## as.factor(group)11 1.4151e+00 4.1170e+00 4.5092e-01 3.1383 0.0016993 **
## as.factor(group)12 1.4212e+00 4.1423e+00 4.1230e-01 3.4471 0.0005666 ***
## as.factor(group)13 2.3621e+00 1.0613e+01 5.8108e-01 4.0649 4.804e-05 ***
## as.factor(group)14 7.6271e-01 2.1441e+00 1.8591e-01 4.1025 4.087e-05 ***
## as.factor(group)15 5.8929e-01 1.8027e+00 5.8023e-01 1.0156 0.3098193
## as.factor(group)16 7.4046e-01 2.0969e+00 4.5100e-01 1.6418 0.1006285
## as.factor(group)17 1.9146e+00 6.7844e+00 3.2216e-01 5.9431 2.796e-09 ***
## as.factor(group)18 2.2235e+00 9.2396e+00 2.3197e-01 9.5852 < 2.2e-16 ***
## as.factor(group)19 -1.2066e+01 5.7542e-06 8.7033e+02 -0.0139 0.9889391
## as.factor(group)20 1.4169e+00 4.1243e+00 1.7097e-01 8.2873 < 2.2e-16 ***
## as.factor(group)21 2.4384e+00 1.1455e+01 4.5154e-01 5.4002 6.656e-08 ***
## as.factor(group)22 -1.2042e+01 5.8892e-06 2.5157e+03 -0.0048 0.9961806
## as.factor(group)23 1.6817e+00 5.3747e+00 5.8041e-01 2.8974 0.0037621 **
## as.factor(group)24 3.0803e+00 2.1764e+01 7.1032e-01 4.3365 1.448e-05 ***
## as.factor(group)26 1.4848e+00 4.4139e+00 7.0992e-01 2.0915 0.0364866 *
## as.factor(group)27 2.3817e+00 1.0823e+01 3.0805e-01 7.7316 1.062e-14 ***
## as.factor(group)28 -1.2064e+01 5.7617e-06 1.7650e+03 -0.0068 0.9945463
## as.factor(group)29 4.9725e+00 1.4439e+02 1.0081e+00 4.9327 8.112e-07 ***
## as.factor(group)30 -1.2048e+01 5.8578e-06 1.9495e+03 -0.0062 0.9950691
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group)2 1.6545e+00 6.0440e-01 1.05215 2.6018
## as.factor(group)3 1.8033e+00 5.5454e-01 1.42063 2.2890
## as.factor(group)4 1.4321e+00 6.9826e-01 1.12195 1.8281
## as.factor(group)5 2.2188e+00 4.5070e-01 1.32103 3.7266
## as.factor(group)6 1.9417e+00 5.1500e-01 1.63920 2.3001
## as.factor(group)7 4.5574e+00 2.1942e-01 3.16223 6.5682
## as.factor(group)8 2.6154e+00 3.8235e-01 2.06156 3.3181
## as.factor(group)9 2.7225e+00 3.6731e-01 2.05330 3.6098
## as.factor(group)10 2.1848e+00 4.5771e-01 0.70036 6.8155
## as.factor(group)11 4.1170e+00 2.4289e-01 1.70121 9.9634
## as.factor(group)12 4.1423e+00 2.4141e-01 1.84623 9.2937
## as.factor(group)13 1.0613e+01 9.4227e-02 3.39790 33.1468
## as.factor(group)14 2.1441e+00 4.6640e-01 1.48933 3.0867
## as.factor(group)15 1.8027e+00 5.5472e-01 0.57813 5.6211
## as.factor(group)16 2.0969e+00 4.7690e-01 0.86633 5.0754
## as.factor(group)17 6.7844e+00 1.4740e-01 3.60821 12.7566
## as.factor(group)18 9.2396e+00 1.0823e-01 5.86408 14.5583
## as.factor(group)19 5.7542e-06 1.7379e+05 0.00000 Inf
## as.factor(group)20 4.1243e+00 2.4246e-01 2.95000 5.7662
## as.factor(group)21 1.1455e+01 8.7298e-02 4.72762 27.7554
## as.factor(group)22 5.8892e-06 1.6980e+05 0.00000 Inf
## as.factor(group)23 5.3747e+00 1.8606e-01 1.72310 16.7648
## as.factor(group)24 2.1764e+01 4.5947e-02 5.40905 87.5731
## as.factor(group)26 4.4139e+00 2.2656e-01 1.09785 17.7463
## as.factor(group)27 1.0823e+01 9.2393e-02 5.91765 19.7957
## as.factor(group)28 5.7617e-06 1.7356e+05 0.00000 Inf
## as.factor(group)29 1.4439e+02 6.9259e-03 20.01937 1041.3516
## as.factor(group)30 5.8578e-06 1.7071e+05 0.00000 Inf
##
## Concordance= 0.637 (se = 0.009 )
## Likelihood ratio test= 286.77 on 28 df, p=<2e-16
## Wald test = 349.07 on 28 df, p=<2e-16
## Score (logrank) test = 478.6 on 28 df, p=<2e-161.2.4 Association for hip fracture
smoke.hip.age.m = coxph(Surv(fu_hipfx, hipfx) ~ age + smoke_bin, data = men)
summary(smoke.hip.age.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ age + smoke_bin, data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age 0.137691 1.147621 0.011253 12.236 < 2.2e-16 ***
## smoke_bin2.Current smoking 1.014170 2.757074 0.299429 3.387 0.0007066 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age 1.1476 0.87137 1.1226 1.1732
## smoke_bin2.Current smoking 2.7571 0.36270 1.5331 4.9582
##
## Concordance= 0.727 (se = 0.016 )
## Likelihood ratio test= 145.19 on 2 df, p=<2e-16
## Wald test = 152.41 on 2 df, p=<2e-16
## Score (logrank) test = 161.88 on 2 df, p=<2e-16all.hip.m = coxph(Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin, data = men)
summary(all.hip.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin, data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 1.14499 3.14239 0.13936 8.2163 < 2e-16 ***
## bmd_bin2.BMD<= -2.5 1.56412 4.77846 0.16806 9.3070 < 2e-16 ***
## fall_bin2.Falls 1+ 0.32338 1.38179 0.14765 2.1902 0.02851 *
## fx50_bin2.Fx 1+ 0.26406 1.30221 0.15705 1.6814 0.09268 .
## smoke_bin2.Current smoking 0.86266 2.36945 0.29981 2.8774 0.00401 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 3.1424 0.31823 2.3913 4.1293
## bmd_bin2.BMD<= -2.5 4.7785 0.20927 3.4375 6.6426
## fall_bin2.Falls 1+ 1.3818 0.72370 1.0346 1.8455
## fx50_bin2.Fx 1+ 1.3022 0.76793 0.9572 1.7716
## smoke_bin2.Current smoking 2.3694 0.42204 1.3166 4.2642
##
## Concordance= 0.731 (se = 0.017 )
## Likelihood ratio test= 168.49 on 5 df, p=<2e-16
## Wald test = 203.79 on 5 df, p=<2e-16
## Score (logrank) test = 255.61 on 5 df, p=<2e-16options(digits = 8)
smoke.hip.m = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(group), data = men)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 15,18,21,23,26,28 ; coefficient may be
## infinite.summary(smoke.hip.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(group), data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 1.1418e+00 3.1324e+00 4.3272e-01 2.6387 0.008324 **
## as.factor(group)3 1.0599e-01 1.1118e+00 3.6266e-01 0.2922 0.770099
## as.factor(group)4 1.5739e-01 1.1704e+00 3.3366e-01 0.4717 0.637139
## as.factor(group)5 1.5099e+00 4.5261e+00 4.6955e-01 3.2156 0.001302 **
## as.factor(group)6 1.0618e+00 2.8916e+00 1.9574e-01 5.4244 5.813e-08 ***
## as.factor(group)7 2.6849e+00 1.4657e+01 2.8298e-01 9.4880 < 2.2e-16 ***
## as.factor(group)8 1.5359e+00 4.6456e+00 2.4769e-01 6.2010 5.610e-10 ***
## as.factor(group)9 1.5914e+00 4.9105e+00 2.8294e-01 5.6245 1.860e-08 ***
## as.factor(group)10 1.6234e+00 5.0703e+00 1.0109e+00 1.6060 0.108285
## as.factor(group)11 2.6143e+00 1.3657e+01 5.9478e-01 4.3953 1.106e-05 ***
## as.factor(group)12 2.0361e+00 7.6606e+00 7.2143e-01 2.8223 0.004768 **
## as.factor(group)13 2.7783e+00 1.6091e+01 1.0106e+00 2.7490 0.005977 **
## as.factor(group)14 -3.0201e-01 7.3933e-01 7.2140e-01 -0.4186 0.675476
## as.factor(group)15 1.3098e+00 3.7052e+00 1.0102e+00 1.2965 0.194797
## as.factor(group)16 -1.3185e+01 1.8777e-06 1.1403e+03 -0.0116 0.990775
## as.factor(group)17 2.9850e+00 1.9786e+01 4.7136e-01 6.3326 2.411e-10 ***
## as.factor(group)18 2.8476e+00 1.7247e+01 4.0567e-01 7.0196 2.226e-12 ***
## as.factor(group)19 -1.3236e+01 1.7857e-06 4.3692e+03 -0.0030 0.997583
## as.factor(group)20 1.8473e+00 6.3425e+00 3.4860e-01 5.2992 1.163e-07 ***
## as.factor(group)21 2.1728e+00 8.7830e+00 1.0102e+00 2.1508 0.031491 *
## as.factor(group)22 -1.3625e+01 1.2100e-06 1.5209e+04 -0.0009 0.999285
## as.factor(group)23 3.0546e+00 2.1214e+01 7.2195e-01 4.2311 2.325e-05 ***
## as.factor(group)24 -1.3172e+01 1.9022e-06 4.1811e+03 -0.0032 0.997486
## as.factor(group)26 2.5838e+00 1.3247e+01 1.0119e+00 2.5533 0.010671 *
## as.factor(group)27 2.7889e+00 1.6262e+01 5.9678e-01 4.6731 2.966e-06 ***
## as.factor(group)28 -1.3196e+01 1.8576e-06 8.8679e+03 -0.0015 0.998813
## as.factor(group)29 7.0361e+00 1.1370e+03 1.0446e+00 6.7359 1.629e-11 ***
## as.factor(group)30 -1.3374e+01 1.5554e-06 1.0780e+04 -0.0012 0.999010
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group)2 3.1324e+00 3.1924e-01 1.34136 7.3149
## as.factor(group)3 1.1118e+00 8.9944e-01 0.54618 2.2632
## as.factor(group)4 1.1704e+00 8.5437e-01 0.60862 2.2509
## as.factor(group)5 4.5261e+00 2.2094e-01 1.80322 11.3608
## as.factor(group)6 2.8916e+00 3.4583e-01 1.97022 4.2437
## as.factor(group)7 1.4657e+01 6.8229e-02 8.41708 25.5212
## as.factor(group)8 4.6456e+00 2.1526e-01 2.85896 7.5488
## as.factor(group)9 4.9105e+00 2.0365e-01 2.82026 8.5499
## as.factor(group)10 5.0703e+00 1.9723e-01 0.69917 36.7694
## as.factor(group)11 1.3657e+01 7.3221e-02 4.25682 43.8172
## as.factor(group)12 7.6606e+00 1.3054e-01 1.86284 31.5027
## as.factor(group)13 1.6091e+01 6.2146e-02 2.21991 116.6384
## as.factor(group)14 7.3933e-01 1.3526e+00 0.17980 3.0401
## as.factor(group)15 3.7052e+00 2.6989e-01 0.51160 26.8353
## as.factor(group)16 1.8777e-06 5.3256e+05 0.00000 Inf
## as.factor(group)17 1.9786e+01 5.0542e-02 7.85457 49.8396
## as.factor(group)18 1.7247e+01 5.7980e-02 7.78769 38.1969
## as.factor(group)19 1.7857e-06 5.6001e+05 0.00000 Inf
## as.factor(group)20 6.3425e+00 1.5767e-01 3.20284 12.5600
## as.factor(group)21 8.7830e+00 1.1386e-01 1.21264 63.6143
## as.factor(group)22 1.2100e-06 8.2642e+05 0.00000 Inf
## as.factor(group)23 2.1214e+01 4.7139e-02 5.15342 87.3249
## as.factor(group)24 1.9022e-06 5.2570e+05 0.00000 Inf
## as.factor(group)26 1.3247e+01 7.5488e-02 1.82289 96.2678
## as.factor(group)27 1.6262e+01 6.1491e-02 5.04897 52.3805
## as.factor(group)28 1.8576e-06 5.3832e+05 0.00000 Inf
## as.factor(group)29 1.1370e+03 8.7954e-04 146.76054 8807.9791
## as.factor(group)30 1.5554e-06 6.4292e+05 0.00000 Inf
##
## Concordance= 0.735 (se = 0.017 )
## Likelihood ratio test= 188.39 on 28 df, p=<2e-16
## Wald test = 232.86 on 28 df, p=<2e-16
## Score (logrank) test = 686.98 on 28 df, p=<2e-161.2 Try different classification of smoking (none vs. ever/current)
1.2.1 Data management
men = men %>% mutate(smoke_bin = case_when(smoke == "Never"~ "1.No/past smoking",
smoke == "Current" | smoke == "Past" ~ "2.Current smoking"))
men = men %>% mutate(group = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 32))
men = men %>% mutate(fu_anyfx = case_when(anyfx == 0 ~ time2end,
anyfx == 1 ~ time2any))
men = men %>% mutate(fu_hipfx = case_when(hipfx == 0 ~ time2end,
hipfx == 1 ~ time2hip))1.2.2 Prevalences
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + smoke_bin + drink_bin + activity_bin + as.factor(group), data = men, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=5992) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 73.0 [69.0, 78.0] |
| age_bin | |
| 1.Age< 75 | 3476 (58.0%) |
| 2.Age>= 75 | 2516 (42.0%) |
| fnbmd | |
| Median [Q1, Q3] | 0.774 [0.696, 0.860] |
| Tscore | |
| Median [Q1, Q3] | -1.17 [-1.73, -0.539] |
| bmd_bin | |
| 1.BMD> -2.5 | 5697 (95.1%) |
| 2.BMD<= -2.5 | 295 (4.9%) |
| fall_bin | |
| 1.No falls | 4725 (78.9%) |
| 2.Falls 1+ | 1267 (21.1%) |
| fx50_bin | |
| 1.No fx | 4961 (82.8%) |
| 2.Fx 1+ | 1031 (17.2%) |
| smoke_bin | |
| 1.No/past smoking | 2249 (37.5%) |
| 2.Current smoking | 3743 (62.5%) |
| drink_bin | |
| 1.Less drinking | 4042 (67.5%) |
| 2.Excessive drinking | 1950 (32.5%) |
| activity_bin | |
| 1.Proactive | 1545 (25.8%) |
| 2.Less active | 4447 (74.2%) |
| as.factor(group) | |
| 1 | 887 (14.8%) |
| 2 | 1484 (24.8%) |
| 3 | 133 (2.2%) |
| 4 | 158 (2.6%) |
| 5 | 20 (0.3%) |
| 6 | 583 (9.7%) |
| 7 | 46 (0.8%) |
| 8 | 180 (3.0%) |
| 9 | 104 (1.7%) |
| 10 | 885 (14.8%) |
| 11 | 3 (0.1%) |
| 12 | 5 (0.1%) |
| 13 | 43 (0.7%) |
| 14 | 33 (0.6%) |
| 15 | 313 (5.2%) |
| 16 | 269 (4.5%) |
| 17 | 13 (0.2%) |
| 18 | 15 (0.3%) |
| 19 | 59 (1.0%) |
| 20 | 60 (1.0%) |
| 21 | 262 (4.4%) |
| 22 | 158 (2.6%) |
| 23 | 1 (0.0%) |
| 24 | 10 (0.2%) |
| 25 | 9 (0.2%) |
| 26 | 103 (1.7%) |
| 27 | 8 (0.1%) |
| 28 | 15 (0.3%) |
| 29 | 25 (0.4%) |
| 30 | 85 (1.4%) |
| 31 | 5 (0.1%) |
| 32 | 18 (0.3%) |
1.2.3 Association for any fracture
library(survival)
smoke.age.m = coxph(Surv(fu_anyfx, anyfx) ~ age + smoke_bin, data = men)
summary(smoke.age.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ age + smoke_bin, data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age 0.0730241 1.0757564 0.0053747 13.5867 < 2e-16 ***
## smoke_bin2.Current smoking 0.1086915 1.1148184 0.0627327 1.7326 0.08316 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age 1.0758 0.92958 1.06448 1.0871
## smoke_bin2.Current smoking 1.1148 0.89701 0.98584 1.2607
##
## Concordance= 0.615 (se = 0.009 )
## Likelihood ratio test= 176.87 on 2 df, p=<2e-16
## Wald test = 185.32 on 2 df, p=<2e-16
## Score (logrank) test = 188.89 on 2 df, p=<2e-16m.any.smoke.m = coxph(Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin, data = men)
summary(m.any.smoke.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin, data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.601950 1.825676 0.062850 9.5775 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.950307 2.586504 0.102918 9.2336 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.329717 1.390574 0.069808 4.7232 2.322e-06 ***
## fx50_bin2.Fx 1+ 0.470967 1.601542 0.071486 6.5882 4.450e-11 ***
## smoke_bin2.Current smoking 0.079467 1.082710 0.062757 1.2663 0.2054
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.8257 0.54774 1.6141 2.0650
## bmd_bin2.BMD<= -2.5 2.5865 0.38662 2.1140 3.1646
## fall_bin2.Falls 1+ 1.3906 0.71913 1.2128 1.5945
## fx50_bin2.Fx 1+ 1.6015 0.62440 1.3922 1.8424
## smoke_bin2.Current smoking 1.0827 0.92361 0.9574 1.2244
##
## Concordance= 0.637 (se = 0.009 )
## Likelihood ratio test= 258.21 on 5 df, p=<2e-16
## Wald test = 299.2 on 5 df, p=<2e-16
## Score (logrank) test = 318.46 on 5 df, p=<2e-16options(digits = 8)
any.smoke.m = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(group), data = men)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 22 ; coefficient may be infinite.summary(any.smoke.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(group), data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 2.0207e-01 1.2239e+00 1.1657e-01 1.7335 0.0829998 .
## as.factor(group)3 6.4588e-01 1.9077e+00 2.0257e-01 3.1884 0.0014304 **
## as.factor(group)4 2.9435e-01 1.3423e+00 2.2086e-01 1.3328 0.1826002
## as.factor(group)5 1.1913e+00 3.2913e+00 3.8945e-01 3.0589 0.0022218 **
## as.factor(group)6 7.8632e-01 2.1953e+00 1.3515e-01 5.8181 5.953e-09 ***
## as.factor(group)7 1.3094e+00 3.7041e+00 3.0387e-01 4.3093 1.638e-05 ***
## as.factor(group)8 1.1636e+00 3.2014e+00 1.7652e-01 6.5917 4.348e-11 ***
## as.factor(group)9 1.1350e+00 3.1113e+00 2.1768e-01 5.2143 1.845e-07 ***
## as.factor(group)10 7.4866e-01 2.1142e+00 1.2598e-01 5.9429 2.801e-09 ***
## as.factor(group)11 9.0207e-01 2.4647e+00 1.0044e+00 0.8981 0.3691132
## as.factor(group)12 1.5440e+00 4.6834e+00 7.1333e-01 2.1645 0.0304250 *
## as.factor(group)13 9.5246e-01 2.5921e+00 3.1580e-01 3.0160 0.0025614 **
## as.factor(group)14 8.4805e-01 2.3351e+00 3.4625e-01 2.4492 0.0143169 *
## as.factor(group)15 5.4898e-01 1.7315e+00 1.5955e-01 3.4408 0.0005801 ***
## as.factor(group)16 7.2551e-01 2.0658e+00 1.5870e-01 4.5715 4.842e-06 ***
## as.factor(group)17 2.2583e+00 9.5670e+00 4.5804e-01 4.9304 8.206e-07 ***
## as.factor(group)18 2.0989e+00 8.1571e+00 3.9012e-01 5.3801 7.445e-08 ***
## as.factor(group)19 1.7937e+00 6.0115e+00 2.4310e-01 7.3782 1.604e-13 ***
## as.factor(group)20 1.6104e+00 5.0048e+00 2.6090e-01 6.1725 6.723e-10 ***
## as.factor(group)21 1.0498e+00 2.8570e+00 1.7172e-01 6.1132 9.763e-10 ***
## as.factor(group)22 1.0719e+00 2.9210e+00 2.0069e-01 5.3412 9.235e-08 ***
## as.factor(group)23 -9.9811e+00 4.6267e-05 4.5676e+02 -0.0219 0.9825662
## as.factor(group)24 2.0453e+00 7.7315e+00 4.1900e-01 4.8814 1.053e-06 ***
## as.factor(group)25 1.5112e+00 4.5322e+00 5.0872e-01 2.9706 0.0029719 **
## as.factor(group)26 9.1121e-01 2.4873e+00 2.2089e-01 4.1253 3.703e-05 ***
## as.factor(group)27 2.4970e+00 1.2147e+01 5.0894e-01 4.9064 9.278e-07 ***
## as.factor(group)28 1.7557e+00 5.7874e+00 4.5731e-01 3.8392 0.0001234 ***
## as.factor(group)29 2.5345e+00 1.2610e+01 2.8424e-01 8.9167 < 2.2e-16 ***
## as.factor(group)30 1.4405e+00 4.2230e+00 2.3342e-01 6.1715 6.765e-10 ***
## as.factor(group)31 2.0106e+00 7.4681e+00 5.8511e-01 3.4363 0.0005897 ***
## as.factor(group)32 2.4696e+00 1.1817e+01 3.9088e-01 6.3179 2.651e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group)2 1.2239e+00 8.1704e-01 0.97395 1.5381
## as.factor(group)3 1.9077e+00 5.2420e-01 1.28255 2.8374
## as.factor(group)4 1.3423e+00 7.4501e-01 0.87065 2.0693
## as.factor(group)5 3.2913e+00 3.0383e-01 1.53413 7.0609
## as.factor(group)6 2.1953e+00 4.5552e-01 1.68443 2.8611
## as.factor(group)7 3.7041e+00 2.6997e-01 2.04188 6.7195
## as.factor(group)8 3.2014e+00 3.1237e-01 2.26507 4.5247
## as.factor(group)9 3.1113e+00 3.2141e-01 2.03071 4.7667
## as.factor(group)10 2.1142e+00 4.7300e-01 1.65162 2.7063
## as.factor(group)11 2.4647e+00 4.0573e-01 0.34422 17.6482
## as.factor(group)12 4.6834e+00 2.1352e-01 1.15709 18.9562
## as.factor(group)13 2.5921e+00 3.8579e-01 1.39584 4.8135
## as.factor(group)14 2.3351e+00 4.2825e-01 1.18460 4.6029
## as.factor(group)15 1.7315e+00 5.7754e-01 1.26651 2.3672
## as.factor(group)16 2.0658e+00 4.8408e-01 1.51355 2.8195
## as.factor(group)17 9.5670e+00 1.0453e-01 3.89845 23.4781
## as.factor(group)18 8.1571e+00 1.2259e-01 3.79719 17.5230
## as.factor(group)19 6.0115e+00 1.6635e-01 3.73297 9.6809
## as.factor(group)20 5.0048e+00 1.9981e-01 3.00128 8.3457
## as.factor(group)21 2.8570e+00 3.5002e-01 2.04052 4.0002
## as.factor(group)22 2.9210e+00 3.4235e-01 1.97108 4.3288
## as.factor(group)23 4.6267e-05 2.1614e+04 0.00000 Inf
## as.factor(group)24 7.7315e+00 1.2934e-01 3.40101 17.5758
## as.factor(group)25 4.5322e+00 2.2064e-01 1.67220 12.2837
## as.factor(group)26 2.4873e+00 4.0204e-01 1.61330 3.8349
## as.factor(group)27 1.2147e+01 8.2328e-02 4.47964 32.9354
## as.factor(group)28 5.7874e+00 1.7279e-01 2.36170 14.1822
## as.factor(group)29 1.2610e+01 7.9300e-02 7.22400 22.0126
## as.factor(group)30 4.2230e+00 2.3680e-01 2.67258 6.6727
## as.factor(group)31 7.4681e+00 1.3390e-01 2.37224 23.5104
## as.factor(group)32 1.1817e+01 8.4620e-02 5.49293 25.4241
##
## Concordance= 0.638 (se = 0.009 )
## Likelihood ratio test= 272.1 on 31 df, p=<2e-16
## Wald test = 318.49 on 31 df, p=<2e-16
## Score (logrank) test = 381.37 on 31 df, p=<2e-161.2.4 Association for hip fracture
hip.smoke.age.m = coxph(Surv(fu_hipfx, hipfx) ~ age + smoke_bin, data = men)
summary(hip.smoke.age.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ age + smoke_bin, data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age 0.134208 1.143630 0.011230 11.9510 <2e-16 ***
## smoke_bin2.Current smoking 0.018378 1.018548 0.132325 0.1389 0.8895
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age 1.1436 0.87441 1.11873 1.1691
## smoke_bin2.Current smoking 1.0185 0.98179 0.78586 1.3201
##
## Concordance= 0.72 (se = 0.016 )
## Likelihood ratio test= 136.52 on 2 df, p=<2e-16
## Wald test = 143.43 on 2 df, p=<2e-16
## Score (logrank) test = 152.81 on 2 df, p=<2e-16m.hip.smoke.m = coxph(Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin, data = men)
summary(m.hip.smoke.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin, data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 1.104599 3.018015 0.138452 7.9782 1.485e-15 ***
## bmd_bin2.BMD<= -2.5 1.575730 4.834267 0.168079 9.3749 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.326225 1.385727 0.147682 2.2090 0.02718 *
## fx50_bin2.Fx 1+ 0.249491 1.283372 0.157112 1.5880 0.11229
## smoke_bin2.Current smoking -0.018263 0.981903 0.132325 -0.1380 0.89023
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 3.0180 0.33134 2.30076 3.9589
## bmd_bin2.BMD<= -2.5 4.8343 0.20686 3.47745 6.7205
## fall_bin2.Falls 1+ 1.3857 0.72164 1.03746 1.8509
## fx50_bin2.Fx 1+ 1.2834 0.77920 0.94323 1.7462
## smoke_bin2.Current smoking 0.9819 1.01843 0.75759 1.2726
##
## Concordance= 0.726 (se = 0.017 )
## Likelihood ratio test= 161.98 on 5 df, p=<2e-16
## Wald test = 198.17 on 5 df, p=<2e-16
## Score (logrank) test = 249.27 on 5 df, p=<2e-16hip.smoke.m = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(group), data = men)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 11,13,22,26 ; coefficient may be infinite.summary(hip.smoke.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(group), data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 -7.7907e-02 9.2505e-01 2.7342e-01 -0.2849 0.7756938
## as.factor(group)3 1.6083e-01 1.1745e+00 5.4174e-01 0.2969 0.7665682
## as.factor(group)4 4.9638e-02 1.0509e+00 5.4175e-01 0.0916 0.9269956
## as.factor(group)5 7.9044e-01 2.2044e+00 1.0215e+00 0.7738 0.4390690
## as.factor(group)6 9.9756e-01 2.7117e+00 2.8749e-01 3.4699 0.0005206 ***
## as.factor(group)7 2.3608e+00 1.0599e+01 4.3274e-01 5.4554 4.886e-08 ***
## as.factor(group)8 1.5841e+00 4.8749e+00 3.4019e-01 4.6565 3.216e-06 ***
## as.factor(group)9 1.6531e+00 5.2232e+00 3.9415e-01 4.1941 2.739e-05 ***
## as.factor(group)10 9.0581e-01 2.4739e+00 2.7333e-01 3.3140 0.0009197 ***
## as.factor(group)11 2.5585e+00 1.2917e+01 1.0216e+00 2.5045 0.0122610 *
## as.factor(group)12 -1.4787e+01 3.7845e-07 5.2389e+03 -0.0028 0.9977479
## as.factor(group)13 1.7528e+00 5.7707e+00 4.9362e-01 3.5509 0.0003840 ***
## as.factor(group)14 -1.4800e+01 3.7372e-07 1.7026e+03 -0.0087 0.9930647
## as.factor(group)15 1.1508e-01 1.1220e+00 4.1053e-01 0.2803 0.7792317
## as.factor(group)16 -2.1738e-01 8.0462e-01 4.9349e-01 -0.4405 0.6595713
## as.factor(group)17 2.8939e+00 1.8064e+01 7.3998e-01 3.9108 9.199e-05 ***
## as.factor(group)18 1.6992e+00 5.4696e+00 1.0222e+00 1.6622 0.0964632 .
## as.factor(group)19 2.6787e+00 1.4566e+01 3.8052e-01 7.0396 1.928e-12 ***
## as.factor(group)20 2.1501e+00 8.5859e+00 4.6050e-01 4.6691 3.025e-06 ***
## as.factor(group)21 1.2760e+00 3.5821e+00 3.5806e-01 3.5636 0.0003658 ***
## as.factor(group)22 1.2910e+00 3.6366e+00 4.1196e-01 3.1339 0.0017249 **
## as.factor(group)23 -1.4730e+01 4.0054e-07 1.1806e+04 -0.0012 0.9990045
## as.factor(group)24 2.2771e+00 9.7484e+00 7.3739e-01 3.0881 0.0020146 **
## as.factor(group)25 2.3070e+00 1.0045e+01 7.3729e-01 3.1291 0.0017536 **
## as.factor(group)26 2.9990e-01 1.3497e+00 6.1390e-01 0.4885 0.6251902
## as.factor(group)27 -1.4763e+01 3.8781e-07 5.1376e+03 -0.0029 0.9977073
## as.factor(group)28 2.7946e+00 1.6357e+01 6.1490e-01 4.5449 5.497e-06 ***
## as.factor(group)29 3.2262e+00 2.5183e+01 4.3361e-01 7.4402 1.005e-13 ***
## as.factor(group)30 1.2969e+00 3.6580e+00 5.4269e-01 2.3898 0.0168590 *
## as.factor(group)31 3.1153e+00 2.2540e+01 7.3778e-01 4.2226 2.415e-05 ***
## as.factor(group)32 3.2909e+00 2.6867e+01 6.1894e-01 5.3170 1.055e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group)2 9.2505e-01 1.0810e+00 0.54129 1.5809
## as.factor(group)3 1.1745e+00 8.5144e-01 0.40618 3.3961
## as.factor(group)4 1.0509e+00 9.5157e-01 0.36343 3.0387
## as.factor(group)5 2.2044e+00 4.5365e-01 0.29767 16.3239
## as.factor(group)6 2.7117e+00 3.6878e-01 1.54356 4.7637
## as.factor(group)7 1.0599e+01 9.4345e-02 4.53864 24.7532
## as.factor(group)8 4.8749e+00 2.0513e-01 2.50262 9.4957
## as.factor(group)9 5.2232e+00 1.9145e-01 2.41234 11.3094
## as.factor(group)10 2.4739e+00 4.0421e-01 1.44787 4.2271
## as.factor(group)11 1.2917e+01 7.7419e-02 1.74423 95.6523
## as.factor(group)12 3.7845e-07 2.6424e+06 0.00000 Inf
## as.factor(group)13 5.7707e+00 1.7329e-01 2.19309 15.1846
## as.factor(group)14 3.7372e-07 2.6758e+06 0.00000 Inf
## as.factor(group)15 1.1220e+00 8.9130e-01 0.50181 2.5085
## as.factor(group)16 8.0462e-01 1.2428e+00 0.30587 2.1166
## as.factor(group)17 1.8064e+01 5.5359e-02 4.23584 77.0345
## as.factor(group)18 5.4696e+00 1.8283e-01 0.73761 40.5579
## as.factor(group)19 1.4566e+01 6.8652e-02 6.90952 30.7074
## as.factor(group)20 8.5859e+00 1.1647e-01 3.48183 21.1719
## as.factor(group)21 3.5821e+00 2.7916e-01 1.77568 7.2263
## as.factor(group)22 3.6366e+00 2.7498e-01 1.62193 8.1537
## as.factor(group)23 4.0054e-07 2.4966e+06 0.00000 Inf
## as.factor(group)24 9.7484e+00 1.0258e-01 2.29757 41.3615
## as.factor(group)25 1.0045e+01 9.9556e-02 2.36783 42.6103
## as.factor(group)26 1.3497e+00 7.4090e-01 0.40522 4.4957
## as.factor(group)27 3.8781e-07 2.5786e+06 0.00000 Inf
## as.factor(group)28 1.6357e+01 6.1137e-02 4.90109 54.5881
## as.factor(group)29 2.5183e+01 3.9709e-02 10.76502 58.9115
## as.factor(group)30 3.6580e+00 2.7338e-01 1.26270 10.5970
## as.factor(group)31 2.2540e+01 4.4365e-02 5.30841 95.7109
## as.factor(group)32 2.6867e+01 3.7220e-02 7.98692 90.3783
##
## Concordance= 0.734 (se = 0.017 )
## Likelihood ratio test= 184.08 on 31 df, p=<2e-16
## Wald test = 221.65 on 31 df, p=<2e-16
## Score (logrank) test = 342.26 on 31 df, p=<2e-161.3 Excessive drinking
1.3.1 Data management
# data = data %>% mutate(drink_bin = case_when(drink4 == "No" | drink4 == "Low" | drink4 == "Moderate" ~ "1.Less drinking",
# drink4 == "High" ~ "2.Excessive drinking"))
men = men %>% mutate(group.d = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 32))1.3.2 Prevalences
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + drink_bin + as.factor(group.d), data = men, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=5992) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 73.0 [69.0, 78.0] |
| age_bin | |
| 1.Age< 75 | 3476 (58.0%) |
| 2.Age>= 75 | 2516 (42.0%) |
| fnbmd | |
| Median [Q1, Q3] | 0.774 [0.696, 0.860] |
| Tscore | |
| Median [Q1, Q3] | -1.17 [-1.73, -0.539] |
| bmd_bin | |
| 1.BMD> -2.5 | 5697 (95.1%) |
| 2.BMD<= -2.5 | 295 (4.9%) |
| fall_bin | |
| 1.No falls | 4725 (78.9%) |
| 2.Falls 1+ | 1267 (21.1%) |
| fx50_bin | |
| 1.No fx | 4961 (82.8%) |
| 2.Fx 1+ | 1031 (17.2%) |
| drink_bin | |
| 1.Less drinking | 4042 (67.5%) |
| 2.Excessive drinking | 1950 (32.5%) |
| as.factor(group.d) | |
| 1 | 1570 (26.2%) |
| 2 | 801 (13.4%) |
| 3 | 276 (4.6%) |
| 4 | 305 (5.1%) |
| 5 | 40 (0.7%) |
| 6 | 1015 (16.9%) |
| 7 | 81 (1.4%) |
| 8 | 305 (5.1%) |
| 9 | 167 (2.8%) |
| 10 | 453 (7.6%) |
| 11 | 9 (0.2%) |
| 12 | 10 (0.2%) |
| 13 | 23 (0.4%) |
| 14 | 81 (1.4%) |
| 15 | 166 (2.8%) |
| 16 | 126 (2.1%) |
| 17 | 24 (0.4%) |
| 18 | 25 (0.4%) |
| 19 | 24 (0.4%) |
| 20 | 106 (1.8%) |
| 21 | 137 (2.3%) |
| 22 | 95 (1.6%) |
| 23 | 6 (0.1%) |
| 24 | 4 (0.1%) |
| 25 | 4 (0.1%) |
| 26 | 55 (0.9%) |
| 27 | 22 (0.4%) |
| 28 | 4 (0.1%) |
| 29 | 15 (0.3%) |
| 30 | 39 (0.7%) |
| 32 | 4 (0.1%) |
1.3.3 Association for any fracture
library(survival)
m.any.drink.m = coxph(Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin, data = men)
summary(m.any.drink.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + drink_bin, data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.597569 1.817694 0.062738 9.5248 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.956198 2.601787 0.103095 9.2749 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.332309 1.394184 0.069781 4.7622 1.915e-06 ***
## fx50_bin2.Fx 1+ 0.472066 1.603303 0.071465 6.6055 3.962e-11 ***
## drink_bin2.Excessive drinking 0.068315 1.070702 0.064095 1.0658 0.2865
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.8177 0.55015 1.6074 2.0555
## bmd_bin2.BMD<= -2.5 2.6018 0.38435 2.1258 3.1844
## fall_bin2.Falls 1+ 1.3942 0.71727 1.2160 1.5985
## fx50_bin2.Fx 1+ 1.6033 0.62371 1.3937 1.8444
## drink_bin2.Excessive drinking 1.0707 0.93397 0.9443 1.2140
##
## Concordance= 0.636 (se = 0.009 )
## Likelihood ratio test= 257.72 on 5 df, p=<2e-16
## Wald test = 298.84 on 5 df, p=<2e-16
## Score (logrank) test = 318.13 on 5 df, p=<2e-16options(digits = 8)
any.drink.m = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(group.d), data = men)
summary(any.drink.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(group.d), data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.d)2 0.15784 1.17097 0.11546 1.3671 0.1716039
## as.factor(group.d)3 0.64269 1.90160 0.14424 4.4556 8.367e-06 ***
## as.factor(group.d)4 0.23854 1.26939 0.16189 1.4735 0.1406140
## as.factor(group.d)5 0.77431 2.16909 0.32396 2.3902 0.0168414 *
## as.factor(group.d)6 0.66880 1.95190 0.10537 6.3472 2.193e-10 ***
## as.factor(group.d)7 1.44360 4.23591 0.21632 6.6735 2.497e-11 ***
## as.factor(group.d)8 1.03436 2.81331 0.14583 7.0928 1.315e-12 ***
## as.factor(group.d)9 1.22578 3.40682 0.16835 7.2811 3.311e-13 ***
## as.factor(group.d)10 0.74269 2.10157 0.12912 5.7520 8.821e-09 ***
## as.factor(group.d)11 1.43287 4.19073 0.50494 2.8377 0.0045436 **
## as.factor(group.d)12 1.54659 4.69545 0.45271 3.4163 0.0006348 ***
## as.factor(group.d)13 1.27902 3.59313 0.36052 3.5477 0.0003886 ***
## as.factor(group.d)14 0.85384 2.34864 0.22924 3.7246 0.0001956 ***
## as.factor(group.d)15 0.63490 1.88683 0.17677 3.5917 0.0003285 ***
## as.factor(group.d)16 0.59535 1.81367 0.19853 2.9988 0.0027100 **
## as.factor(group.d)17 1.90945 6.74936 0.34127 5.5951 2.205e-08 ***
## as.factor(group.d)18 2.50595 12.25514 0.26879 9.3230 < 2.2e-16 ***
## as.factor(group.d)19 1.75333 5.77379 0.36095 4.8575 1.188e-06 ***
## as.factor(group.d)20 1.38288 3.98635 0.20553 6.7285 1.714e-11 ***
## as.factor(group.d)21 1.02587 2.78951 0.19064 5.3813 7.395e-08 ***
## as.factor(group.d)22 0.61451 1.84876 0.26790 2.2938 0.0218014 *
## as.factor(group.d)23 1.70994 5.52862 0.58180 2.9391 0.0032920 **
## as.factor(group.d)24 2.25773 9.56139 0.58165 3.8816 0.0001038 ***
## as.factor(group.d)25 1.07833 2.93976 1.00252 1.0756 0.2820967
## as.factor(group.d)26 0.77689 2.17469 0.28610 2.7154 0.0066190 **
## as.factor(group.d)27 2.58667 13.28547 0.32493 7.9607 1.710e-15 ***
## as.factor(group.d)28 1.85726 6.40616 1.00316 1.8514 0.0641096 .
## as.factor(group.d)29 1.90775 6.73793 0.41465 4.6009 4.207e-06 ***
## as.factor(group.d)30 1.58086 4.85914 0.29759 5.3123 1.083e-07 ***
## as.factor(group.d)32 1.43810 4.21267 1.00296 1.4339 0.1516139
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.d)2 1.1710 0.853989 0.93384 1.4683
## as.factor(group.d)3 1.9016 0.525874 1.43330 2.5229
## as.factor(group.d)4 1.2694 0.787777 0.92427 1.7434
## as.factor(group.d)5 2.1691 0.461023 1.14954 4.0929
## as.factor(group.d)6 1.9519 0.512321 1.58769 2.3997
## as.factor(group.d)7 4.2359 0.236077 2.77215 6.4725
## as.factor(group.d)8 2.8133 0.355454 2.11390 3.7441
## as.factor(group.d)9 3.4068 0.293529 2.44934 4.7386
## as.factor(group.d)10 2.1016 0.475834 1.63169 2.7068
## as.factor(group.d)11 4.1907 0.238622 1.55771 11.2744
## as.factor(group.d)12 4.6954 0.212972 1.93344 11.4031
## as.factor(group.d)13 3.5931 0.278309 1.77254 7.2837
## as.factor(group.d)14 2.3486 0.425778 1.49860 3.6809
## as.factor(group.d)15 1.8868 0.529991 1.33434 2.6681
## as.factor(group.d)16 1.8137 0.551369 1.22906 2.6764
## as.factor(group.d)17 6.7494 0.148162 3.45757 13.1751
## as.factor(group.d)18 12.2551 0.081598 7.23638 20.7546
## as.factor(group.d)19 5.7738 0.173197 2.84590 11.7139
## as.factor(group.d)20 3.9863 0.250856 2.66460 5.9637
## as.factor(group.d)21 2.7895 0.358486 1.91981 4.0532
## as.factor(group.d)22 1.8488 0.540904 1.09356 3.1255
## as.factor(group.d)23 5.5286 0.180877 1.76763 17.2919
## as.factor(group.d)24 9.5614 0.104587 3.05790 29.8964
## as.factor(group.d)25 2.9398 0.340164 0.41207 20.9727
## as.factor(group.d)26 2.1747 0.459835 1.24128 3.8100
## as.factor(group.d)27 13.2855 0.075270 7.02743 25.1164
## as.factor(group.d)28 6.4062 0.156100 0.89683 45.7599
## as.factor(group.d)29 6.7379 0.148413 2.98935 15.1872
## as.factor(group.d)30 4.8591 0.205798 2.71178 8.7069
## as.factor(group.d)32 4.2127 0.237379 0.58998 30.0800
##
## Concordance= 0.638 (se = 0.009 )
## Likelihood ratio test= 277.12 on 30 df, p=<2e-16
## Wald test = 327.11 on 30 df, p=<2e-16
## Score (logrank) test = 395.13 on 30 df, p=<2e-161.3.4 Association for hip fracture
m.hip.drink.m = coxph(Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin, data = men)
summary(m.hip.drink.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + drink_bin, data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 1.10169 3.00926 0.13823 7.9697 1.59e-15 ***
## bmd_bin2.BMD<= -2.5 1.55198 4.72081 0.16849 9.2111 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.32028 1.37751 0.14778 2.1672 0.03022 *
## fx50_bin2.Fx 1+ 0.25454 1.28987 0.15710 1.6202 0.10518
## drink_bin2.Excessive drinking -0.28434 0.75251 0.14825 -1.9180 0.05511 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 3.00926 0.33231 2.29506 3.9457
## bmd_bin2.BMD<= -2.5 4.72081 0.21183 3.39310 6.5680
## fall_bin2.Falls 1+ 1.37751 0.72595 1.03110 1.8403
## fx50_bin2.Fx 1+ 1.28987 0.77527 0.94803 1.7550
## drink_bin2.Excessive drinking 0.75251 1.32888 0.56276 1.0062
##
## Concordance= 0.729 (se = 0.018 )
## Likelihood ratio test= 165.8 on 5 df, p=<2e-16
## Wald test = 202.25 on 5 df, p=<2e-16
## Score (logrank) test = 253.26 on 5 df, p=<2e-16options(digits = 8)
hip.smoke.m = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(group.d), data = men)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 23,24,30 ; coefficient may be infinite.summary(hip.smoke.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(group.d), data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.d)2 4.0723e-02 1.0416e+00 2.8357e-01 0.1436 0.8858077
## as.factor(group.d)3 2.6641e-01 1.3053e+00 3.9088e-01 0.6816 0.4955039
## as.factor(group.d)4 1.8866e-01 1.2076e+00 3.9088e-01 0.4827 0.6293352
## as.factor(group.d)5 1.5745e+00 4.8282e+00 5.2709e-01 2.9871 0.0028164 **
## as.factor(group.d)6 1.1099e+00 3.0339e+00 2.2632e-01 4.9038 9.400e-07 ***
## as.factor(group.d)7 2.6627e+00 1.4335e+01 3.1620e-01 8.4208 < 2.2e-16 ***
## as.factor(group.d)8 1.6407e+00 5.1587e+00 2.8060e-01 5.8471 5.003e-09 ***
## as.factor(group.d)9 1.7317e+00 5.6504e+00 3.2484e-01 5.3310 9.767e-08 ***
## as.factor(group.d)10 7.4709e-01 2.1108e+00 3.0820e-01 2.4240 0.0153502 *
## as.factor(group.d)11 2.9250e+00 1.8635e+01 6.0117e-01 4.8656 1.141e-06 ***
## as.factor(group.d)12 2.2638e+00 9.6194e+00 7.2655e-01 3.1158 0.0018344 **
## as.factor(group.d)13 1.5723e+00 4.8177e+00 7.2660e-01 2.1639 0.0304712 *
## as.factor(group.d)14 1.3117e-01 1.1402e+00 7.2649e-01 0.1806 0.8567159
## as.factor(group.d)15 8.4369e-02 1.0880e+00 5.2705e-01 0.1601 0.8728201
## as.factor(group.d)16 -1.0756e+00 3.4108e-01 1.0138e+00 -1.0610 0.2886949
## as.factor(group.d)17 2.7491e+00 1.5628e+01 5.2854e-01 5.2013 1.979e-07 ***
## as.factor(group.d)18 3.0801e+00 2.1760e+01 4.4279e-01 6.9561 3.499e-12 ***
## as.factor(group.d)19 2.3264e+00 1.0241e+01 6.0208e-01 3.8639 0.0001116 ***
## as.factor(group.d)20 1.6026e+00 4.9662e+00 4.4232e-01 3.6233 0.0002909 ***
## as.factor(group.d)21 1.1049e+00 3.0189e+00 4.4186e-01 2.5005 0.0124002 *
## as.factor(group.d)22 1.0519e+00 2.8631e+00 5.2780e-01 1.9930 0.0462609 *
## as.factor(group.d)23 2.9901e+00 1.9888e+01 7.2702e-01 4.1128 3.908e-05 ***
## as.factor(group.d)24 -1.2747e+01 2.9097e-06 1.8079e+03 -0.0071 0.9943743
## as.factor(group.d)25 -1.2741e+01 2.9299e-06 2.2034e+03 -0.0058 0.9953865
## as.factor(group.d)26 -1.8932e-01 8.2752e-01 1.0138e+00 -0.1867 0.8518634
## as.factor(group.d)27 2.9235e+00 1.8607e+01 6.0265e-01 4.8512 1.227e-06 ***
## as.factor(group.d)28 3.8510e+00 4.7038e+01 1.0180e+00 3.7829 0.0001550 ***
## as.factor(group.d)29 2.5350e+00 1.2616e+01 7.2725e-01 3.4857 0.0004909 ***
## as.factor(group.d)30 2.1179e+00 8.3135e+00 5.2791e-01 4.0118 6.025e-05 ***
## as.factor(group.d)32 -1.2644e+01 3.2255e-06 2.9370e+03 -0.0043 0.9965650
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.d)2 1.0416e+00 9.6009e-01 0.597465 1.8158
## as.factor(group.d)3 1.3053e+00 7.6612e-01 0.606718 2.8081
## as.factor(group.d)4 1.2076e+00 8.2806e-01 0.561327 2.5981
## as.factor(group.d)5 4.8282e+00 2.0712e-01 1.718402 13.5659
## as.factor(group.d)6 3.0339e+00 3.2961e-01 1.946953 4.7277
## as.factor(group.d)7 1.4335e+01 6.9759e-02 7.713377 26.6411
## as.factor(group.d)8 5.1587e+00 1.9385e-01 2.976425 8.9411
## as.factor(group.d)9 5.6504e+00 1.7698e-01 2.989337 10.6803
## as.factor(group.d)10 2.1108e+00 4.7374e-01 1.153753 3.8619
## as.factor(group.d)11 1.8635e+01 5.3663e-02 5.736060 60.5403
## as.factor(group.d)12 9.6194e+00 1.0396e-01 2.315844 39.9565
## as.factor(group.d)13 4.8177e+00 2.0757e-01 1.159731 20.0136
## as.factor(group.d)14 1.1402e+00 8.7707e-01 0.274523 4.7354
## as.factor(group.d)15 1.0880e+00 9.1909e-01 0.387269 3.0568
## as.factor(group.d)16 3.4108e-01 2.9318e+00 0.046764 2.4878
## as.factor(group.d)17 1.5628e+01 6.3986e-02 5.546567 44.0362
## as.factor(group.d)18 2.1760e+01 4.5957e-02 9.135862 51.8262
## as.factor(group.d)19 1.0241e+01 9.7649e-02 3.146599 33.3289
## as.factor(group.d)20 4.9662e+00 2.0136e-01 2.086975 11.8175
## as.factor(group.d)21 3.0189e+00 3.3125e-01 1.269801 7.1772
## as.factor(group.d)22 2.8631e+00 3.4927e-01 1.017592 8.0558
## as.factor(group.d)23 1.9888e+01 5.0281e-02 4.783582 82.6865
## as.factor(group.d)24 2.9097e-06 3.4367e+05 0.000000 Inf
## as.factor(group.d)25 2.9299e-06 3.4130e+05 0.000000 Inf
## as.factor(group.d)26 8.2752e-01 1.2084e+00 0.113458 6.0357
## as.factor(group.d)27 1.8607e+01 5.3743e-02 5.710857 60.6248
## as.factor(group.d)28 4.7038e+01 2.1259e-02 6.396261 345.9163
## as.factor(group.d)29 1.2616e+01 7.9265e-02 3.033075 52.4751
## as.factor(group.d)30 8.3135e+00 1.2029e-01 2.954118 23.3962
## as.factor(group.d)32 3.2255e-06 3.1003e+05 0.000000 Inf
##
## Concordance= 0.736 (se = 0.017 )
## Likelihood ratio test= 182.58 on 30 df, p=<2e-16
## Wald test = 217.09 on 30 df, p=<2e-16
## Score (logrank) test = 325.98 on 30 df, p=<2e-161.4 Proactive physical activity
1.4.1 Data management
men = men %>% mutate(physical_bin = case_when(physical4 == "Moderate" | physical4 == "High" | physical4 == "Low" ~ "1.Proactive",
physical4 == "No" ~ "2.Less active"))
men = men %>% mutate(group.p = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 32))1.4.2 Prevalences
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + physical4 + activity_bin + physical_bin + as.factor(group.p), data = men, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=5992) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 73.0 [69.0, 78.0] |
| age_bin | |
| 1.Age< 75 | 3476 (58.0%) |
| 2.Age>= 75 | 2516 (42.0%) |
| fnbmd | |
| Median [Q1, Q3] | 0.774 [0.696, 0.860] |
| Tscore | |
| Median [Q1, Q3] | -1.17 [-1.73, -0.539] |
| bmd_bin | |
| 1.BMD> -2.5 | 5697 (95.1%) |
| 2.BMD<= -2.5 | 295 (4.9%) |
| fall_bin | |
| 1.No falls | 4725 (78.9%) |
| 2.Falls 1+ | 1267 (21.1%) |
| fx50_bin | |
| 1.No fx | 4961 (82.8%) |
| 2.Fx 1+ | 1031 (17.2%) |
| physical4 | |
| High | 866 (14.5%) |
| Low | 1642 (27.4%) |
| Moderate | 679 (11.3%) |
| No | 2805 (46.8%) |
| activity_bin | |
| 1.Proactive | 1545 (25.8%) |
| 2.Less active | 4447 (74.2%) |
| physical_bin | |
| 1.Proactive | 3187 (53.2%) |
| 2.Less active | 2805 (46.8%) |
| as.factor(group.p) | |
| 1 | 1343 (22.4%) |
| 2 | 1028 (17.2%) |
| 3 | 223 (3.7%) |
| 4 | 270 (4.5%) |
| 5 | 30 (0.5%) |
| 6 | 782 (13.1%) |
| 7 | 38 (0.6%) |
| 8 | 191 (3.2%) |
| 9 | 131 (2.2%) |
| 10 | 686 (11.4%) |
| 11 | 5 (0.1%) |
| 12 | 6 (0.1%) |
| 13 | 33 (0.6%) |
| 14 | 76 (1.3%) |
| 15 | 201 (3.4%) |
| 16 | 179 (3.0%) |
| 17 | 12 (0.2%) |
| 18 | 16 (0.3%) |
| 19 | 67 (1.1%) |
| 20 | 53 (0.9%) |
| 21 | 251 (4.2%) |
| 22 | 131 (2.2%) |
| 23 | 4 (0.1%) |
| 24 | 8 (0.1%) |
| 25 | 8 (0.1%) |
| 26 | 60 (1.0%) |
| 27 | 7 (0.1%) |
| 28 | 16 (0.3%) |
| 29 | 24 (0.4%) |
| 30 | 92 (1.5%) |
| 31 | 2 (0.0%) |
| 32 | 19 (0.3%) |
1.4.3 Association for any fracture
library(survival)
m.any.physical.m = coxph(Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + physical_bin, data = men)
summary(m.any.physical.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + physical_bin, data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.592417 1.808355 0.062857 9.4248 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.940043 2.560091 0.103215 9.1076 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.329209 1.389868 0.069836 4.7140 2.429e-06 ***
## fx50_bin2.Fx 1+ 0.470967 1.601542 0.071491 6.5878 4.464e-11 ***
## physical_bin2.Less active 0.080312 1.083625 0.061337 1.3094 0.1904
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.8084 0.55299 1.59875 2.0454
## bmd_bin2.BMD<= -2.5 2.5601 0.39061 2.09122 3.1341
## fall_bin2.Falls 1+ 1.3899 0.71949 1.21207 1.5937
## fx50_bin2.Fx 1+ 1.6015 0.62440 1.39215 1.8424
## physical_bin2.Less active 1.0836 0.92283 0.96088 1.2221
##
## Concordance= 0.636 (se = 0.009 )
## Likelihood ratio test= 258.31 on 5 df, p=<2e-16
## Wald test = 299.98 on 5 df, p=<2e-16
## Score (logrank) test = 319.16 on 5 df, p=<2e-16options(digits = 8)
any.physical.m = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(group.p), data = men)
summary(any.physical.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(group.p), data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.p)2 -0.019507 0.980682 0.113314 -0.1722 0.8633175
## as.factor(group.p)3 0.445535 1.561326 0.161546 2.7580 0.0058165 **
## as.factor(group.p)4 0.253343 1.288324 0.160224 1.5812 0.1138373
## as.factor(group.p)5 1.321815 3.750223 0.297750 4.4393 9.023e-06 ***
## as.factor(group.p)6 0.582949 1.791312 0.112869 5.1648 2.407e-07 ***
## as.factor(group.p)7 1.055312 2.872872 0.324668 3.2504 0.0011523 **
## as.factor(group.p)8 0.966501 2.628729 0.167819 5.7592 8.452e-09 ***
## as.factor(group.p)9 0.978590 2.660701 0.194043 5.0432 4.579e-07 ***
## as.factor(group.p)10 0.691631 1.996969 0.118576 5.8328 5.450e-09 ***
## as.factor(group.p)11 0.502614 1.653037 1.002640 0.5013 0.6161664
## as.factor(group.p)12 1.705937 5.506543 0.581936 2.9315 0.0033734 **
## as.factor(group.p)13 0.385572 1.470455 0.414665 0.9298 0.3524535
## as.factor(group.p)14 0.327805 1.387919 0.276937 1.1837 0.2365382
## as.factor(group.p)15 0.453947 1.574515 0.181845 2.4963 0.0125482 *
## as.factor(group.p)16 0.712206 2.038483 0.167368 4.2553 2.088e-05 ***
## as.factor(group.p)17 1.698922 5.468052 0.505744 3.3593 0.0007815 ***
## as.factor(group.p)18 2.580432 13.202844 0.310954 8.2984 < 2.2e-16 ***
## as.factor(group.p)19 1.700340 5.475810 0.225979 7.5243 5.299e-14 ***
## as.factor(group.p)20 1.435259 4.200734 0.260683 5.5058 3.676e-08 ***
## as.factor(group.p)21 0.972801 2.645342 0.159660 6.0929 1.109e-09 ***
## as.factor(group.p)22 0.953515 2.594813 0.206200 4.6242 3.760e-06 ***
## as.factor(group.p)23 1.833105 6.253270 0.711006 2.5782 0.0099321 **
## as.factor(group.p)24 2.085499 8.048608 0.414712 5.0288 4.936e-07 ***
## as.factor(group.p)25 1.147552 3.150471 0.581905 1.9721 0.0486029 *
## as.factor(group.p)26 1.236691 3.444199 0.235169 5.2587 1.451e-07 ***
## as.factor(group.p)27 2.256648 9.551024 0.711762 3.1705 0.0015217 **
## as.factor(group.p)28 1.953144 7.050823 0.415312 4.7028 2.566e-06 ***
## as.factor(group.p)29 1.956614 7.075326 0.325262 6.0155 1.793e-09 ***
## as.factor(group.p)30 1.340842 3.822261 0.221595 6.0509 1.441e-09 ***
## as.factor(group.p)31 1.357458 3.886301 1.002800 1.3537 0.1758426
## as.factor(group.p)32 2.368971 10.686386 0.341953 6.9278 4.275e-12 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.p)2 0.98068 1.019699 0.78537 1.2246
## as.factor(group.p)3 1.56133 0.640481 1.13759 2.1429
## as.factor(group.p)4 1.28832 0.776202 0.94111 1.7636
## as.factor(group.p)5 3.75022 0.266651 2.09224 6.7221
## as.factor(group.p)6 1.79131 0.558250 1.43581 2.2348
## as.factor(group.p)7 2.87287 0.348084 1.52040 5.4284
## as.factor(group.p)8 2.62873 0.380412 1.89190 3.6525
## as.factor(group.p)9 2.66070 0.375841 1.81898 3.8919
## as.factor(group.p)10 1.99697 0.500759 1.58285 2.5194
## as.factor(group.p)11 1.65304 0.604947 0.23165 11.7959
## as.factor(group.p)12 5.50654 0.181602 1.76009 17.2276
## as.factor(group.p)13 1.47046 0.680061 0.65236 3.3145
## as.factor(group.p)14 1.38792 0.720503 0.80656 2.3883
## as.factor(group.p)15 1.57452 0.635116 1.10245 2.2487
## as.factor(group.p)16 2.03848 0.490561 1.46839 2.8299
## as.factor(group.p)17 5.46805 0.182880 2.02928 14.7341
## as.factor(group.p)18 13.20284 0.075741 7.17767 24.2858
## as.factor(group.p)19 5.47581 0.182621 3.51637 8.5271
## as.factor(group.p)20 4.20073 0.238054 2.52018 7.0020
## as.factor(group.p)21 2.64534 0.378023 1.93455 3.6173
## as.factor(group.p)22 2.59481 0.385384 1.73216 3.8871
## as.factor(group.p)23 6.25327 0.159916 1.55202 25.1951
## as.factor(group.p)24 8.04861 0.124245 3.57041 18.1436
## as.factor(group.p)25 3.15047 0.317413 1.00706 9.8559
## as.factor(group.p)26 3.44420 0.290343 2.17226 5.4609
## as.factor(group.p)27 9.55102 0.104701 2.36699 38.5393
## as.factor(group.p)28 7.05082 0.141827 3.12411 15.9131
## as.factor(group.p)29 7.07533 0.141336 3.74009 13.3848
## as.factor(group.p)30 3.82226 0.261625 2.47570 5.9012
## as.factor(group.p)31 3.88630 0.257314 0.54444 27.7410
## as.factor(group.p)32 10.68639 0.093577 5.46714 20.8882
##
## Concordance= 0.637 (se = 0.009 )
## Likelihood ratio test= 283.41 on 31 df, p=<2e-16
## Wald test = 337.63 on 31 df, p=<2e-16
## Score (logrank) test = 407.38 on 31 df, p=<2e-161.4.4 Association for hip fracture
m.hip.physical.m = coxph(Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + physical_bin, data = men)
summary(m.hip.physical.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + physical_bin, data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 1.09414 2.98660 0.13835 7.9084 2.608e-15 ***
## bmd_bin2.BMD<= -2.5 1.54736 4.69905 0.16892 9.1605 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.31559 1.37107 0.14789 2.1340 0.03285 *
## fx50_bin2.Fx 1+ 0.23545 1.26548 0.15740 1.4959 0.13468
## physical_bin2.Less active 0.22797 1.25604 0.13163 1.7319 0.08330 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 2.9866 0.33483 2.27725 3.9169
## bmd_bin2.BMD<= -2.5 4.6990 0.21281 3.37465 6.5432
## fall_bin2.Falls 1+ 1.3711 0.72936 1.02607 1.8321
## fx50_bin2.Fx 1+ 1.2655 0.79022 0.92956 1.7228
## physical_bin2.Less active 1.2560 0.79615 0.97042 1.6257
##
## Concordance= 0.725 (se = 0.018 )
## Likelihood ratio test= 164.96 on 5 df, p=<2e-16
## Wald test = 201.47 on 5 df, p=<2e-16
## Score (logrank) test = 252.52 on 5 df, p=<2e-16options(digits = 8)
hip.physical.m = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(group.p), data = men)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 10,26 ; coefficient may be infinite.summary(hip.physical.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(group.p), data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.p)2 -1.3499e-01 8.7372e-01 2.7756e-01 -0.4864 0.6267165
## as.factor(group.p)3 -6.3959e-01 5.2751e-01 6.0229e-01 -1.0619 0.2882610
## as.factor(group.p)4 -1.4436e-01 8.6558e-01 4.4281e-01 -0.3260 0.7444225
## as.factor(group.p)5 1.6094e+00 4.9998e+00 6.0244e-01 2.6715 0.0075518 **
## as.factor(group.p)6 9.5558e-01 2.6002e+00 2.4376e-01 3.9202 8.846e-05 ***
## as.factor(group.p)7 1.8351e+00 6.2660e+00 5.2937e-01 3.4666 0.0005270 ***
## as.factor(group.p)8 6.9435e-01 2.0024e+00 4.4368e-01 1.5650 0.1175892
## as.factor(group.p)9 1.3379e+00 3.8111e+00 3.9392e-01 3.3964 0.0006829 ***
## as.factor(group.p)10 9.1530e-01 2.4975e+00 2.6506e-01 3.4531 0.0005541 ***
## as.factor(group.p)11 -1.2795e+01 2.7745e-06 1.6733e+03 -0.0076 0.9938988
## as.factor(group.p)12 2.2422e+00 9.4139e+00 1.0147e+00 2.2098 0.0271204 *
## as.factor(group.p)13 1.4135e+00 4.1101e+00 6.0233e-01 2.3467 0.0189424 *
## as.factor(group.p)14 -6.4544e-01 5.2443e-01 1.0146e+00 -0.6362 0.5246762
## as.factor(group.p)15 3.8374e-01 1.4678e+00 4.4292e-01 0.8664 0.3862789
## as.factor(group.p)16 4.0384e-01 1.4976e+00 4.4289e-01 0.9118 0.3618568
## as.factor(group.p)17 2.7178e+00 1.5147e+01 7.2860e-01 3.7302 0.0001913 ***
## as.factor(group.p)18 3.4808e+00 3.2486e+01 4.8072e-01 7.2409 4.459e-13 ***
## as.factor(group.p)19 2.8972e+00 1.8123e+01 3.2792e-01 8.8351 < 2.2e-16 ***
## as.factor(group.p)20 1.7101e+00 5.5296e+00 5.2934e-01 3.2306 0.0012352 **
## as.factor(group.p)21 1.8120e+00 6.1229e+00 2.8380e-01 6.3850 1.714e-10 ***
## as.factor(group.p)22 1.5816e+00 4.8629e+00 3.7615e-01 4.2048 2.613e-05 ***
## as.factor(group.p)23 2.7085e+00 1.5007e+01 1.0150e+00 2.6686 0.0076168 **
## as.factor(group.p)24 2.9575e+00 1.9251e+01 6.0249e-01 4.9089 9.160e-07 ***
## as.factor(group.p)25 1.6534e+00 5.2248e+00 1.0146e+00 1.6296 0.1031943
## as.factor(group.p)26 4.6008e-01 1.5842e+00 7.2765e-01 0.6323 0.5272002
## as.factor(group.p)27 -1.2675e+01 3.1281e-06 2.9690e+03 -0.0043 0.9965937
## as.factor(group.p)28 2.9080e+00 1.8320e+01 6.0455e-01 4.8101 1.508e-06 ***
## as.factor(group.p)29 2.2706e+00 9.6850e+00 6.0335e-01 3.7633 0.0001677 ***
## as.factor(group.p)30 1.7147e+00 5.5552e+00 4.4445e-01 3.8581 0.0001143 ***
## as.factor(group.p)31 3.1978e+00 2.4478e+01 1.0156e+00 3.1485 0.0016409 **
## as.factor(group.p)32 2.8476e+00 1.7246e+01 6.0374e-01 4.7166 2.398e-06 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.p)2 8.7372e-01 1.1445e+00 0.507127 1.5053
## as.factor(group.p)3 5.2751e-01 1.8957e+00 0.162018 1.7175
## as.factor(group.p)4 8.6558e-01 1.1553e+00 0.363402 2.0617
## as.factor(group.p)5 4.9998e+00 2.0001e-01 1.535174 16.2837
## as.factor(group.p)6 2.6002e+00 3.8459e-01 1.612574 4.1927
## as.factor(group.p)7 6.2660e+00 1.5959e-01 2.220168 17.6843
## as.factor(group.p)8 2.0024e+00 4.9940e-01 0.839246 4.7777
## as.factor(group.p)9 3.8111e+00 2.6239e-01 1.760918 8.2481
## as.factor(group.p)10 2.4975e+00 4.0040e-01 1.485551 4.1989
## as.factor(group.p)11 2.7745e-06 3.6043e+05 0.000000 Inf
## as.factor(group.p)12 9.4139e+00 1.0623e-01 1.288502 68.7789
## as.factor(group.p)13 4.1101e+00 2.4330e-01 1.262278 13.3831
## as.factor(group.p)14 5.2443e-01 1.9068e+00 0.071789 3.8311
## as.factor(group.p)15 1.4678e+00 6.8131e-01 0.616085 3.4968
## as.factor(group.p)16 1.4976e+00 6.6775e-01 0.628632 3.5676
## as.factor(group.p)17 1.5147e+01 6.6019e-02 3.631983 63.1703
## as.factor(group.p)18 3.2486e+01 3.0782e-02 12.662180 83.3459
## as.factor(group.p)19 1.8123e+01 5.5178e-02 9.530373 34.4636
## as.factor(group.p)20 5.5296e+00 1.8085e-01 1.959355 15.6052
## as.factor(group.p)21 6.1229e+00 1.6332e-01 3.510649 10.6788
## as.factor(group.p)22 4.8629e+00 2.0564e-01 2.326559 10.1643
## as.factor(group.p)23 1.5007e+01 6.6637e-02 2.052851 109.7014
## as.factor(group.p)24 1.9251e+01 5.1947e-02 5.910219 62.7024
## as.factor(group.p)25 5.2248e+00 1.9140e-01 0.715168 38.1703
## as.factor(group.p)26 1.5842e+00 6.3123e-01 0.380572 6.5945
## as.factor(group.p)27 3.1281e-06 3.1968e+05 0.000000 Inf
## as.factor(group.p)28 1.8320e+01 5.4586e-02 5.601754 59.9128
## as.factor(group.p)29 9.6850e+00 1.0325e-01 2.968444 31.5985
## as.factor(group.p)30 5.5552e+00 1.8001e-01 2.324763 13.2745
## as.factor(group.p)31 2.4478e+01 4.0854e-02 3.343951 179.1750
## as.factor(group.p)32 1.7246e+01 5.7983e-02 5.281980 56.3122
##
## Concordance= 0.738 (se = 0.017 )
## Likelihood ratio test= 191.47 on 31 df, p=<2e-16
## Wald test = 233.92 on 31 df, p=<2e-16
## Score (logrank) test = 368.44 on 31 df, p=<2e-161.5 Calcium intake (Adequate: >= 1000 mg/day)
1.5.1 Data management
men = men %>% mutate(calci_bin = case_when(calcium2 >= 1000 ~ "1.Sufficient Calcium",
calcium2 < 1000 ~ "2.Insufficient Calcium"))
men = men %>% mutate(group.c = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 32))1.5.2 Prevalences
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + calcium2 + calci_bin + as.factor(group.c), data = men, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=5992) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 73.0 [69.0, 78.0] |
| age_bin | |
| 1.Age< 75 | 3476 (58.0%) |
| 2.Age>= 75 | 2516 (42.0%) |
| fnbmd | |
| Median [Q1, Q3] | 0.774 [0.696, 0.860] |
| Tscore | |
| Median [Q1, Q3] | -1.17 [-1.73, -0.539] |
| bmd_bin | |
| 1.BMD> -2.5 | 5697 (95.1%) |
| 2.BMD<= -2.5 | 295 (4.9%) |
| fall_bin | |
| 1.No falls | 4725 (78.9%) |
| 2.Falls 1+ | 1267 (21.1%) |
| fx50_bin | |
| 1.No fx | 4961 (82.8%) |
| 2.Fx 1+ | 1031 (17.2%) |
| calcium2 | |
| Median [Q1, Q3] | 728 [522, 991] |
| calci_bin | |
| 1.Sufficient Calcium | 1458 (24.3%) |
| 2.Insufficient Calcium | 4534 (75.7%) |
| as.factor(group.c) | |
| 1 | 554 (9.2%) |
| 2 | 1817 (30.3%) |
| 3 | 100 (1.7%) |
| 4 | 122 (2.0%) |
| 5 | 15 (0.3%) |
| 6 | 364 (6.1%) |
| 7 | 22 (0.4%) |
| 8 | 121 (2.0%) |
| 9 | 62 (1.0%) |
| 10 | 1104 (18.4%) |
| 11 | 6 (0.1%) |
| 12 | 2 (0.0%) |
| 13 | 48 (0.8%) |
| 14 | 32 (0.5%) |
| 15 | 349 (5.8%) |
| 16 | 302 (5.0%) |
| 17 | 5 (0.1%) |
| 18 | 8 (0.1%) |
| 19 | 83 (1.4%) |
| 20 | 39 (0.7%) |
| 21 | 321 (5.4%) |
| 22 | 200 (3.3%) |
| 24 | 7 (0.1%) |
| 25 | 12 (0.2%) |
| 26 | 104 (1.7%) |
| 27 | 6 (0.1%) |
| 28 | 23 (0.4%) |
| 29 | 32 (0.5%) |
| 30 | 106 (1.8%) |
| 31 | 6 (0.1%) |
| 32 | 20 (0.3%) |
1.5.3 Association for any fracture
library(survival)
m.any.calci.m = coxph(Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + calci_bin, data = men)
summary(m.any.calci.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + calci_bin, data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.597585 1.817724 0.062762 9.5215 < 2.2e-16
## bmd_bin2.BMD<= -2.5 0.949808 2.585213 0.102930 9.2277 < 2.2e-16
## fall_bin2.Falls 1+ 0.332225 1.394066 0.069798 4.7598 1.938e-06
## fx50_bin2.Fx 1+ 0.473618 1.605793 0.071454 6.6283 3.395e-11
## calci_bin2.Insufficient Calcium 0.025972 1.026313 0.070796 0.3669 0.7137
##
## age_bin2.Age>= 75 ***
## bmd_bin2.BMD<= -2.5 ***
## fall_bin2.Falls 1+ ***
## fx50_bin2.Fx 1+ ***
## calci_bin2.Insufficient Calcium
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.8177 0.55014 1.60733 2.0557
## bmd_bin2.BMD<= -2.5 2.5852 0.38682 2.11291 3.1631
## fall_bin2.Falls 1+ 1.3941 0.71733 1.21583 1.5984
## fx50_bin2.Fx 1+ 1.6058 0.62275 1.39594 1.8472
## calci_bin2.Insufficient Calcium 1.0263 0.97436 0.89334 1.1791
##
## Concordance= 0.635 (se = 0.009 )
## Likelihood ratio test= 256.73 on 5 df, p=<2e-16
## Wald test = 297.93 on 5 df, p=<2e-16
## Score (logrank) test = 317.22 on 5 df, p=<2e-16options(digits = 8)
any.calci.m = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(group.c), data = men)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 11,16 ; coefficient may be infinite.summary(any.calci.m)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(group.c), data = men)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.c)2 -6.7138e-02 9.3507e-01 1.2952e-01 -0.5184 0.6041958
## as.factor(group.c)3 6.4204e-01 1.9003e+00 2.2610e-01 2.8396 0.0045165 **
## as.factor(group.c)4 3.5101e-01 1.4205e+00 2.3694e-01 1.4814 0.1384903
## as.factor(group.c)5 1.2732e+00 3.5722e+00 4.2353e-01 3.0062 0.0026456 **
## as.factor(group.c)6 4.6777e-01 1.5964e+00 1.7408e-01 2.6871 0.0072074 **
## as.factor(group.c)7 1.1856e+00 3.2728e+00 4.2366e-01 2.7986 0.0051328 **
## as.factor(group.c)8 8.8872e-01 2.4320e+00 2.2984e-01 3.8668 0.0001103 ***
## as.factor(group.c)9 8.3156e-01 2.2969e+00 2.9959e-01 2.7757 0.0055091 **
## as.factor(group.c)10 6.2647e-01 1.8710e+00 1.3386e-01 4.6802 2.866e-06 ***
## as.factor(group.c)11 2.3803e+00 1.0808e+01 4.6174e-01 5.1551 2.535e-07 ***
## as.factor(group.c)12 -1.2188e+01 5.0913e-06 9.2764e+02 -0.0131 0.9895172
## as.factor(group.c)13 7.0636e-01 2.0266e+00 3.0985e-01 2.2797 0.0226264 *
## as.factor(group.c)14 3.3054e-01 1.3917e+00 4.2347e-01 0.7805 0.4350741
## as.factor(group.c)15 2.6881e-01 1.3084e+00 1.6967e-01 1.5843 0.1131344
## as.factor(group.c)16 4.7734e-01 1.6118e+00 1.6677e-01 2.8622 0.0042066 **
## as.factor(group.c)17 -1.2171e+01 5.1797e-06 6.7200e+02 -0.0181 0.9855500
## as.factor(group.c)18 2.0269e+00 7.5908e+00 4.2373e-01 4.7836 1.722e-06 ***
## as.factor(group.c)19 1.4668e+00 4.3354e+00 2.2659e-01 6.4736 9.569e-11 ***
## as.factor(group.c)20 1.3054e+00 3.6890e+00 3.3593e-01 3.8859 0.0001020 ***
## as.factor(group.c)21 9.4067e-01 2.5617e+00 1.6532e-01 5.6901 1.270e-08 ***
## as.factor(group.c)22 9.5185e-01 2.5905e+00 1.8713e-01 5.0865 3.647e-07 ***
## as.factor(group.c)24 7.4727e-01 2.1112e+00 7.1602e-01 1.0436 0.2966563
## as.factor(group.c)25 1.5030e+00 4.4952e+00 4.2348e-01 3.5492 0.0003864 ***
## as.factor(group.c)26 8.2405e-01 2.2797e+00 2.1995e-01 3.7466 0.0001793 ***
## as.factor(group.c)27 2.1166e+00 8.3028e+00 7.1693e-01 2.9523 0.0031544 **
## as.factor(group.c)28 2.0996e+00 8.1627e+00 3.3660e-01 6.2376 4.444e-10 ***
## as.factor(group.c)29 2.2661e+00 9.6419e+00 2.8295e-01 8.0090 1.156e-15 ***
## as.factor(group.c)30 1.3457e+00 3.8408e+00 2.1779e-01 6.1788 6.460e-10 ***
## as.factor(group.c)31 1.6051e+00 4.9782e+00 5.8838e-01 2.7279 0.0063736 **
## as.factor(group.c)32 2.3509e+00 1.0495e+01 3.5252e-01 6.6689 2.577e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.c)2 9.3507e-01 1.0694e+00 0.72543 1.2053
## as.factor(group.c)3 1.9003e+00 5.2622e-01 1.22005 2.9600
## as.factor(group.c)4 1.4205e+00 7.0398e-01 0.89281 2.2601
## as.factor(group.c)5 3.5722e+00 2.7994e-01 1.55752 8.1931
## as.factor(group.c)6 1.5964e+00 6.2640e-01 1.13494 2.2456
## as.factor(group.c)7 3.2728e+00 3.0555e-01 1.42659 7.5081
## as.factor(group.c)8 2.4320e+00 4.1118e-01 1.55000 3.8160
## as.factor(group.c)9 2.2969e+00 4.3537e-01 1.27682 4.1319
## as.factor(group.c)10 1.8710e+00 5.3447e-01 1.43925 2.4323
## as.factor(group.c)11 1.0808e+01 9.2521e-02 4.37243 26.7173
## as.factor(group.c)12 5.0913e-06 1.9641e+05 0.00000 Inf
## as.factor(group.c)13 2.0266e+00 4.9344e-01 1.10414 3.7198
## as.factor(group.c)14 1.3917e+00 7.1854e-01 0.60686 3.1916
## as.factor(group.c)15 1.3084e+00 7.6429e-01 0.93824 1.8246
## as.factor(group.c)16 1.6118e+00 6.2043e-01 1.16238 2.2349
## as.factor(group.c)17 5.1797e-06 1.9306e+05 0.00000 Inf
## as.factor(group.c)18 7.5908e+00 1.3174e-01 3.30836 17.4167
## as.factor(group.c)19 4.3354e+00 2.3066e-01 2.78076 6.7593
## as.factor(group.c)20 3.6890e+00 2.7107e-01 1.90973 7.1262
## as.factor(group.c)21 2.5617e+00 3.9037e-01 1.85272 3.5420
## as.factor(group.c)22 2.5905e+00 3.8603e-01 1.79513 3.7383
## as.factor(group.c)24 2.1112e+00 4.7366e-01 0.51886 8.5904
## as.factor(group.c)25 4.4952e+00 2.2246e-01 1.96011 10.3090
## as.factor(group.c)26 2.2797e+00 4.3865e-01 1.48136 3.5083
## as.factor(group.c)27 8.3028e+00 1.2044e-01 2.03688 33.8437
## as.factor(group.c)28 8.1627e+00 1.2251e-01 4.22008 15.7889
## as.factor(group.c)29 9.6419e+00 1.0371e-01 5.53758 16.7884
## as.factor(group.c)30 3.8408e+00 2.6036e-01 2.50632 5.8857
## as.factor(group.c)31 4.9782e+00 2.0088e-01 1.57121 15.7725
## as.factor(group.c)32 1.0495e+01 9.5282e-02 5.25928 20.9436
##
## Concordance= 0.635 (se = 0.009 )
## Likelihood ratio test= 278.29 on 30 df, p=<2e-16
## Wald test = 328.4 on 30 df, p=<2e-16
## Score (logrank) test = 396.73 on 30 df, p=<2e-161.5.4 Association for hip fracture
m.hip.calci.m = coxph(Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + calci_bin, data = men)
summary(m.hip.calci.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + calci_bin, data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 1.107198 3.025867 0.138169 8.0133 1.116e-15
## bmd_bin2.BMD<= -2.5 1.575406 4.832701 0.168074 9.3733 < 2.2e-16
## fall_bin2.Falls 1+ 0.326992 1.386791 0.147697 2.2139 0.02683
## fx50_bin2.Fx 1+ 0.249872 1.283861 0.157082 1.5907 0.11167
## calci_bin2.Insufficient Calcium 0.056672 1.058309 0.152101 0.3726 0.70945
##
## age_bin2.Age>= 75 ***
## bmd_bin2.BMD<= -2.5 ***
## fall_bin2.Falls 1+ *
## fx50_bin2.Fx 1+
## calci_bin2.Insufficient Calcium
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 3.0259 0.33048 2.30802 3.9670
## bmd_bin2.BMD<= -2.5 4.8327 0.20692 3.47636 6.7182
## fall_bin2.Falls 1+ 1.3868 0.72109 1.03822 1.8524
## fx50_bin2.Fx 1+ 1.2839 0.77890 0.94365 1.7467
## calci_bin2.Insufficient Calcium 1.0583 0.94490 0.78550 1.4259
##
## Concordance= 0.724 (se = 0.017 )
## Likelihood ratio test= 162.1 on 5 df, p=<2e-16
## Wald test = 198.18 on 5 df, p=<2e-16
## Score (logrank) test = 249.33 on 5 df, p=<2e-16options(digits = 8)
hip.calci.m = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(group.c), data = men)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 4,11,16,17,22,25 ; coefficient may be
## infinite.summary(hip.calci.m)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(group.c), data = men)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.c)2 1.8101e-01 1.1984e+00 3.3711e-01 0.5370 0.5913008
## as.factor(group.c)3 7.0271e-01 2.0192e+00 5.8388e-01 1.2035 0.2287750
## as.factor(group.c)4 5.2154e-01 1.6846e+00 5.8388e-01 0.8932 0.3717317
## as.factor(group.c)5 -1.3589e+01 1.2541e-06 1.6820e+03 -0.0081 0.9935538
## as.factor(group.c)6 1.4154e+00 4.1182e+00 3.7601e-01 3.7644 0.0001670 ***
## as.factor(group.c)7 2.1141e+00 8.2825e+00 7.6923e-01 2.7484 0.0059892 **
## as.factor(group.c)8 1.7586e+00 5.8042e+00 4.6556e-01 3.7774 0.0001585 ***
## as.factor(group.c)9 8.8868e-01 2.4319e+00 7.6925e-01 1.1553 0.2479833
## as.factor(group.c)10 1.0151e+00 2.7596e+00 3.4230e-01 2.9656 0.0030214 **
## as.factor(group.c)11 3.5006e+00 3.3135e+01 6.5159e-01 5.3724 7.770e-08 ***
## as.factor(group.c)12 -1.3599e+01 1.2411e-06 5.1648e+03 -0.0026 0.9978991
## as.factor(group.c)13 2.0003e+00 7.3916e+00 5.0758e-01 3.9409 8.117e-05 ***
## as.factor(group.c)14 4.8244e-01 1.6200e+00 1.0445e+00 0.4619 0.6441545
## as.factor(group.c)15 1.7941e-01 1.1965e+00 4.6466e-01 0.3861 0.6994194
## as.factor(group.c)16 -1.8052e-01 8.3483e-01 5.3936e-01 -0.3347 0.7378538
## as.factor(group.c)17 -1.3558e+01 1.2936e-06 3.8022e+03 -0.0036 0.9971549
## as.factor(group.c)18 -1.3564e+01 1.2863e-06 2.5063e+03 -0.0054 0.9956819
## as.factor(group.c)19 2.8429e+00 1.7166e+01 3.9797e-01 7.1435 9.097e-13 ***
## as.factor(group.c)20 1.5198e+00 4.5714e+00 7.6901e-01 1.9763 0.0481180 *
## as.factor(group.c)21 1.5624e+00 4.7702e+00 3.8376e-01 4.0713 4.675e-05 ***
## as.factor(group.c)22 1.8215e+00 6.1813e+00 3.9783e-01 4.5787 4.678e-06 ***
## as.factor(group.c)24 -1.3596e+01 1.2450e-06 2.3660e+03 -0.0057 0.9954149
## as.factor(group.c)25 2.2327e+00 9.3247e+00 7.6875e-01 2.9043 0.0036810 **
## as.factor(group.c)26 5.7266e-03 1.0057e+00 7.6871e-01 0.0074 0.9940561
## as.factor(group.c)27 -1.3547e+01 1.3079e-06 3.7884e+03 -0.0036 0.9971468
## as.factor(group.c)28 3.2706e+00 2.6326e+01 5.4135e-01 6.0415 1.527e-09 ***
## as.factor(group.c)29 3.4356e+00 3.1050e+01 4.6645e-01 7.3655 1.765e-13 ***
## as.factor(group.c)30 2.0343e+00 7.6467e+00 4.6608e-01 4.3646 1.273e-05 ***
## as.factor(group.c)31 3.1191e+00 2.2625e+01 7.6917e-01 4.0551 5.011e-05 ***
## as.factor(group.c)32 3.2210e+00 2.5054e+01 6.5359e-01 4.9282 8.299e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.c)2 1.1984e+00 8.3443e-01 0.61897 2.3204
## as.factor(group.c)3 2.0192e+00 4.9524e-01 0.64296 6.3413
## as.factor(group.c)4 1.6846e+00 5.9361e-01 0.53642 5.2905
## as.factor(group.c)5 1.2541e-06 7.9740e+05 0.00000 Inf
## as.factor(group.c)6 4.1182e+00 2.4282e-01 1.97085 8.6053
## as.factor(group.c)7 8.2825e+00 1.2074e-01 1.83395 37.4053
## as.factor(group.c)8 5.8042e+00 1.7229e-01 2.33054 14.4551
## as.factor(group.c)9 2.4319e+00 4.1120e-01 0.53848 10.9833
## as.factor(group.c)10 2.7596e+00 3.6237e-01 1.41088 5.3978
## as.factor(group.c)11 3.3135e+01 3.0180e-02 9.23956 118.8277
## as.factor(group.c)12 1.2411e-06 8.0572e+05 0.00000 Inf
## as.factor(group.c)13 7.3916e+00 1.3529e-01 2.73326 19.9890
## as.factor(group.c)14 1.6200e+00 6.1728e-01 0.20915 12.5481
## as.factor(group.c)15 1.1965e+00 8.3576e-01 0.48128 2.9747
## as.factor(group.c)16 8.3483e-01 1.1978e+00 0.29006 2.4027
## as.factor(group.c)17 1.2936e-06 7.7306e+05 0.00000 Inf
## as.factor(group.c)18 1.2863e-06 7.7743e+05 0.00000 Inf
## as.factor(group.c)19 1.7166e+01 5.8255e-02 7.86882 37.4470
## as.factor(group.c)20 4.5714e+00 2.1875e-01 1.01266 20.6364
## as.factor(group.c)21 4.7702e+00 2.0964e-01 2.24844 10.1202
## as.factor(group.c)22 6.1813e+00 1.6178e-01 2.83434 13.4806
## as.factor(group.c)24 1.2450e-06 8.0321e+05 0.00000 Inf
## as.factor(group.c)25 9.3247e+00 1.0724e-01 2.06668 42.0725
## as.factor(group.c)26 1.0057e+00 9.9429e-01 0.22293 4.5375
## as.factor(group.c)27 1.3079e-06 7.6459e+05 0.00000 Inf
## as.factor(group.c)28 2.6326e+01 3.7985e-02 9.11153 76.0655
## as.factor(group.c)29 3.1050e+01 3.2206e-02 12.44577 77.4646
## as.factor(group.c)30 7.6467e+00 1.3078e-01 3.06722 19.0636
## as.factor(group.c)31 2.2625e+01 4.4198e-02 5.01048 102.1672
## as.factor(group.c)32 2.5054e+01 3.9914e-02 6.95882 90.2004
##
## Concordance= 0.739 (se = 0.017 )
## Likelihood ratio test= 196.98 on 30 df, p=<2e-16
## Wald test = 239.9 on 30 df, p=<2e-16
## Score (logrank) test = 382.01 on 30 df, p=<2e-162. WOMEN
Data management
women = read.csv("C:\\Thach\\Research projects\\PAR for lifestyle factors\\women.csv")
head(women)## data id visit gender age race education weight height bmi no_falls
## 1 SOF 1 2 FALSE 69 1:WHITE 9 67.3 150.5 29.71270 2
## 2 SOF 2 2 FALSE 84 1:WHITE 10 68.4 151.8 29.68333 1
## 3 SOF 3 2 FALSE 75 1:WHITE 12 72.7 151.0 31.88457 3
## 4 SOF 4 2 FALSE 67 1:WHITE 12 60.6 155.1 25.19121 1
## 5 SOF 5 2 FALSE 84 1:WHITE 17 44.7 157.0 18.13461 0
## 6 SOF 6 2 FALSE 71 1:WHITE 15 84.1 161.6 32.20426 0
## fx50 physical hypertension copd parkinson cancer rheumatoid cvd renal
## 1 1 0 0 0 0 0 0 0 0
## 2 1 0 1 0 0 0 0 1 0
## 3 0 1 0 1 0 1 0 0 0
## 4 0 1 0 0 0 1 0 0 0
## 5 0 0 0 0 0 0 0 0 1
## 6 0 1 1 0 1 0 0 0 0
## depression diabetes medyes deathx fnbmd time2visit anyfx time2any hipfx
## 1 0 0 0 0 0.656 0 0 17.2238 0
## 2 0 2 0 1 0.585 0 0 6.5325 0
## 3 0 0 1 0 0.654 0 0 18.6366 0
## 4 0 0 1 0 0.842 0 0 19.7481 0
## 5 0 0 0 0 0.487 0 0 14.8720 0
## 6 0 0 0 0 0.851 0 0 19.6167 0
## time2hip death time2end tscore osteo smoke physical4 drink4
## 1 17.2238 0 17.223820 -1.6833330 Osteopenia Past No Low
## 2 6.5325 1 6.532512 -2.2750000 Osteopenia Never No No
## 3 18.6366 0 18.636550 -1.7000000 Osteopenia Past No Moderate
## 4 19.7481 0 19.748120 -0.1333333 Normal Never No No
## 5 14.8720 0 14.872010 -3.0916670 Osteoporosis Never No No
## 6 19.6167 0 19.616700 -0.0583333 Normal Never No No
## coffee4 calcium2 protein2
## 1 Low 1787 210
## 2 Low 6727 336
## 3 Moderate 5316 448
## 4 Moderate 8666 484
## 5 Moderate 5216 317
## 6 Moderate 1956 308dim(women)## [1] 7959 40Create variables
women = women %>% mutate(age_bin = case_when(age < 75 ~ "1.Age< 75",
age >= 75 ~ "2.Age>= 75"))
women = women %>% mutate(bmd_bin = case_when(tscore > -2.5 ~ "1.BMD> -2.5",
tscore <= -2.5 ~ "2.BMD<= -2.5"))
women = women %>% mutate(fall_bin = case_when(no_falls == 0 ~ "1.No falls",
no_falls > 0 ~ "2.Falls 1+"))
women = women %>% mutate(fx50_bin = case_when(fx50 == 0 ~ "1.No fx",
fx50 > 0 ~ "2.Fx 1+"))
women = women %>% mutate(smoke_bin0 = case_when(smoke == "Never" | smoke == "Past" ~ "1.No/past smoking",
smoke == "Current" ~ "2.Current smoking"))
women = women %>% mutate(smoke_bin = case_when(smoke == "Never"~ "1.No/past smoking",
smoke == "Current" | smoke == "Past" ~ "2.Current smoking"))
women = women %>% mutate(drink_bin = case_when(drink4 == "No" | drink4 == "Low" | drink4 == "Moderate" ~ "1.Less drinking",
drink4 == "High" ~ "2.Excessive drinking"))
women = women %>% mutate(activity_bin = case_when(physical4 == "Moderate" | physical4 == "High" ~ "1.Proactive",
physical4 == "No" | physical4 == "Low" ~ "2.Less active"))
women = women %>% mutate(calci_bin = case_when(calcium2 >= 6611.5 ~ "1.Sufficient Calcium",
calcium2 < 6611.5 ~ "2.Insufficient Calcium"))
men = men %>% mutate(protein_bin = case_when(protein2 >= 436 ~ "1.Sufficient protein",
protein2 < 436 ~ "2.Insufficient protein"))2.1 Descriptive analysis
table1(~ age + race + fnbmd + tscore + as.factor(no_falls) + as.factor(fx50) + as.factor(smoke) + as.factor(drink4) + as.factor(physical4) + calcium2 + protein2 + as.factor(education) + bmi + as.factor(cvd) + as.factor(hypertension) + as.factor(copd) + as.factor(diabetes) + as.factor(cancer) + as.factor(renal) + as.factor(parkinson) + as.factor(depression) + as.factor(rheumatoid) + as.factor(death) | anyfx, data = women, render.continuous = c(. = "Median [Q1, Q3]"))## Warning in table1.formula(~age + race + fnbmd + tscore + as.factor(no_falls) +
## : Terms to the right of '|' in formula 'x' define table columns and are
## expected to be factors with meaningful labels.| 0 (N=5330) |
1 (N=2629) |
Overall (N=7959) |
|
|---|---|---|---|
| age | |||
| Median [Q1, Q3] | 72.0 [69.0, 76.0] | 73.0 [70.0, 77.0] | 72.0 [69.0, 76.0] |
| race | |||
| 1:WHITE | 5317 (99.8%) | 2620 (99.7%) | 7937 (99.7%) |
| 2 | 13 (0.2%) | 9 (0.3%) | 22 (0.3%) |
| fnbmd | |||
| Median [Q1, Q3] | 0.650 [0.581, 0.724] | 0.617 [0.555, 0.685] | 0.639 [0.571, 0.712] |
| tscore | |||
| Median [Q1, Q3] | -1.73 [-2.31, -1.12] | -2.01 [-2.53, -1.44] | -1.83 [-2.39, -1.22] |
| as.factor(no_falls) | |||
| 0 | 3771 (70.8%) | 1819 (69.2%) | 5590 (70.2%) |
| 1 | 1047 (19.6%) | 525 (20.0%) | 1572 (19.8%) |
| 2 | 337 (6.3%) | 196 (7.5%) | 533 (6.7%) |
| 3 | 103 (1.9%) | 47 (1.8%) | 150 (1.9%) |
| 4 | 31 (0.6%) | 23 (0.9%) | 54 (0.7%) |
| 5 | 13 (0.2%) | 6 (0.2%) | 19 (0.2%) |
| 6 | 12 (0.2%) | 7 (0.3%) | 19 (0.2%) |
| 7 | 2 (0.0%) | 1 (0.0%) | 3 (0.0%) |
| 8 | 5 (0.1%) | 2 (0.1%) | 7 (0.1%) |
| 10 | 1 (0.0%) | 2 (0.1%) | 3 (0.0%) |
| 11 | 1 (0.0%) | 0 (0%) | 1 (0.0%) |
| 12 | 2 (0.0%) | 0 (0%) | 2 (0.0%) |
| 15 | 1 (0.0%) | 0 (0%) | 1 (0.0%) |
| 20 | 2 (0.0%) | 1 (0.0%) | 3 (0.0%) |
| 35 | 1 (0.0%) | 0 (0%) | 1 (0.0%) |
| 98 | 1 (0.0%) | 0 (0%) | 1 (0.0%) |
| as.factor(fx50) | |||
| 0 | 3222 (60.5%) | 1504 (57.2%) | 4726 (59.4%) |
| 1 | 2108 (39.5%) | 1125 (42.8%) | 3233 (40.6%) |
| as.factor(smoke) | |||
| Current | 542 (10.2%) | 215 (8.2%) | 757 (9.5%) |
| Never | 3172 (59.5%) | 1643 (62.5%) | 4815 (60.5%) |
| Past | 1616 (30.3%) | 771 (29.3%) | 2387 (30.0%) |
| as.factor(drink4) | |||
| High | 702 (13.2%) | 355 (13.5%) | 1057 (13.3%) |
| Low | 585 (11.0%) | 283 (10.8%) | 868 (10.9%) |
| Moderate | 354 (6.6%) | 176 (6.7%) | 530 (6.7%) |
| No | 3689 (69.2%) | 1815 (69.0%) | 5504 (69.2%) |
| as.factor(physical4) | |||
| Low | 354 (6.6%) | 161 (6.1%) | 515 (6.5%) |
| Moderate | 28 (0.5%) | 11 (0.4%) | 39 (0.5%) |
| No | 4948 (92.8%) | 2457 (93.5%) | 7405 (93.0%) |
| calcium2 | |||
| Median [Q1, Q3] | 4420 [2850, 6660] | 4330 [2810, 6500] | 4390 [2830, 6610] |
| protein2 | |||
| Median [Q1, Q3] | 346 [265, 437] | 338 [261, 433] | 343 [264, 436] |
| as.factor(education) | |||
| 5 | 11 (0.2%) | 1 (0.0%) | 12 (0.2%) |
| 6 | 30 (0.6%) | 14 (0.5%) | 44 (0.6%) |
| 7 | 61 (1.1%) | 24 (0.9%) | 85 (1.1%) |
| 8 | 384 (7.2%) | 171 (6.5%) | 555 (7.0%) |
| 9 | 185 (3.5%) | 87 (3.3%) | 272 (3.4%) |
| 10 | 299 (5.6%) | 131 (5.0%) | 430 (5.4%) |
| 11 | 203 (3.8%) | 98 (3.7%) | 301 (3.8%) |
| 12 | 2110 (39.6%) | 1044 (39.7%) | 3154 (39.6%) |
| 13 | 420 (7.9%) | 235 (8.9%) | 655 (8.2%) |
| 14 | 428 (8.0%) | 190 (7.2%) | 618 (7.8%) |
| 15 | 223 (4.2%) | 109 (4.1%) | 332 (4.2%) |
| 16 | 453 (8.5%) | 207 (7.9%) | 660 (8.3%) |
| 17 | 192 (3.6%) | 101 (3.8%) | 293 (3.7%) |
| 18 | 144 (2.7%) | 97 (3.7%) | 241 (3.0%) |
| 19 | 180 (3.4%) | 107 (4.1%) | 287 (3.6%) |
| Missing | 7 (0.1%) | 13 (0.5%) | 20 (0.3%) |
| bmi | |||
| Median [Q1, Q3] | 25.8 [23.1, 29.1] | 25.3 [22.8, 28.5] | 25.6 [23.0, 28.8] |
| Missing | 44 (0.8%) | 30 (1.1%) | 74 (0.9%) |
| as.factor(cvd) | |||
| 0 | 4015 (75.3%) | 2033 (77.3%) | 6048 (76.0%) |
| 1 | 989 (18.6%) | 457 (17.4%) | 1446 (18.2%) |
| 2 | 249 (4.7%) | 97 (3.7%) | 346 (4.3%) |
| 3 | 63 (1.2%) | 33 (1.3%) | 96 (1.2%) |
| 4 | 14 (0.3%) | 9 (0.3%) | 23 (0.3%) |
| as.factor(hypertension) | |||
| 0 | 3305 (62.0%) | 1645 (62.6%) | 4950 (62.2%) |
| 1 | 2025 (38.0%) | 984 (37.4%) | 3009 (37.8%) |
| as.factor(copd) | |||
| 0 | 4414 (82.8%) | 2171 (82.6%) | 6585 (82.7%) |
| 1 | 916 (17.2%) | 458 (17.4%) | 1374 (17.3%) |
| as.factor(diabetes) | |||
| 0 | 4978 (93.4%) | 2460 (93.6%) | 7438 (93.5%) |
| 1 | 50 (0.9%) | 28 (1.1%) | 78 (1.0%) |
| 2 | 302 (5.7%) | 141 (5.4%) | 443 (5.6%) |
| as.factor(cancer) | |||
| 0 | 4325 (81.1%) | 2099 (79.8%) | 6424 (80.7%) |
| 1 | 1005 (18.9%) | 530 (20.2%) | 1535 (19.3%) |
| as.factor(renal) | |||
| 0 | 5268 (98.8%) | 2596 (98.7%) | 7864 (98.8%) |
| 1 | 62 (1.2%) | 33 (1.3%) | 95 (1.2%) |
| as.factor(parkinson) | |||
| 0 | 5303 (99.5%) | 2610 (99.3%) | 7913 (99.4%) |
| 1 | 27 (0.5%) | 19 (0.7%) | 46 (0.6%) |
| as.factor(depression) | |||
| 0 | 4944 (92.8%) | 2416 (91.9%) | 7360 (92.5%) |
| 1 | 386 (7.2%) | 213 (8.1%) | 599 (7.5%) |
| as.factor(rheumatoid) | |||
| 0 | 5053 (94.8%) | 2461 (93.6%) | 7514 (94.4%) |
| 1 | 277 (5.2%) | 168 (6.4%) | 445 (5.6%) |
| as.factor(death) | |||
| 0 | 2140 (40.2%) | 1030 (39.2%) | 3170 (39.8%) |
| 1 | 3190 (59.9%) | 1599 (60.8%) | 4789 (60.2%) |
2.2 Current Smoking
2.2.1 Data management
women = women %>% mutate(group.s = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin0 == "1.No/past smoking" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin0 == "2.Current smoking" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "1.No/past smoking" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin0 == "1.No/past smoking" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin0 == "1.No/past smoking" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin0 == "1.No/past smoking" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin0 == "1.No/past smoking" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin0 == "1.No/past smoking" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "1.No/past smoking" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin0 == "2.Current smoking" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin0 == "1.No/past smoking" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "1.No/past smoking" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin0 == "2.Current smoking" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "1.No/past smoking" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin0 == "2.Current smoking" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "2.Current smoking" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin0 == "1.No/past smoking" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "1.No/past smoking" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin0 == "2.Current smoking" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "1.No/past smoking" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin0 == "2.Current smoking" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "2.Current smoking" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "1.No/past smoking" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin0 == "2.Current smoking" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "2.Current smoking" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "2.Current smoking" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "1.No/past smoking" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin0 == "2.Current smoking" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "2.Current smoking" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "2.Current smoking" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "2.Current smoking" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin0 == "2.Current smoking" ~ 32))2.2.2 Prevalences
table1(~ age + age_bin + fnbmd + tscore + bmd_bin + fall_bin + fx50_bin + smoke_bin0 + drink_bin + activity_bin + as.factor(group.s), data = women, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=7959) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 72.0 [69.0, 76.0] |
| age_bin | |
| 1.Age< 75 | 5226 (65.7%) |
| 2.Age>= 75 | 2733 (34.3%) |
| fnbmd | |
| Median [Q1, Q3] | 0.639 [0.571, 0.712] |
| tscore | |
| Median [Q1, Q3] | -1.83 [-2.39, -1.22] |
| bmd_bin | |
| 1.BMD> -2.5 | 6303 (79.2%) |
| 2.BMD<= -2.5 | 1656 (20.8%) |
| fall_bin | |
| 1.No falls | 5590 (70.2%) |
| 2.Falls 1+ | 2369 (29.8%) |
| fx50_bin | |
| 1.No fx | 4726 (59.4%) |
| 2.Fx 1+ | 3233 (40.6%) |
| smoke_bin0 | |
| 1.No/past smoking | 7202 (90.5%) |
| 2.Current smoking | 757 (9.5%) |
| drink_bin | |
| 1.Less drinking | 6902 (86.7%) |
| 2.Excessive drinking | 1057 (13.3%) |
| activity_bin | |
| 1.Proactive | 39 (0.5%) |
| 2.Less active | 7920 (99.5%) |
| as.factor(group.s) | |
| 1 | 1861 (23.4%) |
| 2 | 237 (3.0%) |
| 3 | 890 (11.2%) |
| 4 | 719 (9.0%) |
| 5 | 247 (3.1%) |
| 6 | 744 (9.3%) |
| 7 | 247 (3.1%) |
| 8 | 307 (3.9%) |
| 9 | 475 (6.0%) |
| 10 | 44 (0.6%) |
| 11 | 84 (1.1%) |
| 12 | 237 (3.0%) |
| 13 | 47 (0.6%) |
| 14 | 478 (6.0%) |
| 15 | 61 (0.8%) |
| 16 | 123 (1.5%) |
| 17 | 77 (1.0%) |
| 18 | 315 (4.0%) |
| 19 | 17 (0.2%) |
| 20 | 256 (3.2%) |
| 21 | 17 (0.2%) |
| 22 | 34 (0.4%) |
| 23 | 114 (1.4%) |
| 24 | 13 (0.2%) |
| 25 | 50 (0.6%) |
| 26 | 44 (0.6%) |
| 27 | 151 (1.9%) |
| 28 | 4 (0.1%) |
| 29 | 22 (0.3%) |
| 30 | 13 (0.2%) |
| 31 | 21 (0.3%) |
| 32 | 10 (0.1%) |
2.2.3 Association for any fracture
smoke.age.w = coxph(Surv(time2any, anyfx) ~ age + smoke_bin0, data = women)
summary(smoke.age.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ age + smoke_bin0, data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age 0.0564584 1.0580826 0.0040165 14.0567 <2e-16 ***
## smoke_bin02.Current smoking 0.0572162 1.0588847 0.0715469 0.7997 0.4239
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age 1.0581 0.94511 1.04979 1.0664
## smoke_bin02.Current smoking 1.0589 0.94439 0.92034 1.2183
##
## Concordance= 0.573 (se = 0.006 )
## Likelihood ratio test= 184.6 on 2 df, p=<2e-16
## Wald test = 197.89 on 2 df, p=<2e-16
## Score (logrank) test = 200.06 on 2 df, p=<2e-16m.any.smoke.w = coxph(Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin0, data = women)
summary(m.any.smoke.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin0, data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.408434 1.504460 0.041898 9.7482 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.483787 1.622206 0.045737 10.5776 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.071756 1.074393 0.042450 1.6904 0.090957 .
## fx50_bin2.Fx 1+ 0.110970 1.117362 0.040301 2.7536 0.005895 **
## smoke_bin02.Current smoking 0.018256 1.018424 0.071599 0.2550 0.798741
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.5045 0.66469 1.38585 1.6332
## bmd_bin2.BMD<= -2.5 1.6222 0.61644 1.48311 1.7743
## fall_bin2.Falls 1+ 1.0744 0.93076 0.98862 1.1676
## fx50_bin2.Fx 1+ 1.1174 0.89497 1.03250 1.2092
## smoke_bin02.Current smoking 1.0184 0.98191 0.88508 1.1719
##
## Concordance= 0.589 (se = 0.006 )
## Likelihood ratio test= 257 on 5 df, p=<2e-16
## Wald test = 277.3 on 5 df, p=<2e-16
## Score (logrank) test = 284.05 on 5 df, p=<2e-16options(digits = 8)
any.smoke.w = coxph(Surv(time2any, anyfx) ~ as.factor(group.s), data = women)
summary(any.smoke.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ as.factor(group.s), data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.s)2 -0.044057 0.956899 0.144336 -0.3052 0.7601812
## as.factor(group.s)3 0.398854 1.490116 0.071177 5.6037 2.098e-08 ***
## as.factor(group.s)4 0.187957 1.206782 0.079050 2.3777 0.0174213 *
## as.factor(group.s)5 0.576271 1.779391 0.107611 5.3551 8.549e-08 ***
## as.factor(group.s)6 0.464727 1.591580 0.079972 5.8111 6.206e-09 ***
## as.factor(group.s)7 1.073516 2.925649 0.104843 10.2393 < 2.2e-16 ***
## as.factor(group.s)8 0.665050 1.944588 0.104556 6.3607 2.008e-10 ***
## as.factor(group.s)9 0.506781 1.659938 0.093908 5.3966 6.792e-08 ***
## as.factor(group.s)10 0.439675 1.552203 0.304966 1.4417 0.1493813
## as.factor(group.s)11 0.923850 2.518970 0.157194 5.8771 4.174e-09 ***
## as.factor(group.s)12 0.606618 1.834217 0.111758 5.4280 5.700e-08 ***
## as.factor(group.s)13 1.030824 2.803375 0.222889 4.6248 3.749e-06 ***
## as.factor(group.s)14 0.207808 1.230976 0.093121 2.2316 0.0256424 *
## as.factor(group.s)15 0.421740 1.524612 0.246639 1.7099 0.0872758 .
## as.factor(group.s)16 0.269703 1.309576 0.174808 1.5429 0.1228670
## as.factor(group.s)17 1.410100 4.096366 0.160918 8.7629 < 2.2e-16 ***
## as.factor(group.s)18 1.123470 3.075509 0.096568 11.6340 < 2.2e-16 ***
## as.factor(group.s)19 0.739761 2.095434 0.410815 1.8007 0.0717475 .
## as.factor(group.s)20 0.685671 1.985103 0.116309 5.8953 3.741e-09 ***
## as.factor(group.s)21 0.554362 1.740829 0.449467 1.2334 0.2174356
## as.factor(group.s)22 0.628520 1.874834 0.319463 1.9674 0.0491341 *
## as.factor(group.s)23 0.370930 1.449082 0.164195 2.2591 0.0238782 *
## as.factor(group.s)24 -0.224539 0.798885 0.708537 -0.3169 0.7513157
## as.factor(group.s)25 0.662114 1.938887 0.246685 2.6840 0.0072737 **
## as.factor(group.s)26 0.503240 1.654072 0.261990 1.9208 0.0547521 .
## as.factor(group.s)27 0.896490 2.450984 0.148614 6.0323 1.616e-09 ***
## as.factor(group.s)28 2.309841 10.072820 0.579671 3.9847 6.755e-05 ***
## as.factor(group.s)29 1.300208 3.670059 0.336622 3.8625 0.0001122 ***
## as.factor(group.s)30 0.480057 1.616167 0.502084 0.9561 0.3390067
## as.factor(group.s)31 0.271496 1.311925 0.502094 0.5407 0.5886958
## as.factor(group.s)32 0.757250 2.132404 0.579213 1.3074 0.1910845
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.s)2 0.95690 1.045042 0.72112 1.2698
## as.factor(group.s)3 1.49012 0.671089 1.29609 1.7132
## as.factor(group.s)4 1.20678 0.828650 1.03357 1.4090
## as.factor(group.s)5 1.77939 0.561990 1.44103 2.1972
## as.factor(group.s)6 1.59158 0.628306 1.36068 1.8617
## as.factor(group.s)7 2.92565 0.341805 2.38221 3.5931
## as.factor(group.s)8 1.94459 0.514248 1.58427 2.3869
## as.factor(group.s)9 1.65994 0.602432 1.38089 1.9954
## as.factor(group.s)10 1.55220 0.644246 0.85381 2.8219
## as.factor(group.s)11 2.51897 0.396988 1.85106 3.4279
## as.factor(group.s)12 1.83422 0.545192 1.47341 2.2834
## as.factor(group.s)13 2.80337 0.356713 1.81116 4.3392
## as.factor(group.s)14 1.23098 0.812363 1.02562 1.4775
## as.factor(group.s)15 1.52461 0.655905 0.94020 2.4723
## as.factor(group.s)16 1.30958 0.763606 0.92968 1.8447
## as.factor(group.s)17 4.09637 0.244119 2.98831 5.6153
## as.factor(group.s)18 3.07551 0.325149 2.54518 3.7163
## as.factor(group.s)19 2.09543 0.477228 0.93667 4.6877
## as.factor(group.s)20 1.98510 0.503752 1.58045 2.4934
## as.factor(group.s)21 1.74083 0.574439 0.72139 4.2009
## as.factor(group.s)22 1.87483 0.533381 1.00239 3.5066
## as.factor(group.s)23 1.44908 0.690092 1.05034 1.9992
## as.factor(group.s)24 0.79888 1.251745 0.19924 3.2033
## as.factor(group.s)25 1.93889 0.515760 1.19557 3.1444
## as.factor(group.s)26 1.65407 0.604569 0.98980 2.7641
## as.factor(group.s)27 2.45098 0.407999 1.83164 3.2798
## as.factor(group.s)28 10.07282 0.099277 3.23396 31.3739
## as.factor(group.s)29 3.67006 0.272475 1.89732 7.0992
## as.factor(group.s)30 1.61617 0.618748 0.60410 4.3237
## as.factor(group.s)31 1.31193 0.762239 0.49037 3.5099
## as.factor(group.s)32 2.13240 0.468954 0.68524 6.6358
##
## Concordance= 0.594 (se = 0.006 )
## Likelihood ratio test= 311.52 on 31 df, p=<2e-16
## Wald test = 338.71 on 31 df, p=<2e-16
## Score (logrank) test = 362.5 on 31 df, p=<2e-162.2.4 Association for hip fracture
hip.smoke.age.w = coxph(Surv(time2hip, hipfx) ~ age + smoke_bin, data = women)
summary(hip.smoke.age.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ age + smoke_bin, data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age 0.1069449 1.1128730 0.0071449 14.9680 <2e-16 ***
## smoke_bin2.Current smoking 0.0192798 1.0194669 0.0768971 0.2507 0.802
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age 1.1129 0.89858 1.09740 1.1286
## smoke_bin2.Current smoking 1.0195 0.98090 0.87684 1.1853
##
## Concordance= 0.656 (se = 0.01 )
## Likelihood ratio test= 204.23 on 2 df, p=<2e-16
## Wald test = 226.94 on 2 df, p=<2e-16
## Score (logrank) test = 236.68 on 2 df, p=<2e-16m.hip.smoke.w = coxph(Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin0, data = women)
summary(m.hip.smoke.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin0, data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.6997474 2.0132440 0.0766669 9.1271 <2e-16
## bmd_bin2.BMD<= -2.5 0.9589552 2.6089692 0.0782834 12.2498 <2e-16
## fall_bin2.Falls 1+ -0.0074778 0.9925500 0.0807267 -0.0926 0.9262
## fx50_bin2.Fx 1+ -0.0099828 0.9900668 0.0755091 -0.1322 0.8948
## smoke_bin02.Current smoking -0.1000881 0.9047577 0.1432540 -0.6987 0.4848
##
## age_bin2.Age>= 75 ***
## bmd_bin2.BMD<= -2.5 ***
## fall_bin2.Falls 1+
## fx50_bin2.Fx 1+
## smoke_bin02.Current smoking
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 2.01324 0.49671 1.73236 2.3397
## bmd_bin2.BMD<= -2.5 2.60897 0.38329 2.23787 3.0416
## fall_bin2.Falls 1+ 0.99255 1.00751 0.84730 1.1627
## fx50_bin2.Fx 1+ 0.99007 1.01003 0.85387 1.1480
## smoke_bin02.Current smoking 0.90476 1.10527 0.68327 1.1980
##
## Concordance= 0.656 (se = 0.011 )
## Likelihood ratio test= 259.57 on 5 df, p=<2e-16
## Wald test = 288.25 on 5 df, p=<2e-16
## Score (logrank) test = 314.13 on 5 df, p=<2e-16hip.smoke.w = coxph(Surv(time2hip, hipfx) ~ as.factor(group.s), data = women)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 27,31 ; coefficient may be infinite.summary(hip.smoke.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ as.factor(group.s), data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.s)2 -1.4367e-01 8.6617e-01 3.3021e-01 -0.4351 0.663492
## as.factor(group.s)3 3.6749e-01 1.4441e+00 1.5071e-01 2.4384 0.014751 *
## as.factor(group.s)4 2.7965e-01 1.3227e+00 1.6296e-01 1.7161 0.086140 .
## as.factor(group.s)5 1.2262e+00 3.4084e+00 1.7676e-01 6.9373 3.997e-12 ***
## as.factor(group.s)6 8.2936e-01 2.2919e+00 1.5458e-01 5.3651 8.090e-08 ***
## as.factor(group.s)7 1.9674e+00 7.1522e+00 1.6500e-01 11.9240 < 2.2e-16 ***
## as.factor(group.s)8 1.0165e+00 2.7636e+00 1.9645e-01 5.1744 2.287e-07 ***
## as.factor(group.s)9 7.9026e-01 2.2040e+00 1.8328e-01 4.3118 1.619e-05 ***
## as.factor(group.s)10 7.4287e-01 2.1020e+00 5.8547e-01 1.2689 0.204494
## as.factor(group.s)11 1.3626e+00 3.9062e+00 2.6745e-01 5.0947 3.494e-07 ***
## as.factor(group.s)12 1.1368e+00 3.1168e+00 1.8986e-01 5.9877 2.128e-09 ***
## as.factor(group.s)13 1.2554e+00 3.5091e+00 4.1939e-01 2.9933 0.002760 **
## as.factor(group.s)14 5.0797e-02 1.0521e+00 2.1150e-01 0.2402 0.810198
## as.factor(group.s)15 1.9196e-01 1.2116e+00 5.8521e-01 0.3280 0.742896
## as.factor(group.s)16 1.7021e-02 1.0172e+00 4.1922e-01 0.0406 0.967614
## as.factor(group.s)17 1.9264e+00 6.8649e+00 2.6815e-01 7.1841 6.765e-13 ***
## as.factor(group.s)18 1.8516e+00 6.3697e+00 1.6150e-01 11.4650 < 2.2e-16 ***
## as.factor(group.s)19 5.8150e-01 1.7887e+00 1.0047e+00 0.5788 0.562744
## as.factor(group.s)20 9.3450e-01 2.5459e+00 2.2569e-01 4.1407 3.463e-05 ***
## as.factor(group.s)21 1.3673e+00 3.9246e+00 7.1370e-01 1.9157 0.055398 .
## as.factor(group.s)22 1.3126e+00 3.7159e+00 5.0940e-01 2.5768 0.009973 **
## as.factor(group.s)23 7.5041e-01 2.1179e+00 2.9316e-01 2.5597 0.010477 *
## as.factor(group.s)24 5.3677e-01 1.7105e+00 1.0045e+00 0.5343 0.593101
## as.factor(group.s)25 1.3357e+00 3.8028e+00 3.8996e-01 3.4254 0.000614 ***
## as.factor(group.s)26 7.3395e-01 2.0833e+00 5.0898e-01 1.4420 0.149303
## as.factor(group.s)27 1.3601e+00 3.8966e+00 2.6128e-01 5.2055 1.934e-07 ***
## as.factor(group.s)28 -1.1852e+01 7.1224e-06 9.7630e+02 -0.0121 0.990314
## as.factor(group.s)29 1.5747e+00 4.8295e+00 5.8552e-01 2.6895 0.007156 **
## as.factor(group.s)30 1.5353e+00 4.6428e+00 7.1391e-01 2.1506 0.031511 *
## as.factor(group.s)31 5.3216e-01 1.7026e+00 1.0047e+00 0.5297 0.596348
## as.factor(group.s)32 -1.1854e+01 7.1117e-06 6.8550e+02 -0.0173 0.986204
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.s)2 8.6617e-01 1.1545e+00 0.45345 1.6546
## as.factor(group.s)3 1.4441e+00 6.9247e-01 1.07477 1.9403
## as.factor(group.s)4 1.3227e+00 7.5605e-01 0.96104 1.8204
## as.factor(group.s)5 3.4084e+00 2.9340e-01 2.41040 4.8195
## as.factor(group.s)6 2.2919e+00 4.3633e-01 1.69280 3.1029
## as.factor(group.s)7 7.1522e+00 1.3982e-01 5.17600 9.8829
## as.factor(group.s)8 2.7636e+00 3.6185e-01 1.88039 4.0615
## as.factor(group.s)9 2.2040e+00 4.5373e-01 1.53886 3.1565
## as.factor(group.s)10 2.1020e+00 4.7575e-01 0.66723 6.6217
## as.factor(group.s)11 3.9062e+00 2.5600e-01 2.31260 6.5979
## as.factor(group.s)12 3.1168e+00 3.2084e-01 2.14832 4.5218
## as.factor(group.s)13 3.5091e+00 2.8497e-01 1.54245 7.9834
## as.factor(group.s)14 1.0521e+00 9.5047e-01 0.69507 1.5925
## as.factor(group.s)15 1.2116e+00 8.2534e-01 0.38480 3.8151
## as.factor(group.s)16 1.0172e+00 9.8312e-01 0.44725 2.3133
## as.factor(group.s)17 6.8649e+00 1.4567e-01 4.05866 11.6113
## as.factor(group.s)18 6.3697e+00 1.5699e-01 4.64144 8.7415
## as.factor(group.s)19 1.7887e+00 5.5906e-01 0.24965 12.8159
## as.factor(group.s)20 2.5459e+00 3.9278e-01 1.63585 3.9624
## as.factor(group.s)21 3.9246e+00 2.5480e-01 0.96893 15.8964
## as.factor(group.s)22 3.7159e+00 2.6911e-01 1.36917 10.0848
## as.factor(group.s)23 2.1179e+00 4.7217e-01 1.19222 3.7622
## as.factor(group.s)24 1.7105e+00 5.8463e-01 0.23881 12.2510
## as.factor(group.s)25 3.8028e+00 2.6296e-01 1.77081 8.1665
## as.factor(group.s)26 2.0833e+00 4.8001e-01 0.76825 5.6494
## as.factor(group.s)27 3.8966e+00 2.5663e-01 2.33499 6.5027
## as.factor(group.s)28 7.1224e-06 1.4040e+05 0.00000 Inf
## as.factor(group.s)29 4.8295e+00 2.0706e-01 1.53288 15.2158
## as.factor(group.s)30 4.6428e+00 2.1539e-01 1.14576 18.8131
## as.factor(group.s)31 1.7026e+00 5.8733e-01 0.23763 12.1993
## as.factor(group.s)32 7.1117e-06 1.4061e+05 0.00000 Inf
##
## Concordance= 0.68 (se = 0.01 )
## Likelihood ratio test= 289.84 on 31 df, p=<2e-16
## Wald test = 314.98 on 31 df, p=<2e-16
## Score (logrank) test = 374.06 on 31 df, p=<2e-162.2 Current/Past smoking
2.2.1 Data management
women = women %>% mutate(group = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "1.No/past smoking" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "1.No/past smoking" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smoke_bin == "2.Current smoking" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smoke_bin == "2.Current smoking" ~ 32))2.2.2 Prevalences
table1(~ age + age_bin + fnbmd + tscore + bmd_bin + fall_bin + fx50_bin + smoke_bin + drink_bin + activity_bin + as.factor(group), data = women, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=7959) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 72.0 [69.0, 76.0] |
| age_bin | |
| 1.Age< 75 | 5226 (65.7%) |
| 2.Age>= 75 | 2733 (34.3%) |
| fnbmd | |
| Median [Q1, Q3] | 0.639 [0.571, 0.712] |
| tscore | |
| Median [Q1, Q3] | -1.83 [-2.39, -1.22] |
| bmd_bin | |
| 1.BMD> -2.5 | 6303 (79.2%) |
| 2.BMD<= -2.5 | 1656 (20.8%) |
| fall_bin | |
| 1.No falls | 5590 (70.2%) |
| 2.Falls 1+ | 2369 (29.8%) |
| fx50_bin | |
| 1.No fx | 4726 (59.4%) |
| 2.Fx 1+ | 3233 (40.6%) |
| smoke_bin | |
| 1.No/past smoking | 4815 (60.5%) |
| 2.Current smoking | 3144 (39.5%) |
| drink_bin | |
| 1.Less drinking | 6902 (86.7%) |
| 2.Excessive drinking | 1057 (13.3%) |
| activity_bin | |
| 1.Proactive | 39 (0.5%) |
| 2.Less active | 7920 (99.5%) |
| as.factor(group) | |
| 1 | 1232 (15.5%) |
| 2 | 866 (10.9%) |
| 3 | 564 (7.1%) |
| 4 | 485 (6.1%) |
| 5 | 156 (2.0%) |
| 6 | 533 (6.7%) |
| 7 | 173 (2.2%) |
| 8 | 219 (2.8%) |
| 9 | 330 (4.1%) |
| 10 | 255 (3.2%) |
| 11 | 50 (0.6%) |
| 12 | 146 (1.8%) |
| 13 | 138 (1.7%) |
| 14 | 302 (3.8%) |
| 15 | 295 (3.7%) |
| 16 | 449 (5.6%) |
| 17 | 48 (0.6%) |
| 18 | 217 (2.7%) |
| 19 | 91 (1.1%) |
| 20 | 181 (2.3%) |
| 21 | 105 (1.3%) |
| 22 | 179 (2.2%) |
| 23 | 77 (1.0%) |
| 24 | 47 (0.6%) |
| 25 | 141 (1.8%) |
| 26 | 220 (2.8%) |
| 27 | 102 (1.3%) |
| 28 | 33 (0.4%) |
| 29 | 120 (1.5%) |
| 30 | 88 (1.1%) |
| 31 | 58 (0.7%) |
| 32 | 59 (0.7%) |
2.2.3 Association for any fracture
smoke.age.w = coxph(Surv(time2any, anyfx) ~ age + smoke_bin, data = women)
summary(smoke.age.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ age + smoke_bin, data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age 0.0563351 1.0579522 0.0040211 14.0099 <2e-16 ***
## smoke_bin2.Current smoking 0.0170393 1.0171853 0.0405176 0.4205 0.6741
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age 1.0580 0.94522 1.04965 1.0663
## smoke_bin2.Current smoking 1.0172 0.98311 0.93953 1.1013
##
## Concordance= 0.573 (se = 0.006 )
## Likelihood ratio test= 184.14 on 2 df, p=<2e-16
## Wald test = 197.39 on 2 df, p=<2e-16
## Score (logrank) test = 199.58 on 2 df, p=<2e-16m.any.smoke.w = coxph(Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin, data = women)
summary(m.any.smoke.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin, data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.406291 1.501239 0.041832 9.7124 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.484582 1.623497 0.045735 10.5954 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.071058 1.073643 0.042415 1.6753 0.093878 .
## fx50_bin2.Fx 1+ 0.111520 1.117976 0.040308 2.7667 0.005662 **
## smoke_bin2.Current smoking -0.016469 0.983666 0.040413 -0.4075 0.683638
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.50124 0.66612 1.38306 1.6295
## bmd_bin2.BMD<= -2.5 1.62350 0.61595 1.48430 1.7757
## fall_bin2.Falls 1+ 1.07364 0.93141 0.98800 1.1667
## fx50_bin2.Fx 1+ 1.11798 0.89447 1.03305 1.2099
## smoke_bin2.Current smoking 0.98367 1.01660 0.90876 1.0647
##
## Concordance= 0.589 (se = 0.006 )
## Likelihood ratio test= 257.1 on 5 df, p=<2e-16
## Wald test = 277.44 on 5 df, p=<2e-16
## Score (logrank) test = 284.17 on 5 df, p=<2e-16options(digits = 8)
any.smoke.w = coxph(Surv(time2any, anyfx) ~ as.factor(group), data = women)
summary(any.smoke.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ as.factor(group), data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 0.010473 1.010528 0.086212 0.1215 0.9033098
## as.factor(group)3 0.407032 1.502353 0.087825 4.6346 3.577e-06 ***
## as.factor(group)4 0.197989 1.218949 0.095782 2.0671 0.0387259 *
## as.factor(group)5 0.583675 1.792615 0.132010 4.4214 9.804e-06 ***
## as.factor(group)6 0.477565 1.612144 0.095101 5.0217 5.123e-07 ***
## as.factor(group)7 1.096638 2.994083 0.124643 8.7983 < 2.2e-16 ***
## as.factor(group)8 0.623720 1.865856 0.127025 4.9102 9.097e-07 ***
## as.factor(group)9 0.625067 1.868371 0.109577 5.7044 1.168e-08 ***
## as.factor(group)10 0.458883 1.582305 0.128479 3.5717 0.0003547 ***
## as.factor(group)11 1.058541 2.882164 0.196661 5.3826 7.343e-08 ***
## as.factor(group)12 0.565880 1.760998 0.142030 3.9842 6.770e-05 ***
## as.factor(group)13 0.733077 2.081475 0.144265 5.0814 3.746e-07 ***
## as.factor(group)14 0.187496 1.206225 0.117465 1.5962 0.1104484
## as.factor(group)15 0.233292 1.262750 0.118498 1.9687 0.0489835 *
## as.factor(group)16 0.375223 1.455316 0.098459 3.8109 0.0001384 ***
## as.factor(group)17 1.622341 5.064932 0.193863 8.3685 < 2.2e-16 ***
## as.factor(group)18 1.176462 3.242881 0.115147 10.2170 < 2.2e-16 ***
## as.factor(group)19 0.991746 2.695939 0.171367 5.7873 7.154e-09 ***
## as.factor(group)20 0.649038 1.913699 0.140246 4.6279 3.694e-06 ***
## as.factor(group)21 0.756350 2.130487 0.165433 4.5719 4.832e-06 ***
## as.factor(group)22 0.310613 1.364262 0.157231 1.9755 0.0482089 *
## as.factor(group)23 0.424661 1.529071 0.193419 2.1955 0.0281243 *
## as.factor(group)24 0.578603 1.783545 0.241898 2.3919 0.0167602 *
## as.factor(group)25 0.688397 1.990523 0.146544 4.6976 2.633e-06 ***
## as.factor(group)26 0.310836 1.364565 0.129698 2.3966 0.0165470 *
## as.factor(group)27 0.988297 2.686656 0.173437 5.6983 1.210e-08 ***
## as.factor(group)28 1.216305 3.374695 0.256006 4.7511 2.023e-06 ***
## as.factor(group)29 1.074924 2.929770 0.153227 7.0152 2.296e-12 ***
## as.factor(group)30 0.754775 2.127133 0.187861 4.0177 5.876e-05 ***
## as.factor(group)31 0.271450 1.311865 0.263839 1.0288 0.3035519
## as.factor(group)32 0.710704 2.035423 0.256114 2.7750 0.0055210 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group)2 1.0105 0.98958 0.85342 1.1966
## as.factor(group)3 1.5024 0.66562 1.26478 1.7846
## as.factor(group)4 1.2189 0.82038 1.01031 1.4707
## as.factor(group)5 1.7926 0.55784 1.38395 2.3220
## as.factor(group)6 1.6121 0.62029 1.33799 1.9425
## as.factor(group)7 2.9941 0.33399 2.34514 3.8226
## as.factor(group)8 1.8659 0.53595 1.45464 2.3933
## as.factor(group)9 1.8684 0.53523 1.50727 2.3160
## as.factor(group)10 1.5823 0.63199 1.23007 2.0354
## as.factor(group)11 2.8822 0.34696 1.96029 4.2376
## as.factor(group)12 1.7610 0.56786 1.33310 2.3262
## as.factor(group)13 2.0815 0.48043 1.56882 2.7617
## as.factor(group)14 1.2062 0.82903 0.95817 1.5185
## as.factor(group)15 1.2628 0.79192 1.00104 1.5929
## as.factor(group)16 1.4553 0.68714 1.19991 1.7651
## as.factor(group)17 5.0649 0.19744 3.46384 7.4061
## as.factor(group)18 3.2429 0.30837 2.58772 4.0639
## as.factor(group)19 2.6959 0.37093 1.92682 3.7721
## as.factor(group)20 1.9137 0.52255 1.45377 2.5191
## as.factor(group)21 2.1305 0.46938 1.54050 2.9464
## as.factor(group)22 1.3643 0.73300 1.00245 1.8567
## as.factor(group)23 1.5291 0.65399 1.04662 2.2339
## as.factor(group)24 1.7835 0.56068 1.11015 2.8654
## as.factor(group)25 1.9905 0.50238 1.49358 2.6528
## as.factor(group)26 1.3646 0.73283 1.05827 1.7595
## as.factor(group)27 2.6867 0.37221 1.91242 3.7743
## as.factor(group)28 3.3747 0.29632 2.04325 5.5737
## as.factor(group)29 2.9298 0.34132 2.16973 3.9560
## as.factor(group)30 2.1271 0.47012 1.47193 3.0740
## as.factor(group)31 1.3119 0.76227 0.78218 2.2002
## as.factor(group)32 2.0354 0.49130 1.23211 3.3625
##
## Concordance= 0.593 (se = 0.006 )
## Likelihood ratio test= 310.89 on 31 df, p=<2e-16
## Wald test = 338.15 on 31 df, p=<2e-16
## Score (logrank) test = 360.66 on 31 df, p=<2e-162.2.4 Association for hip fracture
hip.smoke.age.w = coxph(Surv(time2hip, hipfx) ~ age + smoke_bin, data = women)
summary(hip.smoke.age.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ age + smoke_bin, data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age 0.1069449 1.1128730 0.0071449 14.9680 <2e-16 ***
## smoke_bin2.Current smoking 0.0192798 1.0194669 0.0768971 0.2507 0.802
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age 1.1129 0.89858 1.09740 1.1286
## smoke_bin2.Current smoking 1.0195 0.98090 0.87684 1.1853
##
## Concordance= 0.656 (se = 0.01 )
## Likelihood ratio test= 204.23 on 2 df, p=<2e-16
## Wald test = 226.94 on 2 df, p=<2e-16
## Score (logrank) test = 236.68 on 2 df, p=<2e-16m.hip.smoke.w = coxph(Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin, data = women)
summary(m.hip.smoke.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin, data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.7003162 2.0143895 0.0765686 9.1463 <2e-16
## bmd_bin2.BMD<= -2.5 0.9585149 2.6078208 0.0782622 12.2475 <2e-16
## fall_bin2.Falls 1+ -0.0058846 0.9941327 0.0806833 -0.0729 0.9419
## fx50_bin2.Fx 1+ -0.0099806 0.9900690 0.0755168 -0.1322 0.8949
## smoke_bin2.Current smoking -0.0595254 0.9422116 0.0764655 -0.7785 0.4363
##
## age_bin2.Age>= 75 ***
## bmd_bin2.BMD<= -2.5 ***
## fall_bin2.Falls 1+
## fx50_bin2.Fx 1+
## smoke_bin2.Current smoking
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 2.01439 0.49643 1.73368 2.3406
## bmd_bin2.BMD<= -2.5 2.60782 0.38346 2.23697 3.0401
## fall_bin2.Falls 1+ 0.99413 1.00590 0.84872 1.1645
## fx50_bin2.Fx 1+ 0.99007 1.01003 0.85386 1.1480
## smoke_bin2.Current smoking 0.94221 1.06133 0.81107 1.0946
##
## Concordance= 0.66 (se = 0.011 )
## Likelihood ratio test= 259.67 on 5 df, p=<2e-16
## Wald test = 288.31 on 5 df, p=<2e-16
## Score (logrank) test = 314.19 on 5 df, p=<2e-16hip.smoke.w = coxph(Surv(time2hip, hipfx) ~ as.factor(group), data = women)
summary(hip.smoke.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ as.factor(group), data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 -0.32407 0.72320 0.19591 -1.6541 0.0981021 .
## as.factor(group)3 0.31209 1.36628 0.17903 1.7432 0.0812994 .
## as.factor(group)4 0.17388 1.18992 0.19415 0.8956 0.3704514
## as.factor(group)5 1.05317 2.86671 0.21859 4.8180 1.450e-06 ***
## as.factor(group)6 0.70915 2.03226 0.18190 3.8985 9.680e-05 ***
## as.factor(group)7 1.93376 6.91547 0.19049 10.1517 < 2.2e-16 ***
## as.factor(group)8 0.84117 2.31909 0.24027 3.5010 0.0004636 ***
## as.factor(group)9 0.87900 2.40849 0.20416 4.3054 1.667e-05 ***
## as.factor(group)10 0.75856 2.13519 0.23615 3.2122 0.0013174 **
## as.factor(group)11 1.45396 4.28003 0.32095 4.5302 5.893e-06 ***
## as.factor(group)12 0.92843 2.53054 0.23982 3.8713 0.0001083 ***
## as.factor(group)13 1.22961 3.41989 0.23581 5.2145 1.843e-07 ***
## as.factor(group)14 -0.29880 0.74171 0.28895 -1.0341 0.3010907
## as.factor(group)15 0.17501 1.19126 0.24432 0.7163 0.4737883
## as.factor(group)16 0.11536 1.12228 0.21581 0.5345 0.5929695
## as.factor(group)17 1.73586 5.67382 0.35163 4.9366 7.950e-07 ***
## as.factor(group)18 1.73755 5.68339 0.19199 9.0504 < 2.2e-16 ***
## as.factor(group)19 1.54389 4.68279 0.28117 5.4910 3.998e-08 ***
## as.factor(group)20 0.60674 1.83443 0.28934 2.0970 0.0359953 *
## as.factor(group)21 1.09504 2.98929 0.28921 3.7863 0.0001529 ***
## as.factor(group)22 0.36374 1.43871 0.32125 1.1323 0.2575184
## as.factor(group)23 0.87647 2.40240 0.32091 2.7312 0.0063108 **
## as.factor(group)24 0.83353 2.30143 0.42278 1.9716 0.0486585 *
## as.factor(group)25 1.22356 3.39928 0.23997 5.0988 3.417e-07 ***
## as.factor(group)26 0.34997 1.41903 0.26007 1.3457 0.1783979
## as.factor(group)27 1.33533 3.80127 0.29895 4.4668 7.942e-06 ***
## as.factor(group)28 1.80257 6.06520 0.39408 4.5741 4.782e-06 ***
## as.factor(group)29 1.73287 5.65687 0.24082 7.1957 6.214e-13 ***
## as.factor(group)30 1.30021 3.67008 0.30965 4.1990 2.681e-05 ***
## as.factor(group)31 0.04805 1.04922 0.58774 0.0818 0.9348426
## as.factor(group)32 0.83505 2.30493 0.51262 1.6290 0.1033148
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group)2 0.72320 1.38274 0.49260 1.0617
## as.factor(group)3 1.36628 0.73192 0.96193 1.9406
## as.factor(group)4 1.18992 0.84039 0.81331 1.7409
## as.factor(group)5 2.86671 0.34883 1.86776 4.4000
## as.factor(group)6 2.03226 0.49206 1.42279 2.9028
## as.factor(group)7 6.91547 0.14460 4.76079 10.0453
## as.factor(group)8 2.31909 0.43120 1.44810 3.7139
## as.factor(group)9 2.40850 0.41520 1.61421 3.5936
## as.factor(group)10 2.13519 0.46834 1.34408 3.3920
## as.factor(group)11 4.28003 0.23364 2.28168 8.0286
## as.factor(group)12 2.53054 0.39517 1.58152 4.0490
## as.factor(group)13 3.41989 0.29241 2.15424 5.4291
## as.factor(group)14 0.74171 1.34824 0.42100 1.3067
## as.factor(group)15 1.19126 0.83945 0.73798 1.9230
## as.factor(group)16 1.12228 0.89104 0.73519 1.7132
## as.factor(group)17 5.67382 0.17625 2.84817 11.3028
## as.factor(group)18 5.68339 0.17595 3.90111 8.2799
## as.factor(group)19 4.68279 0.21355 2.69881 8.1253
## as.factor(group)20 1.83443 0.54513 1.04044 3.2344
## as.factor(group)21 2.98929 0.33453 1.69586 5.2692
## as.factor(group)22 1.43871 0.69507 0.76652 2.7004
## as.factor(group)23 2.40240 0.41625 1.28081 4.5062
## as.factor(group)24 2.30143 0.43451 1.00492 5.2706
## as.factor(group)25 3.39928 0.29418 2.12386 5.4406
## as.factor(group)26 1.41903 0.70471 0.85236 2.3624
## as.factor(group)27 3.80127 0.26307 2.11574 6.8296
## as.factor(group)28 6.06520 0.16488 2.80158 13.1307
## as.factor(group)29 5.65687 0.17678 3.52850 9.0691
## as.factor(group)30 3.67008 0.27247 2.00032 6.7337
## as.factor(group)31 1.04922 0.95309 0.33158 3.3201
## as.factor(group)32 2.30493 0.43385 0.84395 6.2951
##
## Concordance= 0.684 (se = 0.01 )
## Likelihood ratio test= 297.47 on 31 df, p=<2e-16
## Wald test = 320.18 on 31 df, p=<2e-16
## Score (logrank) test = 380.54 on 31 df, p=<2e-162.3 Excessive drinking
2.3.1 Data management
women = women %>% mutate(group.d = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "1.Less drinking" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "1.Less drinking" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & drink_bin == "2.Excessive drinking" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & drink_bin == "2.Excessive drinking" ~ 32))2.3.2 Prevalences
table1(~ age + age_bin + fnbmd + tscore + bmd_bin + fall_bin + fx50_bin + smoke_bin + drink_bin + activity_bin + as.factor(group.d), data = women, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=7959) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 72.0 [69.0, 76.0] |
| age_bin | |
| 1.Age< 75 | 5226 (65.7%) |
| 2.Age>= 75 | 2733 (34.3%) |
| fnbmd | |
| Median [Q1, Q3] | 0.639 [0.571, 0.712] |
| tscore | |
| Median [Q1, Q3] | -1.83 [-2.39, -1.22] |
| bmd_bin | |
| 1.BMD> -2.5 | 6303 (79.2%) |
| 2.BMD<= -2.5 | 1656 (20.8%) |
| fall_bin | |
| 1.No falls | 5590 (70.2%) |
| 2.Falls 1+ | 2369 (29.8%) |
| fx50_bin | |
| 1.No fx | 4726 (59.4%) |
| 2.Fx 1+ | 3233 (40.6%) |
| smoke_bin | |
| 1.No/past smoking | 4815 (60.5%) |
| 2.Current smoking | 3144 (39.5%) |
| drink_bin | |
| 1.Less drinking | 6902 (86.7%) |
| 2.Excessive drinking | 1057 (13.3%) |
| activity_bin | |
| 1.Proactive | 39 (0.5%) |
| 2.Less active | 7920 (99.5%) |
| as.factor(group.d) | |
| 1 | 1837 (23.1%) |
| 2 | 261 (3.3%) |
| 3 | 867 (10.9%) |
| 4 | 668 (8.4%) |
| 5 | 245 (3.1%) |
| 6 | 691 (8.7%) |
| 7 | 226 (2.8%) |
| 8 | 280 (3.5%) |
| 9 | 441 (5.5%) |
| 10 | 97 (1.2%) |
| 11 | 83 (1.0%) |
| 12 | 249 (3.1%) |
| 13 | 49 (0.6%) |
| 14 | 440 (5.5%) |
| 15 | 112 (1.4%) |
| 16 | 146 (1.8%) |
| 17 | 69 (0.9%) |
| 18 | 304 (3.8%) |
| 19 | 38 (0.5%) |
| 20 | 237 (3.0%) |
| 21 | 44 (0.6%) |
| 22 | 68 (0.9%) |
| 23 | 118 (1.5%) |
| 24 | 14 (0.2%) |
| 25 | 38 (0.5%) |
| 26 | 82 (1.0%) |
| 27 | 147 (1.8%) |
| 28 | 12 (0.2%) |
| 29 | 33 (0.4%) |
| 30 | 32 (0.4%) |
| 31 | 17 (0.2%) |
| 32 | 14 (0.2%) |
2.3.3 Association for any fracture
m.any.drink.w = coxph(Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin, data = women)
summary(m.any.drink.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + drink_bin, data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.407887 1.503638 0.041737 9.7727 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.484239 1.622939 0.045717 10.5920 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.071158 1.073751 0.042411 1.6778 0.093384 .
## fx50_bin2.Fx 1+ 0.111151 1.117563 0.040292 2.7586 0.005805 **
## drink_bin2.Excessive drinking 0.028059 1.028456 0.057085 0.4915 0.623053
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.5036 0.66505 1.38553 1.6318
## bmd_bin2.BMD<= -2.5 1.6229 0.61617 1.48384 1.7751
## fall_bin2.Falls 1+ 1.0738 0.93131 0.98810 1.1668
## fx50_bin2.Fx 1+ 1.1176 0.89480 1.03270 1.2094
## drink_bin2.Excessive drinking 1.0285 0.97233 0.91959 1.1502
##
## Concordance= 0.589 (se = 0.006 )
## Likelihood ratio test= 257.18 on 5 df, p=<2e-16
## Wald test = 277.44 on 5 df, p=<2e-16
## Score (logrank) test = 284.19 on 5 df, p=<2e-16options(digits = 8)
any.drink.w = coxph(Surv(time2any, anyfx) ~ as.factor(group.d), data = women)
summary(any.drink.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ as.factor(group.d), data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.d)2 0.030146 1.030605 0.126184 0.2389 0.8111804
## as.factor(group.d)3 0.442366 1.556385 0.071844 6.1573 7.399e-10 ***
## as.factor(group.d)4 0.198615 1.219712 0.082157 2.4175 0.0156269 *
## as.factor(group.d)5 0.625142 1.868512 0.108849 5.7432 9.290e-09 ***
## as.factor(group.d)6 0.427738 1.533784 0.083725 5.1089 3.241e-07 ***
## as.factor(group.d)7 1.027786 2.794871 0.111065 9.2539 < 2.2e-16 ***
## as.factor(group.d)8 0.627071 1.872119 0.112276 5.5851 2.336e-08 ***
## as.factor(group.d)9 0.538466 1.713377 0.096626 5.5727 2.508e-08 ***
## as.factor(group.d)10 0.760251 2.138813 0.172813 4.3993 1.086e-05 ***
## as.factor(group.d)11 0.905126 2.472244 0.162644 5.5651 2.620e-08 ***
## as.factor(group.d)12 0.642026 1.900327 0.109732 5.8509 4.890e-09 ***
## as.factor(group.d)13 0.753046 2.123459 0.213354 3.5296 0.0004163 ***
## as.factor(group.d)14 0.220594 1.246817 0.096892 2.2767 0.0228037 *
## as.factor(group.d)15 0.277758 1.320167 0.168389 1.6495 0.0990440 .
## as.factor(group.d)16 0.047218 1.048351 0.170486 0.2770 0.7818080
## as.factor(group.d)17 1.435679 4.202495 0.166682 8.6133 < 2.2e-16 ***
## as.factor(group.d)18 1.176461 3.242876 0.097783 12.0314 < 2.2e-16 ***
## as.factor(group.d)19 1.243223 3.466769 0.228375 5.4438 5.216e-08 ***
## as.factor(group.d)20 0.645768 1.907451 0.122848 5.2566 1.467e-07 ***
## as.factor(group.d)21 0.865695 2.376657 0.217975 3.9715 7.141e-05 ***
## as.factor(group.d)22 0.408519 1.504588 0.233914 1.7465 0.0807326 .
## as.factor(group.d)23 0.363798 1.438783 0.166366 2.1867 0.0287622 *
## as.factor(group.d)24 0.436450 1.547205 0.449499 0.9710 0.3315631
## as.factor(group.d)25 0.475007 1.608026 0.292216 1.6255 0.1040485
## as.factor(group.d)26 0.336344 1.399820 0.194299 1.7311 0.0834401 .
## as.factor(group.d)27 0.849109 2.337563 0.153064 5.5474 2.899e-08 ***
## as.factor(group.d)28 1.616800 5.036949 0.411163 3.9323 8.415e-05 ***
## as.factor(group.d)29 0.810518 2.249073 0.292377 2.7722 0.0055685 **
## as.factor(group.d)30 0.919840 2.508888 0.271201 3.3917 0.0006945 ***
## as.factor(group.d)31 0.414554 1.513696 0.449498 0.9223 0.3563926
## as.factor(group.d)32 1.362375 3.905456 0.411035 3.3145 0.0009181 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.d)2 1.0306 0.97030 0.80479 1.3198
## as.factor(group.d)3 1.5564 0.64251 1.35196 1.7917
## as.factor(group.d)4 1.2197 0.81987 1.03831 1.4328
## as.factor(group.d)5 1.8685 0.53519 1.50954 2.3129
## as.factor(group.d)6 1.5338 0.65198 1.30166 1.8073
## as.factor(group.d)7 2.7949 0.35780 2.24814 3.4746
## as.factor(group.d)8 1.8721 0.53415 1.50232 2.3329
## as.factor(group.d)9 1.7134 0.58364 1.41777 2.0706
## as.factor(group.d)10 2.1388 0.46755 1.52431 3.0010
## as.factor(group.d)11 2.4722 0.40449 1.79742 3.4004
## as.factor(group.d)12 1.9003 0.52623 1.53258 2.3563
## as.factor(group.d)13 2.1235 0.47093 1.39777 3.2259
## as.factor(group.d)14 1.2468 0.80204 1.03117 1.5076
## as.factor(group.d)15 1.3202 0.75748 0.94907 1.8364
## as.factor(group.d)16 1.0484 0.95388 0.75057 1.4643
## as.factor(group.d)17 4.2025 0.23795 3.03129 5.8262
## as.factor(group.d)18 3.2429 0.30837 2.67730 3.9279
## as.factor(group.d)19 3.4668 0.28845 2.21581 5.4240
## as.factor(group.d)20 1.9075 0.52426 1.49929 2.4267
## as.factor(group.d)21 2.3767 0.42076 1.55034 3.6434
## as.factor(group.d)22 1.5046 0.66463 0.95128 2.3797
## as.factor(group.d)23 1.4388 0.69503 1.03845 1.9935
## as.factor(group.d)24 1.5472 0.64633 0.64111 3.7339
## as.factor(group.d)25 1.6080 0.62188 0.90690 2.8512
## as.factor(group.d)26 1.3998 0.71438 0.95650 2.0486
## as.factor(group.d)27 2.3376 0.42780 1.73171 3.1554
## as.factor(group.d)28 5.0369 0.19853 2.25001 11.2759
## as.factor(group.d)29 2.2491 0.44463 1.26804 3.9891
## as.factor(group.d)30 2.5089 0.39858 1.47447 4.2690
## as.factor(group.d)31 1.5137 0.66063 0.62723 3.6530
## as.factor(group.d)32 3.9055 0.25605 1.74501 8.7407
##
## Concordance= 0.595 (se = 0.006 )
## Likelihood ratio test= 315.86 on 31 df, p=<2e-16
## Wald test = 341.95 on 31 df, p=<2e-16
## Score (logrank) test = 364.12 on 31 df, p=<2e-162.3.4 Association for hip fracture
m.hip.drink.w = coxph(Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + smoke_bin, data = women)
summary(m.hip.drink.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + smoke_bin, data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.7003162 2.0143895 0.0765686 9.1463 <2e-16
## bmd_bin2.BMD<= -2.5 0.9585149 2.6078208 0.0782622 12.2475 <2e-16
## fall_bin2.Falls 1+ -0.0058846 0.9941327 0.0806833 -0.0729 0.9419
## fx50_bin2.Fx 1+ -0.0099806 0.9900690 0.0755168 -0.1322 0.8949
## smoke_bin2.Current smoking -0.0595254 0.9422116 0.0764655 -0.7785 0.4363
##
## age_bin2.Age>= 75 ***
## bmd_bin2.BMD<= -2.5 ***
## fall_bin2.Falls 1+
## fx50_bin2.Fx 1+
## smoke_bin2.Current smoking
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 2.01439 0.49643 1.73368 2.3406
## bmd_bin2.BMD<= -2.5 2.60782 0.38346 2.23697 3.0401
## fall_bin2.Falls 1+ 0.99413 1.00590 0.84872 1.1645
## fx50_bin2.Fx 1+ 0.99007 1.01003 0.85386 1.1480
## smoke_bin2.Current smoking 0.94221 1.06133 0.81107 1.0946
##
## Concordance= 0.66 (se = 0.011 )
## Likelihood ratio test= 259.67 on 5 df, p=<2e-16
## Wald test = 288.31 on 5 df, p=<2e-16
## Score (logrank) test = 314.19 on 5 df, p=<2e-16hip.drink.w = coxph(Surv(time2hip, hipfx) ~ as.factor(group.d), data = women)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 23,30 ; coefficient may be infinite.summary(hip.drink.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ as.factor(group.d), data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.d)2 -9.4596e-02 9.0974e-01 2.8422e-01 -0.3328 0.7392634
## as.factor(group.d)3 3.9391e-01 1.4828e+00 1.5244e-01 2.5841 0.0097643 **
## as.factor(group.d)4 3.0814e-01 1.3609e+00 1.6797e-01 1.8345 0.0665802 .
## as.factor(group.d)5 1.2049e+00 3.3364e+00 1.8373e-01 6.5580 5.453e-11 ***
## as.factor(group.d)6 8.4218e-01 2.3214e+00 1.5938e-01 5.2839 1.265e-07 ***
## as.factor(group.d)7 1.9748e+00 7.2052e+00 1.7120e-01 11.5351 < 2.2e-16 ***
## as.factor(group.d)8 9.6054e-01 2.6131e+00 2.1273e-01 4.5152 6.324e-06 ***
## as.factor(group.d)9 8.9966e-01 2.4588e+00 1.8425e-01 4.8829 1.046e-06 ***
## as.factor(group.d)10 7.1579e-01 2.0458e+00 3.6668e-01 1.9520 0.0509323 .
## as.factor(group.d)11 1.4804e+00 4.3947e+00 2.6114e-01 5.6690 1.436e-08 ***
## as.factor(group.d)12 1.1947e+00 3.3027e+00 1.8536e-01 6.4455 1.152e-10 ***
## as.factor(group.d)13 1.3458e+00 3.8414e+00 3.3070e-01 4.0697 4.708e-05 ***
## as.factor(group.d)14 1.9332e-01 1.2133e+00 2.0937e-01 0.9233 0.3558398
## as.factor(group.d)15 6.3540e-02 1.0656e+00 3.9015e-01 0.1629 0.8706281
## as.factor(group.d)16 -1.1070e-01 8.9521e-01 3.9018e-01 -0.2837 0.7766296
## as.factor(group.d)17 1.7911e+00 5.9958e+00 2.9427e-01 6.0865 1.154e-09 ***
## as.factor(group.d)18 1.9000e+00 6.6857e+00 1.6246e-01 11.6950 < 2.2e-16 ***
## as.factor(group.d)19 1.5328e+00 4.6309e+00 4.1986e-01 3.6507 0.0002616 ***
## as.factor(group.d)20 7.8000e-01 2.1815e+00 2.4946e-01 3.1267 0.0017678 **
## as.factor(group.d)21 1.3483e+00 3.8508e+00 3.6660e-01 3.6778 0.0002352 ***
## as.factor(group.d)22 2.9646e-01 1.3451e+00 5.0938e-01 0.5820 0.5605637
## as.factor(group.d)23 8.5274e-01 2.3461e+00 2.8424e-01 3.0001 0.0026991 **
## as.factor(group.d)24 -1.3879e+01 9.3828e-07 1.1500e+03 -0.0121 0.9903704
## as.factor(group.d)25 9.2769e-01 2.5287e+00 5.0931e-01 1.8215 0.0685366 .
## as.factor(group.d)26 -4.2621e-01 6.5298e-01 5.8541e-01 -0.7280 0.4665838
## as.factor(group.d)27 1.2294e+00 3.4191e+00 2.7644e-01 4.4472 8.699e-06 ***
## as.factor(group.d)28 2.2835e+00 9.8109e+00 5.8623e-01 3.8952 9.810e-05 ***
## as.factor(group.d)29 1.0519e+00 2.8630e+00 5.8578e-01 1.7957 0.0725475 .
## as.factor(group.d)30 1.8220e+00 6.1842e+00 3.9046e-01 4.6663 3.066e-06 ***
## as.factor(group.d)31 -1.3882e+01 9.3584e-07 1.1949e+03 -0.0116 0.9907306
## as.factor(group.d)32 2.0152e+00 7.5021e+00 7.1446e-01 2.8206 0.0047938 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.d)2 9.0974e-01 1.0992e+00 0.52118 1.5880
## as.factor(group.d)3 1.4828e+00 6.7441e-01 1.09981 1.9991
## as.factor(group.d)4 1.3609e+00 7.3481e-01 0.97915 1.8915
## as.factor(group.d)5 3.3364e+00 2.9972e-01 2.32749 4.7826
## as.factor(group.d)6 2.3214e+00 4.3077e-01 1.69857 3.1726
## as.factor(group.d)7 7.2052e+00 1.3879e-01 5.15136 10.0780
## as.factor(group.d)8 2.6131e+00 3.8268e-01 1.72218 3.9650
## as.factor(group.d)9 2.4588e+00 4.0671e-01 1.71350 3.5282
## as.factor(group.d)10 2.0458e+00 4.8881e-01 0.99710 4.1974
## as.factor(group.d)11 4.3947e+00 2.2755e-01 2.63419 7.3318
## as.factor(group.d)12 3.3027e+00 3.0278e-01 2.29662 4.7494
## as.factor(group.d)13 3.8414e+00 2.6032e-01 2.00907 7.3448
## as.factor(group.d)14 1.2133e+00 8.2422e-01 0.80490 1.8288
## as.factor(group.d)15 1.0656e+00 9.3844e-01 0.49602 2.2892
## as.factor(group.d)16 8.9521e-01 1.1171e+00 0.41668 1.9233
## as.factor(group.d)17 5.9958e+00 1.6678e-01 3.36794 10.6741
## as.factor(group.d)18 6.6857e+00 1.4957e-01 4.86252 9.1925
## as.factor(group.d)19 4.6309e+00 2.1594e-01 2.03368 10.5450
## as.factor(group.d)20 2.1815e+00 4.5841e-01 1.33784 3.5571
## as.factor(group.d)21 3.8508e+00 2.5968e-01 1.87718 7.8996
## as.factor(group.d)22 1.3451e+00 7.4344e-01 0.49564 3.6504
## as.factor(group.d)23 2.3461e+00 4.2625e-01 1.34399 4.0953
## as.factor(group.d)24 9.3828e-07 1.0658e+06 0.00000 Inf
## as.factor(group.d)25 2.5287e+00 3.9546e-01 0.93189 6.8615
## as.factor(group.d)26 6.5298e-01 1.5314e+00 0.20730 2.0569
## as.factor(group.d)27 3.4191e+00 2.9248e-01 1.98888 5.8778
## as.factor(group.d)28 9.8109e+00 1.0193e-01 3.10965 30.9531
## as.factor(group.d)29 2.8630e+00 3.4929e-01 0.90824 9.0248
## as.factor(group.d)30 6.1842e+00 1.6170e-01 2.87692 13.2936
## as.factor(group.d)31 9.3584e-07 1.0686e+06 0.00000 Inf
## as.factor(group.d)32 7.5021e+00 1.3330e-01 1.84941 30.4320
##
## Concordance= 0.684 (se = 0.01 )
## Likelihood ratio test= 303.45 on 31 df, p=<2e-16
## Wald test = 325.27 on 31 df, p=<2e-16
## Score (logrank) test = 391.77 on 31 df, p=<2e-162.4 Proactive physical activity
2.3.1 Data management
women = women %>% mutate(physical_bin = case_when(physical4 == "Moderate" | physical4 == "High" | physical4 == "Low" ~ "1.Proactive",
physical4 == "No" ~ "2.Less active"))
women = women %>% mutate(group.p = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "1.Proactive" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "1.Proactive" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & physical_bin == "2.Less active" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & physical_bin == "2.Less active" ~ 32))2.3.2 Prevalences
table1(~ age + age_bin + fnbmd + tscore + bmd_bin + fall_bin + fx50_bin + physical4 + activity_bin + physical_bin + as.factor(group.p), data = women, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=7959) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 72.0 [69.0, 76.0] |
| age_bin | |
| 1.Age< 75 | 5226 (65.7%) |
| 2.Age>= 75 | 2733 (34.3%) |
| fnbmd | |
| Median [Q1, Q3] | 0.639 [0.571, 0.712] |
| tscore | |
| Median [Q1, Q3] | -1.83 [-2.39, -1.22] |
| bmd_bin | |
| 1.BMD> -2.5 | 6303 (79.2%) |
| 2.BMD<= -2.5 | 1656 (20.8%) |
| fall_bin | |
| 1.No falls | 5590 (70.2%) |
| 2.Falls 1+ | 2369 (29.8%) |
| fx50_bin | |
| 1.No fx | 4726 (59.4%) |
| 2.Fx 1+ | 3233 (40.6%) |
| physical4 | |
| Low | 515 (6.5%) |
| Moderate | 39 (0.5%) |
| No | 7405 (93.0%) |
| activity_bin | |
| 1.Proactive | 39 (0.5%) |
| 2.Less active | 7920 (99.5%) |
| physical_bin | |
| 1.Proactive | 554 (7.0%) |
| 2.Less active | 7405 (93.0%) |
| as.factor(group.p) | |
| 1 | 163 (2.0%) |
| 2 | 1935 (24.3%) |
| 3 | 80 (1.0%) |
| 4 | 67 (0.8%) |
| 5 | 20 (0.3%) |
| 6 | 39 (0.5%) |
| 7 | 16 (0.2%) |
| 8 | 20 (0.3%) |
| 9 | 23 (0.3%) |
| 10 | 749 (9.4%) |
| 11 | 7 (0.1%) |
| 12 | 21 (0.3%) |
| 13 | 274 (3.4%) |
| 14 | 38 (0.5%) |
| 15 | 713 (9.0%) |
| 16 | 933 (11.7%) |
| 17 | 3 (0.0%) |
| 18 | 20 (0.3%) |
| 19 | 248 (3.1%) |
| 20 | 15 (0.2%) |
| 21 | 304 (3.8%) |
| 22 | 486 (6.1%) |
| 23 | 10 (0.1%) |
| 24 | 90 (1.1%) |
| 25 | 266 (3.3%) |
| 26 | 484 (6.1%) |
| 27 | 12 (0.2%) |
| 28 | 78 (1.0%) |
| 29 | 317 (4.0%) |
| 30 | 254 (3.2%) |
| 31 | 125 (1.6%) |
| 32 | 149 (1.9%) |
2.3.3 Association for any fracture
library(survival)
m.any.physical.w = coxph(Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + physical_bin, data = women)
summary(m.any.physical.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + physical_bin, data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.405310 1.499767 0.041767 9.7041 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.484674 1.623646 0.045721 10.6007 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.071814 1.074456 0.042414 1.6932 0.090421 .
## fx50_bin2.Fx 1+ 0.110611 1.116960 0.040298 2.7448 0.006055 **
## physical_bin2.Less active 0.091946 1.096305 0.078975 1.1642 0.244329
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.4998 0.66677 1.38189 1.6277
## bmd_bin2.BMD<= -2.5 1.6236 0.61590 1.48448 1.7759
## fall_bin2.Falls 1+ 1.0745 0.93070 0.98875 1.1676
## fx50_bin2.Fx 1+ 1.1170 0.89529 1.03213 1.2088
## physical_bin2.Less active 1.0963 0.91215 0.93909 1.2798
##
## Concordance= 0.59 (se = 0.006 )
## Likelihood ratio test= 258.33 on 5 df, p=<2e-16
## Wald test = 278.54 on 5 df, p=<2e-16
## Score (logrank) test = 285.29 on 5 df, p=<2e-16options(digits = 8)
any.physical.w = coxph(Surv(time2any, anyfx) ~ as.factor(group.p), data = women)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 16 ; coefficient may be infinite.summary(any.physical.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ as.factor(group.p), data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.p)2 2.1666e-01 1.2419e+00 1.7226e-01 1.2577 0.2084916
## as.factor(group.p)3 4.0131e-01 1.4938e+00 2.6355e-01 1.5227 0.1278302
## as.factor(group.p)4 7.7944e-02 1.0811e+00 2.9428e-01 0.2649 0.7911168
## as.factor(group.p)5 1.0537e+00 2.8683e+00 3.4453e-01 3.0584 0.0022253 **
## as.factor(group.p)6 5.9091e-01 1.8056e+00 3.3339e-01 1.7724 0.0763251 .
## as.factor(group.p)7 9.0174e-01 2.4639e+00 4.4102e-01 2.0447 0.0408877 *
## as.factor(group.p)8 1.0812e+00 2.9482e+00 3.9100e-01 2.7652 0.0056893 **
## as.factor(group.p)9 9.6748e-01 2.6313e+00 3.7282e-01 2.5951 0.0094575 **
## as.factor(group.p)10 6.7368e-01 1.9614e+00 1.7957e-01 3.7515 0.0001758 ***
## as.factor(group.p)11 -3.2053e-01 7.2577e-01 1.0138e+00 -0.3162 0.7518793
## as.factor(group.p)12 2.5431e-01 1.2896e+00 4.7727e-01 0.5328 0.5941438
## as.factor(group.p)13 8.2728e-01 2.2871e+00 1.9123e-01 4.3262 1.517e-05 ***
## as.factor(group.p)14 6.7235e-01 1.9588e+00 3.1498e-01 2.1345 0.0327989 *
## as.factor(group.p)15 4.3672e-01 1.5476e+00 1.7909e-01 2.4386 0.0147456 *
## as.factor(group.p)16 6.0622e-01 1.8335e+00 1.7547e-01 3.4549 0.0005505 ***
## as.factor(group.p)17 -1.1520e+01 9.9307e-06 4.0113e+02 -0.0287 0.9770892
## as.factor(group.p)18 1.8287e+00 6.2260e+00 3.2386e-01 5.6467 1.636e-08 ***
## as.factor(group.p)19 1.2827e+00 3.6065e+00 1.9190e-01 6.6843 2.320e-11 ***
## as.factor(group.p)20 1.5837e+00 4.8730e+00 3.5757e-01 4.4290 9.466e-06 ***
## as.factor(group.p)21 8.5169e-01 2.3436e+00 1.9236e-01 4.4277 9.526e-06 ***
## as.factor(group.p)22 7.0666e-01 2.0272e+00 1.8601e-01 3.7990 0.0001453 ***
## as.factor(group.p)23 -2.3322e-01 7.9198e-01 7.2649e-01 -0.3210 0.7481904
## as.factor(group.p)24 1.1067e+00 3.0243e+00 2.2370e-01 4.9471 7.531e-07 ***
## as.factor(group.p)25 8.5673e-01 2.3554e+00 1.9272e-01 4.4455 8.769e-06 ***
## as.factor(group.p)26 4.1771e-01 1.5185e+00 1.8561e-01 2.2505 0.0244199 *
## as.factor(group.p)27 1.4350e+00 4.1998e+00 5.2727e-01 2.7217 0.0064955 **
## as.factor(group.p)28 1.7320e+00 5.6519e+00 2.2395e-01 7.7338 1.044e-14 ***
## as.factor(group.p)29 1.3024e+00 3.6783e+00 1.8807e-01 6.9253 4.351e-12 ***
## as.factor(group.p)30 8.2109e-01 2.2730e+00 2.0052e-01 4.0948 4.226e-05 ***
## as.factor(group.p)31 6.2721e-01 1.8724e+00 2.2715e-01 2.7613 0.0057576 **
## as.factor(group.p)32 1.0706e+00 2.9172e+00 2.1982e-01 4.8705 1.113e-06 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.p)2 1.2419e+00 8.0520e-01 0.886061 1.7407
## as.factor(group.p)3 1.4938e+00 6.6944e-01 0.891156 2.5039
## as.factor(group.p)4 1.0811e+00 9.2502e-01 0.607233 1.9246
## as.factor(group.p)5 2.8683e+00 3.4864e-01 1.460013 5.6350
## as.factor(group.p)6 1.8056e+00 5.5382e-01 0.939388 3.4707
## as.factor(group.p)7 2.4639e+00 4.0586e-01 1.038062 5.8481
## as.factor(group.p)8 2.9482e+00 3.3919e-01 1.370037 6.3442
## as.factor(group.p)9 2.6313e+00 3.8004e-01 1.267153 5.4640
## as.factor(group.p)10 1.9614e+00 5.0983e-01 1.379499 2.7889
## as.factor(group.p)11 7.2577e-01 1.3779e+00 0.099506 5.2936
## as.factor(group.p)12 1.2896e+00 7.7545e-01 0.506052 3.2862
## as.factor(group.p)13 2.2871e+00 4.3724e-01 1.572215 3.3270
## as.factor(group.p)14 1.9588e+00 5.1051e-01 1.056527 3.6317
## as.factor(group.p)15 1.5476e+00 6.4615e-01 1.089493 2.1984
## as.factor(group.p)16 1.8335e+00 5.4541e-01 1.299931 2.5861
## as.factor(group.p)17 9.9307e-06 1.0070e+05 0.000000 Inf
## as.factor(group.p)18 6.2260e+00 1.6062e-01 3.300197 11.7459
## as.factor(group.p)19 3.6065e+00 2.7728e-01 2.475921 5.2533
## as.factor(group.p)20 4.8730e+00 2.0521e-01 2.417829 9.8211
## as.factor(group.p)21 2.3436e+00 4.2669e-01 1.607500 3.4168
## as.factor(group.p)22 2.0272e+00 4.9329e-01 1.407873 2.9190
## as.factor(group.p)23 7.9198e-01 1.2627e+00 0.190688 3.2893
## as.factor(group.p)24 3.0243e+00 3.3066e-01 1.950773 4.6885
## as.factor(group.p)25 2.3554e+00 4.2455e-01 1.614469 3.4365
## as.factor(group.p)26 1.5185e+00 6.5855e-01 1.055399 2.1847
## as.factor(group.p)27 4.1998e+00 2.3810e-01 1.494242 11.8044
## as.factor(group.p)28 5.6519e+00 1.7693e-01 3.643907 8.7664
## as.factor(group.p)29 3.6783e+00 2.7187e-01 2.544231 5.3177
## as.factor(group.p)30 2.2730e+00 4.3995e-01 1.534297 3.3673
## as.factor(group.p)31 1.8724e+00 5.3408e-01 1.199633 2.9224
## as.factor(group.p)32 2.9172e+00 3.4279e-01 1.896086 4.4883
##
## Concordance= 0.595 (se = 0.006 )
## Likelihood ratio test= 328.52 on 31 df, p=<2e-16
## Wald test = 355.19 on 31 df, p=<2e-16
## Score (logrank) test = 382.5 on 31 df, p=<2e-162.3.4 Association for hip fracture
m.hip.physical.w = coxph(Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + physical_bin, data = women)
summary(m.hip.physical.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + physical_bin, data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.7028830 2.0195668 0.0764034 9.1996 <2e-16 ***
## bmd_bin2.BMD<= -2.5 0.9569915 2.6038511 0.0782193 12.2347 <2e-16 ***
## fall_bin2.Falls 1+ -0.0047955 0.9952160 0.0806828 -0.0594 0.9526
## fx50_bin2.Fx 1+ -0.0107125 0.9893447 0.0755018 -0.1419 0.8872
## physical_bin2.Less active 0.0977472 1.1026840 0.1493287 0.6546 0.5127
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 2.01957 0.49516 1.73870 2.3458
## bmd_bin2.BMD<= -2.5 2.60385 0.38405 2.23376 3.0353
## fall_bin2.Falls 1+ 0.99522 1.00481 0.84965 1.1657
## fx50_bin2.Fx 1+ 0.98934 1.01077 0.85326 1.1471
## physical_bin2.Less active 1.10268 0.90688 0.82289 1.4776
##
## Concordance= 0.657 (se = 0.011 )
## Likelihood ratio test= 259.5 on 5 df, p=<2e-16
## Wald test = 288.04 on 5 df, p=<2e-16
## Score (logrank) test = 313.93 on 5 df, p=<2e-16options(digits = 8)
hip.physical.w = coxph(Surv(time2hip, hipfx) ~ as.factor(group.p), data = women)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 10,16,26 ; coefficient may be infinite.summary(hip.physical.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ as.factor(group.p), data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.p)2 -7.9933e-02 9.2318e-01 3.3019e-01 -0.2421 0.8087194
## as.factor(group.p)3 3.7055e-01 1.4485e+00 4.9283e-01 0.7519 0.4521200
## as.factor(group.p)4 -1.3059e-01 8.7757e-01 5.9164e-01 -0.2207 0.8253016
## as.factor(group.p)5 1.8599e+00 6.4233e+00 4.9285e-01 3.7738 0.0001608 ***
## as.factor(group.p)6 4.7967e-01 1.6155e+00 6.5842e-01 0.7285 0.4662950
## as.factor(group.p)7 1.1741e+00 3.2352e+00 7.7483e-01 1.5153 0.1296968
## as.factor(group.p)8 2.1988e-01 1.2459e+00 1.0490e+00 0.2096 0.8339687
## as.factor(group.p)9 6.9470e-01 2.0031e+00 7.7478e-01 0.8966 0.3699064
## as.factor(group.p)10 7.7957e-01 2.1805e+00 3.3905e-01 2.2992 0.0214917 *
## as.factor(group.p)11 -1.2914e+01 2.4635e-06 1.0076e+03 -0.0128 0.9897740
## as.factor(group.p)12 6.3135e-01 1.8801e+00 7.7461e-01 0.8151 0.4150426
## as.factor(group.p)13 1.0924e+00 2.9813e+00 3.5040e-01 3.1174 0.0018243 **
## as.factor(group.p)14 -1.4523e-01 8.6482e-01 7.7461e-01 -0.1875 0.8512762
## as.factor(group.p)15 2.4405e-01 1.2764e+00 3.4334e-01 0.7108 0.4772065
## as.factor(group.p)16 2.6648e-01 1.3054e+00 3.3753e-01 0.7895 0.4298160
## as.factor(group.p)17 -1.2916e+01 2.4590e-06 1.6941e+03 -0.0076 0.9939169
## as.factor(group.p)18 1.5310e+00 4.6229e+00 6.5870e-01 2.3243 0.0201081 *
## as.factor(group.p)19 1.8917e+00 6.6305e+00 3.4439e-01 5.4928 3.956e-08 ***
## as.factor(group.p)20 1.7531e+00 5.7724e+00 5.9174e-01 2.9626 0.0030504 **
## as.factor(group.p)21 1.0050e+00 2.7320e+00 3.5888e-01 2.8005 0.0051031 **
## as.factor(group.p)22 7.6988e-01 2.1595e+00 3.5146e-01 2.1905 0.0284879 *
## as.factor(group.p)23 5.0910e-01 1.6638e+00 1.0488e+00 0.4854 0.6273933
## as.factor(group.p)24 1.3127e+00 3.7163e+00 3.9858e-01 3.2935 0.0009894 ***
## as.factor(group.p)25 1.1344e+00 3.1092e+00 3.5193e-01 3.2232 0.0012676 **
## as.factor(group.p)26 6.8649e-02 1.0711e+00 3.6520e-01 0.1880 0.8508940
## as.factor(group.p)27 -1.2916e+01 2.4593e-06 1.1418e+03 -0.0113 0.9909750
## as.factor(group.p)28 1.8599e+00 6.4231e+00 4.0373e-01 4.6068 4.088e-06 ***
## as.factor(group.p)29 1.7898e+00 5.9882e+00 3.4224e-01 5.2297 1.698e-07 ***
## as.factor(group.p)30 8.1064e-01 2.2494e+00 3.8184e-01 2.1230 0.0337568 *
## as.factor(group.p)31 6.8596e-01 1.9857e+00 4.2069e-01 1.6306 0.1029795
## as.factor(group.p)32 1.2982e+00 3.6628e+00 3.9918e-01 3.2522 0.0011452 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.p)2 9.2318e-01 1.0832e+00 0.48331 1.7634
## as.factor(group.p)3 1.4485e+00 6.9035e-01 0.55135 3.8056
## as.factor(group.p)4 8.7757e-01 1.1395e+00 0.27522 2.7983
## as.factor(group.p)5 6.4233e+00 1.5568e-01 2.44480 16.8763
## as.factor(group.p)6 1.6155e+00 6.1899e-01 0.44450 5.8717
## as.factor(group.p)7 3.2352e+00 3.0910e-01 0.70855 14.7719
## as.factor(group.p)8 1.2459e+00 8.0262e-01 0.15945 9.7357
## as.factor(group.p)9 2.0031e+00 4.9922e-01 0.43875 9.1453
## as.factor(group.p)10 2.1805e+00 4.5860e-01 1.12191 4.2380
## as.factor(group.p)11 2.4635e-06 4.0593e+05 0.00000 Inf
## as.factor(group.p)12 1.8801e+00 5.3187e-01 0.41195 8.5811
## as.factor(group.p)13 2.9813e+00 3.3542e-01 1.50018 5.9247
## as.factor(group.p)14 8.6482e-01 1.1563e+00 0.18949 3.9471
## as.factor(group.p)15 1.2764e+00 7.8345e-01 0.65124 2.5017
## as.factor(group.p)16 1.3054e+00 7.6607e-01 0.67364 2.5295
## as.factor(group.p)17 2.4590e-06 4.0667e+05 0.00000 Inf
## as.factor(group.p)18 4.6229e+00 2.1631e-01 1.27125 16.8113
## as.factor(group.p)19 6.6305e+00 1.5082e-01 3.37597 13.0225
## as.factor(group.p)20 5.7724e+00 1.7324e-01 1.80996 18.4096
## as.factor(group.p)21 2.7320e+00 3.6603e-01 1.35207 5.5203
## as.factor(group.p)22 2.1595e+00 4.6307e-01 1.08440 4.3005
## as.factor(group.p)23 1.6638e+00 6.0104e-01 0.21298 12.9974
## as.factor(group.p)24 3.7163e+00 2.6908e-01 1.70153 8.1168
## as.factor(group.p)25 3.1092e+00 3.2163e-01 1.55984 6.1974
## as.factor(group.p)26 1.0711e+00 9.3365e-01 0.52355 2.1912
## as.factor(group.p)27 2.4593e-06 4.0661e+05 0.00000 Inf
## as.factor(group.p)28 6.4231e+00 1.5569e-01 2.91134 14.1709
## as.factor(group.p)29 5.9882e+00 1.6700e-01 3.06182 11.7113
## as.factor(group.p)30 2.2494e+00 4.4457e-01 1.06422 4.7543
## as.factor(group.p)31 1.9857e+00 5.0361e-01 0.87060 4.5290
## as.factor(group.p)32 3.6628e+00 2.7302e-01 1.67503 8.0093
##
## Concordance= 0.679 (se = 0.01 )
## Likelihood ratio test= 293.33 on 31 df, p=<2e-16
## Wald test = 319.19 on 31 df, p=<2e-16
## Score (logrank) test = 380.34 on 31 df, p=<2e-162.5 Calcium intake (Adequate: >= 1000 mg/day)
2.5.1 Data management
women$calcium.d = women$calcium2/7
women = women %>% mutate(calci_bin = case_when(calcium.d >= 1300 ~ "1.Sufficient Calcium",
calcium.d < 1300 ~ "2.Insufficient Calcium"))
women = women %>% mutate(group.c = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "1.Sufficient Calcium" ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "1.Sufficient Calcium" ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & calci_bin == "2.Insufficient Calcium" ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & calci_bin == "2.Insufficient Calcium" ~ 32))2.5.2 Prevalences
table1(~ age + age_bin + fnbmd + tscore + bmd_bin + fall_bin + fx50_bin + calcium2 + calci_bin + as.factor(group.c), data = women, render.continuous = c(. = "Median [Q1, Q3]"))| Overall (N=7959) |
|
|---|---|
| age | |
| Median [Q1, Q3] | 72.0 [69.0, 76.0] |
| age_bin | |
| 1.Age< 75 | 5226 (65.7%) |
| 2.Age>= 75 | 2733 (34.3%) |
| fnbmd | |
| Median [Q1, Q3] | 0.639 [0.571, 0.712] |
| tscore | |
| Median [Q1, Q3] | -1.83 [-2.39, -1.22] |
| bmd_bin | |
| 1.BMD> -2.5 | 6303 (79.2%) |
| 2.BMD<= -2.5 | 1656 (20.8%) |
| fall_bin | |
| 1.No falls | 5590 (70.2%) |
| 2.Falls 1+ | 2369 (29.8%) |
| fx50_bin | |
| 1.No fx | 4726 (59.4%) |
| 2.Fx 1+ | 3233 (40.6%) |
| calcium2 | |
| Median [Q1, Q3] | 4390 [2830, 6610] |
| calci_bin | |
| 1.Sufficient Calcium | 788 (9.9%) |
| 2.Insufficient Calcium | 7171 (90.1%) |
| as.factor(group.c) | |
| 1 | 201 (2.5%) |
| 2 | 1897 (23.8%) |
| 3 | 117 (1.5%) |
| 4 | 84 (1.1%) |
| 5 | 29 (0.4%) |
| 6 | 68 (0.9%) |
| 7 | 14 (0.2%) |
| 8 | 24 (0.3%) |
| 9 | 43 (0.5%) |
| 10 | 720 (9.0%) |
| 11 | 7 (0.1%) |
| 12 | 33 (0.4%) |
| 13 | 265 (3.3%) |
| 14 | 72 (0.9%) |
| 15 | 696 (8.7%) |
| 16 | 896 (11.3%) |
| 17 | 5 (0.1%) |
| 18 | 28 (0.4%) |
| 19 | 250 (3.1%) |
| 20 | 27 (0.3%) |
| 21 | 300 (3.8%) |
| 22 | 466 (5.9%) |
| 23 | 18 (0.2%) |
| 24 | 90 (1.1%) |
| 25 | 254 (3.2%) |
| 26 | 450 (5.7%) |
| 27 | 18 (0.2%) |
| 28 | 76 (1.0%) |
| 29 | 309 (3.9%) |
| 30 | 242 (3.0%) |
| 31 | 117 (1.5%) |
| 32 | 143 (1.8%) |
2.5.3 Association for any fracture
library(survival)
m.any.calci.w = coxph(Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + calci_bin, data = women)
summary(m.any.calci.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + calci_bin, data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## age_bin2.Age>= 75 0.405274 1.499713 0.041776 9.7010 < 2e-16
## bmd_bin2.BMD<= -2.5 0.483453 1.621664 0.045722 10.5739 < 2e-16
## fall_bin2.Falls 1+ 0.071970 1.074623 0.042415 1.6968 0.08973
## fx50_bin2.Fx 1+ 0.112747 1.119349 0.040321 2.7962 0.00517
## calci_bin2.Insufficient Calcium 0.071280 1.073882 0.067866 1.0503 0.29358
##
## age_bin2.Age>= 75 ***
## bmd_bin2.BMD<= -2.5 ***
## fall_bin2.Falls 1+ .
## fx50_bin2.Fx 1+ **
## calci_bin2.Insufficient Calcium
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 1.4997 0.66679 1.38181 1.6277
## bmd_bin2.BMD<= -2.5 1.6217 0.61665 1.48266 1.7737
## fall_bin2.Falls 1+ 1.0746 0.93056 0.98890 1.1678
## fx50_bin2.Fx 1+ 1.1193 0.89338 1.03429 1.2114
## calci_bin2.Insufficient Calcium 1.0739 0.93120 0.94013 1.2267
##
## Concordance= 0.59 (se = 0.006 )
## Likelihood ratio test= 258.06 on 5 df, p=<2e-16
## Wald test = 278.32 on 5 df, p=<2e-16
## Score (logrank) test = 285.07 on 5 df, p=<2e-16options(digits = 8)
any.calci.w = coxph(Surv(time2any, anyfx) ~ as.factor(group.c), data = women)
summary(any.calci.w)## Call:
## coxph(formula = Surv(time2any, anyfx) ~ as.factor(group.c), data = women)
##
## n= 7959, number of events= 2629
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.c)2 0.087861 1.091837 0.148148 0.5931 0.5531368
## as.factor(group.c)3 0.193277 1.213219 0.224298 0.8617 0.3888540
## as.factor(group.c)4 -0.181543 0.833982 0.274879 -0.6604 0.5089672
## as.factor(group.c)5 0.561247 1.752857 0.346472 1.6199 0.1052559
## as.factor(group.c)6 0.529016 1.697262 0.275066 1.9232 0.0544511 .
## as.factor(group.c)7 1.304432 3.685593 0.380887 3.4247 0.0006154 ***
## as.factor(group.c)8 1.325540 3.764216 0.311536 4.2549 2.092e-05 ***
## as.factor(group.c)9 0.430932 1.538690 0.321559 1.3401 0.1802017
## as.factor(group.c)10 0.549066 1.731635 0.156769 3.5024 0.0004611 ***
## as.factor(group.c)11 1.023001 2.781530 0.519637 1.9687 0.0489894 *
## as.factor(group.c)12 1.045186 2.843926 0.287280 3.6382 0.0002745 ***
## as.factor(group.c)13 0.739007 2.093856 0.169443 4.3614 1.292e-05 ***
## as.factor(group.c)14 0.499603 1.648066 0.238835 2.0918 0.0364539 *
## as.factor(group.c)15 0.333588 1.395968 0.155926 2.1394 0.0324034 *
## as.factor(group.c)16 0.502354 1.652607 0.151966 3.3057 0.0009474 ***
## as.factor(group.c)17 2.032094 7.630049 0.594853 3.4161 0.0006352 ***
## as.factor(group.c)18 1.058937 2.883305 0.346646 3.0548 0.0022520 **
## as.factor(group.c)19 1.126387 3.084492 0.170873 6.5920 4.341e-11 ***
## as.factor(group.c)20 1.214720 3.369350 0.333276 3.6448 0.0002676 ***
## as.factor(group.c)21 0.690369 1.994451 0.172213 4.0088 6.103e-05 ***
## as.factor(group.c)22 0.613259 1.846438 0.164181 3.7352 0.0001875 ***
## as.factor(group.c)23 0.124532 1.132619 0.519649 0.2396 0.8106038
## as.factor(group.c)24 0.908967 2.481757 0.209389 4.3410 1.418e-05 ***
## as.factor(group.c)25 0.651158 1.917760 0.174430 3.7331 0.0001892 ***
## as.factor(group.c)26 0.282870 1.326933 0.165245 1.7118 0.0869295 .
## as.factor(group.c)27 0.174297 1.190409 0.594600 0.2931 0.7694207
## as.factor(group.c)28 1.506764 4.512106 0.209598 7.1888 6.534e-13 ***
## as.factor(group.c)29 1.229944 3.421040 0.165583 7.4280 1.103e-13 ***
## as.factor(group.c)30 0.710607 2.035227 0.180474 3.9375 8.235e-05 ***
## as.factor(group.c)31 0.483985 1.622528 0.212144 2.2814 0.0225247 *
## as.factor(group.c)32 1.048063 2.852122 0.200297 5.2325 1.672e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.c)2 1.09184 0.91589 0.81668 1.4597
## as.factor(group.c)3 1.21322 0.82425 0.78166 1.8830
## as.factor(group.c)4 0.83398 1.19907 0.48661 1.4293
## as.factor(group.c)5 1.75286 0.57050 0.88885 3.4567
## as.factor(group.c)6 1.69726 0.58918 0.98995 2.9100
## as.factor(group.c)7 3.68559 0.27133 1.74701 7.7753
## as.factor(group.c)8 3.76422 0.26566 2.04407 6.9319
## as.factor(group.c)9 1.53869 0.64990 0.81929 2.8898
## as.factor(group.c)10 1.73163 0.57749 1.27354 2.3545
## as.factor(group.c)11 2.78153 0.35951 1.00454 7.7019
## as.factor(group.c)12 2.84393 0.35163 1.61951 4.9940
## as.factor(group.c)13 2.09386 0.47759 1.50216 2.9186
## as.factor(group.c)14 1.64807 0.60677 1.03199 2.6319
## as.factor(group.c)15 1.39597 0.71635 1.02837 1.8950
## as.factor(group.c)16 1.65261 0.60510 1.22692 2.2260
## as.factor(group.c)17 7.63005 0.13106 2.37787 24.4832
## as.factor(group.c)18 2.88330 0.34682 1.46159 5.6880
## as.factor(group.c)19 3.08449 0.32420 2.20666 4.3115
## as.factor(group.c)20 3.36935 0.29679 1.75332 6.4749
## as.factor(group.c)21 1.99445 0.50139 1.42310 2.7952
## as.factor(group.c)22 1.84644 0.54158 1.33839 2.5473
## as.factor(group.c)23 1.13262 0.88291 0.40903 3.1362
## as.factor(group.c)24 2.48176 0.40294 1.64637 3.7410
## as.factor(group.c)25 1.91776 0.52144 1.36245 2.6994
## as.factor(group.c)26 1.32693 0.75362 0.95982 1.8345
## as.factor(group.c)27 1.19041 0.84005 0.37117 3.8179
## as.factor(group.c)28 4.51211 0.22163 2.99205 6.8044
## as.factor(group.c)29 3.42104 0.29231 2.47294 4.7326
## as.factor(group.c)30 2.03523 0.49135 1.42887 2.8989
## as.factor(group.c)31 1.62253 0.61632 1.07057 2.4591
## as.factor(group.c)32 2.85212 0.35062 1.92608 4.2234
##
## Concordance= 0.595 (se = 0.006 )
## Likelihood ratio test= 321.79 on 31 df, p=<2e-16
## Wald test = 347.17 on 31 df, p=<2e-16
## Score (logrank) test = 370.52 on 31 df, p=<2e-162.5.4 Association for hip fracture
m.hip.calci.w = coxph(Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin + fx50_bin + calci_bin, data = women)
summary(m.hip.calci.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ age_bin + bmd_bin + fall_bin +
## fx50_bin + calci_bin, data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z
## age_bin2.Age>= 75 0.7095551 2.0330865 0.0765137 9.2736
## bmd_bin2.BMD<= -2.5 0.9593318 2.6099519 0.0782616 12.2580
## fall_bin2.Falls 1+ -0.0066476 0.9933744 0.0806889 -0.0824
## fx50_bin2.Fx 1+ -0.0134815 0.9866090 0.0755533 -0.1784
## calci_bin2.Insufficient Calcium -0.1416311 0.8679414 0.1213973 -1.1667
## Pr(>|z|)
## age_bin2.Age>= 75 <2e-16 ***
## bmd_bin2.BMD<= -2.5 <2e-16 ***
## fall_bin2.Falls 1+ 0.9343
## fx50_bin2.Fx 1+ 0.8584
## calci_bin2.Insufficient Calcium 0.2433
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## age_bin2.Age>= 75 2.03309 0.49186 1.74996 2.3620
## bmd_bin2.BMD<= -2.5 2.60995 0.38315 2.23880 3.0426
## fall_bin2.Falls 1+ 0.99337 1.00667 0.84807 1.1636
## fx50_bin2.Fx 1+ 0.98661 1.01357 0.85081 1.1441
## calci_bin2.Insufficient Calcium 0.86794 1.15215 0.68416 1.1011
##
## Concordance= 0.654 (se = 0.011 )
## Likelihood ratio test= 260.37 on 5 df, p=<2e-16
## Wald test = 288.92 on 5 df, p=<2e-16
## Score (logrank) test = 314.84 on 5 df, p=<2e-16options(digits = 8)
hip.calci.w = coxph(Surv(time2hip, hipfx) ~ as.factor(group.c), data = women)
summary(hip.calci.w)## Call:
## coxph(formula = Surv(time2hip, hipfx) ~ as.factor(group.c), data = women)
##
## n= 7959, number of events= 749
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group.c)2 0.2955326 1.3438419 0.3464814 0.8530 0.3936849
## as.factor(group.c)3 0.0067368 1.0067596 0.5577913 0.0121 0.9903637
## as.factor(group.c)4 0.2773318 1.3196042 0.5577760 0.4972 0.6190410
## as.factor(group.c)5 1.1280298 3.0895634 0.6668582 1.6916 0.0907302 .
## as.factor(group.c)6 1.7171168 5.5684503 0.4718648 3.6390 0.0002737 ***
## as.factor(group.c)7 2.7399502 15.4862139 0.5272781 5.1964 2.032e-07 ***
## as.factor(group.c)8 2.1104509 8.2519612 0.5581873 3.7809 0.0001563 ***
## as.factor(group.c)9 1.1508899 3.1610048 0.6011884 1.9144 0.0555744 .
## as.factor(group.c)10 1.0464372 2.8474881 0.3569913 2.9313 0.0033758 **
## as.factor(group.c)11 1.2285744 3.4163558 1.0541135 1.1655 0.2438147
## as.factor(group.c)12 2.2347342 9.3439982 0.4715119 4.7395 2.142e-06 ***
## as.factor(group.c)13 1.5429048 4.6781596 0.3632757 4.2472 2.165e-05 ***
## as.factor(group.c)14 0.2872894 1.3328099 0.6009395 0.4781 0.6326024
## as.factor(group.c)15 0.5879658 1.8003224 0.3595823 1.6351 0.1020207
## as.factor(group.c)16 0.6781583 1.9702459 0.3530467 1.9209 0.0547475 .
## as.factor(group.c)17 3.7482730 42.4477113 0.7836678 4.7830 1.727e-06 ***
## as.factor(group.c)18 2.4787725 11.9266153 0.5279229 4.6953 2.662e-06 ***
## as.factor(group.c)19 2.1539533 8.6188640 0.3620917 5.9486 2.704e-09 ***
## as.factor(group.c)20 2.0544289 7.8023803 0.5581560 3.6807 0.0002326 ***
## as.factor(group.c)21 1.2332546 3.4323823 0.3788854 3.2550 0.0011341 **
## as.factor(group.c)22 1.1082866 3.0291637 0.3683842 3.0085 0.0026253 **
## as.factor(group.c)23 1.3183844 3.7373782 0.7818540 1.6862 0.0917518 .
## as.factor(group.c)24 1.5992982 4.9495575 0.4167136 3.8379 0.0001241 ***
## as.factor(group.c)25 1.3185113 3.7378526 0.3737701 3.5276 0.0004193 ***
## as.factor(group.c)26 0.4148391 1.5141271 0.3832205 1.0825 0.2790270
## as.factor(group.c)27 1.0435580 2.8393012 1.0545944 0.9895 0.3224015
## as.factor(group.c)28 2.0429539 7.7133597 0.4277241 4.7763 1.785e-06 ***
## as.factor(group.c)29 2.0911911 8.0945511 0.3592421 5.8211 5.846e-09 ***
## as.factor(group.c)30 1.1319149 3.1015900 0.3987657 2.8385 0.0045320 **
## as.factor(group.c)31 0.9740749 2.6487159 0.4409693 2.2089 0.0271788 *
## as.factor(group.c)32 1.6250847 5.0788490 0.4171826 3.8954 9.805e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group.c)2 1.3438 0.744135 0.68143 2.6502
## as.factor(group.c)3 1.0068 0.993286 0.33739 3.0041
## as.factor(group.c)4 1.3196 0.757803 0.44225 3.9375
## as.factor(group.c)5 3.0896 0.323670 0.83612 11.4164
## as.factor(group.c)6 5.5685 0.179583 2.20842 14.0406
## as.factor(group.c)7 15.4862 0.064574 5.50967 43.5276
## as.factor(group.c)8 8.2520 0.121183 2.76330 24.6426
## as.factor(group.c)9 3.1610 0.316355 0.97295 10.2697
## as.factor(group.c)10 2.8475 0.351187 1.41446 5.7324
## as.factor(group.c)11 3.4164 0.292710 0.43281 26.9666
## as.factor(group.c)12 9.3440 0.107021 3.70835 23.5442
## as.factor(group.c)13 4.6782 0.213759 2.29538 9.5345
## as.factor(group.c)14 1.3328 0.750295 0.41044 4.3280
## as.factor(group.c)15 1.8003 0.555456 0.88976 3.6427
## as.factor(group.c)16 1.9702 0.507551 0.98629 3.9358
## as.factor(group.c)17 42.4477 0.023558 9.13682 197.2030
## as.factor(group.c)18 11.9266 0.083846 4.23788 33.5649
## as.factor(group.c)19 8.6189 0.116025 4.23874 17.5252
## as.factor(group.c)20 7.8024 0.128166 2.61291 23.2986
## as.factor(group.c)21 3.4324 0.291343 1.63338 7.2128
## as.factor(group.c)22 3.0292 0.330124 1.47148 6.2358
## as.factor(group.c)23 3.7374 0.267567 0.80733 17.3014
## as.factor(group.c)24 4.9496 0.202038 2.18705 11.2014
## as.factor(group.c)25 3.7379 0.267533 1.79667 7.7764
## as.factor(group.c)26 1.5141 0.660447 0.71444 3.2089
## as.factor(group.c)27 2.8393 0.352199 0.35937 22.4328
## as.factor(group.c)28 7.7134 0.129645 3.33553 17.8370
## as.factor(group.c)29 8.0946 0.123540 4.00318 16.3674
## as.factor(group.c)30 3.1016 0.322415 1.41956 6.7766
## as.factor(group.c)31 2.6487 0.377541 1.11604 6.2862
## as.factor(group.c)32 5.0788 0.196895 2.24212 11.5046
##
## Concordance= 0.682 (se = 0.01 )
## Likelihood ratio test= 301.51 on 31 df, p=<2e-16
## Wald test = 336.51 on 31 df, p=<2e-16
## Score (logrank) test = 411.97 on 31 df, p=<2e-163. Graph to represent PAR
3.1 Smoking:
Data management:
par = read.csv("C:\\Thach\\Research projects\\PAR for lifestyle factors\\par_smoking.csv")3.1.1 Current smoking:
3.1.1.1 Any fracture in men
library(ggplot2)
m.anyfx = subset(par, lifestyle == 0 & sex == 0 & fx == 1)
m.anyfx$group.n = -m.anyfx$group
p0 = ggplot(data = m.anyfx, aes(x = group.n, y = par, fill = group.n)) + geom_bar(stat = "identity", width = 0.9)
p0 + coord_flip() + theme_minimal() + theme(legend.position = "none")## Warning: Removed 6 rows containing missing values (`position_stack()`).
# scale_fill_manual(values = c("blue", "red"))
# scale: 570 x 6003.1.1.2 Hip fracture in men
m.hipfx = subset(par, lifestyle == 0 & sex == 0 & fx == 2)
m.hipfx$group.n = -m.hipfx$group
p0 = ggplot(data = m.hipfx, aes(x = group.n, y = par, fill = group.n)) + geom_bar(stat = "identity", width = 0.9)
p0 + coord_flip() + theme_minimal() + theme(legend.position = "none")## Warning: Removed 9 rows containing missing values (`position_stack()`).
3.1.2 Current/past smoking:
3.1.2.1 Any fracture in men
library(ggplot2)
m.anyfx = subset(par, lifestyle == 1 & sex == 0 & fx == 1)
m.anyfx$group.n = -m.anyfx$group
p0 = ggplot(data = m.anyfx, aes(x = group.n, y = par, fill = group.n)) + geom_bar(stat = "identity", width = 0.9)
p0 + coord_flip() + theme_minimal() + theme(legend.position = "none")
# scale_fill_manual(values = c("blue", "red"))
# scale: 570 x 6003.1.2.2 Hip fracture in men
m.hipfx = subset(par, lifestyle == 1 & sex == 0 & fx == 2)
m.hipfx$group.n = -m.hipfx$group
p0 = ggplot(data = m.hipfx, aes(x = group.n, y = par, fill = group.n)) + geom_bar(stat = "identity", width = 0.9)
p0 + coord_flip() + theme_minimal() + theme(legend.position = "none")## Warning: Removed 4 rows containing missing values (`position_stack()`).