Smoking and Risks of Fractures
Nick Tran + Thach Tran
2024-11-20
Cumulative and reversible impact of cigarette smoking on fragility fractures
Statistical analysis plan: - Aims: to quantify the association between cigarette smoking and risks of (i) any fracture and (ii) hip fracture to quantify number of fractures possibly prevented if smokers woult quit - Design: + Participants: MrOS participants + Outcomes: (i) any fracture, (ii) hip fracture, and (iii) post-fracture death + Exposures: (i) Smoking status (smoke_status): none, past and current (ii) Number of pack-years (smoke_packyrs): continuous; quintiles; excess smoking (different thresholds: 20 pack-years) (iii) No. cigarettes smoked per day over a lifetime (smoke_perddlife): (iv) Duration of smoking: [smoke_agestop (or age if no smoke_agestop) - smoke_age1st] (v) Whether the participants smoked 100+ cigarettes in their lifetime (smoke_100life) + Covariates: risk factors for fractures (age, FNBMD, history of falls, history of fractures), lifestyle factors (alcohol drinking, calcium/ protein intake, physical activity) and comorbidity. - Analysis: + Descriptive analysis + Cox’s regression + Heuristic PAR
libraries
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## varslibrary(ggfortify)## Warning: package 'ggfortify' was built under R version 4.3.2Data set-up:
data = read.csv("C:\\Thach\\Research projects\\PAR for lifestyle factors\\SOF_MrOS_Nick_lifestyle_02aug24.csv")
data = 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(fall_bin = case_when(no_falls == 0 ~ "1.No falls",
no_falls > 0 ~ "2.Falls 1+"))
data = data %>% mutate(smoke_bin = case_when(smoke == "Never" | smoke == "Past" ~ "1.No/past smoking",
smoke == "Current" ~ "2.Current smoking"))
data = data %>% mutate(physical_bin = case_when(physical4 == "Moderate" | physical4 == "High" | physical4 == "Low" ~ "1.Proactive",
physical4 == "No" ~ "2.Less active"))
data = data %>% mutate(calci_bin = case_when(calcium2 >= 1000 ~ "1.Sufficient Calcium",
calcium2 < 1000 ~ "2.Insufficient Calcium"))
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(fx50_bin = case_when(fx50 == 0 ~ "1.No fx",
fx50 > 0 ~ "2.Fx 1+"))
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"))
men = subset(data, gender == "M")
# Combination of risk factors for smoking (Current vs. None/Past):
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"))Smoking data
smoke = read.csv("C:\\Thach\\Research projects\\PAR for lifestyle factors\\Smoking\\smoking_data.csv")
head(smoke)## ID smoke_status smoke_packyrs cigar_yrs cigar_perwk cigar_status
## 1 BI0001 0:NO NA NA NA 0: No
## 2 BI0002 1:PAST 0.15 NA NA 0: No
## 3 BI0003 1:PAST 6.50 NA NA 0: No
## 4 BI0004 1:PAST 27.00 3 8 1: Yes
## 5 BI0005 1:PAST 72.50 NA NA 0: No
## 6 BI0006 1:PAST 24.00 NA NA 0: No
## smoke_age1st smoke_perdd smoke_perddlife smoke_agestop smoke_100life
## 1 NA NA NA NA 0: No
## 2 21 NA 3 22 1: Yes
## 3 18 NA 10 31 1: Yes
## 4 13 NA 20 40 1: Yes
## 5 21 NA 50 50 1: Yes
## 6 16 NA 20 40 1: Yes
## smoke_yrsstop snuff_age1st snuff_perwk snuff_current snuff_agestop snuff_ever
## 1 NA NA NA NA 0: No
## 2 45 NA NA NA 0: No
## 3 41 NA NA NA 0: No
## 4 25 NA NA NA 0: No
## 5 28 NA NA NA 0: No
## 6 38 NA NA NA 0: Nomen.smk = merge(men, smoke, by = "ID", all.x = TRUE)
men.smk = men.smk %>% mutate(smk_dur = case_when(smoke_status == "1:PAST" ~ smoke_agestop - smoke_age1st,
smoke_status == "2:CURRENT" ~ age - smoke_age1st,
smoke_status == "0:NO" ~ 0))
men.smk[is.na(men.smk)] = 0
head(men.smk)## ID data Visit gender age race education weight height BMI
## 1 BI0001 MrOS 1 M 67 1:WHITE 7 87.8 172.75 29.42107
## 2 BI0002 MrOS 1 M 67 1:WHITE 7 99.4 176.60 31.87168
## 3 BI0003 MrOS 1 M 72 1:WHITE 5 83.1 178.45 26.09564
## 4 BI0004 MrOS 1 M 65 1:WHITE 7 97.4 184.65 28.56672
## 5 BI0005 MrOS 1 M 78 1:WHITE 5 82.9 168.75 29.11166
## 6 BI0006 MrOS 1 M 78 1:WHITE 3 76.3 163.75 28.45522
## no_falls fx50 physical hypertension copd parkinson cancer rheumatoid cvd
## 1 0 0 1 0 0 1 0 0 0
## 2 0 0 1 1 0 1 0 1 1
## 3 0 1 1 0 0 0 0 0 1
## 4 0 0 0 0 0 0 0 0 0
## 5 1 0 1 0 0 0 1 0 0
## 6 1 0 0 0 1 0 0 1 0
## renal depression diabetes MedYes DeathX fnbmd time2visit anyfx time2any
## 1 1 0 0 0 0 0.8674233 0 0 13.971300
## 2 1 0 0 0 0 0.7402350 0 0 14.636600
## 3 0 0 0 0 1 0.6918427 0 1 8.421629
## 4 0 0 0 0 1 0.8783067 0 0 19.540000
## 5 0 0 0 0 3 0.9194940 0 0 3.036300
## 6 0 1 0 0 3 0.8862731 0 0 13.149900
## hipfx time2hip death time2end Tscore Osteo smoke physical4 physical7
## 1 0 13.9713 1 13.9713 -0.4859616 Normal Never High 0
## 2 0 14.6366 1 14.6366 -1.4143433 Osteopenia Past No 8897
## 3 0 13.9493 1 13.9493 -1.7675718 Osteopenia Past Low 5957
## 4 0 19.5400 0 19.5400 -0.4065204 Normal Past Low 2905
## 5 0 3.0363 1 3.0363 -0.1058833 Normal Past No 0
## 6 0 13.1499 0 13.1499 -0.3483715 Normal Past No 714
## drink4 drink7 coffee4 calcium2 protein2 race.n fall_bin smoke_bin
## 1 No 0 Moderate 1588.5 74.2 1_White 1.No falls 1.No/past smoking
## 2 No 0 Moderate 416.8 58.1 1_White 1.No falls 1.No/past smoking
## 3 High 5 Moderate 815.1 50.0 1_White 1.No falls 1.No/past smoking
## 4 Low 1 Low 900.0 85.5 1_White 1.No falls 1.No/past smoking
## 5 No 0 No 569.1 41.4 1_White 2.Falls 1+ 1.No/past smoking
## 6 No 0 Low 797.7 46.2 1_White 2.Falls 1+ 1.No/past smoking
## physical_bin calci_bin age_bin bmd_bin fx50_bin
## 1 1.Proactive 1.Sufficient Calcium 1.Age< 75 1.BMD> -2.5 1.No fx
## 2 2.Less active 2.Insufficient Calcium 1.Age< 75 1.BMD> -2.5 1.No fx
## 3 1.Proactive 2.Insufficient Calcium 1.Age< 75 1.BMD> -2.5 2.Fx 1+
## 4 1.Proactive 2.Insufficient Calcium 1.Age< 75 1.BMD> -2.5 1.No fx
## 5 2.Less active 2.Insufficient Calcium 2.Age>= 75 1.BMD> -2.5 1.No fx
## 6 2.Less active 2.Insufficient Calcium 2.Age>= 75 1.BMD> -2.5 1.No fx
## drink_bin activity_bin group fu_anyfx fu_hipfx
## 1 1.Less drinking 1.Proactive 1 13.971300 13.9713
## 2 1.Less drinking 2.Less active 1 14.636600 14.6366
## 3 2.Excessive drinking 2.Less active 3 8.421629 13.9493
## 4 1.Less drinking 2.Less active 1 19.540000 19.5400
## 5 1.Less drinking 2.Less active 8 3.036300 3.0363
## 6 1.Less drinking 2.Less active 8 13.149900 13.1499
## protein_bin smoke_status smoke_packyrs cigar_yrs cigar_perwk
## 1 2.Insufficient protein 0:NO 0.00 0 0
## 2 2.Insufficient protein 1:PAST 0.15 0 0
## 3 2.Insufficient protein 1:PAST 6.50 0 0
## 4 1.Sufficient protein 1:PAST 27.00 3 8
## 5 2.Insufficient protein 1:PAST 72.50 0 0
## 6 2.Insufficient protein 1:PAST 24.00 0 0
## cigar_status smoke_age1st smoke_perdd smoke_perddlife smoke_agestop
## 1 0: No 0 0 0 0
## 2 0: No 21 0 3 22
## 3 0: No 18 0 10 31
## 4 1: Yes 13 0 20 40
## 5 0: No 21 0 50 50
## 6 0: No 16 0 20 40
## smoke_100life smoke_yrsstop snuff_age1st snuff_perwk snuff_current
## 1 0: No 0 0 0
## 2 1: Yes 45 0 0
## 3 1: Yes 41 0 0
## 4 1: Yes 25 0 0
## 5 1: Yes 28 0 0
## 6 1: Yes 38 0 0
## snuff_agestop snuff_ever smk_dur
## 1 0 0: No 0
## 2 0 0: No 1
## 3 0 0: No 13
## 4 0 0: No 27
## 5 0 0: No 29
## 6 0 0: No 24Flowchart
Data management
men.smk = men.smk %>% mutate(fx_death = case_when(anyfx == 0 & death == 0 ~ "Event-free",
anyfx == 1 & death == 0 ~ "Fractured",
anyfx == 0 & death == 1 ~ "Dead w/o fracture"))
men.smk = men.smk %>% mutate(hip_death = case_when(hipfx == 0 & death == 0 ~ "Event-free",
hipfx == 1 & death == 0 ~ "Fractured",
hipfx == 0 & death == 1 ~ "Dead w/o fracture"))
men.anyfx = subset(men.smk, anyfx == 1)
men.anyfx$postfx_death = ifelse(men.anyfx$death == 1, 1, 0)
men.hipfx = subset(men.smk, hipfx == 1)
men.hipfx$postfx_death = ifelse(men.hipfx$death == 1, 1, 0)Flowchart
table(men.smk$fx_death)##
## Dead w/o fracture Event-free Fractured
## 2918 1990 391table(men.smk$hip_death)##
## Dead w/o fracture Event-free Fractured
## 3437 2318 63table(men.anyfx$postfx_death)##
## 0 1
## 391 693table(men.hipfx$postfx_death)##
## 0 1
## 63 174(1) Descriptive analysis
(1.1) Any fracture:
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) + smoke_status + smoke_packyrs + smoke_perddlife + smoke_perdd + smk_dur + smoke_age1st + smoke_agestop + as.factor(smoke_100life) + 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.smk, render.continuous = c(. = "Mean(SD)", . = "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 | |||
| Mean(SD) | 73.5(5.86) | 74.5(5.88) | 73.7(5.87) |
| 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 | |||
| Mean(SD) | 0.794(0.127) | 0.739(0.122) | 0.784(0.128) |
| Median [Q1, Q3] | 0.783 [0.707, 0.870] | 0.728 [0.652, 0.812] | 0.774 [0.696, 0.860] |
| Tscore | |||
| Mean(SD) | -1.02(0.930) | -1.43(0.887) | -1.09(0.935) |
| 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%) |
| smoke_status | |||
| 1 (0.0%) | 0 (0%) | 1 (0.0%) | |
| 0:NO | 1836 (37.4%) | 412 (38.0%) | 2248 (37.5%) |
| 1:PAST | 2909 (59.3%) | 628 (57.9%) | 3537 (59.0%) |
| 2:CURRENT | 162 (3.3%) | 44 (4.1%) | 206 (3.4%) |
| smoke_packyrs | |||
| Mean(SD) | 18.1(24.6) | 17.7(24.6) | 18.1(24.6) |
| Median [Q1, Q3] | 7.40 [0, 29.0] | 5.65 [0, 29.0] | 7.00 [0, 29.0] |
| smoke_perddlife | |||
| Mean(SD) | 12.6(13.9) | 12.1(13.6) | 12.5(13.8) |
| Median [Q1, Q3] | 10.0 [0, 20.0] | 10.0 [0, 20.0] | 10.0 [0, 20.0] |
| smoke_perdd | |||
| Mean(SD) | 0.540(3.45) | 0.705(3.96) | 0.570(3.55) |
| Median [Q1, Q3] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] |
| smk_dur | |||
| Mean(SD) | 16.7(17.6) | 16.6(18.0) | 16.7(17.6) |
| Median [Q1, Q3] | 12.0 [0, 30.0] | 11.0 [0, 30.0] | 12.0 [0, 30.0] |
| smoke_age1st | |||
| Mean(SD) | 11.4(9.55) | 11.6(9.89) | 11.5(9.61) |
| Median [Q1, Q3] | 15.0 [0, 18.0] | 16.0 [0, 19.0] | 15.0 [0, 18.0] |
| smoke_agestop | |||
| Mean(SD) | 25.8(23.8) | 25.3(24.0) | 25.7(23.8) |
| Median [Q1, Q3] | 30.0 [0, 45.0] | 27.0 [0, 45.0] | 29.0 [0, 45.0] |
| as.factor(smoke_100life) | |||
| 0: No | 1836 (37.4%) | 412 (38.0%) | 2248 (37.5%) |
| 1: Yes | 3072 (62.6%) | 672 (62.0%) | 3744 (62.5%) |
| 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 | |||
| Mean(SD) | 795(392) | 784(388) | 793(391) |
| 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 | |||
| Mean(SD) | 64.4(27.6) | 62.6(26.1) | 64.1(27.4) |
| 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 | |||
| Mean(SD) | 27.4(3.95) | 27.1(3.88) | 27.3(3.94) |
| Median [Q1, Q3] | 26.9 [24.9, 29.5] | 26.6 [24.4, 29.3] | 26.9 [24.8, 29.5] |
| 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 | 4472 (91.1%) | 967 (89.2%) | 5439 (90.8%) |
| 1 | 436 (8.9%) | 117 (10.8%) | 553 (9.2%) |
| 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 | 4750 (96.8%) | 1031 (95.1%) | 5781 (96.5%) |
| 1 | 158 (3.2%) | 53 (4.9%) | 211 (3.5%) |
| 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%) |
createTable(compareGroups(anyfx ~ age + age_bin + race + fnbmd + Tscore + bmd_bin + no_falls + fall_bin + fx50 + fx50_bin + smoke + smoke_bin + smoke_status + smoke_packyrs + smoke_perddlife + smoke_perdd + smk_dur + smoke_age1st + smoke_agestop + smoke_100life + drink4 + drink_bin + physical4 + activity_bin + calcium2 + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)) ## Warning in chisq.test(xx, correct = FALSE): Chi-squared approximation may be
## incorrect## Warning in chisq.test(xx, correct = FALSE): Chi-squared approximation may be
## incorrect##
## --------Summary descriptives table by 'anyfx'---------
##
## __________________________________________________________________________________
## 0 1 p.overall
## N=4908 N=1084
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
## age 73.5 (5.86) 74.5 (5.88) <0.001
## age_bin: <0.001
## 1.Age< 75 2909 (59.3%) 567 (52.3%)
## 2.Age>= 75 1999 (40.7%) 517 (47.7%)
## race: .
## 1:WHITE 4368 (89.0%) 1016 (93.7%)
## 2:AFRICAN AMERICAN 226 (4.60%) 18 (1.66%)
## 3:ASIAN 166 (3.38%) 26 (2.40%)
## 4:NATIVE HAWIIAN OR OTHER PACIFIC ISLANDER 6 (0.12%) 1 (0.09%)
## 5:AMERICAN INDIAN OR ALASKAN NATIVE 6 (0.12%) 1 (0.09%)
## 6:MULTI RACIAL 58 (1.18%) 3 (0.28%)
## 7:UNKNOWN 78 (1.59%) 19 (1.75%)
## fnbmd 0.79 (0.13) 0.74 (0.12) <0.001
## Tscore -1.02 (0.93) -1.43 (0.89) <0.001
## bmd_bin: <0.001
## 1.BMD> -2.5 4721 (96.2%) 976 (90.0%)
## 2.BMD<= -2.5 187 (3.81%) 108 (9.96%)
## no_falls 0.20 (0.40) 0.26 (0.44) <0.001
## fall_bin: <0.001
## 1.No falls 3924 (80.0%) 801 (73.9%)
## 2.Falls 1+ 984 (20.0%) 283 (26.1%)
## fx50 0.20 (0.53) 0.35 (0.73) <0.001
## fx50_bin: <0.001
## 1.No fx 4141 (84.4%) 820 (75.6%)
## 2.Fx 1+ 767 (15.6%) 264 (24.4%)
## smoke: 0.400
## Current 162 (3.30%) 44 (4.06%)
## Never 1837 (37.4%) 412 (38.0%)
## Past 2909 (59.3%) 628 (57.9%)
## smoke_bin: 0.251
## 1.No/past smoking 4746 (96.7%) 1040 (95.9%)
## 2.Current smoking 162 (3.30%) 44 (4.06%)
## smoke_status: 0.497
## 1 (0.02%) 0 (0.00%)
## 0:NO 1836 (37.4%) 412 (38.0%)
## 1:PAST 2909 (59.3%) 628 (57.9%)
## 2:CURRENT 162 (3.30%) 44 (4.06%)
## smoke_packyrs 18.1 (24.6) 17.7 (24.6) 0.586
## smoke_perddlife 12.6 (13.9) 12.1 (13.6) 0.312
## smoke_perdd 0.54 (3.45) 0.70 (3.96) 0.205
## smk_dur 16.7 (17.6) 16.6 (18.0) 0.871
## smoke_age1st 11.4 (9.55) 11.6 (9.89) 0.658
## smoke_agestop 25.8 (23.8) 25.3 (24.0) 0.501
## smoke_100life: 0.738
## 0: No 1836 (37.4%) 412 (38.0%)
## 1: Yes 3072 (62.6%) 672 (62.0%)
## drink4: 0.242
## High 1578 (32.2%) 372 (34.3%)
## Low 726 (14.8%) 155 (14.3%)
## Moderate 393 (8.01%) 70 (6.46%)
## No 2211 (45.0%) 487 (44.9%)
## drink_bin: 0.180
## 1.Less drinking 3330 (67.8%) 712 (65.7%)
## 2.Excessive drinking 1578 (32.2%) 372 (34.3%)
## physical4: 0.436
## High 695 (14.2%) 171 (15.8%)
## Low 1361 (27.7%) 281 (25.9%)
## Moderate 558 (11.4%) 121 (11.2%)
## No 2294 (46.7%) 511 (47.1%)
## activity_bin: 0.357
## 1.Proactive 1253 (25.5%) 292 (26.9%)
## 2.Less active 3655 (74.5%) 792 (73.1%)
## calcium2 795 (392) 784 (388) 0.409
## calci_bin: 1.000
## 1.Sufficient Calcium 1194 (24.3%) 264 (24.4%)
## 2.Insufficient Calcium 3714 (75.7%) 820 (75.6%)
## protein2 64.4 (27.6) 62.6 (26.1) 0.049
## education 5.78 (1.66) 5.89 (1.59) 0.051
## BMI 27.4 (3.95) 27.1 (3.88) 0.016
## cvd 0.21 (0.41) 0.21 (0.41) 0.641
## hypertension 0.43 (0.49) 0.44 (0.50) 0.496
## copd 0.10 (0.31) 0.12 (0.32) 0.330
## diabetes 0.11 (0.31) 0.11 (0.31) 0.734
## cancer 0.18 (0.39) 0.18 (0.38) 0.824
## renal 0.09 (0.28) 0.11 (0.31) 0.063
## parkinson 0.13 (0.34) 0.12 (0.33) 0.376
## depression 0.03 (0.18) 0.05 (0.22) 0.017
## rheumatoid 0.48 (0.50) 0.47 (0.50) 0.753
## death 0.59 (0.49) 0.64 (0.48) 0.006
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯(1.2) Hip fracture:
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) + smoke_status + smoke_packyrs + smoke_perddlife + smoke_perdd + smk_dur + smoke_age1st + smoke_agestop + as.factor(smoke_100life) + 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) | hipfx, data = men.smk, render.continuous = c(. = "Mean(SD)", . = "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=5755) |
1 (N=237) |
Overall (N=5992) |
|
|---|---|---|---|
| age | |||
| Mean(SD) | 73.5(5.84) | 76.4(6.09) | 73.7(5.87) |
| Median [Q1, Q3] | 73.0 [69.0, 78.0] | 76.0 [72.0, 80.0] | 73.0 [69.0, 78.0] |
| as.factor(age_bin) | |||
| 1.Age< 75 | 3384 (58.8%) | 92 (38.8%) | 3476 (58.0%) |
| 2.Age>= 75 | 2371 (41.2%) | 145 (61.2%) | 2516 (42.0%) |
| race | |||
| 1:WHITE | 5157 (89.6%) | 227 (95.8%) | 5384 (89.9%) |
| 2:AFRICAN AMERICAN | 241 (4.2%) | 3 (1.3%) | 244 (4.1%) |
| 3:ASIAN | 188 (3.3%) | 4 (1.7%) | 192 (3.2%) |
| 4:NATIVE HAWIIAN OR OTHER PACIFIC ISLANDER | 7 (0.1%) | 0 (0%) | 7 (0.1%) |
| 5:AMERICAN INDIAN OR ALASKAN NATIVE | 7 (0.1%) | 0 (0%) | 7 (0.1%) |
| 6:MULTI RACIAL | 60 (1.0%) | 1 (0.4%) | 61 (1.0%) |
| 7:UNKNOWN | 95 (1.7%) | 2 (0.8%) | 97 (1.6%) |
| fnbmd | |||
| Mean(SD) | 0.788(0.127) | 0.689(0.115) | 0.784(0.128) |
| Median [Q1, Q3] | 0.778 [0.701, 0.863] | 0.671 [0.605, 0.752] | 0.774 [0.696, 0.860] |
| Tscore | |||
| Mean(SD) | -1.06(0.928) | -1.79(0.843) | -1.09(0.935) |
| Median [Q1, Q3] | -1.14 [-1.70, -0.519] | -1.92 [-2.40, -1.33] | -1.17 [-1.73, -0.539] |
| as.factor(bmd_bin) | |||
| 1.BMD> -2.5 | 5506 (95.7%) | 191 (80.6%) | 5697 (95.1%) |
| 2.BMD<= -2.5 | 249 (4.3%) | 46 (19.4%) | 295 (4.9%) |
| as.factor(no_falls) | |||
| 0 | 4552 (79.1%) | 173 (73.0%) | 4725 (78.9%) |
| 1 | 1203 (20.9%) | 64 (27.0%) | 1267 (21.1%) |
| as.factor(fall_bin) | |||
| 1.No falls | 4552 (79.1%) | 173 (73.0%) | 4725 (78.9%) |
| 2.Falls 1+ | 1203 (20.9%) | 64 (27.0%) | 1267 (21.1%) |
| as.factor(fx50) | |||
| 0 | 4778 (83.0%) | 183 (77.2%) | 4961 (82.8%) |
| 1 | 741 (12.9%) | 38 (16.0%) | 779 (13.0%) |
| 2 | 183 (3.2%) | 9 (3.8%) | 192 (3.2%) |
| 3 | 39 (0.7%) | 4 (1.7%) | 43 (0.7%) |
| 4 | 11 (0.2%) | 2 (0.8%) | 13 (0.2%) |
| 5 | 1 (0.0%) | 1 (0.4%) | 2 (0.0%) |
| 6 | 2 (0.0%) | 0 (0%) | 2 (0.0%) |
| as.factor(fx50_bin) | |||
| 1.No fx | 4778 (83.0%) | 183 (77.2%) | 4961 (82.8%) |
| 2.Fx 1+ | 977 (17.0%) | 54 (22.8%) | 1031 (17.2%) |
| as.factor(smoke) | |||
| Current | 194 (3.4%) | 12 (5.1%) | 206 (3.4%) |
| Never | 2151 (37.4%) | 98 (41.4%) | 2249 (37.5%) |
| Past | 3410 (59.3%) | 127 (53.6%) | 3537 (59.0%) |
| as.factor(smoke_bin) | |||
| 1.No/past smoking | 5561 (96.6%) | 225 (94.9%) | 5786 (96.6%) |
| 2.Current smoking | 194 (3.4%) | 12 (5.1%) | 206 (3.4%) |
| smoke_status | |||
| 1 (0.0%) | 0 (0%) | 1 (0.0%) | |
| 0:NO | 2150 (37.4%) | 98 (41.4%) | 2248 (37.5%) |
| 1:PAST | 3410 (59.3%) | 127 (53.6%) | 3537 (59.0%) |
| 2:CURRENT | 194 (3.4%) | 12 (5.1%) | 206 (3.4%) |
| smoke_packyrs | |||
| Mean(SD) | 18.1(24.6) | 17.6(25.3) | 18.1(24.6) |
| Median [Q1, Q3] | 7.05 [0, 29.0] | 3.00 [0, 29.3] | 7.00 [0, 29.0] |
| smoke_perddlife | |||
| Mean(SD) | 12.5(13.8) | 11.5(13.6) | 12.5(13.8) |
| Median [Q1, Q3] | 10.0 [0, 20.0] | 8.00 [0, 20.0] | 10.0 [0, 20.0] |
| smoke_perdd | |||
| Mean(SD) | 0.560(3.53) | 0.819(3.86) | 0.570(3.55) |
| Median [Q1, Q3] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] |
| smk_dur | |||
| Mean(SD) | 16.7(17.6) | 16.3(18.7) | 16.7(17.6) |
| Median [Q1, Q3] | 12.0 [0, 30.0] | 9.00 [0, 29.0] | 12.0 [0, 30.0] |
| smoke_age1st | |||
| Mean(SD) | 11.5(9.61) | 10.8(9.47) | 11.5(9.61) |
| Median [Q1, Q3] | 15.0 [0, 18.0] | 15.0 [0, 18.0] | 15.0 [0, 18.0] |
| smoke_agestop | |||
| Mean(SD) | 25.8(23.8) | 23.4(24.4) | 25.7(23.8) |
| Median [Q1, Q3] | 30.0 [0, 45.0] | 23.0 [0, 45.0] | 29.0 [0, 45.0] |
| as.factor(smoke_100life) | |||
| 0: No | 2150 (37.4%) | 98 (41.4%) | 2248 (37.5%) |
| 1: Yes | 3605 (62.6%) | 139 (58.6%) | 3744 (62.5%) |
| drink4 | |||
| High | 1888 (32.8%) | 62 (26.2%) | 1950 (32.5%) |
| Low | 849 (14.8%) | 32 (13.5%) | 881 (14.7%) |
| Moderate | 445 (7.7%) | 18 (7.6%) | 463 (7.7%) |
| No | 2573 (44.7%) | 125 (52.7%) | 2698 (45.0%) |
| as.factor(drink_bin) | |||
| 1.Less drinking | 3867 (67.2%) | 175 (73.8%) | 4042 (67.5%) |
| 2.Excessive drinking | 1888 (32.8%) | 62 (26.2%) | 1950 (32.5%) |
| physical4 | |||
| High | 829 (14.4%) | 37 (15.6%) | 866 (14.5%) |
| Low | 1583 (27.5%) | 59 (24.9%) | 1642 (27.4%) |
| Moderate | 663 (11.5%) | 16 (6.8%) | 679 (11.3%) |
| No | 2680 (46.6%) | 125 (52.7%) | 2805 (46.8%) |
| as.factor(activity_bin) | |||
| 1.Proactive | 1492 (25.9%) | 53 (22.4%) | 1545 (25.8%) |
| 2.Less active | 4263 (74.1%) | 184 (77.6%) | 4447 (74.2%) |
| calcium2 | |||
| Mean(SD) | 793(391) | 779(387) | 793(391) |
| Median [Q1, Q3] | 727 [523, 991] | 738 [500, 994] | 728 [522, 991] |
| as.factor(calci_bin) | |||
| 1.Sufficient Calcium | 1401 (24.3%) | 57 (24.1%) | 1458 (24.3%) |
| 2.Insufficient Calcium | 4354 (75.7%) | 180 (75.9%) | 4534 (75.7%) |
| protein2 | |||
| Mean(SD) | 64.2(27.3) | 62.2(27.9) | 64.1(27.4) |
| Median [Q1, Q3] | 60.2 [45.7, 78.3] | 58.2 [45.3, 76.9] | 60.2 [45.7, 78.2] |
| as.factor(education) | |||
| 1 | 16 (0.3%) | 0 (0%) | 16 (0.3%) |
| 2 | 93 (1.6%) | 4 (1.7%) | 97 (1.6%) |
| 3 | 265 (4.6%) | 13 (5.5%) | 278 (4.6%) |
| 4 | 992 (17.2%) | 44 (18.6%) | 1036 (17.3%) |
| 5 | 1329 (23.1%) | 48 (20.3%) | 1377 (23.0%) |
| 6 | 1043 (18.1%) | 51 (21.5%) | 1094 (18.3%) |
| 7 | 603 (10.5%) | 30 (12.7%) | 633 (10.6%) |
| 8 | 1414 (24.6%) | 47 (19.8%) | 1461 (24.4%) |
| BMI | |||
| Mean(SD) | 27.4(3.95) | 26.7(3.73) | 27.3(3.94) |
| Median [Q1, Q3] | 26.9 [24.8, 29.5] | 26.1 [23.9, 28.7] | 26.9 [24.8, 29.5] |
| as.factor(cvd) | |||
| 0 | 4566 (79.3%) | 175 (73.8%) | 4741 (79.1%) |
| 1 | 1189 (20.7%) | 62 (26.2%) | 1251 (20.9%) |
| as.factor(hypertension) | |||
| 0 | 3298 (57.3%) | 113 (47.7%) | 3411 (56.9%) |
| 1 | 2457 (42.7%) | 124 (52.3%) | 2581 (43.1%) |
| as.factor(copd) | |||
| 0 | 5140 (89.3%) | 212 (89.5%) | 5352 (89.3%) |
| 1 | 615 (10.7%) | 25 (10.5%) | 640 (10.7%) |
| as.factor(diabetes) | |||
| 0 | 5126 (89.1%) | 213 (89.9%) | 5339 (89.1%) |
| 1 | 629 (10.9%) | 24 (10.1%) | 653 (10.9%) |
| as.factor(cancer) | |||
| 0 | 4705 (81.8%) | 195 (82.3%) | 4900 (81.8%) |
| 1 | 1050 (18.2%) | 42 (17.7%) | 1092 (18.2%) |
| as.factor(renal) | |||
| 0 | 5226 (90.8%) | 213 (89.9%) | 5439 (90.8%) |
| 1 | 529 (9.2%) | 24 (10.1%) | 553 (9.2%) |
| as.factor(parkinson) | |||
| 0 | 5002 (86.9%) | 201 (84.8%) | 5203 (86.8%) |
| 1 | 753 (13.1%) | 36 (15.2%) | 789 (13.2%) |
| as.factor(depression) | |||
| 0 | 5556 (96.5%) | 225 (94.9%) | 5781 (96.5%) |
| 1 | 199 (3.5%) | 12 (5.1%) | 211 (3.5%) |
| as.factor(rheumatoid) | |||
| 0 | 3030 (52.6%) | 117 (49.4%) | 3147 (52.5%) |
| 1 | 2725 (47.4%) | 120 (50.6%) | 2845 (47.5%) |
| as.factor(death) | |||
| 0 | 2318 (40.3%) | 63 (26.6%) | 2381 (39.7%) |
| 1 | 3437 (59.7%) | 174 (73.4%) | 3611 (60.3%) |
createTable(compareGroups(hipfx ~ age + age_bin + race + fnbmd + Tscore + bmd_bin + no_falls + fall_bin + fx50 + fx50_bin + smoke + smoke_bin + smoke_status + smoke_packyrs + smoke_perddlife + smoke_perdd + smk_dur + smoke_age1st + smoke_agestop + smoke_100life + drink4 + drink_bin + physical4 + activity_bin + calcium2 + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)) ##
## --------Summary descriptives table by 'hipfx'---------
##
## __________________________________________________________________________________
## 0 1 p.overall
## N=5755 N=237
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
## age 73.5 (5.84) 76.4 (6.09) <0.001
## age_bin: <0.001
## 1.Age< 75 3384 (58.8%) 92 (38.8%)
## 2.Age>= 75 2371 (41.2%) 145 (61.2%)
## race: 0.142
## 1:WHITE 5157 (89.6%) 227 (95.8%)
## 2:AFRICAN AMERICAN 241 (4.19%) 3 (1.27%)
## 3:ASIAN 188 (3.27%) 4 (1.69%)
## 4:NATIVE HAWIIAN OR OTHER PACIFIC ISLANDER 7 (0.12%) 0 (0.00%)
## 5:AMERICAN INDIAN OR ALASKAN NATIVE 7 (0.12%) 0 (0.00%)
## 6:MULTI RACIAL 60 (1.04%) 1 (0.42%)
## 7:UNKNOWN 95 (1.65%) 2 (0.84%)
## fnbmd 0.79 (0.13) 0.69 (0.12) <0.001
## Tscore -1.06 (0.93) -1.79 (0.84) <0.001
## bmd_bin: <0.001
## 1.BMD> -2.5 5506 (95.7%) 191 (80.6%)
## 2.BMD<= -2.5 249 (4.33%) 46 (19.4%)
## no_falls 0.21 (0.41) 0.27 (0.44) 0.039
## fall_bin: 0.030
## 1.No falls 4552 (79.1%) 173 (73.0%)
## 2.Falls 1+ 1203 (20.9%) 64 (27.0%)
## fx50 0.22 (0.56) 0.34 (0.77) 0.020
## fx50_bin: 0.025
## 1.No fx 4778 (83.0%) 183 (77.2%)
## 2.Fx 1+ 977 (17.0%) 54 (22.8%)
## smoke: 0.129
## Current 194 (3.37%) 12 (5.06%)
## Never 2151 (37.4%) 98 (41.4%)
## Past 3410 (59.3%) 127 (53.6%)
## smoke_bin: 0.223
## 1.No/past smoking 5561 (96.6%) 225 (94.9%)
## 2.Current smoking 194 (3.37%) 12 (5.06%)
## smoke_status: 0.154
## 1 (0.02%) 0 (0.00%)
## 0:NO 2150 (37.4%) 98 (41.4%)
## 1:PAST 3410 (59.3%) 127 (53.6%)
## 2:CURRENT 194 (3.37%) 12 (5.06%)
## smoke_packyrs 18.1 (24.6) 17.6 (25.3) 0.770
## smoke_perddlife 12.5 (13.8) 11.5 (13.6) 0.259
## smoke_perdd 0.56 (3.53) 0.82 (3.86) 0.311
## smk_dur 16.7 (17.6) 16.3 (18.7) 0.746
## smoke_age1st 11.5 (9.61) 10.8 (9.47) 0.262
## smoke_agestop 25.8 (23.8) 23.4 (24.4) 0.142
## smoke_100life: 0.240
## 0: No 2150 (37.4%) 98 (41.4%)
## 1: Yes 3605 (62.6%) 139 (58.6%)
## drink4: 0.086
## High 1888 (32.8%) 62 (26.2%)
## Low 849 (14.8%) 32 (13.5%)
## Moderate 445 (7.73%) 18 (7.59%)
## No 2573 (44.7%) 125 (52.7%)
## drink_bin: 0.039
## 1.Less drinking 3867 (67.2%) 175 (73.8%)
## 2.Excessive drinking 1888 (32.8%) 62 (26.2%)
## physical4: 0.065
## High 829 (14.4%) 37 (15.6%)
## Low 1583 (27.5%) 59 (24.9%)
## Moderate 663 (11.5%) 16 (6.75%)
## No 2680 (46.6%) 125 (52.7%)
## activity_bin: 0.249
## 1.Proactive 1492 (25.9%) 53 (22.4%)
## 2.Less active 4263 (74.1%) 184 (77.6%)
## calcium2 793 (391) 779 (387) 0.579
## calci_bin: 0.979
## 1.Sufficient Calcium 1401 (24.3%) 57 (24.1%)
## 2.Insufficient Calcium 4354 (75.7%) 180 (75.9%)
## protein2 64.2 (27.3) 62.2 (27.9) 0.294
## education 5.80 (1.65) 5.72 (1.60) 0.416
## BMI 27.4 (3.95) 26.7 (3.73) 0.004
## cvd 0.21 (0.40) 0.26 (0.44) 0.060
## hypertension 0.43 (0.49) 0.52 (0.50) 0.004
## copd 0.11 (0.31) 0.11 (0.31) 0.946
## diabetes 0.11 (0.31) 0.10 (0.30) 0.689
## cancer 0.18 (0.39) 0.18 (0.38) 0.837
## renal 0.09 (0.29) 0.10 (0.30) 0.641
## parkinson 0.13 (0.34) 0.15 (0.36) 0.377
## depression 0.03 (0.18) 0.05 (0.22) 0.268
## rheumatoid 0.47 (0.50) 0.51 (0.50) 0.324
## death 0.60 (0.49) 0.73 (0.44) <0.001
## ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯(2) Smoking status:
(2.1) Classification 1: Current vs. Past/None
(2.1.1) Prevalence
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + smoke_bin + drink_bin + activity_bin + as.factor(group) | anyfx, data = men.smk, render.continuous = c(. = "Mean(SD)", . = "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 | |||
| Mean(SD) | 73.5(5.86) | 74.5(5.88) | 73.7(5.87) |
| 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 | |||
| Mean(SD) | 0.794(0.127) | 0.739(0.122) | 0.784(0.128) |
| Median [Q1, Q3] | 0.783 [0.707, 0.870] | 0.728 [0.652, 0.812] | 0.774 [0.696, 0.860] |
| Tscore | |||
| Mean(SD) | -1.02(0.930) | -1.43(0.887) | -1.09(0.935) |
| 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%) |
(2.1.2) Association for any fracture
Original format of 3 categories: Never, Past vs Current
men.smk$smoke.c = factor(men.smk$smoke, levels = c("Never", "Past", "Current"))
men.smk$fnbmd.sd = men.smk$fnbmd / 0.10
any.smk.age = coxph(Surv(fu_anyfx, anyfx) ~ smoke.c + age, data = men.smk)
summary(any.smk.age)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke.c + age, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast 0.082228 1.085703 0.063516 1.295 0.195
## smoke.cCurrent 0.627575 1.873063 0.160191 3.918 8.94e-05 ***
## age 0.074815 1.077685 0.005404 13.844 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.086 0.9211 0.9586 1.230
## smoke.cCurrent 1.873 0.5339 1.3684 2.564
## age 1.078 0.9279 1.0663 1.089
##
## Concordance= 0.618 (se = 0.009 )
## Likelihood ratio test= 187.3 on 3 df, p=<2e-16
## Wald test = 195.8 on 3 df, p=<2e-16
## Score (logrank) test = 199.6 on 3 df, p=<2e-16any.smk.all1 = coxph(Surv(fu_anyfx, anyfx) ~ smoke.c + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(any.smk.all1)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke.c + age_bin + bmd_bin +
## fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast 0.05447 1.05598 0.06355 0.857 0.391394
## smoke.cCurrent 0.55135 1.73559 0.15998 3.446 0.000568 ***
## age_bin2.Age>= 75 0.61935 1.85772 0.06324 9.793 < 2e-16 ***
## bmd_bin2.BMD<= -2.5 0.94642 2.57646 0.10294 9.194 < 2e-16 ***
## fall_bin2.Falls 1+ 0.33337 1.39566 0.06982 4.774 1.80e-06 ***
## fx50_bin2.Fx 1+ 0.47510 1.60818 0.07147 6.647 2.99e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.056 0.9470 0.9323 1.196
## smoke.cCurrent 1.736 0.5762 1.2684 2.375
## age_bin2.Age>= 75 1.858 0.5383 1.6412 2.103
## bmd_bin2.BMD<= -2.5 2.576 0.3881 2.1057 3.152
## fall_bin2.Falls 1+ 1.396 0.7165 1.2172 1.600
## fx50_bin2.Fx 1+ 1.608 0.6218 1.3980 1.850
##
## Concordance= 0.638 (se = 0.009 )
## Likelihood ratio test= 267 on 6 df, p=<2e-16
## Wald test = 307.3 on 6 df, p=<2e-16
## Score (logrank) test = 327.1 on 6 df, p=<2e-16any.smk.all2 = coxph(Surv(fu_anyfx, anyfx) ~ smoke.c + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid, data = men.smk)
summary(any.smk.all2)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke.c + age_bin + bmd_bin +
## fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin +
## protein2 + education + BMI + cvd + hypertension + copd +
## diabetes + cancer + renal + parkinson + depression + rheumatoid,
## data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast 0.028192 1.028593 0.065577 0.430 0.667268
## smoke.cCurrent 0.553899 1.740025 0.162155 3.416 0.000636
## age_bin2.Age>= 75 0.583400 1.792122 0.065229 8.944 < 2e-16
## bmd_bin2.BMD<= -2.5 0.963598 2.621110 0.105499 9.134 < 2e-16
## fall_bin2.Falls 1+ 0.308458 1.361325 0.071011 4.344 1.4e-05
## fx50_bin2.Fx 1+ 0.478196 1.613162 0.071720 6.668 2.6e-11
## drink_bin2.Excessive drinking 0.080176 1.083478 0.065870 1.217 0.223531
## activity_bin2.Less active 0.007088 1.007114 0.070160 0.101 0.919525
## calci_bin2.Insufficient Calcium -0.080404 0.922744 0.081915 -0.982 0.326320
## protein2 -0.003309 0.996697 0.001372 -2.412 0.015873
## education 0.001935 1.001937 0.019381 0.100 0.920485
## BMI -0.004690 0.995321 0.008664 -0.541 0.588294
## cvd 0.157894 1.171043 0.076513 2.064 0.039053
## hypertension 0.124935 1.133075 0.063345 1.972 0.048575
## copd 0.138593 1.148656 0.096460 1.437 0.150778
## diabetes 0.204408 1.226799 0.101378 2.016 0.043769
## cancer 0.051299 1.052638 0.079917 0.642 0.520932
## renal 0.018369 1.018539 0.128268 0.143 0.886124
## parkinson -0.071625 0.930879 0.120286 -0.595 0.551537
## depression 0.179663 1.196814 0.142363 1.262 0.206948
## rheumatoid -0.015625 0.984497 0.062836 -0.249 0.803623
##
## smoke.cPast
## smoke.cCurrent ***
## age_bin2.Age>= 75 ***
## bmd_bin2.BMD<= -2.5 ***
## fall_bin2.Falls 1+ ***
## fx50_bin2.Fx 1+ ***
## drink_bin2.Excessive drinking
## activity_bin2.Less active
## calci_bin2.Insufficient Calcium
## protein2 *
## education
## BMI
## cvd *
## hypertension *
## copd
## diabetes *
## cancer
## renal
## parkinson
## depression
## rheumatoid
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.0286 0.9722 0.9045 1.1697
## smoke.cCurrent 1.7400 0.5747 1.2663 2.3910
## age_bin2.Age>= 75 1.7921 0.5580 1.5770 2.0365
## bmd_bin2.BMD<= -2.5 2.6211 0.3815 2.1315 3.2232
## fall_bin2.Falls 1+ 1.3613 0.7346 1.1845 1.5646
## fx50_bin2.Fx 1+ 1.6132 0.6199 1.4016 1.8566
## drink_bin2.Excessive drinking 1.0835 0.9230 0.9523 1.2328
## activity_bin2.Less active 1.0071 0.9929 0.8777 1.1556
## calci_bin2.Insufficient Calcium 0.9227 1.0837 0.7859 1.0834
## protein2 0.9967 1.0033 0.9940 0.9994
## education 1.0019 0.9981 0.9646 1.0407
## BMI 0.9953 1.0047 0.9786 1.0124
## cvd 1.1710 0.8539 1.0080 1.3605
## hypertension 1.1331 0.8826 1.0008 1.2829
## copd 1.1487 0.8706 0.9508 1.3877
## diabetes 1.2268 0.8151 1.0057 1.4965
## cancer 1.0526 0.9500 0.9000 1.2311
## renal 1.0185 0.9818 0.7921 1.3097
## parkinson 0.9309 1.0743 0.7354 1.1784
## depression 1.1968 0.8356 0.9054 1.5820
## rheumatoid 0.9845 1.0157 0.8704 1.1135
##
## Concordance= 0.647 (se = 0.009 )
## Likelihood ratio test= 292.5 on 21 df, p=<2e-16
## Wald test = 331.8 on 21 df, p=<2e-16
## Score (logrank) test = 352.6 on 21 df, p=<2e-16Binary format for PAR
any.smk.age = coxph(Surv(fu_anyfx, anyfx) ~ smoke_bin + age, data = men.smk)
summary(any.smk.age)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke_bin + age, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke_bin2.Current smoking 0.577225 1.781089 0.155247 3.718 0.000201 ***
## age 0.074439 1.077279 0.005392 13.804 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_bin2.Current smoking 1.781 0.5615 1.314 2.415
## age 1.077 0.9283 1.066 1.089
##
## 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-16any.smk.all1 = coxph(Surv(fu_anyfx, anyfx) ~ smoke_bin + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(any.smk.all1)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke_bin + age_bin +
## bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke_bin2.Current smoking 0.51810 1.67883 0.15511 3.340 0.000837 ***
## age_bin2.Age>= 75 0.61663 1.85267 0.06317 9.761 < 2e-16 ***
## bmd_bin2.BMD<= -2.5 0.94618 2.57586 0.10295 9.191 < 2e-16 ***
## fall_bin2.Falls 1+ 0.33490 1.39780 0.06980 4.798 1.60e-06 ***
## fx50_bin2.Fx 1+ 0.47695 1.61115 0.07144 6.677 2.45e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_bin2.Current smoking 1.679 0.5957 1.239 2.275
## age_bin2.Age>= 75 1.853 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
##
## Concordance= 0.636 (se = 0.009 )
## Likelihood ratio test= 266.2 on 5 df, p=<2e-16
## Wald test = 306.7 on 5 df, p=<2e-16
## Score (logrank) test = 326.5 on 5 df, p=<2e-16any.smk.all2 = coxph(Surv(fu_anyfx, anyfx) ~ smoke_bin + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid, data = men.smk)
summary(any.smk.all2)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke_bin + age_bin +
## bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin +
## calci_bin + protein2 + education + BMI + cvd + hypertension +
## copd + diabetes + cancer + renal + parkinson + depression +
## rheumatoid, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z
## smoke_bin2.Current smoking 0.5358238 1.7088555 0.1565659 3.422
## age_bin2.Age>= 75 0.5818252 1.7893014 0.0651334 8.933
## bmd_bin2.BMD<= -2.5 0.9647256 2.6240674 0.1054818 9.146
## fall_bin2.Falls 1+ 0.3089229 1.3619573 0.0710001 4.351
## fx50_bin2.Fx 1+ 0.4790486 1.6145376 0.0716910 6.682
## drink_bin2.Excessive drinking 0.0845968 1.0882782 0.0650693 1.300
## activity_bin2.Less active 0.0072301 1.0072563 0.0701555 0.103
## calci_bin2.Insufficient Calcium -0.0801932 0.9229380 0.0819197 -0.979
## protein2 -0.0033096 0.9966958 0.0013715 -2.413
## education 0.0008118 1.0008122 0.0192043 0.042
## BMI -0.0044180 0.9955918 0.0086419 -0.511
## cvd 0.1595742 1.1730113 0.0764134 2.088
## hypertension 0.1256238 1.1338555 0.0633292 1.984
## copd 0.1417496 1.1522881 0.0961836 1.474
## diabetes 0.2042303 1.2265805 0.1013885 2.014
## cancer 0.0510206 1.0523445 0.0799109 0.638
## renal 0.0182944 1.0184628 0.1282469 0.143
## parkinson -0.0719417 0.9305851 0.1202642 -0.598
## depression 0.1804831 1.1977958 0.1423518 1.268
## rheumatoid -0.0145294 0.9855757 0.0627836 -0.231
## Pr(>|z|)
## smoke_bin2.Current smoking 0.000621 ***
## age_bin2.Age>= 75 < 2e-16 ***
## bmd_bin2.BMD<= -2.5 < 2e-16 ***
## fall_bin2.Falls 1+ 1.36e-05 ***
## fx50_bin2.Fx 1+ 2.35e-11 ***
## drink_bin2.Excessive drinking 0.193566
## activity_bin2.Less active 0.917917
## calci_bin2.Insufficient Calcium 0.327618
## protein2 0.015817 *
## education 0.966281
## BMI 0.609190
## cvd 0.036771 *
## hypertension 0.047293 *
## copd 0.140552
## diabetes 0.043974 *
## cancer 0.523169
## renal 0.886567
## parkinson 0.549708
## depression 0.204846
## rheumatoid 0.816989
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_bin2.Current smoking 1.7089 0.5852 1.2573 2.3226
## age_bin2.Age>= 75 1.7893 0.5589 1.5749 2.0329
## bmd_bin2.BMD<= -2.5 2.6241 0.3811 2.1340 3.2267
## fall_bin2.Falls 1+ 1.3620 0.7342 1.1850 1.5653
## fx50_bin2.Fx 1+ 1.6145 0.6194 1.4029 1.8581
## drink_bin2.Excessive drinking 1.0883 0.9189 0.9580 1.2363
## activity_bin2.Less active 1.0073 0.9928 0.8779 1.1557
## calci_bin2.Insufficient Calcium 0.9229 1.0835 0.7860 1.0837
## protein2 0.9967 1.0033 0.9940 0.9994
## education 1.0008 0.9992 0.9638 1.0392
## BMI 0.9956 1.0044 0.9789 1.0126
## cvd 1.1730 0.8525 1.0099 1.3625
## hypertension 1.1339 0.8819 1.0015 1.2837
## copd 1.1523 0.8678 0.9543 1.3913
## diabetes 1.2266 0.8153 1.0055 1.4962
## cancer 1.0523 0.9503 0.8998 1.2308
## renal 1.0185 0.9819 0.7921 1.3095
## parkinson 0.9306 1.0746 0.7352 1.1779
## depression 1.1978 0.8349 0.9062 1.5833
## rheumatoid 0.9856 1.0146 0.8715 1.1146
##
## Concordance= 0.647 (se = 0.009 )
## Likelihood ratio test= 292.3 on 20 df, p=<2e-16
## Wald test = 331.6 on 20 df, p=<2e-16
## Score (logrank) test = 352.5 on 20 df, p=<2e-16Sensitivity analysis to account for a competing risk of death
Data management:
men.smk = men.smk %>% mutate(anyfx_crr = case_when(anyfx == 0 & death == 0 ~ 0,
anyfx == 1 & death == 0 ~ 1,
anyfx == 0 & death == 1 ~ 2))
library(cmprsk)## Warning: package 'cmprsk' was built under R version 4.3.3library(finalfit)## Warning: package 'finalfit' was built under R version 4.3.3Age-adjusted
cov_age = c("smoke_bin", "age")
anyfx_cph = "Surv(fu_anyfx, anyfx)"
anyfx_crr = "Surv(fu_anyfx, anyfx_crr)"
men.smk %>%
# Summary table
summary_factorlist(anyfx_cph, cov_age,
column = TRUE, fit_id = TRUE) %>%
# CPH multivariable
ff_merge(
men.smk %>%
coxphmulti(anyfx_cph, cov_age) %>%
fit2df(estimate_suffix = " (Cause-specific)")
) %>%
# Fine and Gray competing risks regression
ff_merge(
men.smk %>%
crrmulti(anyfx_crr, cov_age) %>%
fit2df(estimate_suffix = " (Fine-Gray subdistribution)")
) %>%
select(-fit_id, -index) %>%
dependent_label(men.smk, "Survival")## Dependent variable is a survival object## 693 cases omitted due to missing values## Dependent: Survival all HR (Cause-specific)
## 2 smoke_bin 1.No/past smoking 5786 (96.6) -
## 3 2.Current smoking 206 (3.4) 1.78 (1.31-2.41, p<0.001)
## 1 age Mean (SD) 73.7 (5.9) 1.08 (1.07-1.09, p<0.001)
## HR (Fine-Gray subdistribution)
## 2 -
## 3 0.73 (0.40-1.34, p=0.310)
## 1 0.94 (0.93-0.96, p<0.001)Multivariable-adjusted (only fracture risk factors)
cov_multi1 = c("smoke_bin", "age_bin", "bmd_bin", "fall_bin", "fx50_bin")
anyfx_cph = "Surv(fu_anyfx, anyfx)"
anyfx_crr = "Surv(fu_anyfx, anyfx_crr)"
men.smk %>%
# Summary table
summary_factorlist(anyfx_cph, cov_multi1,
column = TRUE, fit_id = TRUE) %>%
# CPH multivariable
ff_merge(
men.smk %>%
coxphmulti(anyfx_cph, cov_multi1) %>%
fit2df(estimate_suffix = " (Cause-specific)")
) %>%
# Fine and Gray competing risks regression
ff_merge(
men.smk %>%
crrmulti(anyfx_crr, cov_multi1) %>%
fit2df(estimate_suffix = " (Fine-Gray distribution)")
) %>%
select(-fit_id, -index) %>%
dependent_label(men.smk, "Survival")## Dependent variable is a survival object## 693 cases omitted due to missing values## Dependent: Survival all HR (Cause-specific)
## 9 smoke_bin 1.No/past smoking 5786 (96.6) -
## 10 2.Current smoking 206 (3.4) 1.68 (1.24-2.28, p=0.001)
## 1 age_bin 1.Age< 75 3476 (58.0) -
## 2 2.Age>= 75 2516 (42.0) 1.85 (1.64-2.10, p<0.001)
## 3 bmd_bin 1.BMD> -2.5 5697 (95.1) -
## 4 2.BMD<= -2.5 295 (4.9) 2.58 (2.11-3.15, p<0.001)
## 5 fall_bin 1.No falls 4725 (78.9) -
## 6 2.Falls 1+ 1267 (21.1) 1.40 (1.22-1.60, p<0.001)
## 7 fx50_bin 1.No fx 4961 (82.8) -
## 8 2.Fx 1+ 1031 (17.2) 1.61 (1.40-1.85, p<0.001)
## HR (Fine-Gray distribution)
## 9 -
## 10 0.74 (0.40-1.34, p=0.320)
## 1 -
## 2 0.47 (0.37-0.59, p<0.001)
## 3 -
## 4 1.90 (1.24-2.89, p=0.003)
## 5 -
## 6 0.97 (0.75-1.26, p=0.810)
## 7 -
## 8 1.59 (1.26-2.02, p<0.001)Multivariable-adjusted (only fracture risk factors)
cov_multi2 = c("smoke_bin", "age_bin", "bmd_bin", "fall_bin", "fx50_bin", "drink_bin", "activity_bin", "calci_bin", "protein2", "education", "BMI", "cvd", "hypertension", "copd", "diabetes", "cancer", "renal", "parkinson", "depression", "rheumatoid")
anyfx_cph = "Surv(fu_anyfx, anyfx)"
anyfx_crr = "Surv(fu_anyfx, anyfx_crr)"
men.smk %>%
# Summary table
summary_factorlist(anyfx_cph, cov_multi2,
column = TRUE, fit_id = TRUE) %>%
# CPH multivariable
ff_merge(
men.smk %>%
coxphmulti(anyfx_cph, cov_multi2) %>%
fit2df(estimate_suffix = " (Cause-specific)")
) %>%
# Fine and Gray competing risks regression
ff_merge(
men.smk %>%
crrmulti(anyfx_crr, cov_multi2) %>%
fit2df(estimate_suffix = " (Fine-Gray subdistribution)")
) %>%
select(-fit_id, -index) %>%
dependent_label(men.smk, "Survival")## Dependent variable is a survival object## 693 cases omitted due to missing values## Dependent: Survival all
## 45 smoke_bin 1.No/past smoking 5786 (96.6)
## 46 2.Current smoking 206 (3.4)
## 3 age_bin 1.Age< 75 3476 (58.0)
## 4 2.Age>= 75 2516 (42.0)
## 5 bmd_bin 1.BMD> -2.5 5697 (95.1)
## 6 2.BMD<= -2.5 295 (4.9)
## 28 fall_bin 1.No falls 4725 (78.9)
## 29 2.Falls 1+ 1267 (21.1)
## 30 fx50_bin 1.No fx 4961 (82.8)
## 31 2.Fx 1+ 1031 (17.2)
## 25 drink_bin 1.Less drinking 4042 (67.5)
## 26 2.Excessive drinking 1950 (32.5)
## 1 activity_bin 1.Proactive 1545 (25.8)
## 2 2.Less active 4447 (74.2)
## 8 calci_bin 1.Sufficient Calcium 1458 (24.3)
## 9 2.Insufficient Calcium 4534 (75.7)
## 38 protein2 Mean (SD) 64.1 (27.4)
## 27 education Mean (SD) 5.8 (1.6)
## 7 BMI Mean (SD) 27.3 (3.9)
## 17 cvd 0 4741 (79.1)
## 18 1 1251 (20.9)
## 33 hypertension 0 3411 (56.9)
## 34 1 2581 (43.1)
## 14 copd 0 5352 (89.3)
## 15 1 640 (10.7)
## 23 diabetes 0 5339 (89.1)
## 24 1 653 (10.9)
## 11 cancer 0 4900 (81.8)
## 12 1 1092 (18.2)
## 40 renal 0 5439 (90.8)
## 41 1 553 (9.2)
## 36 parkinson 0 5203 (86.8)
## 37 1 789 (13.2)
## 20 depression 0 5781 (96.5)
## 21 1 211 (3.5)
## 43 rheumatoid 0 3147 (52.5)
## 44 1 2845 (47.5)
## 10 <NA> <NA> <NA>
## 13 <NA> <NA> <NA>
## 16 <NA> <NA> <NA>
## 19 <NA> <NA> <NA>
## 22 <NA> <NA> <NA>
## 32 <NA> <NA> <NA>
## 35 <NA> <NA> <NA>
## 39 <NA> <NA> <NA>
## 42 <NA> <NA> <NA>
## HR (Cause-specific) HR (Fine-Gray subdistribution)
## 45 - -
## 46 1.71 (1.26-2.32, p=0.001) 0.82 (0.45-1.49, p=0.510)
## 3 - -
## 4 1.79 (1.57-2.03, p<0.001) 0.52 (0.41-0.66, p<0.001)
## 5 - -
## 6 2.62 (2.13-3.23, p<0.001) 1.86 (1.21-2.85, p=0.004)
## 28 - -
## 29 1.36 (1.19-1.57, p<0.001) 0.98 (0.75-1.27, p=0.860)
## 30 - -
## 31 1.61 (1.40-1.86, p<0.001) 1.60 (1.26-2.03, p<0.001)
## 25 - -
## 26 1.09 (0.96-1.24, p=0.194) 1.03 (0.83-1.27, p=0.820)
## 1 - -
## 2 1.01 (0.88-1.16, p=0.918) 0.81 (0.66-1.01, p=0.065)
## 8 - -
## 9 0.92 (0.79-1.08, p=0.328) 0.92 (0.71-1.19, p=0.530)
## 38 1.00 (0.99-1.00, p=0.016) 1.00 (1.00-1.00, p=0.840)
## 27 1.00 (0.96-1.04, p=0.966) 1.07 (1.00-1.14, p=0.036)
## 7 1.00 (0.98-1.01, p=0.609) 0.99 (0.96-1.01, p=0.350)
## 17 - -
## 18 - -
## 33 - -
## 34 - -
## 14 - -
## 15 - -
## 23 - -
## 24 - -
## 11 - -
## 12 - -
## 40 - -
## 41 - -
## 36 - -
## 37 - -
## 20 - -
## 21 - -
## 43 - -
## 44 - -
## 10 1.05 (0.90-1.23, p=0.523) 0.87 (0.66-1.15, p=0.340)
## 13 1.15 (0.95-1.39, p=0.141) 0.78 (0.54-1.15, p=0.210)
## 16 1.17 (1.01-1.36, p=0.037) 0.87 (0.66-1.15, p=0.330)
## 19 1.20 (0.91-1.58, p=0.205) 1.22 (0.74-2.02, p=0.430)
## 22 1.23 (1.01-1.50, p=0.044) 0.93 (0.65-1.34, p=0.710)
## 32 1.13 (1.00-1.28, p=0.047) 0.86 (0.70-1.07, p=0.170)
## 35 0.93 (0.74-1.18, p=0.550) 0.75 (0.54-1.04, p=0.085)
## 39 1.02 (0.79-1.31, p=0.887) 1.86 (1.33-2.59, p<0.001)
## 42 0.99 (0.87-1.11, p=0.817) 0.93 (0.75-1.14, p=0.480)To obtain HR for PAR calculation
options(digits = 8)
any.smk.par = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(group), data = men.smk)## 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(any.smk.par)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(group), data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 5.0358e-01 1.6546e+00 2.3097e-01 2.1803 0.0292352 *
## as.factor(group)3 5.8961e-01 1.8033e+00 1.2169e-01 4.8451 1.266e-06 ***
## as.factor(group)4 3.5915e-01 1.4321e+00 1.2454e-01 2.8838 0.0039292 **
## as.factor(group)5 7.9699e-01 2.2189e+00 2.6457e-01 3.0124 0.0025918 **
## as.factor(group)6 6.6369e-01 1.9419e+00 8.6418e-02 7.6801 1.590e-14 ***
## as.factor(group)7 1.5168e+00 4.5578e+00 1.8648e-01 8.1343 4.143e-16 ***
## as.factor(group)8 9.6153e-01 2.6157e+00 1.2141e-01 7.9198 2.380e-15 ***
## as.factor(group)9 1.0017e+00 2.7228e+00 1.4393e-01 6.9592 3.421e-12 ***
## as.factor(group)10 7.8150e-01 2.1848e+00 5.8046e-01 1.3464 0.1781893
## as.factor(group)11 1.4151e+00 4.1168e+00 4.5092e-01 3.1382 0.0016999 **
## as.factor(group)12 1.4212e+00 4.1420e+00 4.1230e-01 3.4470 0.0005669 ***
## as.factor(group)13 2.3621e+00 1.0613e+01 5.8108e-01 4.0650 4.804e-05 ***
## as.factor(group)14 7.6270e-01 2.1441e+00 1.8591e-01 4.1024 4.088e-05 ***
## as.factor(group)15 5.8924e-01 1.8026e+00 5.8023e-01 1.0155 0.3098597
## as.factor(group)16 7.4042e-01 2.0968e+00 4.5100e-01 1.6417 0.1006461
## as.factor(group)17 1.9150e+00 6.7869e+00 3.2216e-01 5.9443 2.777e-09 ***
## as.factor(group)18 2.2236e+00 9.2408e+00 2.3197e-01 9.5857 < 2.2e-16 ***
## as.factor(group)19 -1.2066e+01 5.7544e-06 8.7033e+02 -0.0139 0.9889391
## as.factor(group)20 1.4171e+00 4.1251e+00 1.7097e-01 8.2883 < 2.2e-16 ***
## as.factor(group)21 2.4387e+00 1.1458e+01 4.5154e-01 5.4009 6.631e-08 ***
## as.factor(group)22 -1.2042e+01 5.8897e-06 2.5250e+03 -0.0048 0.9961947
## as.factor(group)23 1.6817e+00 5.3745e+00 5.8041e-01 2.8974 0.0037628 **
## as.factor(group)24 3.0803e+00 2.1765e+01 7.1032e-01 4.3365 1.448e-05 ***
## as.factor(group)26 1.4848e+00 4.4139e+00 7.0992e-01 2.0915 0.0364863 *
## as.factor(group)27 2.3819e+00 1.0826e+01 3.0805e-01 7.7323 1.056e-14 ***
## as.factor(group)28 -1.2064e+01 5.7619e-06 1.7650e+03 -0.0068 0.9945463
## as.factor(group)29 4.9726e+00 1.4440e+02 1.0081e+00 4.9327 8.109e-07 ***
## as.factor(group)30 -1.2048e+01 5.8583e-06 1.9519e+03 -0.0062 0.9950752
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group)2 1.6546e+00 6.0437e-01 1.05221 2.6020
## as.factor(group)3 1.8033e+00 5.5454e-01 1.42062 2.2890
## as.factor(group)4 1.4321e+00 6.9827e-01 1.12193 1.8280
## as.factor(group)5 2.2189e+00 4.5068e-01 1.32107 3.7268
## as.factor(group)6 1.9419e+00 5.1495e-01 1.63938 2.3004
## as.factor(group)7 4.5578e+00 2.1940e-01 3.16249 6.5688
## as.factor(group)8 2.6157e+00 3.8231e-01 2.06179 3.3184
## as.factor(group)9 2.7228e+00 3.6726e-01 2.05355 3.6103
## as.factor(group)10 2.1848e+00 4.5772e-01 0.70035 6.8154
## as.factor(group)11 4.1168e+00 2.4291e-01 1.70112 9.9629
## as.factor(group)12 4.1420e+00 2.4143e-01 1.84613 9.2932
## as.factor(group)13 1.0613e+01 9.4225e-02 3.39796 33.1474
## as.factor(group)14 2.1441e+00 4.6641e-01 1.48931 3.0866
## as.factor(group)15 1.8026e+00 5.5475e-01 0.57810 5.6208
## as.factor(group)16 2.0968e+00 4.7691e-01 0.86630 5.0752
## as.factor(group)17 6.7869e+00 1.4734e-01 3.60953 12.7613
## as.factor(group)18 9.2408e+00 1.0822e-01 5.86480 14.5601
## as.factor(group)19 5.7544e-06 1.7378e+05 0.00000 Inf
## as.factor(group)20 4.1251e+00 2.4242e-01 2.95054 5.7673
## as.factor(group)21 1.1458e+01 8.7272e-02 4.72905 27.7639
## as.factor(group)22 5.8897e-06 1.6979e+05 0.00000 Inf
## as.factor(group)23 5.3745e+00 1.8606e-01 1.72304 16.7643
## as.factor(group)24 2.1765e+01 4.5946e-02 5.40913 87.5743
## as.factor(group)26 4.4139e+00 2.2656e-01 1.09785 17.7463
## as.factor(group)27 1.0826e+01 9.2373e-02 5.91893 19.8000
## as.factor(group)28 5.7619e-06 1.7355e+05 0.00000 Inf
## as.factor(group)29 1.4440e+02 6.9254e-03 20.02080 1041.4260
## as.factor(group)30 5.8583e-06 1.7070e+05 0.00000 Inf
##
## Concordance= 0.637 (se = 0.009 )
## Likelihood ratio test= 286.81 on 28 df, p=<2e-16
## Wald test = 349.13 on 28 df, p=<2e-16
## Score (logrank) test = 478.67 on 28 df, p=<2e-16(2.1.3) Association for hip fracture
Original format of 3 categories: Never, Past vs Current
hip.smk.age = coxph(Surv(fu_hipfx, hipfx) ~ smoke.c + age, data = men.smk)
summary(hip.smk.age)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke.c + age, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast -0.035764 0.964868 0.134783 -0.2653 0.790743
## smoke.cCurrent 0.993289 2.700101 0.309664 3.2076 0.001338 **
## age 0.137513 1.147417 0.011277 12.1944 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 0.96487 1.03641 0.74087 1.2566
## smoke.cCurrent 2.70010 0.37036 1.47161 4.9541
## age 1.14742 0.87152 1.12233 1.1731
##
## Concordance= 0.727 (se = 0.016 )
## Likelihood ratio test= 145.29 on 3 df, p=<2e-16
## Wald test = 152.53 on 3 df, p=<2e-16
## Score (logrank) test = 162.11 on 3 df, p=<2e-16hip.smk.all1 = coxph(Surv(fu_hipfx, hipfx) ~ smoke.c + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(hip.smk.all1)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke.c + age_bin + bmd_bin +
## fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast -0.068273 0.934005 0.134787 -0.5065 0.612487
## smoke.cCurrent 0.822679 2.276591 0.309869 2.6549 0.007933 **
## age_bin2.Age>= 75 1.141116 3.130258 0.139612 8.1735 2.996e-16 ***
## bmd_bin2.BMD<= -2.5 1.563392 4.774992 0.168082 9.3013 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.324356 1.383140 0.147666 2.1966 0.028052 *
## fx50_bin2.Fx 1+ 0.266081 1.304841 0.157093 1.6938 0.090306 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 0.93401 1.07066 0.71716 1.2164
## smoke.cCurrent 2.27659 0.43925 1.24029 4.1787
## age_bin2.Age>= 75 3.13026 0.31946 2.38091 4.1155
## bmd_bin2.BMD<= -2.5 4.77499 0.20942 3.43479 6.6381
## fall_bin2.Falls 1+ 1.38314 0.72299 1.03555 1.8474
## fx50_bin2.Fx 1+ 1.30484 0.76638 0.95905 1.7753
##
## Concordance= 0.735 (se = 0.017 )
## Likelihood ratio test= 168.76 on 6 df, p=<2e-16
## Wald test = 204.2 on 6 df, p=<2e-16
## Score (logrank) test = 256.01 on 6 df, p=<2e-16hip.smk.all2 = coxph(Surv(fu_hipfx, hipfx) ~ smoke.c + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid, data = men.smk)
summary(hip.smk.all2)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke.c + age_bin + bmd_bin +
## fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin +
## protein2 + education + BMI + cvd + hypertension + copd +
## diabetes + cancer + renal + parkinson + depression + rheumatoid,
## data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z
## smoke.cPast -0.1003479 0.9045227 0.1395985 -0.7188
## smoke.cCurrent 0.8093504 2.2464482 0.3149415 2.5698
## age_bin2.Age>= 75 1.0376338 2.8225304 0.1436818 7.2217
## bmd_bin2.BMD<= -2.5 1.5458572 4.6919921 0.1760006 8.7832
## fall_bin2.Falls 1+ 0.2848979 1.3296263 0.1500361 1.8989
## fx50_bin2.Fx 1+ 0.2833728 1.3276000 0.1576854 1.7971
## drink_bin2.Excessive drinking -0.2304198 0.7942002 0.1516925 -1.5190
## activity_bin2.Less active 0.1723060 1.1880413 0.1592610 1.0819
## calci_bin2.Insufficient Calcium -0.0648584 0.9372002 0.1776294 -0.3651
## protein2 -0.0024005 0.9976024 0.0029877 -0.8035
## education -0.0393954 0.9613705 0.0409012 -0.9632
## BMI -0.0244095 0.9758860 0.0188013 -1.2983
## cvd 0.3401319 1.4051329 0.1534947 2.2159
## hypertension 0.4892259 1.6310531 0.1349313 3.6257
## copd -0.0427253 0.9581746 0.2143931 -0.1993
## diabetes 0.1086192 1.1147378 0.2213135 0.4908
## cancer -0.0354437 0.9651771 0.1722312 -0.2058
## renal -0.3907790 0.6765297 0.2714743 -1.4395
## parkinson 0.3909541 1.4783906 0.2275320 1.7182
## depression 0.1732430 1.1891550 0.2999132 0.5776
## rheumatoid 0.1117549 1.1182388 0.1345257 0.8307
## Pr(>|z|)
## smoke.cPast 0.4722444
## smoke.cCurrent 0.0101745 *
## age_bin2.Age>= 75 5.132e-13 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.0575826 .
## fx50_bin2.Fx 1+ 0.0723233 .
## drink_bin2.Excessive drinking 0.1287644
## activity_bin2.Less active 0.2792930
## calci_bin2.Insufficient Calcium 0.7150120
## protein2 0.4217106
## education 0.3354553
## BMI 0.1941880
## cvd 0.0266970 *
## hypertension 0.0002881 ***
## copd 0.8420399
## diabetes 0.6235725
## cancer 0.8369537
## renal 0.1500175
## parkinson 0.0857533 .
## depression 0.5635046
## rheumatoid 0.4061244
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 0.90452 1.10556 0.68801 1.1892
## smoke.cCurrent 2.24645 0.44515 1.21176 4.1646
## age_bin2.Age>= 75 2.82253 0.35429 2.12979 3.7406
## bmd_bin2.BMD<= -2.5 4.69199 0.21313 3.32311 6.6247
## fall_bin2.Falls 1+ 1.32963 0.75209 0.99087 1.7842
## fx50_bin2.Fx 1+ 1.32760 0.75324 0.97464 1.8084
## drink_bin2.Excessive drinking 0.79420 1.25913 0.58994 1.0692
## activity_bin2.Less active 1.18804 0.84172 0.86950 1.6233
## calci_bin2.Insufficient Calcium 0.93720 1.06701 0.66166 1.3275
## protein2 0.99760 1.00240 0.99178 1.0035
## education 0.96137 1.04018 0.88731 1.0416
## BMI 0.97589 1.02471 0.94058 1.0125
## cvd 1.40513 0.71168 1.04007 1.8983
## hypertension 1.63105 0.61310 1.25203 2.1248
## copd 0.95817 1.04365 0.62944 1.4586
## diabetes 1.11474 0.89707 0.72242 1.7201
## cancer 0.96518 1.03608 0.68866 1.3527
## renal 0.67653 1.47813 0.39738 1.1518
## parkinson 1.47839 0.67641 0.94648 2.3092
## depression 1.18916 0.84093 0.66062 2.1405
## rheumatoid 1.11824 0.89426 0.85907 1.4556
##
## Concordance= 0.757 (se = 0.017 )
## Likelihood ratio test= 202.49 on 21 df, p=<2e-16
## Wald test = 237.6 on 21 df, p=<2e-16
## Score (logrank) test = 291.98 on 21 df, p=<2e-16Binary format for PAR calculation
hip.smk.age = coxph(Surv(fu_hipfx, hipfx) ~ smoke_bin + age, data = men.smk)
summary(hip.smk.age)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke_bin + age, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke_bin2.Current smoking 1.014385 2.757666 0.299428 3.3877 0.0007047 ***
## age 0.137710 1.147642 0.011253 12.2372 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_bin2.Current smoking 2.7577 0.36263 1.5334 4.9592
## age 1.1476 0.87135 1.1226 1.1732
##
## Concordance= 0.727 (se = 0.016 )
## Likelihood ratio test= 145.22 on 2 df, p=<2e-16
## Wald test = 152.44 on 2 df, p=<2e-16
## Score (logrank) test = 161.92 on 2 df, p=<2e-16hip.smk.all1 = coxph(Surv(fu_hipfx, hipfx) ~ smoke_bin + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(hip.smk.all1)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke_bin + age_bin +
## bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke_bin2.Current smoking 0.86289 2.36999 0.29980 2.8782 0.00400 **
## age_bin2.Age>= 75 1.14509 3.14272 0.13936 8.2170 < 2e-16 ***
## bmd_bin2.BMD<= -2.5 1.56407 4.77824 0.16806 9.3067 < 2e-16 ***
## fall_bin2.Falls 1+ 0.32342 1.38185 0.14765 2.1905 0.02849 *
## fx50_bin2.Fx 1+ 0.26396 1.30207 0.15705 1.6808 0.09281 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_bin2.Current smoking 2.3700 0.42194 1.3169 4.2652
## age_bin2.Age>= 75 3.1427 0.31820 2.3916 4.1298
## bmd_bin2.BMD<= -2.5 4.7782 0.20928 3.4373 6.6423
## fall_bin2.Falls 1+ 1.3819 0.72367 1.0346 1.8456
## fx50_bin2.Fx 1+ 1.3021 0.76801 0.9571 1.7714
##
## Concordance= 0.731 (se = 0.017 )
## Likelihood ratio test= 168.5 on 5 df, p=<2e-16
## Wald test = 203.81 on 5 df, p=<2e-16
## Score (logrank) test = 255.62 on 5 df, p=<2e-16hip.smk.all2 = coxph(Surv(fu_hipfx, hipfx) ~ smoke_bin + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid, data = men.smk)
summary(hip.smk.all2)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke_bin + age_bin +
## bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin +
## calci_bin + protein2 + education + BMI + cvd + hypertension +
## copd + diabetes + cancer + renal + parkinson + depression +
## rheumatoid, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z
## smoke_bin2.Current smoking 0.8702020 2.3873931 0.3036858 2.8655
## age_bin2.Age>= 75 1.0443334 2.8415036 0.1432956 7.2880
## bmd_bin2.BMD<= -2.5 1.5430984 4.6790654 0.1758326 8.7760
## fall_bin2.Falls 1+ 0.2841194 1.3285916 0.1500526 1.8935
## fx50_bin2.Fx 1+ 0.2790259 1.3218416 0.1575941 1.7705
## drink_bin2.Excessive drinking -0.2464582 0.7815640 0.1499755 -1.6433
## activity_bin2.Less active 0.1703902 1.1857674 0.1592740 1.0698
## calci_bin2.Insufficient Calcium -0.0674420 0.9347819 0.1775400 -0.3799
## protein2 -0.0023977 0.9976052 0.0029897 -0.8020
## education -0.0355068 0.9651161 0.0405423 -0.8758
## BMI -0.0254591 0.9748623 0.0187126 -1.3605
## cvd 0.3341880 1.3968057 0.1532614 2.1805
## hypertension 0.4855621 1.6250882 0.1348297 3.6013
## copd -0.0530674 0.9483160 0.2139154 -0.2481
## diabetes 0.1093723 1.1155776 0.2212235 0.4944
## cancer -0.0340719 0.9665021 0.1722659 -0.1978
## renal -0.3930198 0.6750154 0.2715806 -1.4472
## parkinson 0.3941973 1.4831931 0.2275817 1.7321
## depression 0.1730032 1.1888700 0.2999022 0.5769
## rheumatoid 0.1057541 1.1115485 0.1342510 0.7877
## Pr(>|z|)
## smoke_bin2.Current smoking 0.0041639 **
## age_bin2.Age>= 75 3.147e-13 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.0582960 .
## fx50_bin2.Fx 1+ 0.0766380 .
## drink_bin2.Excessive drinking 0.1003160
## activity_bin2.Less active 0.2847127
## calci_bin2.Insufficient Calcium 0.7040422
## protein2 0.4225676
## education 0.3811399
## BMI 0.1736626
## cvd 0.0292197 *
## hypertension 0.0003166 ***
## copd 0.8040749
## diabetes 0.6210256
## cancer 0.8432121
## renal 0.1478529
## parkinson 0.0832534 .
## depression 0.5640303
## rheumatoid 0.4308522
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_bin2.Current smoking 2.38739 0.41887 1.31652 4.3293
## age_bin2.Age>= 75 2.84150 0.35193 2.14573 3.7629
## bmd_bin2.BMD<= -2.5 4.67907 0.21372 3.31505 6.6043
## fall_bin2.Falls 1+ 1.32859 0.75268 0.99007 1.7829
## fx50_bin2.Fx 1+ 1.32184 0.75652 0.97059 1.8002
## drink_bin2.Excessive drinking 0.78156 1.27949 0.58251 1.0486
## activity_bin2.Less active 1.18577 0.84334 0.86781 1.6202
## calci_bin2.Insufficient Calcium 0.93478 1.06977 0.66007 1.3238
## protein2 0.99761 1.00240 0.99178 1.0035
## education 0.96512 1.03614 0.89139 1.0449
## BMI 0.97486 1.02579 0.93976 1.0113
## cvd 1.39681 0.71592 1.03438 1.8862
## hypertension 1.62509 0.61535 1.24770 2.1166
## copd 0.94832 1.05450 0.62355 1.4422
## diabetes 1.11558 0.89640 0.72309 1.7211
## cancer 0.96650 1.03466 0.68956 1.3547
## renal 0.67502 1.48145 0.39641 1.1494
## parkinson 1.48319 0.67422 0.94947 2.3169
## depression 1.18887 0.84113 0.66048 2.1400
## rheumatoid 1.11155 0.89965 0.85439 1.4461
##
## Concordance= 0.756 (se = 0.017 )
## Likelihood ratio test= 201.98 on 20 df, p=<2e-16
## Wald test = 236.96 on 20 df, p=<2e-16
## Score (logrank) test = 291.26 on 20 df, p=<2e-16Sensitivity analysis to account for a competing risk of death
Data management:
men.smk = men.smk %>% mutate(hipfx_crr = case_when(hipfx == 0 & death == 0 ~ 0,
hipfx == 1 & death == 0 ~ 1,
hipfx == 0 & death == 1 ~ 2))Age-adjusted
cov_age = c("smoke_bin", "age")
hipfx_cph = "Surv(fu_hipfx, hipfx)"
hipfx_crr = "Surv(fu_hipfx, hipfx_crr)"
men.smk %>%
# Summary table
summary_factorlist(hipfx_cph, cov_age,
column = TRUE, fit_id = TRUE) %>%
# CPH multivariable
ff_merge(
men.smk %>%
coxphmulti(hipfx_cph, cov_age) %>%
fit2df(estimate_suffix = " (Cause-specific)")
) %>%
# Fine and Gray competing risks regression
ff_merge(
men.smk %>%
crrmulti(hipfx_crr, cov_age) %>%
fit2df(estimate_suffix = " (Fine-Gray subdistribution)")
) %>%
select(-fit_id, -index) %>%
dependent_label(men.smk, "Survival")## Dependent variable is a survival object## 174 cases omitted due to missing values## Dependent: Survival all HR (Cause-specific)
## 2 smoke_bin 1.No/past smoking 5786 (96.6) -
## 3 2.Current smoking 206 (3.4) 2.76 (1.53-4.96, p=0.001)
## 1 age Mean (SD) 73.7 (5.9) 1.15 (1.12-1.17, p<0.001)
## HR (Fine-Gray subdistribution)
## 2 -
## 3 0.50 (0.07-3.53, p=0.485)
## 1 1.02 (0.98-1.06, p=0.405)Multivariable-adjusted (only fracture risk factors)
cov_multi1 = c("smoke_bin", "age_bin", "bmd_bin", "fall_bin", "fx50_bin")
hipfx_cph = "Surv(fu_hipfx, hipfx)"
hipfx_crr = "Surv(fu_hipfx, hipfx_crr)"
men.smk %>%
# Summary table
summary_factorlist(hipfx_cph, cov_multi1,
column = TRUE, fit_id = TRUE) %>%
# CPH multivariable
ff_merge(
men.smk %>%
coxphmulti(hipfx_cph, cov_multi1) %>%
fit2df(estimate_suffix = " (Cause-specific)")
) %>%
# Fine and Gray competing risks regression
ff_merge(
men.smk %>%
crrmulti(hipfx_crr, cov_multi1) %>%
fit2df(estimate_suffix = " (Fine-Gray distribution)")
) %>%
select(-fit_id, -index) %>%
dependent_label(men.smk, "Survival")## Dependent variable is a survival object## 174 cases omitted due to missing values## Dependent: Survival all HR (Cause-specific)
## 9 smoke_bin 1.No/past smoking 5786 (96.6) -
## 10 2.Current smoking 206 (3.4) 2.37 (1.32-4.27, p=0.004)
## 1 age_bin 1.Age< 75 3476 (58.0) -
## 2 2.Age>= 75 2516 (42.0) 3.14 (2.39-4.13, p<0.001)
## 3 bmd_bin 1.BMD> -2.5 5697 (95.1) -
## 4 2.BMD<= -2.5 295 (4.9) 4.78 (3.44-6.64, p<0.001)
## 5 fall_bin 1.No falls 4725 (78.9) -
## 6 2.Falls 1+ 1267 (21.1) 1.38 (1.03-1.85, p=0.028)
## 7 fx50_bin 1.No fx 4961 (82.8) -
## 8 2.Fx 1+ 1031 (17.2) 1.30 (0.96-1.77, p=0.093)
## HR (Fine-Gray distribution)
## 9 -
## 10 0.43 (0.06-3.12, p=0.405)
## 1 -
## 2 0.89 (0.53-1.49, p=0.652)
## 3 -
## 4 4.75 (2.40-9.38, p<0.001)
## 5 -
## 6 0.67 (0.34-1.34, p=0.261)
## 7 -
## 8 1.55 (0.86-2.79, p=0.146)Multivariable-adjusted (only fracture risk factors)
cov_multi2 = c("smoke_bin", "age_bin", "bmd_bin", "fall_bin", "fx50_bin", "drink_bin", "activity_bin", "calci_bin", "protein2", "education", "BMI", "cvd", "hypertension", "copd", "diabetes", "cancer", "renal", "parkinson", "depression", "rheumatoid")
hipfx_cph = "Surv(fu_hipfx, hipfx)"
hipfx_crr = "Surv(fu_hipfx, hipfx_crr)"
men.smk %>%
# Summary table
summary_factorlist(hipfx_cph, cov_multi2,
column = TRUE, fit_id = TRUE) %>%
# CPH multivariable
ff_merge(
men.smk %>%
coxphmulti(hipfx_cph, cov_multi2) %>%
fit2df(estimate_suffix = " (Cause-specific)")
) %>%
# Fine and Gray competing risks regression
ff_merge(
men.smk %>%
crrmulti(hipfx_crr, cov_multi2) %>%
fit2df(estimate_suffix = " (Fine-Gray subdistribution)")
) %>%
select(-fit_id, -index) %>%
dependent_label(men.smk, "Survival")## Dependent variable is a survival object## 174 cases omitted due to missing values## Dependent: Survival all
## 45 smoke_bin 1.No/past smoking 5786 (96.6)
## 46 2.Current smoking 206 (3.4)
## 3 age_bin 1.Age< 75 3476 (58.0)
## 4 2.Age>= 75 2516 (42.0)
## 5 bmd_bin 1.BMD> -2.5 5697 (95.1)
## 6 2.BMD<= -2.5 295 (4.9)
## 28 fall_bin 1.No falls 4725 (78.9)
## 29 2.Falls 1+ 1267 (21.1)
## 30 fx50_bin 1.No fx 4961 (82.8)
## 31 2.Fx 1+ 1031 (17.2)
## 25 drink_bin 1.Less drinking 4042 (67.5)
## 26 2.Excessive drinking 1950 (32.5)
## 1 activity_bin 1.Proactive 1545 (25.8)
## 2 2.Less active 4447 (74.2)
## 8 calci_bin 1.Sufficient Calcium 1458 (24.3)
## 9 2.Insufficient Calcium 4534 (75.7)
## 38 protein2 Mean (SD) 64.1 (27.4)
## 27 education Mean (SD) 5.8 (1.6)
## 7 BMI Mean (SD) 27.3 (3.9)
## 17 cvd 0 4741 (79.1)
## 18 1 1251 (20.9)
## 33 hypertension 0 3411 (56.9)
## 34 1 2581 (43.1)
## 14 copd 0 5352 (89.3)
## 15 1 640 (10.7)
## 23 diabetes 0 5339 (89.1)
## 24 1 653 (10.9)
## 11 cancer 0 4900 (81.8)
## 12 1 1092 (18.2)
## 40 renal 0 5439 (90.8)
## 41 1 553 (9.2)
## 36 parkinson 0 5203 (86.8)
## 37 1 789 (13.2)
## 20 depression 0 5781 (96.5)
## 21 1 211 (3.5)
## 43 rheumatoid 0 3147 (52.5)
## 44 1 2845 (47.5)
## 10 <NA> <NA> <NA>
## 13 <NA> <NA> <NA>
## 16 <NA> <NA> <NA>
## 19 <NA> <NA> <NA>
## 22 <NA> <NA> <NA>
## 32 <NA> <NA> <NA>
## 35 <NA> <NA> <NA>
## 39 <NA> <NA> <NA>
## 42 <NA> <NA> <NA>
## HR (Cause-specific) HR (Fine-Gray subdistribution)
## 45 - -
## 46 2.39 (1.32-4.33, p=0.004) 0.50 (0.07-3.63, p=0.491)
## 3 - -
## 4 2.84 (2.15-3.76, p<0.001) 0.95 (0.56-1.63, p=0.861)
## 5 - -
## 6 4.68 (3.32-6.60, p<0.001) 4.75 (2.28-9.88, p<0.001)
## 28 - -
## 29 1.33 (0.99-1.78, p=0.058) 0.66 (0.33-1.34, p=0.255)
## 30 - -
## 31 1.32 (0.97-1.80, p=0.077) 1.51 (0.83-2.75, p=0.181)
## 25 - -
## 26 0.78 (0.58-1.05, p=0.100) 0.84 (0.48-1.45, p=0.523)
## 1 - -
## 2 1.19 (0.87-1.62, p=0.285) 1.05 (0.57-1.94, p=0.873)
## 8 - -
## 9 0.93 (0.66-1.32, p=0.704) 1.36 (0.67-2.76, p=0.389)
## 38 1.00 (0.99-1.00, p=0.423) 1.01 (1.00-1.02, p=0.275)
## 27 0.97 (0.89-1.04, p=0.381) 1.08 (0.93-1.26, p=0.321)
## 7 0.97 (0.94-1.01, p=0.174) 0.99 (0.93-1.06, p=0.845)
## 17 - -
## 18 - -
## 33 - -
## 34 - -
## 14 - -
## 15 - -
## 23 - -
## 24 - -
## 11 - -
## 12 - -
## 40 - -
## 41 - -
## 36 - -
## 37 - -
## 20 - -
## 21 - -
## 43 - -
## 44 - -
## 10 0.97 (0.69-1.35, p=0.843) 0.82 (0.41-1.64, p=0.571)
## 13 0.95 (0.62-1.44, p=0.804) 0.41 (0.13-1.31, p=0.132)
## 16 1.40 (1.03-1.89, p=0.029) 0.99 (0.52-1.89, p=0.969)
## 19 1.19 (0.66-2.14, p=0.564) 1.34 (0.41-4.36, p=0.626)
## 22 1.12 (0.72-1.72, p=0.621) 0.58 (0.22-1.52, p=0.266)
## 32 1.63 (1.25-2.12, p<0.001) 1.51 (0.91-2.50, p=0.112)
## 35 1.48 (0.95-2.32, p=0.083) 0.86 (0.42-1.75, p=0.671)
## 39 0.68 (0.40-1.15, p=0.148) 1.39 (0.65-2.96, p=0.392)
## 42 1.11 (0.85-1.45, p=0.431) 1.16 (0.69-1.95, p=0.587)To calculate PAR
options(digits = 8)
hip.smk.par = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(group), data = men.smk)## 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(hip.smk.par)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(group), data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 1.1421e+00 3.1332e+00 4.3272e-01 2.6392 0.008309 **
## as.factor(group)3 1.0598e-01 1.1118e+00 3.6266e-01 0.2922 0.770102
## as.factor(group)4 1.5744e-01 1.1705e+00 3.3366e-01 0.4719 0.637026
## as.factor(group)5 1.5098e+00 4.5258e+00 4.6955e-01 3.2154 0.001303 **
## as.factor(group)6 1.0619e+00 2.8920e+00 1.9574e-01 5.4251 5.791e-08 ***
## as.factor(group)7 2.6850e+00 1.4658e+01 2.8298e-01 9.4883 < 2.2e-16 ***
## as.factor(group)8 1.5361e+00 4.6464e+00 2.4769e-01 6.2017 5.587e-10 ***
## as.factor(group)9 1.5914e+00 4.9104e+00 2.8294e-01 5.6245 1.861e-08 ***
## as.factor(group)10 1.6234e+00 5.0702e+00 1.0109e+00 1.6059 0.108291
## as.factor(group)11 2.6142e+00 1.3656e+01 5.9478e-01 4.3952 1.107e-05 ***
## as.factor(group)12 2.0360e+00 7.6599e+00 7.2143e-01 2.8222 0.004770 **
## as.factor(group)13 2.7782e+00 1.6091e+01 1.0106e+00 2.7490 0.005978 **
## as.factor(group)14 -3.0209e-01 7.3927e-01 7.2140e-01 -0.4188 0.675395
## as.factor(group)15 1.3097e+00 3.7050e+00 1.0102e+00 1.2964 0.194822
## as.factor(group)16 -1.3185e+01 1.8779e-06 1.1403e+03 -0.0116 0.990774
## as.factor(group)17 2.9849e+00 1.9785e+01 4.7136e-01 6.3325 2.412e-10 ***
## as.factor(group)18 2.8476e+00 1.7247e+01 4.0567e-01 7.0195 2.227e-12 ***
## as.factor(group)19 -1.3236e+01 1.7859e-06 4.3690e+03 -0.0030 0.997583
## as.factor(group)20 1.8474e+00 6.3430e+00 3.4860e-01 5.2994 1.162e-07 ***
## as.factor(group)21 2.1735e+00 8.7893e+00 1.0102e+00 2.1515 0.031435 *
## as.factor(group)22 -1.3625e+01 1.2102e-06 1.5209e+04 -0.0009 0.999285
## as.factor(group)23 3.0546e+00 2.1212e+01 7.2195e-01 4.2310 2.326e-05 ***
## as.factor(group)24 -1.3173e+01 1.9021e-06 4.1879e+03 -0.0031 0.997490
## as.factor(group)26 2.5838e+00 1.3247e+01 1.0119e+00 2.5533 0.010670 *
## as.factor(group)27 2.7888e+00 1.6262e+01 5.9678e-01 4.6731 2.966e-06 ***
## as.factor(group)28 -1.3196e+01 1.8579e-06 8.8675e+03 -0.0015 0.998813
## as.factor(group)29 7.0362e+00 1.1370e+03 1.0446e+00 6.7360 1.628e-11 ***
## as.factor(group)30 -1.3374e+01 1.5556e-06 1.0779e+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 3.1332e+00 3.1916e-01 1.34170 7.3168
## as.factor(group)3 1.1118e+00 8.9944e-01 0.54617 2.2632
## as.factor(group)4 1.1705e+00 8.5433e-01 0.60865 2.2510
## as.factor(group)5 4.5258e+00 2.2096e-01 1.80308 11.3599
## as.factor(group)6 2.8920e+00 3.4578e-01 1.97050 4.2444
## as.factor(group)7 1.4658e+01 6.8223e-02 8.41786 25.5236
## as.factor(group)8 4.6464e+00 2.1522e-01 2.85945 7.5501
## as.factor(group)9 4.9104e+00 2.0365e-01 2.82023 8.5498
## as.factor(group)10 5.0702e+00 1.9723e-01 0.69915 36.7684
## as.factor(group)11 1.3656e+01 7.3227e-02 4.25648 43.8137
## as.factor(group)12 7.6599e+00 1.3055e-01 1.86268 31.5000
## as.factor(group)13 1.6091e+01 6.2148e-02 2.21984 116.6344
## as.factor(group)14 7.3927e-01 1.3527e+00 0.17978 3.0399
## as.factor(group)15 3.7050e+00 2.6991e-01 0.51156 26.8333
## as.factor(group)16 1.8779e-06 5.3252e+05 0.00000 Inf
## as.factor(group)17 1.9785e+01 5.0543e-02 7.85443 49.8387
## as.factor(group)18 1.7247e+01 5.7982e-02 7.78745 38.1958
## as.factor(group)19 1.7859e-06 5.5995e+05 0.00000 Inf
## as.factor(group)20 6.3430e+00 1.5765e-01 3.20307 12.5609
## as.factor(group)21 8.7893e+00 1.1378e-01 1.21351 63.6596
## as.factor(group)22 1.2102e-06 8.2634e+05 0.00000 Inf
## as.factor(group)23 2.1212e+01 4.7142e-02 5.15310 87.3195
## as.factor(group)24 1.9021e-06 5.2574e+05 0.00000 Inf
## as.factor(group)26 1.3247e+01 7.5487e-02 1.82292 96.2692
## as.factor(group)27 1.6262e+01 6.1492e-02 5.04891 52.3800
## as.factor(group)28 1.8579e-06 5.3826e+05 0.00000 Inf
## as.factor(group)29 1.1370e+03 8.7949e-04 146.76977 8808.5434
## as.factor(group)30 1.5556e-06 6.4285e+05 0.00000 Inf
##
## Concordance= 0.735 (se = 0.017 )
## Likelihood ratio test= 188.4 on 28 df, p=<2e-16
## Wald test = 232.87 on 28 df, p=<2e-16
## Score (logrank) test = 686.98 on 28 df, p=<2e-16par = read.csv("C:\\Thach\\Research projects\\PAR for lifestyle factors\\par_smoking.csv")library(tidyverse)
library(ggplot2)
## Any fracture
m.anyfx = par %>%
filter(lifestyle == 10 & sex == 0 & fx == 1) %>%
mutate(group = factor(as.factor(group), levels = rev(unique(group)))
,color = as.factor(ifelse(group %in% c(1,9,12,14,15,18,20,21,23,24,25,27,28,29,30,31),1,0)))
ggplot(data = m.anyfx, aes(x = group, y = par, fill = color)) +
geom_bar(stat = "identity", width = 0.9) +
scale_fill_manual(values = c("0" = "gray", "1" = "darkblue")) +
coord_flip() +
theme_minimal() + theme(legend.position = "none")
## Hip fracture
m.hipfx = par %>%
filter(lifestyle == 10 & sex == 0 & fx == 2) %>%
mutate(group = factor(as.factor(group), levels = rev(unique(group)))
,color = as.factor(ifelse(group %in% c(1,9,12,14,15,18,20,21,23,24,25,27,28,29,30,31),1,0)))
ggplot(data = m.hipfx, aes(x = group, y = par, fill = color)) +
geom_bar(stat = "identity", width = 0.9) +
scale_fill_manual(values = c("0" = "gray", "1" = "darkblue")) +
coord_flip() +
theme_minimal() + theme(legend.position = "none")## Warning: Removed 4 rows containing missing values (`position_stack()`).
(2.2) Classification 2: Current/Past vs. None
Data management
men.smk = men.smk %>% mutate(smoke2_bin = case_when(smoke == "Never"~ "1.No/past smoking",
smoke == "Current" | smoke == "Past" ~ "2.Current smoking"))
men.smk = men.smk %>% mutate(group2 = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smoke2_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" & smoke2_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+" & smoke2_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" & smoke2_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" & smoke2_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" & smoke2_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" & smoke2_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" & smoke2_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+" & smoke2_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" & smoke2_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" & smoke2_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+" & smoke2_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" & smoke2_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+" & smoke2_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" & smoke2_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+" & smoke2_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" & smoke2_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+" & smoke2_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" & smoke2_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+" & smoke2_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" & smoke2_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+" & smoke2_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+" & smoke2_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" & smoke2_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+" & smoke2_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+" & smoke2_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+" & smoke2_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" & smoke2_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+" & smoke2_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+" & smoke2_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+" & smoke2_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+" & smoke2_bin == "2.Current smoking" ~ 32))(2.2.1) Prevalence
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + smoke2_bin + drink_bin + activity_bin + as.factor(group2) | anyfx, data = men.smk, render.continuous = c(. = "Mean(SD)", . = "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 | |||
| Mean(SD) | 73.5(5.86) | 74.5(5.88) | 73.7(5.87) |
| 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 | |||
| Mean(SD) | 0.794(0.127) | 0.739(0.122) | 0.784(0.128) |
| Median [Q1, Q3] | 0.783 [0.707, 0.870] | 0.728 [0.652, 0.812] | 0.774 [0.696, 0.860] |
| Tscore | |||
| Mean(SD) | -1.02(0.930) | -1.43(0.887) | -1.09(0.935) |
| 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%) |
| smoke2_bin | |||
| 1.No/past smoking | 1837 (37.4%) | 412 (38.0%) | 2249 (37.5%) |
| 2.Current smoking | 3071 (62.6%) | 672 (62.0%) | 3743 (62.5%) |
| 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(group2) | |||
| 1 | 773 (15.7%) | 114 (10.5%) | 887 (14.8%) |
| 2 | 1276 (26.0%) | 208 (19.2%) | 1484 (24.8%) |
| 3 | 102 (2.1%) | 31 (2.9%) | 133 (2.2%) |
| 4 | 133 (2.7%) | 25 (2.3%) | 158 (2.6%) |
| 5 | 13 (0.3%) | 7 (0.6%) | 20 (0.3%) |
| 6 | 476 (9.7%) | 107 (9.9%) | 583 (9.7%) |
| 7 | 34 (0.7%) | 12 (1.1%) | 46 (0.8%) |
| 8 | 135 (2.8%) | 45 (4.2%) | 180 (3.0%) |
| 9 | 78 (1.6%) | 26 (2.4%) | 104 (1.7%) |
| 10 | 740 (15.1%) | 145 (13.4%) | 885 (14.8%) |
| 11 | 2 (0.0%) | 1 (0.1%) | 3 (0.1%) |
| 12 | 3 (0.1%) | 2 (0.2%) | 5 (0.1%) |
| 13 | 32 (0.7%) | 11 (1.0%) | 43 (0.7%) |
| 14 | 24 (0.5%) | 9 (0.8%) | 33 (0.6%) |
| 15 | 253 (5.2%) | 60 (5.5%) | 313 (5.2%) |
| 16 | 208 (4.2%) | 61 (5.6%) | 269 (4.5%) |
| 17 | 8 (0.2%) | 5 (0.5%) | 13 (0.2%) |
| 18 | 8 (0.2%) | 7 (0.6%) | 15 (0.3%) |
| 19 | 39 (0.8%) | 20 (1.8%) | 59 (1.0%) |
| 20 | 43 (0.9%) | 17 (1.6%) | 60 (1.0%) |
| 21 | 213 (4.3%) | 49 (4.5%) | 262 (4.4%) |
| 22 | 126 (2.6%) | 32 (3.0%) | 158 (2.6%) |
| 23 | 1 (0.0%) | 0 (0%) | 1 (0.0%) |
| 24 | 4 (0.1%) | 6 (0.6%) | 10 (0.2%) |
| 25 | 5 (0.1%) | 4 (0.4%) | 9 (0.2%) |
| 26 | 78 (1.6%) | 25 (2.3%) | 103 (1.7%) |
| 27 | 4 (0.1%) | 4 (0.4%) | 8 (0.1%) |
| 28 | 10 (0.2%) | 5 (0.5%) | 15 (0.3%) |
| 29 | 11 (0.2%) | 14 (1.3%) | 25 (0.4%) |
| 30 | 63 (1.3%) | 22 (2.0%) | 85 (1.4%) |
| 31 | 2 (0.0%) | 3 (0.3%) | 5 (0.1%) |
| 32 | 11 (0.2%) | 7 (0.6%) | 18 (0.3%) |
(2.2.2) Association for any fracture
any2.smk.age = coxph(Surv(fu_anyfx, anyfx) ~ smoke2_bin + age, data = men.smk)
summary(any2.smk.age)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke2_bin + age, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke2_bin2.Current smoking 0.1087108 1.1148398 0.0627327 1.7329 0.08311 .
## age 0.0730360 1.0757693 0.0053748 13.5887 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke2_bin2.Current smoking 1.1148 0.89699 0.98586 1.2607
## age 1.0758 0.92957 1.06450 1.0872
##
## Concordance= 0.615 (se = 0.009 )
## Likelihood ratio test= 176.93 on 2 df, p=<2e-16
## Wald test = 185.38 on 2 df, p=<2e-16
## Score (logrank) test = 188.95 on 2 df, p=<2e-16any2.smk.all1 = coxph(Surv(fu_anyfx, anyfx) ~ smoke2_bin + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(any2.smk.all1)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke2_bin + age_bin +
## bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke2_bin2.Current smoking 0.079488 1.082733 0.062757 1.2666 0.2053
## age_bin2.Age>= 75 0.602075 1.825903 0.062851 9.5794 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.950327 2.586555 0.102918 9.2338 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.329733 1.390596 0.069808 4.7234 2.319e-06 ***
## fx50_bin2.Fx 1+ 0.470980 1.601563 0.071486 6.5884 4.445e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke2_bin2.Current smoking 1.0827 0.92359 0.95742 1.2244
## age_bin2.Age>= 75 1.8259 0.54767 1.61428 2.0653
## bmd_bin2.BMD<= -2.5 2.5866 0.38661 2.11406 3.1647
## fall_bin2.Falls 1+ 1.3906 0.71912 1.21277 1.5945
## fx50_bin2.Fx 1+ 1.6016 0.62439 1.39218 1.8424
##
## Concordance= 0.637 (se = 0.009 )
## Likelihood ratio test= 258.25 on 5 df, p=<2e-16
## Wald test = 299.24 on 5 df, p=<2e-16
## Score (logrank) test = 318.51 on 5 df, p=<2e-16any2.smk.all2 = coxph(Surv(fu_anyfx, anyfx) ~ smoke2_bin + age_bin + bmd_bin + fall_bin + fx50_bin + drink4 + drink_bin + physical4 + activity_bin + calcium2 + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)
summary(any2.smk.all2)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke2_bin + age_bin +
## bmd_bin + fall_bin + fx50_bin + drink4 + drink_bin + physical4 +
## activity_bin + calcium2 + calci_bin + protein2 + education +
## BMI + cvd + hypertension + copd + diabetes + cancer + renal +
## parkinson + depression + rheumatoid + death, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z
## smoke2_bin2.Current smoking 0.04123680 1.04209885 0.06518567 0.6326
## age_bin2.Age>= 75 0.39135516 1.47898369 0.06777266 5.7745
## bmd_bin2.BMD<= -2.5 0.92912480 2.53229195 0.10562367 8.7966
## fall_bin2.Falls 1+ 0.30321273 1.35420251 0.07100833 4.2701
## fx50_bin2.Fx 1+ 0.45981029 1.58377350 0.07177577 6.4062
## drink4Low -0.10134706 0.90361937 0.09617339 -1.0538
## drink4Moderate -0.23431962 0.79110892 0.13082499 -1.7911
## drink4No -0.01959307 0.98059762 0.07244860 -0.2704
## drink_bin2.Excessive drinking NA NA 0.00000000 NA
## physical4Low -0.06928500 0.93306072 0.09792801 -0.7075
## physical4Moderate -0.04187566 0.95898901 0.11926548 -0.3511
## physical4No -0.00090664 0.99909377 0.09043806 -0.0100
## activity_bin2.Less active NA NA 0.00000000 NA
## calcium2 -0.00013052 0.99986949 0.00015140 -0.8621
## calci_bin2.Insufficient Calcium -0.12485705 0.88262306 0.11519514 -1.0839
## protein2 -0.00240856 0.99759434 0.00159859 -1.5067
## education 0.00896632 1.00900664 0.01945063 0.4610
## BMI -0.00700430 0.99302017 0.00853147 -0.8210
## cvd 0.09144803 1.09575982 0.07662271 1.1935
## hypertension 0.07605203 1.07901871 0.06351385 1.1974
## copd 0.10267154 1.10812738 0.09658648 1.0630
## diabetes 0.13589319 1.14555953 0.10207621 1.3313
## cancer 0.01735082 1.01750222 0.07996238 0.2170
## renal 0.05364690 1.05511198 0.12749641 0.4208
## parkinson -0.11376414 0.89246843 0.11960656 -0.9512
## depression 0.13109674 1.14007806 0.14240416 0.9206
## rheumatoid -0.03328686 0.96726105 0.06284896 -0.5296
## death 0.60369415 1.82886243 0.07183722 8.4036
## Pr(>|z|)
## smoke2_bin2.Current smoking 0.52699
## age_bin2.Age>= 75 7.717e-09 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 1.954e-05 ***
## fx50_bin2.Fx 1+ 1.492e-10 ***
## drink4Low 0.29198
## drink4Moderate 0.07328 .
## drink4No 0.78682
## drink_bin2.Excessive drinking NA
## physical4Low 0.47925
## physical4Moderate 0.72550
## physical4No 0.99200
## activity_bin2.Less active NA
## calcium2 0.38865
## calci_bin2.Insufficient Calcium 0.27842
## protein2 0.13189
## education 0.64481
## BMI 0.41165
## cvd 0.23268
## hypertension 0.23115
## copd 0.28778
## diabetes 0.18309
## cancer 0.82822
## renal 0.67392
## parkinson 0.34153
## depression 0.35726
## rheumatoid 0.59637
## death < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke2_bin2.Current smoking 1.04210 0.95960 0.91711 1.1841
## age_bin2.Age>= 75 1.47898 0.67614 1.29502 1.6891
## bmd_bin2.BMD<= -2.5 2.53229 0.39490 2.05876 3.1147
## fall_bin2.Falls 1+ 1.35420 0.73844 1.17826 1.5564
## fx50_bin2.Fx 1+ 1.58377 0.63140 1.37593 1.8230
## drink4Low 0.90362 1.10666 0.74838 1.0911
## drink4Moderate 0.79111 1.26405 0.61218 1.0223
## drink4No 0.98060 1.01979 0.85079 1.1302
## drink_bin2.Excessive drinking NA NA NA NA
## physical4Low 0.93306 1.07174 0.77011 1.1305
## physical4Moderate 0.95899 1.04276 0.75909 1.2115
## physical4No 0.99909 1.00091 0.83681 1.1929
## activity_bin2.Less active NA NA NA NA
## calcium2 0.99987 1.00013 0.99957 1.0002
## calci_bin2.Insufficient Calcium 0.88262 1.13299 0.70424 1.1062
## protein2 0.99759 1.00241 0.99447 1.0007
## education 1.00901 0.99107 0.97126 1.0482
## BMI 0.99302 1.00703 0.97655 1.0098
## cvd 1.09576 0.91261 0.94296 1.2733
## hypertension 1.07902 0.92677 0.95272 1.2221
## copd 1.10813 0.90242 0.91701 1.3391
## diabetes 1.14556 0.87294 0.93784 1.3993
## cancer 1.01750 0.98280 0.86990 1.1901
## renal 1.05511 0.94777 0.82181 1.3546
## parkinson 0.89247 1.12049 0.70597 1.1282
## depression 1.14008 0.87713 0.86242 1.5071
## rheumatoid 0.96726 1.03385 0.85516 1.0941
## death 1.82886 0.54679 1.58867 2.1054
##
## Concordance= 0.661 (se = 0.009 )
## Likelihood ratio test= 361.08 on 26 df, p=<2e-16
## Wald test = 388.34 on 26 df, p=<2e-16
## Score (logrank) test = 415.22 on 26 df, p=<2e-16To obtain HR for PAR calculation
options(digits = 8)
any2.smk.par = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(group), data = men.smk)## 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(any2.smk.par)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(group), data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group)2 5.0358e-01 1.6546e+00 2.3097e-01 2.1803 0.0292352 *
## as.factor(group)3 5.8961e-01 1.8033e+00 1.2169e-01 4.8451 1.266e-06 ***
## as.factor(group)4 3.5915e-01 1.4321e+00 1.2454e-01 2.8838 0.0039292 **
## as.factor(group)5 7.9699e-01 2.2189e+00 2.6457e-01 3.0124 0.0025918 **
## as.factor(group)6 6.6369e-01 1.9419e+00 8.6418e-02 7.6801 1.590e-14 ***
## as.factor(group)7 1.5168e+00 4.5578e+00 1.8648e-01 8.1343 4.143e-16 ***
## as.factor(group)8 9.6153e-01 2.6157e+00 1.2141e-01 7.9198 2.380e-15 ***
## as.factor(group)9 1.0017e+00 2.7228e+00 1.4393e-01 6.9592 3.421e-12 ***
## as.factor(group)10 7.8150e-01 2.1848e+00 5.8046e-01 1.3464 0.1781893
## as.factor(group)11 1.4151e+00 4.1168e+00 4.5092e-01 3.1382 0.0016999 **
## as.factor(group)12 1.4212e+00 4.1420e+00 4.1230e-01 3.4470 0.0005669 ***
## as.factor(group)13 2.3621e+00 1.0613e+01 5.8108e-01 4.0650 4.804e-05 ***
## as.factor(group)14 7.6270e-01 2.1441e+00 1.8591e-01 4.1024 4.088e-05 ***
## as.factor(group)15 5.8924e-01 1.8026e+00 5.8023e-01 1.0155 0.3098597
## as.factor(group)16 7.4042e-01 2.0968e+00 4.5100e-01 1.6417 0.1006461
## as.factor(group)17 1.9150e+00 6.7869e+00 3.2216e-01 5.9443 2.777e-09 ***
## as.factor(group)18 2.2236e+00 9.2408e+00 2.3197e-01 9.5857 < 2.2e-16 ***
## as.factor(group)19 -1.2066e+01 5.7544e-06 8.7033e+02 -0.0139 0.9889391
## as.factor(group)20 1.4171e+00 4.1251e+00 1.7097e-01 8.2883 < 2.2e-16 ***
## as.factor(group)21 2.4387e+00 1.1458e+01 4.5154e-01 5.4009 6.631e-08 ***
## as.factor(group)22 -1.2042e+01 5.8897e-06 2.5250e+03 -0.0048 0.9961947
## as.factor(group)23 1.6817e+00 5.3745e+00 5.8041e-01 2.8974 0.0037628 **
## as.factor(group)24 3.0803e+00 2.1765e+01 7.1032e-01 4.3365 1.448e-05 ***
## as.factor(group)26 1.4848e+00 4.4139e+00 7.0992e-01 2.0915 0.0364863 *
## as.factor(group)27 2.3819e+00 1.0826e+01 3.0805e-01 7.7323 1.056e-14 ***
## as.factor(group)28 -1.2064e+01 5.7619e-06 1.7650e+03 -0.0068 0.9945463
## as.factor(group)29 4.9726e+00 1.4440e+02 1.0081e+00 4.9327 8.109e-07 ***
## as.factor(group)30 -1.2048e+01 5.8583e-06 1.9519e+03 -0.0062 0.9950752
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(group)2 1.6546e+00 6.0437e-01 1.05221 2.6020
## as.factor(group)3 1.8033e+00 5.5454e-01 1.42062 2.2890
## as.factor(group)4 1.4321e+00 6.9827e-01 1.12193 1.8280
## as.factor(group)5 2.2189e+00 4.5068e-01 1.32107 3.7268
## as.factor(group)6 1.9419e+00 5.1495e-01 1.63938 2.3004
## as.factor(group)7 4.5578e+00 2.1940e-01 3.16249 6.5688
## as.factor(group)8 2.6157e+00 3.8231e-01 2.06179 3.3184
## as.factor(group)9 2.7228e+00 3.6726e-01 2.05355 3.6103
## as.factor(group)10 2.1848e+00 4.5772e-01 0.70035 6.8154
## as.factor(group)11 4.1168e+00 2.4291e-01 1.70112 9.9629
## as.factor(group)12 4.1420e+00 2.4143e-01 1.84613 9.2932
## as.factor(group)13 1.0613e+01 9.4225e-02 3.39796 33.1474
## as.factor(group)14 2.1441e+00 4.6641e-01 1.48931 3.0866
## as.factor(group)15 1.8026e+00 5.5475e-01 0.57810 5.6208
## as.factor(group)16 2.0968e+00 4.7691e-01 0.86630 5.0752
## as.factor(group)17 6.7869e+00 1.4734e-01 3.60953 12.7613
## as.factor(group)18 9.2408e+00 1.0822e-01 5.86480 14.5601
## as.factor(group)19 5.7544e-06 1.7378e+05 0.00000 Inf
## as.factor(group)20 4.1251e+00 2.4242e-01 2.95054 5.7673
## as.factor(group)21 1.1458e+01 8.7272e-02 4.72905 27.7639
## as.factor(group)22 5.8897e-06 1.6979e+05 0.00000 Inf
## as.factor(group)23 5.3745e+00 1.8606e-01 1.72304 16.7643
## as.factor(group)24 2.1765e+01 4.5946e-02 5.40913 87.5743
## as.factor(group)26 4.4139e+00 2.2656e-01 1.09785 17.7463
## as.factor(group)27 1.0826e+01 9.2373e-02 5.91893 19.8000
## as.factor(group)28 5.7619e-06 1.7355e+05 0.00000 Inf
## as.factor(group)29 1.4440e+02 6.9254e-03 20.02080 1041.4260
## as.factor(group)30 5.8583e-06 1.7070e+05 0.00000 Inf
##
## Concordance= 0.637 (se = 0.009 )
## Likelihood ratio test= 286.81 on 28 df, p=<2e-16
## Wald test = 349.13 on 28 df, p=<2e-16
## Score (logrank) test = 478.67 on 28 df, p=<2e-16(2.2.3) Association for hip fracture
hip2.smk.age = coxph(Surv(fu_hipfx, hipfx) ~ smoke2_bin + age, data = men.smk)
summary(hip2.smk.age)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke2_bin + age, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke2_bin2.Current smoking 0.018386 1.018556 0.132324 0.1389 0.8895
## age 0.134226 1.143651 0.011230 11.9522 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke2_bin2.Current smoking 1.0186 0.98178 0.78587 1.3201
## age 1.1437 0.87439 1.11875 1.1691
##
## Concordance= 0.72 (se = 0.016 )
## Likelihood ratio test= 136.55 on 2 df, p=<2e-16
## Wald test = 143.46 on 2 df, p=<2e-16
## Score (logrank) test = 152.84 on 2 df, p=<2e-16hip2.smk.all1 = coxph(Surv(fu_hipfx, hipfx) ~ smoke2_bin + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(hip2.smk.all1)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke2_bin + age_bin +
## bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke2_bin2.Current smoking -0.018219 0.981946 0.132325 -0.1377 0.89049
## age_bin2.Age>= 75 1.104707 3.018341 0.138454 7.9789 1.476e-15 ***
## bmd_bin2.BMD<= -2.5 1.575669 4.833975 0.168079 9.3746 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.326256 1.385770 0.147682 2.2092 0.02716 *
## fx50_bin2.Fx 1+ 0.249391 1.283243 0.157112 1.5873 0.11243
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke2_bin2.Current smoking 0.98195 1.01839 0.75762 1.2727
## age_bin2.Age>= 75 3.01834 0.33131 2.30100 3.9593
## bmd_bin2.BMD<= -2.5 4.83398 0.20687 3.47724 6.7201
## fall_bin2.Falls 1+ 1.38577 0.72162 1.03749 1.8510
## fx50_bin2.Fx 1+ 1.28324 0.77928 0.94314 1.7460
##
## Concordance= 0.726 (se = 0.017 )
## Likelihood ratio test= 161.99 on 5 df, p=<2e-16
## Wald test = 198.17 on 5 df, p=<2e-16
## Score (logrank) test = 249.28 on 5 df, p=<2e-16hip2.smk.all2 = coxph(Surv(fu_hipfx, hipfx) ~ smoke2_bin + age_bin + bmd_bin + fall_bin + fx50_bin + drink4 + drink_bin + physical4 + activity_bin + calcium2 + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)
summary(hip2.smk.all2)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke2_bin + age_bin +
## bmd_bin + fall_bin + fx50_bin + drink4 + drink_bin + physical4 +
## activity_bin + calcium2 + calci_bin + protein2 + education +
## BMI + cvd + hypertension + copd + diabetes + cancer + renal +
## parkinson + depression + rheumatoid + death, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z
## smoke2_bin2.Current smoking -0.05987512 0.94188215 0.13830957 -0.4329
## age_bin2.Age>= 75 0.75079849 2.11869109 0.14814666 5.0679
## bmd_bin2.BMD<= -2.5 1.45639433 4.29046160 0.17626798 8.2624
## fall_bin2.Falls 1+ 0.28737207 1.33292006 0.15024817 1.9126
## fx50_bin2.Fx 1+ 0.24588167 1.27874825 0.15803510 1.5559
## drink4Low 0.12047641 1.12803413 0.21920550 0.5496
## drink4Moderate 0.23999662 1.27124486 0.26947837 0.8906
## drink4No 0.32749362 1.38748619 0.16325579 2.0060
## drink_bin2.Excessive drinking NA NA 0.00000000 NA
## physical4Low -0.07188955 0.93063368 0.21195529 -0.3392
## physical4Moderate -0.47186920 0.62383511 0.30060432 -1.5697
## physical4No 0.00124075 1.00124153 0.19243252 0.0064
## activity_bin2.Less active NA NA 0.00000000 NA
## calcium2 -0.00024788 0.99975215 0.00032267 -0.7682
## calci_bin2.Insufficient Calcium -0.16749582 0.84578015 0.24805001 -0.6753
## protein2 -0.00059458 0.99940560 0.00343410 -0.1731
## education -0.03181628 0.96868454 0.04125872 -0.7711
## BMI -0.03037786 0.97007891 0.01849086 -1.6429
## cvd 0.25402041 1.28919811 0.15363758 1.6534
## hypertension 0.41796570 1.51886857 0.13516257 3.0923
## copd -0.08124107 0.92197141 0.21450307 -0.3787
## diabetes 0.01512104 1.01523594 0.22249524 0.0680
## cancer -0.05572664 0.94579765 0.17234253 -0.3233
## renal -0.34970740 0.70489431 0.26773253 -1.3062
## parkinson 0.35519467 1.42645832 0.22406128 1.5853
## depression 0.07351039 1.07627971 0.30023065 0.2448
## rheumatoid 0.06892847 1.07135957 0.13481996 0.5113
## death 0.92549656 2.52312084 0.16747975 5.5260
## Pr(>|z|)
## smoke2_bin2.Current smoking 0.665083
## age_bin2.Age>= 75 4.021e-07 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.055793 .
## fx50_bin2.Fx 1+ 0.119740
## drink4Low 0.582590
## drink4Moderate 0.373145
## drink4No 0.044855 *
## drink_bin2.Excessive drinking NA
## physical4Low 0.734479
## physical4Moderate 0.116477
## physical4No 0.994855
## activity_bin2.Less active NA
## calcium2 0.442349
## calci_bin2.Insufficient Calcium 0.499517
## protein2 0.862541
## education 0.440624
## BMI 0.100412
## cvd 0.098255 .
## hypertension 0.001986 **
## copd 0.704880
## diabetes 0.945817
## cancer 0.746432
## renal 0.191491
## parkinson 0.112908
## depression 0.806575
## rheumatoid 0.609167
## death 3.276e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke2_bin2.Current smoking 0.94188 1.06170 0.71824 1.2352
## age_bin2.Age>= 75 2.11869 0.47199 1.58477 2.8325
## bmd_bin2.BMD<= -2.5 4.29046 0.23308 3.03714 6.0610
## fall_bin2.Falls 1+ 1.33292 0.75023 0.99292 1.7894
## fx50_bin2.Fx 1+ 1.27875 0.78201 0.93813 1.7430
## drink4Low 1.12803 0.88650 0.73406 1.7334
## drink4Moderate 1.27124 0.78663 0.74963 2.1558
## drink4No 1.38749 0.72073 1.00755 1.9107
## drink_bin2.Excessive drinking NA NA NA NA
## physical4Low 0.93063 1.07454 0.61427 1.4099
## physical4Moderate 0.62384 1.60299 0.34609 1.1245
## physical4No 1.00124 0.99876 0.68666 1.4599
## activity_bin2.Less active NA NA NA NA
## calcium2 0.99975 1.00025 0.99912 1.0004
## calci_bin2.Insufficient Calcium 0.84578 1.18234 0.52014 1.3753
## protein2 0.99941 1.00059 0.99270 1.0062
## education 0.96868 1.03233 0.89343 1.0503
## BMI 0.97008 1.03084 0.93555 1.0059
## cvd 1.28920 0.77568 0.95399 1.7422
## hypertension 1.51887 0.65838 1.16539 1.9796
## copd 0.92197 1.08463 0.60553 1.4038
## diabetes 1.01524 0.98499 0.65642 1.5702
## cancer 0.94580 1.05731 0.67468 1.3259
## renal 0.70489 1.41865 0.41709 1.1913
## parkinson 1.42646 0.70104 0.91947 2.2130
## depression 1.07628 0.92913 0.59754 1.9386
## rheumatoid 1.07136 0.93339 0.82258 1.3954
## death 2.52312 0.39633 1.81710 3.5035
##
## Concordance= 0.781 (se = 0.015 )
## Likelihood ratio test= 233.46 on 26 df, p=<2e-16
## Wald test = 254.12 on 26 df, p=<2e-16
## Score (logrank) test = 316.51 on 26 df, p=<2e-16To calculate PAR
options(digits = 8)
hip2.smk.par = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(group2), data = men.smk)## 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(hip2.smk.par)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(group2), data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(group2)2 -7.7915e-02 9.2504e-01 2.7342e-01 -0.2850 0.7756729
## as.factor(group2)3 1.6073e-01 1.1744e+00 5.4174e-01 0.2967 0.7667010
## as.factor(group2)4 4.9648e-02 1.0509e+00 5.4175e-01 0.0916 0.9269810
## as.factor(group2)5 7.9035e-01 2.2042e+00 1.0215e+00 0.7737 0.4391206
## as.factor(group2)6 9.9764e-01 2.7119e+00 2.8749e-01 3.4702 0.0005200 ***
## as.factor(group2)7 2.3607e+00 1.0599e+01 4.3274e-01 5.4553 4.890e-08 ***
## as.factor(group2)8 1.5843e+00 4.8758e+00 3.4019e-01 4.6571 3.206e-06 ***
## as.factor(group2)9 1.6531e+00 5.2229e+00 3.9415e-01 4.1940 2.741e-05 ***
## as.factor(group2)10 9.0597e-01 2.4743e+00 2.7333e-01 3.3146 0.0009179 ***
## as.factor(group2)11 2.5584e+00 1.2915e+01 1.0216e+00 2.5044 0.0122642 *
## as.factor(group2)12 -1.4787e+01 3.7845e-07 5.2386e+03 -0.0028 0.9977478
## as.factor(group2)13 1.7527e+00 5.7703e+00 4.9362e-01 3.5507 0.0003842 ***
## as.factor(group2)14 -1.4800e+01 3.7372e-07 1.7026e+03 -0.0087 0.9930643
## as.factor(group2)15 1.1513e-01 1.1220e+00 4.1053e-01 0.2804 0.7791413
## as.factor(group2)16 -2.1736e-01 8.0464e-01 4.9349e-01 -0.4405 0.6596048
## as.factor(group2)17 2.8939e+00 1.8064e+01 7.3998e-01 3.9108 9.200e-05 ***
## as.factor(group2)18 1.6992e+00 5.4693e+00 1.0222e+00 1.6622 0.0964716 .
## as.factor(group2)19 2.6789e+00 1.4569e+01 3.8052e-01 7.0402 1.920e-12 ***
## as.factor(group2)20 2.1502e+00 8.5869e+00 4.6050e-01 4.6694 3.021e-06 ***
## as.factor(group2)21 1.2761e+00 3.5826e+00 3.5806e-01 3.5640 0.0003653 ***
## as.factor(group2)22 1.2910e+00 3.6366e+00 4.1196e-01 3.1339 0.0017248 **
## as.factor(group2)23 -1.4730e+01 4.0055e-07 1.1805e+04 -0.0012 0.9990044
## as.factor(group2)24 2.2775e+00 9.7527e+00 7.3738e-01 3.0887 0.0020105 **
## as.factor(group2)25 2.3069e+00 1.0044e+01 7.3729e-01 3.1289 0.0017544 **
## as.factor(group2)26 2.9981e-01 1.3496e+00 6.1390e-01 0.4884 0.6252901
## as.factor(group2)27 -1.4763e+01 3.8781e-07 5.1373e+03 -0.0029 0.9977072
## as.factor(group2)28 2.7946e+00 1.6356e+01 6.1490e-01 4.5448 5.499e-06 ***
## as.factor(group2)29 3.2261e+00 2.5182e+01 4.3361e-01 7.4401 1.006e-13 ***
## as.factor(group2)30 1.2969e+00 3.6580e+00 5.4269e-01 2.3898 0.0168578 *
## as.factor(group2)31 3.1152e+00 2.2539e+01 7.3778e-01 4.2224 2.417e-05 ***
## as.factor(group2)32 3.2909e+00 2.6868e+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(group2)2 9.2504e-01 1.0810e+00 0.54129 1.5809
## as.factor(group2)3 1.1744e+00 8.5152e-01 0.40614 3.3958
## as.factor(group2)4 1.0509e+00 9.5156e-01 0.36344 3.0388
## as.factor(group2)5 2.2042e+00 4.5369e-01 0.29765 16.3224
## as.factor(group2)6 2.7119e+00 3.6875e-01 1.54369 4.7641
## as.factor(group2)7 1.0599e+01 9.4351e-02 4.53836 24.7516
## as.factor(group2)8 4.8758e+00 2.0509e-01 2.50313 9.4977
## as.factor(group2)9 5.2229e+00 1.9146e-01 2.41219 11.3087
## as.factor(group2)10 2.4743e+00 4.0415e-01 1.44810 4.2278
## as.factor(group2)11 1.2915e+01 7.7427e-02 1.74407 95.6432
## as.factor(group2)12 3.7845e-07 2.6423e+06 0.00000 Inf
## as.factor(group2)13 5.7703e+00 1.7330e-01 2.19291 15.1834
## as.factor(group2)14 3.7372e-07 2.6758e+06 0.00000 Inf
## as.factor(group2)15 1.1220e+00 8.9125e-01 0.50183 2.5087
## as.factor(group2)16 8.0464e-01 1.2428e+00 0.30588 2.1167
## as.factor(group2)17 1.8064e+01 5.5359e-02 4.23580 77.0340
## as.factor(group2)18 5.4693e+00 1.8284e-01 0.73758 40.5562
## as.factor(group2)19 1.4569e+01 6.8638e-02 6.91096 30.7139
## as.factor(group2)20 8.5869e+00 1.1646e-01 3.48225 21.1744
## as.factor(group2)21 3.5826e+00 2.7912e-01 1.77592 7.2274
## as.factor(group2)22 3.6366e+00 2.7498e-01 1.62194 8.1537
## as.factor(group2)23 4.0055e-07 2.4966e+06 0.00000 Inf
## as.factor(group2)24 9.7527e+00 1.0254e-01 2.29860 41.3798
## as.factor(group2)25 1.0044e+01 9.9566e-02 2.36759 42.6059
## as.factor(group2)26 1.3496e+00 7.4096e-01 0.40518 4.4953
## as.factor(group2)27 3.8781e-07 2.5786e+06 0.00000 Inf
## as.factor(group2)28 1.6356e+01 6.1140e-02 4.90085 54.5854
## as.factor(group2)29 2.5182e+01 3.9711e-02 10.76452 58.9087
## as.factor(group2)30 3.6580e+00 2.7337e-01 1.26272 10.5971
## as.factor(group2)31 2.2539e+01 4.4369e-02 5.30795 95.7025
## as.factor(group2)32 2.6868e+01 3.7220e-02 7.98704 90.3796
##
## Concordance= 0.734 (se = 0.017 )
## Likelihood ratio test= 184.09 on 31 df, p=<2e-16
## Wald test = 221.66 on 31 df, p=<2e-16
## Score (logrank) test = 342.27 on 31 df, p=<2e-16(3) Number of pack-years:
(3.1) Descriptive analysis
hipfx = subset(men.smk, hipfx == 1)
hipfx$site = 2
men.smk$site[men.smk$anyfx == 0] = 0
men.smk$site[men.smk$anyfx == 1] = 1
smk.box = rbind(men.smk, hipfx)
var_lab(smk.box$site) = "Fracture status"
val_lab(smk.box$site) = num_lab(" 0 Event-free
1 Any fracture
2 Hip fracture")
table(smk.box$site)##
## Event-free Any fracture Hip fracture
## 4908 1084 237smk.box$smk_excess = ifelse(smk.box$smoke_packyrs >= 20, 1, 0)
smk.box$smk_30excess = ifelse(smk.box$smoke_packyrs >= 30, 1, 0)
smk.box = smk.box %>% mutate(quin.packyrs = case_when(smoke_packyrs == 0 ~ 1,
smoke_packyrs > 0 & smoke_packyrs<= 9.75 ~ 2,
smoke_packyrs > 9.75 & smoke_packyrs<= 22.5 ~ 3,
smoke_packyrs > 22.5 & smoke_packyrs<= 42 ~ 4,
smoke_packyrs > 42 ~ 5))
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) + smoke_status + smoke_packyrs + smk_excess + smk_30excess + quin.packyrs + smoke_perddlife + smoke_perdd + smk_dur + smoke_age1st + smoke_agestop + as.factor(smoke_100life) + 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) | site, data = smk.box, render.continuous = c(. = "Mean(SD)", . = "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.| Event-free (N=4908) |
Any fracture (N=1084) |
Hip fracture (N=237) |
Overall (N=6229) |
|
|---|---|---|---|---|
| age | ||||
| Mean(SD) | 73.5(5.86) | 74.5(5.88) | 76.4(6.09) | 73.8(5.90) |
| Median [Q1, Q3] | 73.0 [69.0, 78.0] | 74.0 [70.0, 78.0] | 76.0 [72.0, 80.0] | 73.0 [69.0, 78.0] |
| as.factor(age_bin) | ||||
| 1.Age< 75 | 2909 (59.3%) | 567 (52.3%) | 92 (38.8%) | 3568 (57.3%) |
| 2.Age>= 75 | 1999 (40.7%) | 517 (47.7%) | 145 (61.2%) | 2661 (42.7%) |
| race | ||||
| 1:WHITE | 4368 (89.0%) | 1016 (93.7%) | 227 (95.8%) | 5611 (90.1%) |
| 2:AFRICAN AMERICAN | 226 (4.6%) | 18 (1.7%) | 3 (1.3%) | 247 (4.0%) |
| 3:ASIAN | 166 (3.4%) | 26 (2.4%) | 4 (1.7%) | 196 (3.1%) |
| 4:NATIVE HAWIIAN OR OTHER PACIFIC ISLANDER | 6 (0.1%) | 1 (0.1%) | 0 (0%) | 7 (0.1%) |
| 5:AMERICAN INDIAN OR ALASKAN NATIVE | 6 (0.1%) | 1 (0.1%) | 0 (0%) | 7 (0.1%) |
| 6:MULTI RACIAL | 58 (1.2%) | 3 (0.3%) | 1 (0.4%) | 62 (1.0%) |
| 7:UNKNOWN | 78 (1.6%) | 19 (1.8%) | 2 (0.8%) | 99 (1.6%) |
| fnbmd | ||||
| Mean(SD) | 0.794(0.127) | 0.739(0.122) | 0.689(0.115) | 0.781(0.129) |
| Median [Q1, Q3] | 0.783 [0.707, 0.870] | 0.728 [0.652, 0.812] | 0.671 [0.605, 0.752] | 0.770 [0.692, 0.857] |
| Tscore | ||||
| Mean(SD) | -1.02(0.930) | -1.43(0.887) | -1.79(0.843) | -1.12(0.941) |
| Median [Q1, Q3] | -1.10 [-1.66, -0.466] | -1.50 [-2.06, -0.894] | -1.92 [-2.40, -1.33] | -1.20 [-1.77, -0.561] |
| as.factor(bmd_bin) | ||||
| 1.BMD> -2.5 | 4721 (96.2%) | 976 (90.0%) | 191 (80.6%) | 5888 (94.5%) |
| 2.BMD<= -2.5 | 187 (3.8%) | 108 (10.0%) | 46 (19.4%) | 341 (5.5%) |
| as.factor(no_falls) | ||||
| 0 | 3924 (80.0%) | 801 (73.9%) | 173 (73.0%) | 4898 (78.6%) |
| 1 | 984 (20.0%) | 283 (26.1%) | 64 (27.0%) | 1331 (21.4%) |
| as.factor(fall_bin) | ||||
| 1.No falls | 3924 (80.0%) | 801 (73.9%) | 173 (73.0%) | 4898 (78.6%) |
| 2.Falls 1+ | 984 (20.0%) | 283 (26.1%) | 64 (27.0%) | 1331 (21.4%) |
| as.factor(fx50) | ||||
| 0 | 4141 (84.4%) | 820 (75.6%) | 183 (77.2%) | 5144 (82.6%) |
| 1 | 595 (12.1%) | 184 (17.0%) | 38 (16.0%) | 817 (13.1%) |
| 2 | 133 (2.7%) | 59 (5.4%) | 9 (3.8%) | 201 (3.2%) |
| 3 | 31 (0.6%) | 12 (1.1%) | 4 (1.7%) | 47 (0.8%) |
| 4 | 7 (0.1%) | 6 (0.6%) | 2 (0.8%) | 15 (0.2%) |
| 5 | 0 (0%) | 2 (0.2%) | 1 (0.4%) | 3 (0.0%) |
| 6 | 1 (0.0%) | 1 (0.1%) | 0 (0%) | 2 (0.0%) |
| as.factor(fx50_bin) | ||||
| 1.No fx | 4141 (84.4%) | 820 (75.6%) | 183 (77.2%) | 5144 (82.6%) |
| 2.Fx 1+ | 767 (15.6%) | 264 (24.4%) | 54 (22.8%) | 1085 (17.4%) |
| as.factor(smoke) | ||||
| Current | 162 (3.3%) | 44 (4.1%) | 12 (5.1%) | 218 (3.5%) |
| Never | 1837 (37.4%) | 412 (38.0%) | 98 (41.4%) | 2347 (37.7%) |
| Past | 2909 (59.3%) | 628 (57.9%) | 127 (53.6%) | 3664 (58.8%) |
| as.factor(smoke_bin) | ||||
| 1.No/past smoking | 4746 (96.7%) | 1040 (95.9%) | 225 (94.9%) | 6011 (96.5%) |
| 2.Current smoking | 162 (3.3%) | 44 (4.1%) | 12 (5.1%) | 218 (3.5%) |
| smoke_status | ||||
| 1 (0.0%) | 0 (0%) | 0 (0%) | 1 (0.0%) | |
| 0:NO | 1836 (37.4%) | 412 (38.0%) | 98 (41.4%) | 2346 (37.7%) |
| 1:PAST | 2909 (59.3%) | 628 (57.9%) | 127 (53.6%) | 3664 (58.8%) |
| 2:CURRENT | 162 (3.3%) | 44 (4.1%) | 12 (5.1%) | 218 (3.5%) |
| smoke_packyrs | ||||
| Mean(SD) | 18.1(24.6) | 17.7(24.6) | 17.6(25.3) | 18.0(24.7) |
| Median [Q1, Q3] | 7.40 [0, 29.0] | 5.65 [0, 29.0] | 3.00 [0, 29.3] | 7.00 [0, 29.0] |
| smk_excess | ||||
| Mean(SD) | 0.343(0.475) | 0.339(0.473) | 0.342(0.475) | 0.342(0.475) |
| Median [Q1, Q3] | 0 [0, 1.00] | 0 [0, 1.00] | 0 [0, 1.00] | 0 [0, 1.00] |
| smk_30excess | ||||
| Mean(SD) | 0.247(0.431) | 0.245(0.431) | 0.249(0.433) | 0.247(0.431) |
| Median [Q1, Q3] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] |
| quin.packyrs | ||||
| Mean(SD) | 2.55(1.50) | 2.52(1.49) | 2.47(1.54) | 2.54(1.50) |
| Median [Q1, Q3] | 2.00 [1.00, 4.00] | 2.00 [1.00, 4.00] | 2.00 [1.00, 4.00] | 2.00 [1.00, 4.00] |
| smoke_perddlife | ||||
| Mean(SD) | 12.6(13.9) | 12.1(13.6) | 11.5(13.6) | 12.4(13.8) |
| Median [Q1, Q3] | 10.0 [0, 20.0] | 10.0 [0, 20.0] | 8.00 [0, 20.0] | 10.0 [0, 20.0] |
| smoke_perdd | ||||
| Mean(SD) | 0.540(3.45) | 0.705(3.96) | 0.819(3.86) | 0.579(3.56) |
| Median [Q1, Q3] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] | 0 [0, 0] |
| smk_dur | ||||
| Mean(SD) | 16.7(17.6) | 16.6(18.0) | 16.3(18.7) | 16.7(17.7) |
| Median [Q1, Q3] | 12.0 [0, 30.0] | 11.0 [0, 30.0] | 9.00 [0, 29.0] | 12.0 [0, 30.0] |
| smoke_age1st | ||||
| Mean(SD) | 11.4(9.55) | 11.6(9.89) | 10.8(9.47) | 11.4(9.60) |
| Median [Q1, Q3] | 15.0 [0, 18.0] | 16.0 [0, 19.0] | 15.0 [0, 18.0] | 15.0 [0, 18.0] |
| smoke_agestop | ||||
| Mean(SD) | 25.8(23.8) | 25.3(24.0) | 23.4(24.4) | 25.6(23.9) |
| Median [Q1, Q3] | 30.0 [0, 45.0] | 27.0 [0, 45.0] | 23.0 [0, 45.0] | 29.0 [0, 45.0] |
| as.factor(smoke_100life) | ||||
| 0: No | 1836 (37.4%) | 412 (38.0%) | 98 (41.4%) | 2346 (37.7%) |
| 1: Yes | 3072 (62.6%) | 672 (62.0%) | 139 (58.6%) | 3883 (62.3%) |
| drink4 | ||||
| High | 1578 (32.2%) | 372 (34.3%) | 62 (26.2%) | 2012 (32.3%) |
| Low | 726 (14.8%) | 155 (14.3%) | 32 (13.5%) | 913 (14.7%) |
| Moderate | 393 (8.0%) | 70 (6.5%) | 18 (7.6%) | 481 (7.7%) |
| No | 2211 (45.0%) | 487 (44.9%) | 125 (52.7%) | 2823 (45.3%) |
| as.factor(drink_bin) | ||||
| 1.Less drinking | 3330 (67.8%) | 712 (65.7%) | 175 (73.8%) | 4217 (67.7%) |
| 2.Excessive drinking | 1578 (32.2%) | 372 (34.3%) | 62 (26.2%) | 2012 (32.3%) |
| physical4 | ||||
| High | 695 (14.2%) | 171 (15.8%) | 37 (15.6%) | 903 (14.5%) |
| Low | 1361 (27.7%) | 281 (25.9%) | 59 (24.9%) | 1701 (27.3%) |
| Moderate | 558 (11.4%) | 121 (11.2%) | 16 (6.8%) | 695 (11.2%) |
| No | 2294 (46.7%) | 511 (47.1%) | 125 (52.7%) | 2930 (47.0%) |
| as.factor(activity_bin) | ||||
| 1.Proactive | 1253 (25.5%) | 292 (26.9%) | 53 (22.4%) | 1598 (25.7%) |
| 2.Less active | 3655 (74.5%) | 792 (73.1%) | 184 (77.6%) | 4631 (74.3%) |
| calcium2 | ||||
| Mean(SD) | 795(392) | 784(388) | 779(387) | 792(391) |
| Median [Q1, Q3] | 730 [523, 991] | 720 [515, 993] | 738 [500, 994] | 729 [522, 991] |
| as.factor(calci_bin) | ||||
| 1.Sufficient Calcium | 1194 (24.3%) | 264 (24.4%) | 57 (24.1%) | 1515 (24.3%) |
| 2.Insufficient Calcium | 3714 (75.7%) | 820 (75.6%) | 180 (75.9%) | 4714 (75.7%) |
| protein2 | ||||
| Mean(SD) | 64.4(27.6) | 62.6(26.1) | 62.2(27.9) | 64.0(27.4) |
| Median [Q1, Q3] | 60.2 [45.8, 78.7] | 59.5 [45.2, 76.7] | 58.2 [45.3, 76.9] | 60.1 [45.7, 78.1] |
| as.factor(education) | ||||
| 1 | 13 (0.3%) | 3 (0.3%) | 0 (0%) | 16 (0.3%) |
| 2 | 82 (1.7%) | 15 (1.4%) | 4 (1.7%) | 101 (1.6%) |
| 3 | 243 (5.0%) | 35 (3.2%) | 13 (5.5%) | 291 (4.7%) |
| 4 | 860 (17.5%) | 176 (16.2%) | 44 (18.6%) | 1080 (17.3%) |
| 5 | 1132 (23.1%) | 245 (22.6%) | 48 (20.3%) | 1425 (22.9%) |
| 6 | 874 (17.8%) | 220 (20.3%) | 51 (21.5%) | 1145 (18.4%) |
| 7 | 507 (10.3%) | 126 (11.6%) | 30 (12.7%) | 663 (10.6%) |
| 8 | 1197 (24.4%) | 264 (24.4%) | 47 (19.8%) | 1508 (24.2%) |
| BMI | ||||
| Mean(SD) | 27.4(3.95) | 27.1(3.88) | 26.7(3.73) | 27.3(3.94) |
| Median [Q1, Q3] | 26.9 [24.9, 29.5] | 26.6 [24.4, 29.3] | 26.1 [23.9, 28.7] | 26.9 [24.7, 29.5] |
| as.factor(cvd) | ||||
| 0 | 3889 (79.2%) | 852 (78.6%) | 175 (73.8%) | 4916 (78.9%) |
| 1 | 1019 (20.8%) | 232 (21.4%) | 62 (26.2%) | 1313 (21.1%) |
| as.factor(hypertension) | ||||
| 0 | 2804 (57.1%) | 607 (56.0%) | 113 (47.7%) | 3524 (56.6%) |
| 1 | 2104 (42.9%) | 477 (44.0%) | 124 (52.3%) | 2705 (43.4%) |
| as.factor(copd) | ||||
| 0 | 4393 (89.5%) | 959 (88.5%) | 212 (89.5%) | 5564 (89.3%) |
| 1 | 515 (10.5%) | 125 (11.5%) | 25 (10.5%) | 665 (10.7%) |
| as.factor(diabetes) | ||||
| 0 | 4370 (89.0%) | 969 (89.4%) | 213 (89.9%) | 5552 (89.1%) |
| 1 | 538 (11.0%) | 115 (10.6%) | 24 (10.1%) | 677 (10.9%) |
| as.factor(cancer) | ||||
| 0 | 4011 (81.7%) | 889 (82.0%) | 195 (82.3%) | 5095 (81.8%) |
| 1 | 897 (18.3%) | 195 (18.0%) | 42 (17.7%) | 1134 (18.2%) |
| as.factor(renal) | ||||
| 0 | 4472 (91.1%) | 967 (89.2%) | 213 (89.9%) | 5652 (90.7%) |
| 1 | 436 (8.9%) | 117 (10.8%) | 24 (10.1%) | 577 (9.3%) |
| as.factor(parkinson) | ||||
| 0 | 4253 (86.7%) | 950 (87.6%) | 201 (84.8%) | 5404 (86.8%) |
| 1 | 655 (13.3%) | 134 (12.4%) | 36 (15.2%) | 825 (13.2%) |
| as.factor(depression) | ||||
| 0 | 4750 (96.8%) | 1031 (95.1%) | 225 (94.9%) | 6006 (96.4%) |
| 1 | 158 (3.2%) | 53 (4.9%) | 12 (5.1%) | 223 (3.6%) |
| as.factor(rheumatoid) | ||||
| 0 | 2573 (52.4%) | 574 (53.0%) | 117 (49.4%) | 3264 (52.4%) |
| 1 | 2335 (47.6%) | 510 (47.0%) | 120 (50.6%) | 2965 (47.6%) |
| as.factor(death) | ||||
| 0 | 1990 (40.5%) | 391 (36.1%) | 63 (26.6%) | 2444 (39.2%) |
| 1 | 2918 (59.5%) | 693 (63.9%) | 174 (73.4%) | 3785 (60.8%) |
Boxplots
# Number of pack-years:
p1 = ggplot(data = smk.box, aes(y = smoke_packyrs, x = as.factor(site), fill = as.factor(site))) + geom_boxplot() +
geom_jitter(alpha=0.2) + theme_bw() + theme(legend.position="none") +
labs(title = "Number of pack-years by fracture status", x = "Fracture status", y = "Number of pack-years") + theme(axis.text.x = element_text(angle = 45, hjust = 1))
p1
# Number of cigarettes smoked per day during lifetime:
p2 = ggplot(data = smk.box, aes(y = smoke_perddlife, x = as.factor(site), fill = as.factor(site))) + geom_boxplot() +
geom_jitter(alpha=0.2) + theme_bw() + theme(legend.position="none") +
labs(title = "Number of cigarettes smoked per day during lifetime by fracture status", x = "Fracture status", y = "Number of cigarettes smoked per day") + theme(axis.text.x = element_text(angle = 45, hjust = 1))
p2
# Number of cigarettes currently smoked per day:
p3 = ggplot(data = smk.box, aes(y = smoke_perdd, x = as.factor(site), fill = as.factor(site))) + geom_boxplot() +
geom_jitter(alpha=0.2) + theme_bw() + theme(legend.position="none") +
labs(title = "Number of cigarettes currently smoked per day by fracture status", x = "Fracture status", y = "Number of cigarettes currently smoked per day") + theme(axis.text.x = element_text(angle = 45, hjust = 1))
p3
# Duration of smoking:
p4 = ggplot(data = smk.box, aes(y = smk_dur, x = as.factor(site), fill = as.factor(site))) + geom_boxplot() +
geom_jitter(alpha=0.2) + theme_bw() + theme(legend.position="none") +
labs(title = "Duration of smoking by fracture status", x = "Fracture status", y = "Duration of smoking") + theme(axis.text.x = element_text(angle = 45, hjust = 1))
p4
(3.2) Excessive smoking
men.smk$smk_excess = ifelse(men.smk$smoke_packyrs >= 20, 1, 0)
men.smk$smk_30excess = ifelse(men.smk$smoke_packyrs >= 30, 1, 0)
table(men.smk$smk_excess, men.smk$smk_30excess)##
## 0 1
## 0 3940 0
## 1 573 1479(3.2.1) Single factor
Association for any fracture
# Prevalence:
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + smoke_packyrs + as.factor(smk_excess) + drink_bin + activity_bin | anyfx, data = men.smk, render.continuous = c(. = "Mean (SD)", . = "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 | |||
| Mean (SD) | 73.5 (5.86) | 74.5 (5.88) | 73.7 (5.87) |
| 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 | |||
| Mean (SD) | 0.794 (0.127) | 0.739 (0.122) | 0.784 (0.128) |
| Median [Q1, Q3] | 0.783 [0.707, 0.870] | 0.728 [0.652, 0.812] | 0.774 [0.696, 0.860] |
| Tscore | |||
| Mean (SD) | -1.02 (0.930) | -1.43 (0.887) | -1.09 (0.935) |
| 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_packyrs | |||
| Mean (SD) | 18.1 (24.6) | 17.7 (24.6) | 18.1 (24.6) |
| Median [Q1, Q3] | 7.40 [0, 29.0] | 5.65 [0, 29.0] | 7.00 [0, 29.0] |
| as.factor(smk_excess) | |||
| 0 | 3223 (65.7%) | 717 (66.1%) | 3940 (65.8%) |
| 1 | 1685 (34.3%) | 367 (33.9%) | 2052 (34.2%) |
| 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%) |
# Association with No.pack-years:
any.packyr.age = coxph(Surv(fu_anyfx, anyfx) ~ smoke_packyrs + age, data = men.smk)
summary(any.packyr.age)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke_packyrs + age,
## data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke_packyrs 0.0038050 1.0038122 0.0012554 3.0308 0.002439 **
## age 0.0736938 1.0764771 0.0053959 13.6573 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_packyrs 1.0038 0.99620 1.0013 1.0063
## age 1.0765 0.92896 1.0652 1.0879
##
## Concordance= 0.616 (se = 0.009 )
## Likelihood ratio test= 182.59 on 2 df, p=<2e-16
## Wald test = 190.11 on 2 df, p=<2e-16
## Score (logrank) test = 193.96 on 2 df, p=<2e-16any.packyr.all1 = coxph(Surv(fu_anyfx, anyfx) ~ smoke_packyrs + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(any.packyr.all1)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke_packyrs + age_bin +
## bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke_packyrs 0.0031249 1.0031298 0.0012544 2.4912 0.01273 *
## age_bin2.Age>= 75 0.6044216 1.8301934 0.0627962 9.6251 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.9532970 2.5942488 0.1029092 9.2635 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.3311431 1.3925590 0.0698033 4.7439 2.096e-06 ***
## fx50_bin2.Fx 1+ 0.4701525 1.6002382 0.0714737 6.5780 4.769e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_packyrs 1.0031 0.99688 1.0007 1.0056
## age_bin2.Age>= 75 1.8302 0.54639 1.6182 2.0699
## bmd_bin2.BMD<= -2.5 2.5942 0.38547 2.1204 3.1740
## fall_bin2.Falls 1+ 1.3926 0.71810 1.2145 1.5967
## fx50_bin2.Fx 1+ 1.6002 0.62491 1.3911 1.8409
##
## Concordance= 0.639 (se = 0.009 )
## Likelihood ratio test= 262.57 on 5 df, p=<2e-16
## Wald test = 302.94 on 5 df, p=<2e-16
## Score (logrank) test = 322.46 on 5 df, p=<2e-16any.packyr.all2 = coxph(Surv(fu_anyfx, anyfx) ~ smoke_packyrs + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)
summary(any.packyr.all2)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smoke_packyrs + age_bin +
## bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin +
## calci_bin + protein2 + education + BMI + cvd + hypertension +
## copd + diabetes + cancer + renal + parkinson + depression +
## rheumatoid + death, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z
## smoke_packyrs 0.0014724 1.0014735 0.0013353 1.1027
## age_bin2.Age>= 75 0.3932977 1.4818595 0.0676967 5.8097
## bmd_bin2.BMD<= -2.5 0.9444981 2.5715224 0.1052744 8.9718
## fall_bin2.Falls 1+ 0.3073235 1.3597808 0.0709683 4.3304
## fx50_bin2.Fx 1+ 0.4631354 1.5890486 0.0717118 6.4583
## drink_bin2.Excessive drinking 0.0563734 1.0579927 0.0655826 0.8596
## activity_bin2.Less active -0.0065639 0.9934576 0.0701420 -0.0936
## calci_bin2.Insufficient Calcium -0.0639958 0.9380090 0.0821203 -0.7793
## protein2 -0.0032663 0.9967390 0.0013670 -2.3895
## education 0.0063819 1.0064023 0.0193712 0.3295
## BMI -0.0073404 0.9926865 0.0085404 -0.8595
## cvd 0.0928716 1.0973209 0.0766508 1.2116
## hypertension 0.0843253 1.0879828 0.0634152 1.3297
## copd 0.0965469 1.1013612 0.0976122 0.9891
## diabetes 0.1526573 1.1649257 0.1015822 1.5028
## cancer 0.0196669 1.0198615 0.0799395 0.2460
## renal 0.0573823 1.0590606 0.1275867 0.4498
## parkinson -0.1107990 0.8951186 0.1196246 -0.9262
## depression 0.1339828 1.1433732 0.1424048 0.9409
## rheumatoid -0.0314913 0.9689994 0.0627927 -0.5015
## death 0.5980168 1.8185088 0.0721182 8.2922
## Pr(>|z|)
## smoke_packyrs 0.27017
## age_bin2.Age>= 75 6.258e-09 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 1.488e-05 ***
## fx50_bin2.Fx 1+ 1.059e-10 ***
## drink_bin2.Excessive drinking 0.39002
## activity_bin2.Less active 0.92544
## calci_bin2.Insufficient Calcium 0.43581
## protein2 0.01687 *
## education 0.74181
## BMI 0.39007
## cvd 0.22566
## hypertension 0.18361
## copd 0.32262
## diabetes 0.13289
## cancer 0.80567
## renal 0.65289
## parkinson 0.35433
## depression 0.34678
## rheumatoid 0.61601
## death < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_packyrs 1.00147 0.99853 0.99886 1.00410
## age_bin2.Age>= 75 1.48186 0.67483 1.29773 1.69212
## bmd_bin2.BMD<= -2.5 2.57152 0.38887 2.09209 3.16082
## fall_bin2.Falls 1+ 1.35978 0.73541 1.18321 1.56271
## fx50_bin2.Fx 1+ 1.58905 0.62931 1.38069 1.82885
## drink_bin2.Excessive drinking 1.05799 0.94519 0.93038 1.20311
## activity_bin2.Less active 0.99346 1.00659 0.86585 1.13987
## calci_bin2.Insufficient Calcium 0.93801 1.06609 0.79856 1.10181
## protein2 0.99674 1.00327 0.99407 0.99941
## education 1.00640 0.99364 0.96891 1.04535
## BMI 0.99269 1.00737 0.97621 1.00944
## cvd 1.09732 0.91131 0.94425 1.27520
## hypertension 1.08798 0.91913 0.96082 1.23197
## copd 1.10136 0.90797 0.90958 1.33357
## diabetes 1.16493 0.85842 0.95462 1.42156
## cancer 1.01986 0.98053 0.87196 1.19285
## renal 1.05906 0.94423 0.82474 1.35995
## parkinson 0.89512 1.11717 0.70804 1.13163
## depression 1.14337 0.87461 0.86491 1.51148
## rheumatoid 0.96900 1.03199 0.85679 1.09590
## death 1.81851 0.54990 1.57880 2.09461
##
## Concordance= 0.659 (se = 0.009 )
## Likelihood ratio test= 356.89 on 21 df, p=<2e-16
## Wald test = 384.41 on 21 df, p=<2e-16
## Score (logrank) test = 411.31 on 21 df, p=<2e-16# Association with excessive smoking:
any.excess.age = coxph(Surv(fu_anyfx, anyfx) ~ smk_excess + age, data = men.smk)
summary(any.excess.age)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smk_excess + age, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smk_excess 0.1562445 1.1691120 0.0644094 2.4258 0.01527 *
## age 0.0732774 1.0760289 0.0053867 13.6034 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smk_excess 1.1691 0.85535 1.0305 1.3264
## age 1.0760 0.92934 1.0647 1.0874
##
## Concordance= 0.617 (se = 0.009 )
## Likelihood ratio test= 179.68 on 2 df, p=<2e-16
## Wald test = 187.34 on 2 df, p=<2e-16
## Score (logrank) test = 191.2 on 2 df, p=<2e-16any.excess.all1 = coxph(Surv(fu_anyfx, anyfx) ~ smk_excess + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(any.excess.all1)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smk_excess + age_bin +
## bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smk_excess 0.133244 1.142528 0.064312 2.0718 0.03828 *
## age_bin2.Age>= 75 0.600906 1.823770 0.062753 9.5757 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.952881 2.593169 0.102918 9.2587 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.332672 1.394690 0.069801 4.7660 1.879e-06 ***
## fx50_bin2.Fx 1+ 0.472964 1.604744 0.071462 6.6184 3.632e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smk_excess 1.1425 0.87525 1.0072 1.2960
## age_bin2.Age>= 75 1.8238 0.54831 1.6127 2.0625
## bmd_bin2.BMD<= -2.5 2.5932 0.38563 2.1195 3.1727
## fall_bin2.Falls 1+ 1.3947 0.71701 1.2164 1.5992
## fx50_bin2.Fx 1+ 1.6047 0.62315 1.3950 1.8460
##
## Concordance= 0.638 (se = 0.009 )
## Likelihood ratio test= 260.87 on 5 df, p=<2e-16
## Wald test = 301.45 on 5 df, p=<2e-16
## Score (logrank) test = 320.82 on 5 df, p=<2e-16any.excess.all2 = coxph(Surv(fu_anyfx, anyfx) ~ smk_excess + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)
summary(any.excess.all2)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ smk_excess + age_bin +
## bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin +
## calci_bin + protein2 + education + BMI + cvd + hypertension +
## copd + diabetes + cancer + renal + parkinson + depression +
## rheumatoid + death, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z
## smk_excess 0.0643305 1.0664447 0.0674112 0.9543
## age_bin2.Age>= 75 0.3904544 1.4776521 0.0675341 5.7816
## bmd_bin2.BMD<= -2.5 0.9447589 2.5721932 0.1052801 8.9738
## fall_bin2.Falls 1+ 0.3075845 1.3601357 0.0709783 4.3335
## fx50_bin2.Fx 1+ 0.4642935 1.5908898 0.0717035 6.4752
## drink_bin2.Excessive drinking 0.0574792 1.0591632 0.0656069 0.8761
## activity_bin2.Less active -0.0056893 0.9943269 0.0701205 -0.0811
## calci_bin2.Insufficient Calcium -0.0632424 0.9387159 0.0820965 -0.7703
## protein2 -0.0032432 0.9967620 0.0013661 -2.3741
## education 0.0057227 1.0057391 0.0193400 0.2959
## BMI -0.0073061 0.9927206 0.0085494 -0.8546
## cvd 0.0940105 1.0985713 0.0766272 1.2269
## hypertension 0.0837284 1.0873336 0.0634229 1.3202
## copd 0.1018768 1.1072470 0.0970972 1.0492
## diabetes 0.1551040 1.1677794 0.1015096 1.5280
## cancer 0.0200417 1.0202439 0.0799342 0.2507
## renal 0.0577378 1.0594371 0.1275399 0.4527
## parkinson -0.1111080 0.8948421 0.1195798 -0.9292
## depression 0.1329853 1.1422332 0.1424219 0.9337
## rheumatoid -0.0317660 0.9687333 0.0628071 -0.5058
## death 0.6006898 1.8233761 0.0719519 8.3485
## Pr(>|z|)
## smk_excess 0.33993
## age_bin2.Age>= 75 7.400e-09 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 1.468e-05 ***
## fx50_bin2.Fx 1+ 9.470e-11 ***
## drink_bin2.Excessive drinking 0.38097
## activity_bin2.Less active 0.93533
## calci_bin2.Insufficient Calcium 0.44110
## protein2 0.01759 *
## education 0.76731
## BMI 0.39279
## cvd 0.21988
## hypertension 0.18678
## copd 0.29407
## diabetes 0.12652
## cancer 0.80203
## renal 0.65076
## parkinson 0.35281
## depression 0.35044
## rheumatoid 0.61302
## death < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smk_excess 1.06644 0.93770 0.93445 1.21708
## age_bin2.Age>= 75 1.47765 0.67675 1.29446 1.68678
## bmd_bin2.BMD<= -2.5 2.57219 0.38877 2.09261 3.16168
## fall_bin2.Falls 1+ 1.36014 0.73522 1.18349 1.56314
## fx50_bin2.Fx 1+ 1.59089 0.62858 1.38231 1.83094
## drink_bin2.Excessive drinking 1.05916 0.94414 0.93136 1.20450
## activity_bin2.Less active 0.99433 1.00571 0.86665 1.14082
## calci_bin2.Insufficient Calcium 0.93872 1.06529 0.79920 1.10259
## protein2 0.99676 1.00325 0.99410 0.99943
## education 1.00574 0.99429 0.96833 1.04459
## BMI 0.99272 1.00733 0.97622 1.00950
## cvd 1.09857 0.91027 0.94537 1.27660
## hypertension 1.08733 0.91968 0.96023 1.23126
## copd 1.10725 0.90314 0.91537 1.33935
## diabetes 1.16778 0.85633 0.95710 1.42484
## cancer 1.02024 0.98016 0.87230 1.19328
## renal 1.05944 0.94390 0.82511 1.36031
## parkinson 0.89484 1.11752 0.70788 1.13118
## depression 1.14223 0.87548 0.86402 1.51003
## rheumatoid 0.96873 1.03228 0.85653 1.09563
## death 1.82338 0.54843 1.58355 2.09953
##
## Concordance= 0.658 (se = 0.009 )
## Likelihood ratio test= 356.6 on 21 df, p=<2e-16
## Wald test = 384.17 on 21 df, p=<2e-16
## Score (logrank) test = 411.03 on 21 df, p=<2e-16EXploratory analysis with quintiles of cigarette packyears:
men.smk = men.smk %>% mutate(quin.packyrs = case_when(smoke_packyrs == 0 ~ 1,
smoke_packyrs > 0 & smoke_packyrs<= 9.75 ~ 2,
smoke_packyrs > 9.75 & smoke_packyrs<= 22.5 ~ 3,
smoke_packyrs > 22.5 & smoke_packyrs<= 42 ~ 4,
smoke_packyrs > 42 ~ 5))
table(men.smk$quin.packyrs)##
## 1 2 3 4 5
## 2272 935 943 926 916# Any fracture:
km_quin = survfit(Surv(fu_anyfx, anyfx) ~ as.factor(quin.packyrs), data = men.smk)
autoplot(km_quin)
any.quin.age = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(quin.packyrs) + age, data = men.smk)
summary(any.quin.age)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(quin.packyrs) +
## age, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(quin.packyrs)2 0.0876029 1.0915546 0.0890597 0.9836 0.325292
## as.factor(quin.packyrs)3 0.0042472 1.0042562 0.0928972 0.0457 0.963534
## as.factor(quin.packyrs)4 0.1021626 1.1075635 0.0924205 1.1054 0.268982
## as.factor(quin.packyrs)5 0.2709893 1.3112611 0.0930155 2.9134 0.003575 **
## age 0.0734825 1.0762497 0.0053976 13.6140 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(quin.packyrs)2 1.0916 0.91612 0.91672 1.2997
## as.factor(quin.packyrs)3 1.0043 0.99576 0.83709 1.2048
## as.factor(quin.packyrs)4 1.1076 0.90288 0.92406 1.3275
## as.factor(quin.packyrs)5 1.3113 0.76262 1.09273 1.5735
## age 1.0762 0.92915 1.06492 1.0877
##
## Concordance= 0.617 (se = 0.009 )
## Likelihood ratio test= 182.97 on 5 df, p=<2e-16
## Wald test = 190.55 on 5 df, p=<2e-16
## Score (logrank) test = 194.51 on 5 df, p=<2e-16any.quin.all1 = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(quin.packyrs) + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(any.quin.all1)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(quin.packyrs) +
## age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(quin.packyrs)2 0.058016 1.059732 0.089193 0.6505 0.5154
## as.factor(quin.packyrs)3 -0.021282 0.978943 0.092970 -0.2289 0.8189
## as.factor(quin.packyrs)4 0.086258 1.090087 0.092327 0.9343 0.3502
## as.factor(quin.packyrs)5 0.212106 1.236279 0.092951 2.2819 0.0225 *
## age_bin2.Age>= 75 0.602637 1.826929 0.062838 9.5903 < 2.2e-16 ***
## bmd_bin2.BMD<= -2.5 0.949908 2.585471 0.102922 9.2294 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.332044 1.393814 0.069846 4.7540 1.995e-06 ***
## fx50_bin2.Fx 1+ 0.470388 1.600615 0.071519 6.5771 4.798e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(quin.packyrs)2 1.05973 0.94363 0.88976 1.2622
## as.factor(quin.packyrs)3 0.97894 1.02151 0.81587 1.1746
## as.factor(quin.packyrs)4 1.09009 0.91736 0.90965 1.3063
## as.factor(quin.packyrs)5 1.23628 0.80888 1.03038 1.4833
## age_bin2.Age>= 75 1.82693 0.54737 1.61523 2.0664
## bmd_bin2.BMD<= -2.5 2.58547 0.38678 2.11316 3.1633
## fall_bin2.Falls 1+ 1.39381 0.71746 1.21549 1.5983
## fx50_bin2.Fx 1+ 1.60062 0.62476 1.39126 1.8415
##
## Concordance= 0.638 (se = 0.009 )
## Likelihood ratio test= 262.76 on 8 df, p=<2e-16
## Wald test = 302.94 on 8 df, p=<2e-16
## Score (logrank) test = 322.58 on 8 df, p=<2e-16any.quin.all2 = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(quin.packyrs) + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)
summary(any.quin.all2)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(quin.packyrs) +
## age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin +
## calci_bin + protein2 + education + BMI + cvd + hypertension +
## copd + diabetes + cancer + renal + parkinson + depression +
## rheumatoid + death, data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z
## as.factor(quin.packyrs)2 0.0610249 1.0629254 0.0896012 0.6811
## as.factor(quin.packyrs)3 -0.0474907 0.9536193 0.0941722 -0.5043
## as.factor(quin.packyrs)4 0.0399628 1.0407720 0.0944648 0.4230
## as.factor(quin.packyrs)5 0.0958893 1.1006373 0.0981833 0.9766
## age_bin2.Age>= 75 0.3906955 1.4780084 0.0677667 5.7653
## bmd_bin2.BMD<= -2.5 0.9427803 2.5671089 0.1053341 8.9504
## fall_bin2.Falls 1+ 0.3081181 1.3608617 0.0710082 4.3392
## fx50_bin2.Fx 1+ 0.4628684 1.5886243 0.0717840 6.4481
## drink_bin2.Excessive drinking 0.0604816 1.0623480 0.0660143 0.9162
## activity_bin2.Less active -0.0073629 0.9926642 0.0701762 -0.1049
## calci_bin2.Insufficient Calcium -0.0613045 0.9405368 0.0820946 -0.7468
## protein2 -0.0032693 0.9967360 0.0013671 -2.3915
## education 0.0058054 1.0058223 0.0194313 0.2988
## BMI -0.0071030 0.9929221 0.0085600 -0.8298
## cvd 0.0925418 1.0969590 0.0766792 1.2069
## hypertension 0.0840385 1.0876707 0.0634861 1.3237
## copd 0.1001812 1.1053712 0.0976131 1.0263
## diabetes 0.1550746 1.1677450 0.1015824 1.5266
## cancer 0.0197949 1.0199921 0.0799457 0.2476
## renal 0.0545193 1.0560329 0.1275933 0.4273
## parkinson -0.1108593 0.8950647 0.1196176 -0.9268
## depression 0.1344636 1.1439230 0.1424222 0.9441
## rheumatoid -0.0310043 0.9694714 0.0628419 -0.4934
## death 0.6000047 1.8221273 0.0721708 8.3137
## Pr(>|z|)
## as.factor(quin.packyrs)2 0.49583
## as.factor(quin.packyrs)3 0.61405
## as.factor(quin.packyrs)4 0.67226
## as.factor(quin.packyrs)5 0.32875
## age_bin2.Age>= 75 8.151e-09 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 1.430e-05 ***
## fx50_bin2.Fx 1+ 1.133e-10 ***
## drink_bin2.Excessive drinking 0.35957
## activity_bin2.Less active 0.91644
## calci_bin2.Insufficient Calcium 0.45521
## protein2 0.01678 *
## education 0.76512
## BMI 0.40666
## cvd 0.22748
## hypertension 0.18559
## copd 0.30475
## diabetes 0.12686
## cancer 0.80444
## renal 0.66917
## parkinson 0.35404
## depression 0.34511
## rheumatoid 0.62175
## death < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(quin.packyrs)2 1.06293 0.94080 0.89173 1.26699
## as.factor(quin.packyrs)3 0.95362 1.04864 0.79289 1.14692
## as.factor(quin.packyrs)4 1.04077 0.96083 0.86486 1.25246
## as.factor(quin.packyrs)5 1.10064 0.90856 0.90797 1.33419
## age_bin2.Age>= 75 1.47801 0.67659 1.29418 1.68795
## bmd_bin2.BMD<= -2.5 2.56711 0.38954 2.08826 3.15577
## fall_bin2.Falls 1+ 1.36086 0.73483 1.18405 1.56407
## fx50_bin2.Fx 1+ 1.58862 0.62948 1.38013 1.82862
## drink_bin2.Excessive drinking 1.06235 0.94131 0.93342 1.20909
## activity_bin2.Less active 0.99266 1.00739 0.86510 1.13903
## calci_bin2.Insufficient Calcium 0.94054 1.06322 0.80075 1.10473
## protein2 0.99674 1.00327 0.99407 0.99941
## education 1.00582 0.99421 0.96824 1.04487
## BMI 0.99292 1.00713 0.97640 1.00972
## cvd 1.09696 0.91161 0.94389 1.27485
## hypertension 1.08767 0.91940 0.96041 1.23179
## copd 1.10537 0.90467 0.91289 1.33843
## diabetes 1.16775 0.85635 0.95693 1.42500
## cancer 1.01999 0.98040 0.87206 1.19302
## renal 1.05603 0.94694 0.82237 1.35608
## parkinson 0.89506 1.11724 0.70800 1.13155
## depression 1.14392 0.87418 0.86530 1.51226
## rheumatoid 0.96947 1.03149 0.85712 1.09654
## death 1.82213 0.54881 1.58178 2.09899
##
## Concordance= 0.659 (se = 0.009 )
## Likelihood ratio test= 357.78 on 24 df, p=<2e-16
## Wald test = 385.3 on 24 df, p=<2e-16
## Score (logrank) test = 412.24 on 24 df, p=<2e-16# Hip fracture:
hip_km_quin = survfit(Surv(fu_hipfx, hipfx) ~ as.factor(quin.packyrs), data = men.smk)
autoplot(hip_km_quin)
hip.quin.age = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(quin.packyrs) + age, data = men.smk)
summary(hip.quin.age)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(quin.packyrs) +
## age, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(quin.packyrs)2 0.017392 1.017544 0.187380 0.0928 0.92605
## as.factor(quin.packyrs)3 -0.390401 0.676786 0.223967 -1.7431 0.08131 .
## as.factor(quin.packyrs)4 0.066723 1.068999 0.199719 0.3341 0.73832
## as.factor(quin.packyrs)5 0.371516 1.449931 0.190161 1.9537 0.05074 .
## age 0.135814 1.145469 0.011344 11.9722 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(quin.packyrs)2 1.01754 0.98276 0.70478 1.4691
## as.factor(quin.packyrs)3 0.67679 1.47757 0.43632 1.0498
## as.factor(quin.packyrs)4 1.06900 0.93545 0.72273 1.5812
## as.factor(quin.packyrs)5 1.44993 0.68969 0.99881 2.1048
## age 1.14547 0.87300 1.12028 1.1712
##
## Concordance= 0.728 (se = 0.016 )
## Likelihood ratio test= 145.75 on 5 df, p=<2e-16
## Wald test = 150.29 on 5 df, p=<2e-16
## Score (logrank) test = 160.51 on 5 df, p=<2e-16hip.quin.all1 = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(quin.packyrs) + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(hip.quin.all1)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(quin.packyrs) +
## age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(quin.packyrs)2 -0.010548 0.989507 0.187625 -0.0562 0.95517
## as.factor(quin.packyrs)3 -0.404335 0.667420 0.224038 -1.8048 0.07111 .
## as.factor(quin.packyrs)4 0.016334 1.016468 0.199265 0.0820 0.93467
## as.factor(quin.packyrs)5 0.274243 1.315534 0.189902 1.4441 0.14870
## age_bin2.Age>= 75 1.110522 3.035942 0.138323 8.0285 9.87e-16 ***
## bmd_bin2.BMD<= -2.5 1.569289 4.803232 0.167816 9.3512 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.331826 1.393510 0.147716 2.2464 0.02468 *
## fx50_bin2.Fx 1+ 0.252012 1.286612 0.157004 1.6051 0.10846
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(quin.packyrs)2 0.98951 1.01060 0.68503 1.4293
## as.factor(quin.packyrs)3 0.66742 1.49831 0.43023 1.0354
## as.factor(quin.packyrs)4 1.01647 0.98380 0.68783 1.5021
## as.factor(quin.packyrs)5 1.31553 0.76015 0.90669 1.9087
## age_bin2.Age>= 75 3.03594 0.32939 2.31501 3.9814
## bmd_bin2.BMD<= -2.5 4.80323 0.20819 3.45691 6.6739
## fall_bin2.Falls 1+ 1.39351 0.71761 1.04322 1.8614
## fx50_bin2.Fx 1+ 1.28661 0.77724 0.94581 1.7502
##
## Concordance= 0.737 (se = 0.017 )
## Likelihood ratio test= 169.3 on 8 df, p=<2e-16
## Wald test = 203.15 on 8 df, p=<2e-16
## Score (logrank) test = 255.08 on 8 df, p=<2e-16hip.quin.all2 = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(quin.packyrs) + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)
summary(hip.quin.all2)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(quin.packyrs) +
## age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin +
## calci_bin + protein2 + education + BMI + cvd + hypertension +
## copd + diabetes + cancer + renal + parkinson + depression +
## rheumatoid + death, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z
## as.factor(quin.packyrs)2 -0.0077329 0.9922969 0.1889085 -0.0409
## as.factor(quin.packyrs)3 -0.4257446 0.6532832 0.2268768 -1.8765
## as.factor(quin.packyrs)4 -0.0171095 0.9830360 0.2037235 -0.0840
## as.factor(quin.packyrs)5 0.1340713 1.1434743 0.2020525 0.6635
## age_bin2.Age>= 75 0.7532487 2.1238888 0.1483915 5.0761
## bmd_bin2.BMD<= -2.5 1.4764803 4.3775109 0.1753594 8.4197
## fall_bin2.Falls 1+ 0.2965626 1.3452268 0.1500106 1.9769
## fx50_bin2.Fx 1+ 0.2464051 1.2794178 0.1575451 1.5640
## drink_bin2.Excessive drinking -0.2742804 0.7601189 0.1522204 -1.8019
## activity_bin2.Less active 0.1519000 1.1640438 0.1593264 0.9534
## calci_bin2.Insufficient Calcium -0.0476843 0.9534348 0.1783006 -0.2674
## protein2 -0.0024239 0.9975790 0.0029674 -0.8169
## education -0.0319701 0.9685355 0.0410879 -0.7781
## BMI -0.0302729 0.9701807 0.0184090 -1.6445
## cvd 0.2484717 1.2820646 0.1538211 1.6153
## hypertension 0.4457491 1.5616596 0.1349507 3.3031
## copd -0.1092333 0.8965212 0.2172074 -0.5029
## diabetes 0.0325410 1.0330762 0.2221281 0.1465
## cancer -0.0640654 0.9379436 0.1722674 -0.3719
## renal -0.3398806 0.7118553 0.2681345 -1.2676
## parkinson 0.3518289 1.4216653 0.2245056 1.5671
## depression 0.0997464 1.1048907 0.2999141 0.3326
## rheumatoid 0.0777146 1.0808142 0.1346409 0.5772
## death 0.9137172 2.4935744 0.1681286 5.4346
## Pr(>|z|)
## as.factor(quin.packyrs)2 0.9673481
## as.factor(quin.packyrs)3 0.0605805 .
## as.factor(quin.packyrs)4 0.9330691
## as.factor(quin.packyrs)5 0.5069804
## age_bin2.Age>= 75 3.853e-07 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.0480479 *
## fx50_bin2.Fx 1+ 0.1178108
## drink_bin2.Excessive drinking 0.0715668 .
## activity_bin2.Less active 0.3403933
## calci_bin2.Insufficient Calcium 0.7891323
## protein2 0.4140140
## education 0.4365155
## BMI 0.1000808
## cvd 0.1062393
## hypertension 0.0009564 ***
## copd 0.6150355
## diabetes 0.8835294
## cancer 0.7099709
## renal 0.2049497
## parkinson 0.1170849
## depression 0.7394489
## rheumatoid 0.5638049
## death 5.491e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(quin.packyrs)2 0.99230 1.00776 0.68524 1.4369
## as.factor(quin.packyrs)3 0.65328 1.53073 0.41878 1.0191
## as.factor(quin.packyrs)4 0.98304 1.01726 0.65942 1.4655
## as.factor(quin.packyrs)5 1.14347 0.87453 0.76955 1.6991
## age_bin2.Age>= 75 2.12389 0.47083 1.58789 2.8408
## bmd_bin2.BMD<= -2.5 4.37751 0.22844 3.10428 6.1730
## fall_bin2.Falls 1+ 1.34523 0.74337 1.00255 1.8050
## fx50_bin2.Fx 1+ 1.27942 0.78161 0.93953 1.7423
## drink_bin2.Excessive drinking 0.76012 1.31558 0.56404 1.0244
## activity_bin2.Less active 1.16404 0.85907 0.85183 1.5907
## calci_bin2.Insufficient Calcium 0.95343 1.04884 0.67224 1.3523
## protein2 0.99758 1.00243 0.99179 1.0034
## education 0.96854 1.03249 0.89360 1.0498
## BMI 0.97018 1.03074 0.93580 1.0058
## cvd 1.28206 0.77999 0.94837 1.7332
## hypertension 1.56166 0.64034 1.19872 2.0345
## copd 0.89652 1.11542 0.58570 1.3723
## diabetes 1.03308 0.96798 0.66843 1.5966
## cancer 0.93794 1.06616 0.66918 1.3147
## renal 0.71186 1.40478 0.42088 1.2040
## parkinson 1.42167 0.70340 0.91558 2.2075
## depression 1.10489 0.90507 0.61381 1.9889
## rheumatoid 1.08081 0.92523 0.83013 1.4072
## death 2.49357 0.40103 1.79354 3.4668
##
## Concordance= 0.78 (se = 0.015 )
## Likelihood ratio test= 234.18 on 24 df, p=<2e-16
## Wald test = 255.52 on 24 df, p=<2e-16
## Score (logrank) test = 316.72 on 24 df, p=<2e-16Association for hip fracture
# Prevalence:
table1(~ age + age_bin + fnbmd + Tscore + bmd_bin + fall_bin + fx50_bin + smoke_packyrs + as.factor(smk_excess) + drink_bin + activity_bin | hipfx, data = men.smk, render.continuous = c(. = "Mean (SD)", . = "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=5755) |
1 (N=237) |
Overall (N=5992) |
|
|---|---|---|---|
| age | |||
| Mean (SD) | 73.5 (5.84) | 76.4 (6.09) | 73.7 (5.87) |
| Median [Q1, Q3] | 73.0 [69.0, 78.0] | 76.0 [72.0, 80.0] | 73.0 [69.0, 78.0] |
| age_bin | |||
| 1.Age< 75 | 3384 (58.8%) | 92 (38.8%) | 3476 (58.0%) |
| 2.Age>= 75 | 2371 (41.2%) | 145 (61.2%) | 2516 (42.0%) |
| fnbmd | |||
| Mean (SD) | 0.788 (0.127) | 0.689 (0.115) | 0.784 (0.128) |
| Median [Q1, Q3] | 0.778 [0.701, 0.863] | 0.671 [0.605, 0.752] | 0.774 [0.696, 0.860] |
| Tscore | |||
| Mean (SD) | -1.06 (0.928) | -1.79 (0.843) | -1.09 (0.935) |
| Median [Q1, Q3] | -1.14 [-1.70, -0.519] | -1.92 [-2.40, -1.33] | -1.17 [-1.73, -0.539] |
| bmd_bin | |||
| 1.BMD> -2.5 | 5506 (95.7%) | 191 (80.6%) | 5697 (95.1%) |
| 2.BMD<= -2.5 | 249 (4.3%) | 46 (19.4%) | 295 (4.9%) |
| fall_bin | |||
| 1.No falls | 4552 (79.1%) | 173 (73.0%) | 4725 (78.9%) |
| 2.Falls 1+ | 1203 (20.9%) | 64 (27.0%) | 1267 (21.1%) |
| fx50_bin | |||
| 1.No fx | 4778 (83.0%) | 183 (77.2%) | 4961 (82.8%) |
| 2.Fx 1+ | 977 (17.0%) | 54 (22.8%) | 1031 (17.2%) |
| smoke_packyrs | |||
| Mean (SD) | 18.1 (24.6) | 17.6 (25.3) | 18.1 (24.6) |
| Median [Q1, Q3] | 7.05 [0, 29.0] | 3.00 [0, 29.3] | 7.00 [0, 29.0] |
| as.factor(smk_excess) | |||
| 0 | 3784 (65.8%) | 156 (65.8%) | 3940 (65.8%) |
| 1 | 1971 (34.2%) | 81 (34.2%) | 2052 (34.2%) |
| drink_bin | |||
| 1.Less drinking | 3867 (67.2%) | 175 (73.8%) | 4042 (67.5%) |
| 2.Excessive drinking | 1888 (32.8%) | 62 (26.2%) | 1950 (32.5%) |
| activity_bin | |||
| 1.Proactive | 1492 (25.9%) | 53 (22.4%) | 1545 (25.8%) |
| 2.Less active | 4263 (74.1%) | 184 (77.6%) | 4447 (74.2%) |
# Association with No.pack-years:
hip.packyr.age = coxph(Surv(fu_hipfx, hipfx) ~ smoke_packyrs + age, data = men.smk)
summary(hip.packyr.age)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke_packyrs + age,
## data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke_packyrs 0.0052532 1.0052670 0.0026812 1.9593 0.05008 .
## age 0.1363256 1.1460550 0.0112991 12.0652 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_packyrs 1.0053 0.99476 1.000 1.0106
## age 1.1461 0.87256 1.121 1.1717
##
## Concordance= 0.723 (se = 0.016 )
## Likelihood ratio test= 140.09 on 2 df, p=<2e-16
## Wald test = 145.98 on 2 df, p=<2e-16
## Score (logrank) test = 155.31 on 2 df, p=<2e-16hip.packyr.all1 = coxph(Surv(fu_hipfx, hipfx) ~ smoke_packyrs + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(hip.packyr.all1)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke_packyrs + age_bin +
## bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke_packyrs 0.0042320 1.0042410 0.0026998 1.5675 0.11699
## age_bin2.Age>= 75 1.1191695 3.0623100 0.1383152 8.0914 5.896e-16 ***
## bmd_bin2.BMD<= -2.5 1.5801484 4.8556765 0.1679869 9.4064 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.3272941 1.3872094 0.1476993 2.2159 0.02669 *
## fx50_bin2.Fx 1+ 0.2479865 1.2814427 0.1570552 1.5790 0.11434
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_packyrs 1.0042 0.99578 0.99894 1.0096
## age_bin2.Age>= 75 3.0623 0.32655 2.33515 4.0159
## bmd_bin2.BMD<= -2.5 4.8557 0.20594 3.49349 6.7490
## fall_bin2.Falls 1+ 1.3872 0.72087 1.03853 1.8530
## fx50_bin2.Fx 1+ 1.2814 0.78037 0.94192 1.7434
##
## Concordance= 0.726 (se = 0.018 )
## Likelihood ratio test= 164.28 on 5 df, p=<2e-16
## Wald test = 199.39 on 5 df, p=<2e-16
## Score (logrank) test = 250.91 on 5 df, p=<2e-16hip.packyr.all2 = coxph(Surv(fu_hipfx, hipfx) ~ smoke_packyrs + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)
summary(hip.packyr.all2)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smoke_packyrs + age_bin +
## bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin +
## calci_bin + protein2 + education + BMI + cvd + hypertension +
## copd + diabetes + cancer + renal + parkinson + depression +
## rheumatoid + death, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z
## smoke_packyrs 0.0025955 1.0025989 0.0028672 0.9052
## age_bin2.Age>= 75 0.7686095 2.1567652 0.1480240 5.1925
## bmd_bin2.BMD<= -2.5 1.4824707 4.4038126 0.1750178 8.4704
## fall_bin2.Falls 1+ 0.2879961 1.3337522 0.1500882 1.9188
## fx50_bin2.Fx 1+ 0.2418719 1.2736310 0.1574717 1.5360
## drink_bin2.Excessive drinking -0.3017210 0.7395444 0.1512295 -1.9951
## activity_bin2.Less active 0.1525109 1.1647552 0.1592326 0.9578
## calci_bin2.Insufficient Calcium -0.0539710 0.9474595 0.1783150 -0.3027
## protein2 -0.0022535 0.9977490 0.0029624 -0.7607
## education -0.0272649 0.9731034 0.0409533 -0.6658
## BMI -0.0306834 0.9697826 0.0183208 -1.6748
## cvd 0.2535132 1.2885445 0.1536105 1.6504
## hypertension 0.4319385 1.5402404 0.1346891 3.2069
## copd -0.1049585 0.9003619 0.2166311 -0.4845
## diabetes 0.0394556 1.0402443 0.2217127 0.1780
## cancer -0.0615283 0.9403263 0.1722850 -0.3571
## renal -0.3425194 0.7099793 0.2679567 -1.2783
## parkinson 0.3548854 1.4260172 0.2243360 1.5819
## depression 0.0932486 1.0977346 0.2997711 0.3111
## rheumatoid 0.0708944 1.0734678 0.1344589 0.5273
## death 0.9130339 2.4918712 0.1678226 5.4405
## Pr(>|z|)
## smoke_packyrs 0.365341
## age_bin2.Age>= 75 2.075e-07 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.055004 .
## fx50_bin2.Fx 1+ 0.124546
## drink_bin2.Excessive drinking 0.046030 *
## activity_bin2.Less active 0.338170
## calci_bin2.Insufficient Calcium 0.762140
## protein2 0.446838
## education 0.505567
## BMI 0.093976 .
## cvd 0.098868 .
## hypertension 0.001342 **
## copd 0.628029
## diabetes 0.858756
## cancer 0.720994
## renal 0.201156
## parkinson 0.113664
## depression 0.755750
## rheumatoid 0.598015
## death 5.314e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke_packyrs 1.00260 0.99741 0.99698 1.0082
## age_bin2.Age>= 75 2.15677 0.46366 1.61363 2.8827
## bmd_bin2.BMD<= -2.5 4.40381 0.22708 3.12502 6.2059
## fall_bin2.Falls 1+ 1.33375 0.74976 0.99385 1.7899
## fx50_bin2.Fx 1+ 1.27363 0.78516 0.93541 1.7341
## drink_bin2.Excessive drinking 0.73954 1.35218 0.54984 0.9947
## activity_bin2.Less active 1.16476 0.85855 0.85250 1.5914
## calci_bin2.Insufficient Calcium 0.94746 1.05545 0.66800 1.3438
## protein2 0.99775 1.00226 0.99197 1.0036
## education 0.97310 1.02764 0.89805 1.0544
## BMI 0.96978 1.03116 0.93558 1.0052
## cvd 1.28854 0.77607 0.95356 1.7412
## hypertension 1.54024 0.64925 1.18288 2.0056
## copd 0.90036 1.11066 0.58887 1.3766
## diabetes 1.04024 0.96131 0.67362 1.6064
## cancer 0.94033 1.06346 0.67086 1.3180
## renal 0.70998 1.40849 0.41991 1.2004
## parkinson 1.42602 0.70125 0.91869 2.2135
## depression 1.09773 0.91097 0.61000 1.9754
## rheumatoid 1.07347 0.93156 0.82478 1.3971
## death 2.49187 0.40130 1.79339 3.4624
##
## Concordance= 0.776 (se = 0.015 )
## Likelihood ratio test= 229.49 on 21 df, p=<2e-16
## Wald test = 251.27 on 21 df, p=<2e-16
## Score (logrank) test = 312.9 on 21 df, p=<2e-16# Association with excess smoking:
hip.excess.age = coxph(Surv(fu_hipfx, hipfx) ~ smk_excess + age, data = men.smk)
summary(hip.excess.age)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smk_excess + age, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smk_excess 0.25025 1.28435 0.13783 1.8156 0.06943 .
## age 0.13617 1.14588 0.01131 12.0398 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smk_excess 1.2843 0.77861 0.9803 1.6827
## age 1.1459 0.87269 1.1208 1.1716
##
## Concordance= 0.722 (se = 0.016 )
## Likelihood ratio test= 139.74 on 2 df, p=<2e-16
## Wald test = 145.25 on 2 df, p=<2e-16
## Score (logrank) test = 154.95 on 2 df, p=<2e-16hip.excess.all1 = coxph(Surv(fu_hipfx, hipfx) ~ smk_excess + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk)
summary(hip.excess.all1)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smk_excess + age_bin +
## bmd_bin + fall_bin + fx50_bin, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smk_excess 0.19240 1.21215 0.13738 1.4005 0.16136
## age_bin2.Age>= 75 1.11510 3.04987 0.13820 8.0689 7.093e-16 ***
## bmd_bin2.BMD<= -2.5 1.57844 4.84737 0.16801 9.3951 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.32943 1.39018 0.14771 2.2303 0.02573 *
## fx50_bin2.Fx 1+ 0.24917 1.28296 0.15709 1.5862 0.11270
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smk_excess 1.2122 0.82498 0.92602 1.5867
## age_bin2.Age>= 75 3.0499 0.32788 2.32620 3.9987
## bmd_bin2.BMD<= -2.5 4.8474 0.20630 3.48738 6.7377
## fall_bin2.Falls 1+ 1.3902 0.71933 1.04074 1.8570
## fx50_bin2.Fx 1+ 1.2830 0.77945 0.94297 1.7455
##
## Concordance= 0.729 (se = 0.017 )
## Likelihood ratio test= 163.89 on 5 df, p=<2e-16
## Wald test = 199.24 on 5 df, p=<2e-16
## Score (logrank) test = 250.6 on 5 df, p=<2e-16hip.excess.all2 = coxph(Surv(fu_hipfx, hipfx) ~ smk_excess + age_bin + bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin + calci_bin + protein2 + education + BMI + cvd + hypertension + copd + diabetes + cancer + renal + parkinson + depression + rheumatoid + death, data = men.smk)
summary(hip.excess.all2)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ smk_excess + age_bin +
## bmd_bin + fall_bin + fx50_bin + drink_bin + activity_bin +
## calci_bin + protein2 + education + BMI + cvd + hypertension +
## copd + diabetes + cancer + renal + parkinson + depression +
## rheumatoid + death, data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z
## smk_excess 0.1258583 1.1341215 0.1439466 0.8743
## age_bin2.Age>= 75 0.7642097 2.1472968 0.1475123 5.1807
## bmd_bin2.BMD<= -2.5 1.4815682 4.3998401 0.1750314 8.4646
## fall_bin2.Falls 1+ 0.2879610 1.3337052 0.1501200 1.9182
## fx50_bin2.Fx 1+ 0.2423852 1.2742850 0.1574776 1.5392
## drink_bin2.Excessive drinking -0.3010834 0.7400161 0.1512290 -1.9909
## activity_bin2.Less active 0.1547754 1.1673957 0.1591672 0.9724
## calci_bin2.Insufficient Calcium -0.0535837 0.9478266 0.1782880 -0.3005
## protein2 -0.0022177 0.9977847 0.0029595 -0.7494
## education -0.0277586 0.9726231 0.0409180 -0.6784
## BMI -0.0308416 0.9696291 0.0183385 -1.6818
## cvd 0.2547328 1.2901169 0.1535478 1.6590
## hypertension 0.4304534 1.5379547 0.1347311 3.1949
## copd -0.0985056 0.9061906 0.2155987 -0.4569
## diabetes 0.0423579 1.0432678 0.2215286 0.1912
## cancer -0.0584386 0.9432362 0.1722641 -0.3392
## renal -0.3424385 0.7100368 0.2679153 -1.2782
## parkinson 0.3537174 1.4243527 0.2242661 1.5772
## depression 0.0897282 1.0938769 0.2998600 0.2992
## rheumatoid 0.0697488 1.0722388 0.1345492 0.5184
## death 0.9157343 2.4986094 0.1676026 5.4637
## Pr(>|z|)
## smk_excess 0.381933
## age_bin2.Age>= 75 2.211e-07 ***
## bmd_bin2.BMD<= -2.5 < 2.2e-16 ***
## fall_bin2.Falls 1+ 0.055085 .
## fx50_bin2.Fx 1+ 0.123762
## drink_bin2.Excessive drinking 0.046491 *
## activity_bin2.Less active 0.330848
## calci_bin2.Insufficient Calcium 0.763761
## protein2 0.453634
## education 0.497521
## BMI 0.092609 .
## cvd 0.097120 .
## hypertension 0.001399 **
## copd 0.647748
## diabetes 0.848363
## cancer 0.734430
## renal 0.201193
## parkinson 0.114744
## depression 0.764762
## rheumatoid 0.604187
## death 4.663e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smk_excess 1.13412 0.88174 0.85533 1.50379
## age_bin2.Age>= 75 2.14730 0.46570 1.60816 2.86718
## bmd_bin2.BMD<= -2.5 4.39984 0.22728 3.12212 6.20046
## fall_bin2.Falls 1+ 1.33371 0.74979 0.99375 1.78996
## fx50_bin2.Fx 1+ 1.27428 0.78475 0.93588 1.73505
## drink_bin2.Excessive drinking 0.74002 1.35132 0.55019 0.99533
## activity_bin2.Less active 1.16740 0.85661 0.85454 1.59478
## calci_bin2.Insufficient Calcium 0.94783 1.05505 0.66830 1.34427
## protein2 0.99778 1.00222 0.99201 1.00359
## education 0.97262 1.02815 0.89767 1.05384
## BMI 0.96963 1.03132 0.93540 1.00511
## cvd 1.29012 0.77512 0.95484 1.74313
## hypertension 1.53795 0.65021 1.18103 2.00275
## copd 0.90619 1.10352 0.59388 1.38273
## diabetes 1.04327 0.95853 0.67582 1.61050
## cancer 0.94324 1.06018 0.67296 1.32206
## renal 0.71004 1.40838 0.41998 1.20041
## parkinson 1.42435 0.70207 0.91774 2.21062
## depression 1.09388 0.91418 0.60775 1.96884
## rheumatoid 1.07224 0.93263 0.82369 1.39579
## death 2.49861 0.40022 1.79901 3.47026
##
## Concordance= 0.776 (se = 0.015 )
## Likelihood ratio test= 229.45 on 21 df, p=<2e-16
## Wald test = 251.46 on 21 df, p=<2e-16
## Score (logrank) test = 312.98 on 21 df, p=<2e-16Exploratory - Patterns of association between No. pack-years and fracture risk
library(smoothHR)## Loading required package: splines# Any fracture
fit = coxph(Surv(fu_anyfx, anyfx) ~ pspline(smoke_packyrs) + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk, x = TRUE)
hr1 = smoothHR(data = men.smk, coxfit = fit)
plot(hr1, predictor = "smoke_packyrs", xlim = c(0, 150), ref.label = "Ref")
# Hip fracture
fit2 = coxph(Surv(fu_hipfx, hipfx) ~ pspline(smoke_packyrs) + age_bin + bmd_bin + fall_bin + fx50_bin, data = men.smk, x = TRUE)
hr2 = smoothHR(data = men.smk, coxfit = fit2)## Warning: a global p-value of 0.046582968 was obtained when testing the proportional hazards assumptionplot(hr2, predictor = "smoke_packyrs", xlim = c(0, 150), ref.label = "Ref")
(3.2.2) Combination of risk factors
Data management
men.smk = men.smk %>% mutate(ex.group = case_when(age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smk_excess == 0 ~ 1,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smk_excess == 1 ~ 2,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smk_excess == 0 ~ 3,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smk_excess == 0 ~ 4,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smk_excess == 0 ~ 5,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smk_excess == 0 ~ 6,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smk_excess == 0 ~ 7,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smk_excess == 0 ~ 8,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smk_excess == 0 ~ 9,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smk_excess == 1 ~ 10,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smk_excess == 0 ~ 11,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smk_excess == 0 ~ 12,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smk_excess == 1 ~ 13,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smk_excess == 0 ~ 14,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smk_excess == 1 ~ 15,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smk_excess == 1 ~ 16,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smk_excess == 0 ~ 17,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smk_excess == 0 ~ 18,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "1.No fx" & smk_excess == 1 ~ 19,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smk_excess == 0 ~ 20,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smk_excess == 1 ~ 21,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smk_excess == 1 ~ 22,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smk_excess == 0 ~ 23,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smk_excess == 1 ~ 24,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smk_excess == 1 ~ 25,
age_bin == "1.Age< 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smk_excess == 1 ~ 26,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smk_excess == 0 ~ 27,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "1.No fx" & smk_excess == 1 ~ 28,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "1.No falls" & fx50_bin == "2.Fx 1+" & smk_excess == 1 ~ 29,
age_bin == "2.Age>= 75" & bmd_bin == "1.BMD> -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smk_excess == 1 ~ 30,
age_bin == "1.Age< 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smk_excess == 1 ~ 31,
age_bin == "2.Age>= 75" & bmd_bin == "2.BMD<= -2.5" & fall_bin == "2.Falls 1+" & fx50_bin == "2.Fx 1+" & smk_excess == 1 ~ 32))Association for any fracture
table1(~ as.factor(ex.group) | anyfx, data = men.smk)## Warning in table1.formula(~as.factor(ex.group) | anyfx, data = men.smk): 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) |
|
|---|---|---|---|
| as.factor(ex.group) | |||
| 1 | 1361 (27.7%) | 202 (18.6%) | 1563 (26.1%) |
| 2 | 688 (14.0%) | 120 (11.1%) | 808 (13.5%) |
| 3 | 196 (4.0%) | 53 (4.9%) | 249 (4.2%) |
| 4 | 254 (5.2%) | 53 (4.9%) | 307 (5.1%) |
| 5 | 22 (0.4%) | 11 (1.0%) | 33 (0.6%) |
| 6 | 798 (16.3%) | 178 (16.4%) | 976 (16.3%) |
| 7 | 52 (1.1%) | 19 (1.8%) | 71 (1.2%) |
| 8 | 222 (4.5%) | 73 (6.7%) | 295 (4.9%) |
| 9 | 140 (2.9%) | 42 (3.9%) | 182 (3.0%) |
| 10 | 418 (8.5%) | 74 (6.8%) | 492 (8.2%) |
| 11 | 5 (0.1%) | 3 (0.3%) | 8 (0.1%) |
| 12 | 4 (0.1%) | 4 (0.4%) | 8 (0.1%) |
| 13 | 23 (0.5%) | 7 (0.6%) | 30 (0.5%) |
| 14 | 57 (1.2%) | 20 (1.8%) | 77 (1.3%) |
| 15 | 132 (2.7%) | 32 (3.0%) | 164 (2.7%) |
| 16 | 114 (2.3%) | 39 (3.6%) | 153 (2.6%) |
| 17 | 14 (0.3%) | 7 (0.6%) | 21 (0.4%) |
| 18 | 12 (0.2%) | 15 (1.4%) | 27 (0.5%) |
| 19 | 21 (0.4%) | 13 (1.2%) | 34 (0.6%) |
| 20 | 73 (1.5%) | 27 (2.5%) | 100 (1.7%) |
| 21 | 126 (2.6%) | 21 (1.9%) | 147 (2.5%) |
| 22 | 64 (1.3%) | 16 (1.5%) | 80 (1.3%) |
| 23 | 2 (0.0%) | 1 (0.1%) | 3 (0.1%) |
| 24 | 1 (0.0%) | 4 (0.4%) | 5 (0.1%) |
| 25 | 4 (0.1%) | 2 (0.2%) | 6 (0.1%) |
| 26 | 45 (0.9%) | 14 (1.3%) | 59 (1.0%) |
| 27 | 11 (0.2%) | 9 (0.8%) | 20 (0.3%) |
| 28 | 4 (0.1%) | 3 (0.3%) | 7 (0.1%) |
| 29 | 7 (0.1%) | 6 (0.6%) | 13 (0.2%) |
| 30 | 33 (0.7%) | 12 (1.1%) | 45 (0.8%) |
| 31 | 1 (0.0%) | 2 (0.2%) | 3 (0.1%) |
| 32 | 4 (0.1%) | 2 (0.2%) | 6 (0.1%) |
options(digits = 8)
any.exgrp = coxph(Surv(fu_anyfx, anyfx) ~ as.factor(ex.group), data = men.smk)
summary(any.exgrp)## Call:
## coxph(formula = Surv(fu_anyfx, anyfx) ~ as.factor(ex.group),
## data = men.smk)
##
## n= 5992, number of events= 1084
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(ex.group)2 0.29944 1.34910 0.11532 2.5965 0.0094168 **
## as.factor(ex.group)3 0.52198 1.68536 0.15434 3.3820 0.0007196 ***
## as.factor(ex.group)4 0.34999 1.41905 0.15434 2.2676 0.0233539 *
## as.factor(ex.group)5 1.08449 2.95792 0.30964 3.5024 0.0004611 ***
## as.factor(ex.group)6 0.78265 2.18725 0.10351 7.5613 3.990e-14 ***
## as.factor(ex.group)7 1.35156 3.86345 0.24034 5.6234 1.872e-08 ***
## as.factor(ex.group)8 1.15994 3.18973 0.13723 8.4523 < 2.2e-16 ***
## as.factor(ex.group)9 1.05838 2.88169 0.17006 6.2235 4.862e-10 ***
## as.factor(ex.group)10 0.65059 1.91668 0.13667 4.7601 1.935e-06 ***
## as.factor(ex.group)11 1.10640 3.02347 0.58163 1.9022 0.0571392 .
## as.factor(ex.group)12 1.47589 4.37494 0.50495 2.9228 0.0034684 **
## as.factor(ex.group)13 0.91495 2.49666 0.38457 2.3792 0.0173515 *
## as.factor(ex.group)14 0.81047 2.24896 0.23442 3.4573 0.0005456 ***
## as.factor(ex.group)15 0.61916 1.85737 0.19034 3.2529 0.0011422 **
## as.factor(ex.group)16 0.92605 2.52451 0.17503 5.2908 1.218e-07 ***
## as.factor(ex.group)17 1.84167 6.30703 0.38506 4.7827 1.729e-06 ***
## as.factor(ex.group)18 2.35189 10.50543 0.26872 8.7523 < 2.2e-16 ***
## as.factor(ex.group)19 1.97998 7.24258 0.28707 6.8973 5.301e-12 ***
## as.factor(ex.group)20 1.52066 4.57525 0.20575 7.3908 1.459e-13 ***
## as.factor(ex.group)21 0.84509 2.32819 0.23005 3.6735 0.0002392 ***
## as.factor(ex.group)22 1.12929 3.09347 0.26030 4.3384 1.435e-05 ***
## as.factor(ex.group)23 0.97116 2.64102 1.00258 0.9687 0.3327108
## as.factor(ex.group)24 2.91044 18.36482 0.50559 5.7565 8.588e-09 ***
## as.factor(ex.group)25 1.54272 4.67729 0.71065 2.1709 0.0299422 *
## as.factor(ex.group)26 0.96160 2.61588 0.27643 3.4786 0.0005040 ***
## as.factor(ex.group)27 2.55562 12.87934 0.34173 7.4785 7.517e-14 ***
## as.factor(ex.group)28 2.28400 9.81583 0.58236 3.9220 8.783e-05 ***
## as.factor(ex.group)29 2.33269 10.30563 0.41488 5.6226 1.881e-08 ***
## as.factor(ex.group)30 1.42252 4.14758 0.29758 4.7803 1.751e-06 ***
## as.factor(ex.group)31 2.67306 14.48429 0.71134 3.7578 0.0001714 ***
## as.factor(ex.group)32 2.11178 8.26294 0.71118 2.9694 0.0029839 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(ex.group)2 1.3491 0.741236 1.07617 1.6912
## as.factor(ex.group)3 1.6854 0.593347 1.24543 2.2807
## as.factor(ex.group)4 1.4191 0.704694 1.04863 1.9203
## as.factor(ex.group)5 2.9579 0.338076 1.61220 5.4269
## as.factor(ex.group)6 2.1873 0.457195 1.78564 2.6792
## as.factor(ex.group)7 3.8634 0.258836 2.41209 6.1881
## as.factor(ex.group)8 3.1897 0.313506 2.43748 4.1741
## as.factor(ex.group)9 2.8817 0.347019 2.06486 4.0216
## as.factor(ex.group)10 1.9167 0.521736 1.46626 2.5055
## as.factor(ex.group)11 3.0235 0.330746 0.96699 9.4535
## as.factor(ex.group)12 4.3749 0.228575 1.62614 11.7703
## as.factor(ex.group)13 2.4967 0.400535 1.17494 5.3052
## as.factor(ex.group)14 2.2490 0.444650 1.42050 3.5606
## as.factor(ex.group)15 1.8574 0.538394 1.27903 2.6972
## as.factor(ex.group)16 2.5245 0.396117 1.79140 3.5576
## as.factor(ex.group)17 6.3070 0.158553 2.96523 13.4151
## as.factor(ex.group)18 10.5054 0.095189 6.20414 17.7888
## as.factor(ex.group)19 7.2426 0.138072 4.12612 12.7129
## as.factor(ex.group)20 4.5753 0.218567 3.05690 6.8478
## as.factor(ex.group)21 2.3282 0.429518 1.48320 3.6546
## as.factor(ex.group)22 3.0935 0.323262 1.85728 5.1524
## as.factor(ex.group)23 2.6410 0.378642 0.37015 18.8437
## as.factor(ex.group)24 18.3648 0.054452 6.81752 49.4706
## as.factor(ex.group)25 4.6773 0.213799 1.16168 18.8322
## as.factor(ex.group)26 2.6159 0.382280 1.52167 4.4969
## as.factor(ex.group)27 12.8793 0.077644 6.59194 25.1637
## as.factor(ex.group)28 9.8158 0.101876 3.13489 30.7349
## as.factor(ex.group)29 10.3056 0.097034 4.57013 23.2392
## as.factor(ex.group)30 4.1476 0.241105 2.31469 7.4318
## as.factor(ex.group)31 14.4843 0.069040 3.59255 58.3972
## as.factor(ex.group)32 8.2629 0.121022 2.05009 33.3040
##
## Concordance= 0.643 (se = 0.009 )
## Likelihood ratio test= 286.23 on 31 df, p=<2e-16
## Wald test = 338.05 on 31 df, p=<2e-16
## Score (logrank) test = 412.94 on 31 df, p=<2e-16Association for hip fracture
table1(~ as.factor(ex.group) | hipfx, data = men.smk)## Warning in table1.formula(~as.factor(ex.group) | hipfx, data = men.smk): Terms
## to the right of '|' in formula 'x' define table columns and are expected to be
## factors with meaningful labels.| 0 (N=5755) |
1 (N=237) |
Overall (N=5992) |
|
|---|---|---|---|
| as.factor(ex.group) | |||
| 1 | 1530 (26.6%) | 33 (13.9%) | 1563 (26.1%) |
| 2 | 786 (13.7%) | 22 (9.3%) | 808 (13.5%) |
| 3 | 241 (4.2%) | 8 (3.4%) | 249 (4.2%) |
| 4 | 299 (5.2%) | 8 (3.4%) | 307 (5.1%) |
| 5 | 31 (0.5%) | 2 (0.8%) | 33 (0.6%) |
| 6 | 938 (16.3%) | 38 (16.0%) | 976 (16.3%) |
| 7 | 62 (1.1%) | 9 (3.8%) | 71 (1.2%) |
| 8 | 274 (4.8%) | 21 (8.9%) | 295 (4.9%) |
| 9 | 170 (3.0%) | 12 (5.1%) | 182 (3.0%) |
| 10 | 471 (8.2%) | 21 (8.9%) | 492 (8.2%) |
| 11 | 6 (0.1%) | 2 (0.8%) | 8 (0.1%) |
| 12 | 6 (0.1%) | 2 (0.8%) | 8 (0.1%) |
| 13 | 26 (0.5%) | 4 (1.7%) | 30 (0.5%) |
| 14 | 75 (1.3%) | 2 (0.8%) | 77 (1.3%) |
| 15 | 160 (2.8%) | 4 (1.7%) | 164 (2.7%) |
| 16 | 152 (2.6%) | 1 (0.4%) | 153 (2.6%) |
| 17 | 18 (0.3%) | 3 (1.3%) | 21 (0.4%) |
| 18 | 23 (0.4%) | 4 (1.7%) | 27 (0.5%) |
| 19 | 26 (0.5%) | 8 (3.4%) | 34 (0.6%) |
| 20 | 92 (1.6%) | 8 (3.4%) | 100 (1.7%) |
| 21 | 142 (2.5%) | 5 (2.1%) | 147 (2.5%) |
| 22 | 75 (1.3%) | 5 (2.1%) | 80 (1.3%) |
| 23 | 2 (0.0%) | 1 (0.4%) | 3 (0.1%) |
| 24 | 4 (0.1%) | 1 (0.4%) | 5 (0.1%) |
| 25 | 6 (0.1%) | 0 (0%) | 6 (0.1%) |
| 26 | 58 (1.0%) | 1 (0.4%) | 59 (1.0%) |
| 27 | 17 (0.3%) | 3 (1.3%) | 20 (0.3%) |
| 28 | 5 (0.1%) | 2 (0.8%) | 7 (0.1%) |
| 29 | 9 (0.2%) | 4 (1.7%) | 13 (0.2%) |
| 30 | 43 (0.7%) | 2 (0.8%) | 45 (0.8%) |
| 31 | 2 (0.0%) | 1 (0.4%) | 3 (0.1%) |
| 32 | 6 (0.1%) | 0 (0%) | 6 (0.1%) |
options(digits = 8)
hip.exgrp = coxph(Surv(fu_hipfx, hipfx) ~ as.factor(ex.group), data = men.smk)## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 24,31 ; coefficient may be infinite.summary(hip.exgrp)## Call:
## coxph(formula = Surv(fu_hipfx, hipfx) ~ as.factor(ex.group),
## data = men.smk)
##
## n= 5992, number of events= 237
##
## coef exp(coef) se(coef) z Pr(>|z|)
## as.factor(ex.group)2 4.2016e-01 1.5222e+00 2.7537e-01 1.5258 0.1270585
## as.factor(ex.group)3 4.2415e-01 1.5283e+00 3.9409e-01 1.0763 0.2817991
## as.factor(ex.group)4 2.6181e-01 1.2993e+00 3.9410e-01 0.6643 0.5064774
## as.factor(ex.group)5 1.1510e+00 3.1614e+00 7.2825e-01 1.5805 0.1139879
## as.factor(ex.group)6 1.0719e+00 2.9210e+00 2.3935e-01 4.4785 7.519e-06 ***
## as.factor(ex.group)7 2.4055e+00 1.1084e+01 3.7708e-01 6.3792 1.781e-10 ***
## as.factor(ex.group)8 1.7300e+00 5.6405e+00 2.8070e-01 6.1630 7.138e-10 ***
## as.factor(ex.group)9 1.6044e+00 4.9750e+00 3.3831e-01 4.7424 2.112e-06 ***
## as.factor(ex.group)10 1.2740e+00 3.5752e+00 2.8105e-01 4.5331 5.812e-06 ***
## as.factor(ex.group)11 2.5136e+00 1.2349e+01 7.2824e-01 3.4516 0.0005573 ***
## as.factor(ex.group)12 2.5713e+00 1.3083e+01 7.2827e-01 3.5307 0.0004144 ***
## as.factor(ex.group)13 2.1735e+00 8.7893e+00 5.2973e-01 4.1031 4.076e-05 ***
## as.factor(ex.group)14 1.8471e-01 1.2029e+00 7.2822e-01 0.2536 0.7997685
## as.factor(ex.group)15 3.3795e-01 1.4021e+00 5.2952e-01 0.6382 0.5233333
## as.factor(ex.group)16 -9.9012e-01 3.7153e-01 1.0151e+00 -0.9754 0.3293670
## as.factor(ex.group)17 2.7600e+00 1.5800e+01 6.0431e-01 4.5671 4.944e-06 ***
## as.factor(ex.group)18 2.6843e+00 1.4648e+01 5.3093e-01 5.0559 4.284e-07 ***
## as.factor(ex.group)19 3.2925e+00 2.6909e+01 3.9663e-01 8.3012 < 2.2e-16 ***
## as.factor(ex.group)20 2.0477e+00 7.7498e+00 3.9579e-01 5.1736 2.297e-07 ***
## as.factor(ex.group)21 1.2725e+00 3.5698e+00 4.8158e-01 2.6423 0.0082340 **
## as.factor(ex.group)22 1.8087e+00 6.1022e+00 4.8142e-01 3.7570 0.0001720 ***
## as.factor(ex.group)23 2.8866e+00 1.7933e+01 1.0157e+00 2.8420 0.0044831 **
## as.factor(ex.group)24 2.6492e+00 1.4143e+01 1.0156e+00 2.6086 0.0090919 **
## as.factor(ex.group)25 -1.2588e+01 3.4141e-06 1.7981e+03 -0.0070 0.9944144
## as.factor(ex.group)26 7.3530e-02 1.0763e+00 1.0151e+00 0.0724 0.9422558
## as.factor(ex.group)27 3.1220e+00 2.2691e+01 6.0480e-01 5.1620 2.443e-07 ***
## as.factor(ex.group)28 3.6452e+00 3.8290e+01 7.3137e-01 4.9841 6.227e-07 ***
## as.factor(ex.group)29 3.6261e+00 3.7566e+01 5.3075e-01 6.8321 8.369e-12 ***
## as.factor(ex.group)30 1.5060e+00 4.5085e+00 7.2902e-01 2.0657 0.0388524 *
## as.factor(ex.group)31 3.4366e+00 3.1081e+01 1.0155e+00 3.3841 0.0007141 ***
## as.factor(ex.group)32 -1.2491e+01 3.7611e-06 2.5773e+03 -0.0048 0.9961330
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## as.factor(ex.group)2 1.5222e+00 6.5694e-01 0.88732 2.6114
## as.factor(ex.group)3 1.5283e+00 6.5433e-01 0.70593 3.3087
## as.factor(ex.group)4 1.2993e+00 7.6965e-01 0.60013 2.8130
## as.factor(ex.group)5 3.1614e+00 3.1632e-01 0.75856 13.1754
## as.factor(ex.group)6 2.9210e+00 3.4235e-01 1.82723 4.6694
## as.factor(ex.group)7 1.1084e+01 9.0224e-02 5.29306 23.2088
## as.factor(ex.group)8 5.6405e+00 1.7729e-01 3.25375 9.7781
## as.factor(ex.group)9 4.9750e+00 2.0101e-01 2.56340 9.6553
## as.factor(ex.group)10 3.5752e+00 2.7970e-01 2.06098 6.2020
## as.factor(ex.group)11 1.2349e+01 8.0979e-02 2.96312 51.4644
## as.factor(ex.group)12 1.3083e+01 7.6435e-02 3.13907 54.5272
## as.factor(ex.group)13 8.7893e+00 1.1378e-01 3.11207 24.8231
## as.factor(ex.group)14 1.2029e+00 8.3134e-01 0.28864 5.0128
## as.factor(ex.group)15 1.4021e+00 7.1323e-01 0.49664 3.9582
## as.factor(ex.group)16 3.7153e-01 2.6915e+00 0.05081 2.7168
## as.factor(ex.group)17 1.5800e+01 6.3293e-02 4.83339 51.6459
## as.factor(ex.group)18 1.4648e+01 6.8269e-02 5.17429 41.4671
## as.factor(ex.group)19 2.6909e+01 3.7162e-02 12.36769 58.5473
## as.factor(ex.group)20 7.7498e+00 1.2904e-01 3.56773 16.8342
## as.factor(ex.group)21 3.5698e+00 2.8013e-01 1.38904 9.1741
## as.factor(ex.group)22 6.1022e+00 1.6387e-01 2.37524 15.6773
## as.factor(ex.group)23 1.7933e+01 5.5763e-02 2.44952 131.2867
## as.factor(ex.group)24 1.4143e+01 7.0706e-02 1.93232 103.5163
## as.factor(ex.group)25 3.4141e-06 2.9290e+05 0.00000 Inf
## as.factor(ex.group)26 1.0763e+00 9.2911e-01 0.14719 7.8704
## as.factor(ex.group)27 2.2691e+01 4.4070e-02 6.93510 74.2440
## as.factor(ex.group)28 3.8290e+01 2.6116e-02 9.13154 160.5587
## as.factor(ex.group)29 3.7566e+01 2.6620e-02 13.27469 106.3083
## as.factor(ex.group)30 4.5085e+00 2.2180e-01 1.08017 18.8180
## as.factor(ex.group)31 3.1081e+01 3.2174e-02 4.24707 227.4640
## as.factor(ex.group)32 3.7611e-06 2.6588e+05 0.00000 Inf
##
## Concordance= 0.737 (se = 0.017 )
## Likelihood ratio test= 185.88 on 31 df, p=<2e-16
## Wald test = 223.68 on 31 df, p=<2e-16
## Score (logrank) test = 350.86 on 31 df, p=<2e-16Export data in csv format
write.csv(men.smk, "C:\\Thach\\Research projects\\PAR for lifestyle factors\\smoking_final.csv", row.names = FALSE)(4) Additional analysis: Post-fracture mortality risk
Data management
men.anyfx$fu = men.anyfx$time2end - men.anyfx$time2any
men.hipfx$fu = men.hipfx$time2end - men.hipfx$time2any(4.1) Following any fracture
men.anyfx$smoke.c = factor(men.anyfx$smoke, levels = c("Never", "Past", "Current"))
men.anyfx$fnbmd.sd = men.anyfx$fnbmd / 0.10
pany.age = coxph(Surv(fu, death) ~ smoke.c + age, data = men.anyfx)
summary(pany.age)## Call:
## coxph(formula = Surv(fu, death) ~ smoke.c + age, data = men.anyfx)
##
## n= 1084, number of events= 693
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast 0.1250210 1.1331722 0.0801782 1.5593 0.1189280
## smoke.cCurrent 0.6407731 1.8979476 0.1869827 3.4269 0.0006105 ***
## age 0.0949590 1.0996138 0.0066602 14.2576 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.1332 0.88248 0.96839 1.3260
## smoke.cCurrent 1.8979 0.52688 1.31560 2.7381
## age 1.0996 0.90941 1.08535 1.1141
##
## Concordance= 0.641 (se = 0.012 )
## Likelihood ratio test= 197.05 on 3 df, p=<2e-16
## Wald test = 205.12 on 3 df, p=<2e-16
## Score (logrank) test = 210.71 on 3 df, p=<2e-16pany.multi1 = coxph(Surv(fu, death) ~ smoke.c + age + fnbmd.sd + cvd + diabetes + renal + copd + cancer + depression, data = men.anyfx)
summary(pany.multi1)## Call:
## coxph(formula = Surv(fu, death) ~ smoke.c + age + fnbmd.sd +
## cvd + diabetes + renal + copd + cancer + depression, data = men.anyfx)
##
## n= 1084, number of events= 693
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast 0.1314561 1.1404878 0.0808410 1.6261 0.1039268
## smoke.cCurrent 0.6731738 1.9604495 0.1882506 3.5759 0.0003490 ***
## age 0.0923883 1.0967907 0.0069735 13.2484 < 2.2e-16 ***
## fnbmd.sd -0.0941156 0.9101776 0.0323780 -2.9068 0.0036518 **
## cvd 0.1394747 1.1496697 0.0900416 1.5490 0.1213809
## diabetes 0.3136288 1.3683817 0.1207121 2.5982 0.0093726 **
## renal -0.5895430 0.5545807 0.1393249 -4.2314 2.322e-05 ***
## copd 0.3675655 1.4442143 0.1112217 3.3048 0.0009504 ***
## cancer 0.0192445 1.0194309 0.0966124 0.1992 0.8421117
## depression 0.2634095 1.3013595 0.1733104 1.5199 0.1285433
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.14049 0.87682 0.97337 1.33630
## smoke.cCurrent 1.96045 0.51009 1.35555 2.83527
## age 1.09679 0.91175 1.08190 1.11188
## fnbmd.sd 0.91018 1.09869 0.85421 0.96981
## cvd 1.14967 0.86982 0.96367 1.37157
## diabetes 1.36838 0.73079 1.08008 1.73363
## renal 0.55458 1.80316 0.42206 0.72872
## copd 1.44421 0.69242 1.16134 1.79599
## cancer 1.01943 0.98094 0.84357 1.23195
## depression 1.30136 0.76843 0.92656 1.82776
##
## Concordance= 0.659 (se = 0.011 )
## Likelihood ratio test= 244.84 on 10 df, p=<2e-16
## Wald test = 243.92 on 10 df, p=<2e-16
## Score (logrank) test = 254.16 on 10 df, p=<2e-16pany.multi2 = coxph(Surv(fu, death) ~ smoke.c + age + fnbmd.sd + BMI + drink_bin + physical_bin + calci_bin + protein2 + cvd + diabetes + renal + copd + cancer + depression, data = men.anyfx)
summary(pany.multi2)## Call:
## coxph(formula = Surv(fu, death) ~ smoke.c + age + fnbmd.sd +
## BMI + drink_bin + physical_bin + calci_bin + protein2 + cvd +
## diabetes + renal + copd + cancer + depression, data = men.anyfx)
##
## n= 1084, number of events= 693
##
## coef exp(coef) se(coef) z
## smoke.cPast 0.1161753 1.1231928 0.0830216 1.3993
## smoke.cCurrent 0.6850054 1.9837825 0.1922742 3.5626
## age 0.0925601 1.0969790 0.0070580 13.1143
## fnbmd.sd -0.1071279 0.8984108 0.0347817 -3.0800
## BMI 0.0163228 1.0164568 0.0110481 1.4774
## drink_bin2.Excessive drinking 0.0562688 1.0578820 0.0841257 0.6689
## physical_bin2.Less active 0.0589665 1.0607397 0.0793367 0.7432
## calci_bin2.Insufficient Calcium -0.0654520 0.9366440 0.1064066 -0.6151
## protein2 -0.0017090 0.9982924 0.0018165 -0.9408
## cvd 0.1253799 1.1335790 0.0907256 1.3820
## diabetes 0.2909403 1.3376848 0.1226505 2.3721
## renal -0.6091720 0.5438010 0.1399476 -4.3529
## copd 0.3692164 1.4466006 0.1120072 3.2964
## cancer -0.0032143 0.9967909 0.0974182 -0.0330
## depression 0.2618845 1.2993764 0.1738727 1.5062
## Pr(>|z|)
## smoke.cPast 0.1617115
## smoke.cCurrent 0.0003671 ***
## age < 2.2e-16 ***
## fnbmd.sd 0.0020700 **
## BMI 0.1395607
## drink_bin2.Excessive drinking 0.5035812
## physical_bin2.Less active 0.4573344
## calci_bin2.Insufficient Calcium 0.5384809
## protein2 0.3467961
## cvd 0.1669813
## diabetes 0.0176869 *
## renal 1.344e-05 ***
## copd 0.0009795 ***
## cancer 0.9736787
## depression 0.1320196
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.12319 0.89032 0.95452 1.32167
## smoke.cCurrent 1.98378 0.50409 1.36091 2.89173
## age 1.09698 0.91159 1.08191 1.11226
## fnbmd.sd 0.89841 1.11308 0.83921 0.96179
## BMI 1.01646 0.98381 0.99468 1.03871
## drink_bin2.Excessive drinking 1.05788 0.94529 0.89708 1.24751
## physical_bin2.Less active 1.06074 0.94274 0.90798 1.23920
## calci_bin2.Insufficient Calcium 0.93664 1.06764 0.76033 1.15385
## protein2 0.99829 1.00171 0.99474 1.00185
## cvd 1.13358 0.88216 0.94891 1.35418
## diabetes 1.33768 0.74756 1.05185 1.70120
## renal 0.54380 1.83891 0.41335 0.71542
## copd 1.44660 0.69128 1.16147 1.80173
## cancer 0.99679 1.00322 0.82353 1.20650
## depression 1.29938 0.76960 0.92413 1.82699
##
## Concordance= 0.66 (se = 0.011 )
## Likelihood ratio test= 248.8 on 15 df, p=<2e-16
## Wald test = 246.74 on 15 df, p=<2e-16
## Score (logrank) test = 256.98 on 15 df, p=<2e-16(4.2) Following hip fracture
men.hipfx$smoke.c = factor(men.hipfx$smoke, levels = c("Never", "Past", "Current"))
men.hipfx$fnbmd.sd = men.hipfx$fnbmd / 0.10
phip.age = coxph(Surv(fu, death) ~ smoke.c + age, data = men.anyfx)
summary(phip.age)## Call:
## coxph(formula = Surv(fu, death) ~ smoke.c + age, data = men.anyfx)
##
## n= 1084, number of events= 693
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast 0.1250210 1.1331722 0.0801782 1.5593 0.1189280
## smoke.cCurrent 0.6407731 1.8979476 0.1869827 3.4269 0.0006105 ***
## age 0.0949590 1.0996138 0.0066602 14.2576 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.1332 0.88248 0.96839 1.3260
## smoke.cCurrent 1.8979 0.52688 1.31560 2.7381
## age 1.0996 0.90941 1.08535 1.1141
##
## Concordance= 0.641 (se = 0.012 )
## Likelihood ratio test= 197.05 on 3 df, p=<2e-16
## Wald test = 205.12 on 3 df, p=<2e-16
## Score (logrank) test = 210.71 on 3 df, p=<2e-16phip.multi1 = coxph(Surv(fu, death) ~ smoke.c + age + fnbmd.sd + cvd + diabetes + renal + copd + cancer + depression, data = men.anyfx)
summary(phip.multi1)## Call:
## coxph(formula = Surv(fu, death) ~ smoke.c + age + fnbmd.sd +
## cvd + diabetes + renal + copd + cancer + depression, data = men.anyfx)
##
## n= 1084, number of events= 693
##
## coef exp(coef) se(coef) z Pr(>|z|)
## smoke.cPast 0.1314561 1.1404878 0.0808410 1.6261 0.1039268
## smoke.cCurrent 0.6731738 1.9604495 0.1882506 3.5759 0.0003490 ***
## age 0.0923883 1.0967907 0.0069735 13.2484 < 2.2e-16 ***
## fnbmd.sd -0.0941156 0.9101776 0.0323780 -2.9068 0.0036518 **
## cvd 0.1394747 1.1496697 0.0900416 1.5490 0.1213809
## diabetes 0.3136288 1.3683817 0.1207121 2.5982 0.0093726 **
## renal -0.5895430 0.5545807 0.1393249 -4.2314 2.322e-05 ***
## copd 0.3675655 1.4442143 0.1112217 3.3048 0.0009504 ***
## cancer 0.0192445 1.0194309 0.0966124 0.1992 0.8421117
## depression 0.2634095 1.3013595 0.1733104 1.5199 0.1285433
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.14049 0.87682 0.97337 1.33630
## smoke.cCurrent 1.96045 0.51009 1.35555 2.83527
## age 1.09679 0.91175 1.08190 1.11188
## fnbmd.sd 0.91018 1.09869 0.85421 0.96981
## cvd 1.14967 0.86982 0.96367 1.37157
## diabetes 1.36838 0.73079 1.08008 1.73363
## renal 0.55458 1.80316 0.42206 0.72872
## copd 1.44421 0.69242 1.16134 1.79599
## cancer 1.01943 0.98094 0.84357 1.23195
## depression 1.30136 0.76843 0.92656 1.82776
##
## Concordance= 0.659 (se = 0.011 )
## Likelihood ratio test= 244.84 on 10 df, p=<2e-16
## Wald test = 243.92 on 10 df, p=<2e-16
## Score (logrank) test = 254.16 on 10 df, p=<2e-16phip.multi2 = coxph(Surv(fu, death) ~ smoke.c + age + fnbmd.sd + BMI + drink_bin + physical_bin + calci_bin + protein2 + cvd + diabetes + renal + copd + cancer + depression, data = men.anyfx)
summary(phip.multi2)## Call:
## coxph(formula = Surv(fu, death) ~ smoke.c + age + fnbmd.sd +
## BMI + drink_bin + physical_bin + calci_bin + protein2 + cvd +
## diabetes + renal + copd + cancer + depression, data = men.anyfx)
##
## n= 1084, number of events= 693
##
## coef exp(coef) se(coef) z
## smoke.cPast 0.1161753 1.1231928 0.0830216 1.3993
## smoke.cCurrent 0.6850054 1.9837825 0.1922742 3.5626
## age 0.0925601 1.0969790 0.0070580 13.1143
## fnbmd.sd -0.1071279 0.8984108 0.0347817 -3.0800
## BMI 0.0163228 1.0164568 0.0110481 1.4774
## drink_bin2.Excessive drinking 0.0562688 1.0578820 0.0841257 0.6689
## physical_bin2.Less active 0.0589665 1.0607397 0.0793367 0.7432
## calci_bin2.Insufficient Calcium -0.0654520 0.9366440 0.1064066 -0.6151
## protein2 -0.0017090 0.9982924 0.0018165 -0.9408
## cvd 0.1253799 1.1335790 0.0907256 1.3820
## diabetes 0.2909403 1.3376848 0.1226505 2.3721
## renal -0.6091720 0.5438010 0.1399476 -4.3529
## copd 0.3692164 1.4466006 0.1120072 3.2964
## cancer -0.0032143 0.9967909 0.0974182 -0.0330
## depression 0.2618845 1.2993764 0.1738727 1.5062
## Pr(>|z|)
## smoke.cPast 0.1617115
## smoke.cCurrent 0.0003671 ***
## age < 2.2e-16 ***
## fnbmd.sd 0.0020700 **
## BMI 0.1395607
## drink_bin2.Excessive drinking 0.5035812
## physical_bin2.Less active 0.4573344
## calci_bin2.Insufficient Calcium 0.5384809
## protein2 0.3467961
## cvd 0.1669813
## diabetes 0.0176869 *
## renal 1.344e-05 ***
## copd 0.0009795 ***
## cancer 0.9736787
## depression 0.1320196
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## smoke.cPast 1.12319 0.89032 0.95452 1.32167
## smoke.cCurrent 1.98378 0.50409 1.36091 2.89173
## age 1.09698 0.91159 1.08191 1.11226
## fnbmd.sd 0.89841 1.11308 0.83921 0.96179
## BMI 1.01646 0.98381 0.99468 1.03871
## drink_bin2.Excessive drinking 1.05788 0.94529 0.89708 1.24751
## physical_bin2.Less active 1.06074 0.94274 0.90798 1.23920
## calci_bin2.Insufficient Calcium 0.93664 1.06764 0.76033 1.15385
## protein2 0.99829 1.00171 0.99474 1.00185
## cvd 1.13358 0.88216 0.94891 1.35418
## diabetes 1.33768 0.74756 1.05185 1.70120
## renal 0.54380 1.83891 0.41335 0.71542
## copd 1.44660 0.69128 1.16147 1.80173
## cancer 0.99679 1.00322 0.82353 1.20650
## depression 1.29938 0.76960 0.92413 1.82699
##
## Concordance= 0.66 (se = 0.011 )
## Likelihood ratio test= 248.8 on 15 df, p=<2e-16
## Wald test = 246.74 on 15 df, p=<2e-16
## Score (logrank) test = 256.98 on 15 df, p=<2e-16