library("haven")Warning: package ‘haven’ was built under R version 4.3.3library("tidyverse")Warning: package ‘tidyverse’ was built under R version 4.3.3Warning: package ‘readr’ was built under R version 4.3.3Warning: package ‘forcats’ was built under R version 4.3.3Warning: package ‘lubridate’ was built under R version 4.3.3── Attaching core tidyverse packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
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ℹ Use the ]8;;http://conflicted.r-lib.org/conflicted package]8;; to force all conflicts to become errorslibrary("dplyr")
library("foreign")
library("survey")Warning: package ‘survey’ was built under R version 4.3.3Loading required package: grid
Loading required package: Matrix
Attaching package: ‘Matrix’
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expand, pack, unpack
Loading required package: survival
Attaching package: ‘survey’
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dotchartlibrary("ggplot2")
library("car")Loading required package: carData
Attaching package: ‘car’
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recode
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somelibrary("SciViews")Warning: package ‘SciViews’ was built under R version 4.3.3#list variable
colnames(Fulldat_mediation_pfas) [1] "SEQN" "chronological_age" "Gender" "Race"
[5] "Pregnancy" "Marital_Status" "Ratio_income_poverty" "Interview_Weight"
[9] "MEC_Weight" "psu" "Strata" "BMI"
[13] "Vitamin_A" "Vitamin_C" "Vitamin_E" "Zinc"
[17] "Selenium" "sleep_disorders" "Smoked_days" "now_smoke"
[21] "quit_smoking" "Avg_alcohol_drinks" "equipment_walk" "walk_difficulty"
[25] "had_cancer" "weight_2" "Perfluorohexane_sulfonic_acid" "Perfluorohexane_sulfonic_acid_comment"
[29] "Perfluorononanoic_acid" "Perfluorononanoic_acid_comment" "perfluorooctanoic_acid" "perfluorooctanoic_acid_comment"
[33] "perfluorooctane_sulfonic_acid" "perfluorooctane_sulfonic_acid_comment" "White_blood_cell_count" "Lymphocyte_percent"
[37] "Red_cell_distribution_width" "Mean_cell_volume" "Albumin" "Creatinine"
[41] "Glucose_serum" "Alkaline_phosphotase" "xb" "Phenotypic_Age"
[45] "cate_age" "age_binary" "BMI_cat" "income_cat"
[49] "triglycerides" "fastglucose" "TriGlu_BMI" "pfas_comment" Fulldat_Pheno <- Fulldat_mediation_pfas#Examine the pfas and Phenotypic_Age
ggplot(Fulldat_Pheno, aes(x = Perfluorohexane_sulfonic_acid)) +
geom_histogram(binwidth = 100, color = "skyblue", fill = "red", alpha = 0.7) +
labs(title = "Distribution of Perfluorohexane_sulfonic_acid",
x = "Perfluorohexane_sulfonic_acid",
y = "Frequency") +
theme_minimal()
ggplot(Fulldat_Pheno, aes(x = Perfluorohexane_sulfonic_acid, y = Phenotypic_Age)) +
geom_point() +
geom_smooth(method = "lm", se = FALSE) +
labs(x = "Perfluorohexane_sulfonic_acid", y = "Phenotypic_Age", title = "Scatter Plot Perfluorohexane_sulfonic_acid vs Phenotypic_Age with Regression Line")
# Define breaks for age groups
breaks <- c(20, 45, 65, Inf) # Breaks represent the age boundaries
# Define labels for the age groups
labels <- c("1", "2", "3")
# Categorize chronological_age into groups and assign custom labels
Fulldat_Pheno$cate_age <- cut(Fulldat_Pheno$chronological_age, breaks = breaks, labels = labels, include.lowest = TRUE)#sample density curves of pfas concentrations among accelerated and delayed age
Fulldat_Pheno <- Fulldat_Pheno %>% mutate(age_binary = case_when(
Phenotypic_Age-chronological_age >= 0 ~"accelerated",
Phenotypic_Age-chronological_age < 0 ~"delayed"
))
library(ggplot2)
cols <- c("#F76D5E", "#72D8FF")
#Perfluorohexane_sulfonic_acid
ggplot(Fulldat_Pheno, aes(x = Perfluorohexane_sulfonic_acid, colour = age_binary)) +
geom_density(lwd = 1.2, linetype = 1) +
scale_color_manual(values = cols)
#Perfluorohexane_sulfonic_acid_comment
ggplot(Fulldat_Pheno, aes(x = Perfluorononanoic_acid, colour = age_binary)) +
geom_density(lwd = 1.2, linetype = 1) +
scale_color_manual(values = cols)
#Perfluorononanoic_acid
ggplot(Fulldat_Pheno, aes(x = perfluorooctanoic_acid, colour = age_binary)) +
geom_density(lwd = 1.2, linetype = 1) +
scale_color_manual(values = cols)
#Perfluorononanoic_acid_comment
ggplot(Fulldat_Pheno, aes(x = perfluorooctane_sulfonic_acid, colour = age_binary)) +
geom_density(lwd = 1.2, linetype = 1) +
scale_color_manual(values = cols)
#Main model of regression for association, and adjust for covariates (Table 2) #Perfluorohexane_sulfonic_acid
Call:
svyglm(formula = Phenotypic_Age ~ Perfluorohexane_sulfonic_acid_comment,
design = des, family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 45.4975 0.2657 171.230 <2e-16 ***
Perfluorohexane_sulfonic_acid_comment 5.2534 2.1305 2.466 0.0149 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 377.0007)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 44.971890 46.023018
Perfluorohexane_sulfonic_acid_comment 1.039329 9.467451
Call:
svyglm(formula = Phenotypic_Age ~ Perfluorohexane_sulfonic_acid_comment +
Gender + Race + Marital_Status + Ratio_income_poverty, design = des,
family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 49.2560 0.9008 54.679 < 2e-16 ***
Perfluorohexane_sulfonic_acid_comment 6.3596 1.8483 3.441 0.000795 ***
Gender -2.0185 0.4008 -5.037 1.66e-06 ***
Race 1.1056 0.1625 6.803 4.07e-10 ***
Marital_Status2 19.0699 0.8281 23.027 < 2e-16 ***
Marital_Status3 -3.1127 0.7573 -4.110 7.19e-05 ***
Marital_Status4 -3.4031 1.0380 -3.278 0.001360 **
Marital_Status5 -18.6684 0.5279 -35.367 < 2e-16 ***
Marital_Status6 -15.0139 0.7636 -19.661 < 2e-16 ***
Marital_Status77 3.9023 6.7186 0.581 0.562431
Marital_Status99 24.6696 1.9110 12.909 < 2e-16 ***
Marital_StatusNone -31.6353 0.5365 -58.971 < 2e-16 ***
Ratio_income_poverty -0.3013 0.1332 -2.263 0.025431 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 269.9044)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 47.4727632 51.0393027
Perfluorohexane_sulfonic_acid_comment 2.7006431 10.0186161
Gender -2.8118785 -1.2252172
Race 0.7838548 1.4272723
Marital_Status2 17.4304736 20.7092267
Marital_Status3 -4.6117763 -1.6136183
Marital_Status4 -5.4579197 -1.3482062
Marital_Status5 -19.7133385 -17.6234541
Marital_Status6 -16.5256218 -13.5022627
Marital_Status77 -9.3978364 17.2024857
Marital_Status99 20.8865419 28.4526800
Marital_StatusNone -32.6972241 -30.5732818
Ratio_income_poverty -0.5649918 -0.0376875
Call:
svyglm(formula = Phenotypic_Age ~ Perfluorohexane_sulfonic_acid_comment +
Gender + Race + Marital_Status + Ratio_income_poverty + BMI +
sleep_disorders + Smoked_days + now_smoke + quit_smoking +
Avg_alcohol_drinks + had_cancer, design = des, family = "gaussian",
data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.360e+01 1.666e+00 32.170 < 2e-16 ***
Perfluorohexane_sulfonic_acid_comment 6.938e+00 1.685e+00 4.118 7.51e-05 ***
Gender -2.167e+00 3.754e-01 -5.772 7.59e-08 ***
Race 1.044e+00 1.509e-01 6.921 3.34e-10 ***
Marital_Status2 1.664e+01 7.706e-01 21.592 < 2e-16 ***
Marital_Status3 -2.754e+00 7.392e-01 -3.726 0.000312 ***
Marital_Status4 -2.844e+00 9.695e-01 -2.934 0.004093 **
Marital_Status5 -1.601e+01 4.902e-01 -32.660 < 2e-16 ***
Marital_Status6 -1.320e+01 7.551e-01 -17.482 < 2e-16 ***
Marital_Status77 -2.274e+00 4.920e+00 -0.462 0.644846
Marital_Status99 2.860e+01 4.468e-01 64.024 < 2e-16 ***
Marital_StatusNone 8.131e+00 5.139e+00 1.582 0.116549
Ratio_income_poverty -2.794e-01 1.297e-01 -2.154 0.033495 *
BMI 1.828e-01 2.437e-02 7.502 1.87e-11 ***
sleep_disorders2 -3.483e+00 4.911e-01 -7.093 1.43e-10 ***
sleep_disorders7 2.541e+01 5.839e+00 4.353 3.07e-05 ***
sleep_disorders9 -6.457e+00 1.021e+01 -0.632 0.528534
sleep_disordersNone -3.813e+00 7.186e-01 -5.306 6.03e-07 ***
Smoked_days 1.477e+00 6.129e-01 2.410 0.017659 *
now_smoke 2.405e+00 2.845e-01 8.454 1.47e-13 ***
quit_smoking 2.106e-04 2.878e-05 7.318 4.70e-11 ***
Avg_alcohol_drinks2 4.719e+00 4.839e-01 9.753 < 2e-16 ***
Avg_alcohol_drinks9 6.143e+00 5.696e+00 1.078 0.283245
Avg_alcohol_drinksNone -3.823e-01 5.627e-01 -0.679 0.498395
had_cancer2 -1.359e+01 5.484e-01 -24.781 < 2e-16 ***
had_cancer9 -6.299e+00 4.171e+00 -1.510 0.133941
had_cancerNone -4.943e+01 5.179e+00 -9.545 5.06e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 244.5291)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 5.030027e+01 5.690590e+01
Perfluorohexane_sulfonic_acid_comment 3.598050e+00 1.027767e+01
Gender -2.910682e+00 -1.422594e+00
Race 7.450227e-01 1.343050e+00
Marital_Status2 1.511057e+01 1.816535e+01
Marital_Status3 -4.219357e+00 -1.288781e+00
Marital_Status4 -4.765659e+00 -9.223144e-01
Marital_Status5 -1.698296e+01 -1.503947e+01
Marital_Status6 -1.469834e+01 -1.170468e+01
Marital_Status77 -1.202639e+01 7.478069e+00
Marital_Status99 2.771837e+01 2.948952e+01
Marital_StatusNone -2.055954e+00 1.831711e+01
Ratio_income_poverty -5.364708e-01 -2.223747e-02
BMI 1.345141e-01 2.311232e-01
sleep_disorders2 -4.456752e+00 -2.509972e+00
sleep_disorders7 1.384063e+01 3.698710e+01
sleep_disorders9 -2.670012e+01 1.378565e+01
sleep_disordersNone -5.237270e+00 -2.388390e+00
Smoked_days 2.620016e-01 2.691841e+00
now_smoke 1.841021e+00 2.968824e+00
quit_smoking 1.535791e-04 2.676827e-04
Avg_alcohol_drinks2 3.760201e+00 5.678488e+00
Avg_alcohol_drinks9 -5.147558e+00 1.743261e+01
Avg_alcohol_drinksNone -1.497630e+00 7.331279e-01
had_cancer2 -1.467606e+01 -1.250213e+01
had_cancer9 -1.456638e+01 1.969087e+00
had_cancerNone -5.969745e+01 -3.916659e+01
Call:
svyglm(formula = Phenotypic_Age ~ ln(Perfluorohexane_sulfonic_acid),
design = des, family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 44.9501 0.2767 162.427 < 2e-16 ***
ln(Perfluorohexane_sulfonic_acid) 1.7040 0.2593 6.571 1.04e-09 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 374.8053)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 44.402761 45.49753
ln(Perfluorohexane_sulfonic_acid) 1.191031 2.21689
Call:
svyglm(formula = Phenotypic_Age ~ ln(Perfluorohexane_sulfonic_acid) +
Gender + Race + Marital_Status + Ratio_income_poverty, design = des,
family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 48.0439 0.9771 49.172 < 2e-16 ***
ln(Perfluorohexane_sulfonic_acid) 1.4648 0.2652 5.523 1.91e-07 ***
Gender -1.1838 0.4710 -2.514 0.01325 *
Race 1.0604 0.1538 6.896 2.54e-10 ***
Marital_Status2 18.6290 0.8280 22.499 < 2e-16 ***
Marital_Status3 -3.0927 0.7319 -4.226 4.62e-05 ***
Marital_Status4 -3.5611 1.0720 -3.322 0.00118 **
Marital_Status5 -18.7433 0.5347 -35.052 < 2e-16 ***
Marital_Status6 -15.1011 0.7862 -19.208 < 2e-16 ***
Marital_Status77 3.2268 6.9485 0.464 0.64320
Marital_Status99 23.0357 3.4388 6.699 6.86e-10 ***
Marital_StatusNone -31.6577 0.5538 -57.160 < 2e-16 ***
Ratio_income_poverty -0.4140 0.1353 -3.060 0.00272 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 268.7147)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 46.1096892 49.9780639
ln(Perfluorohexane_sulfonic_acid) 0.9398148 1.9897695
Gender -2.1161471 -0.2515361
Race 0.7560248 1.3648672
Marital_Status2 16.9898922 20.2681162
Marital_Status3 -4.5414770 -1.6438950
Marital_Status4 -5.6833547 -1.4389165
Marital_Status5 -19.8018521 -17.6847432
Marital_Status6 -16.6574133 -13.5448147
Marital_Status77 -10.5285297 16.9821114
Marital_Status99 16.2282848 29.8432140
Marital_StatusNone -32.7541129 -30.5613166
Ratio_income_poverty -0.6818136 -0.1462218
Call:
svyglm(formula = Phenotypic_Age ~ ln(Perfluorohexane_sulfonic_acid) +
Gender + Race + Marital_Status + Ratio_income_poverty + BMI +
sleep_disorders + Smoked_days + now_smoke + quit_smoking +
Avg_alcohol_drinks + had_cancer, design = des, family = "gaussian",
data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.206e+01 1.708e+00 30.470 < 2e-16 ***
ln(Perfluorohexane_sulfonic_acid) 1.451e+00 2.589e-01 5.604 1.62e-07 ***
Gender -1.356e+00 4.396e-01 -3.085 0.002585 **
Race 9.981e-01 1.442e-01 6.920 3.35e-10 ***
Marital_Status2 1.622e+01 7.728e-01 20.989 < 2e-16 ***
Marital_Status3 -2.732e+00 7.164e-01 -3.814 0.000228 ***
Marital_Status4 -2.975e+00 9.932e-01 -2.996 0.003396 **
Marital_Status5 -1.606e+01 4.949e-01 -32.445 < 2e-16 ***
Marital_Status6 -1.326e+01 7.753e-01 -17.101 < 2e-16 ***
Marital_Status77 -3.179e+00 4.984e+00 -0.638 0.524949
Marital_Status99 2.692e+01 1.635e+00 16.459 < 2e-16 ***
Marital_StatusNone 7.971e+00 4.931e+00 1.617 0.108894
Ratio_income_poverty -3.883e-01 1.299e-01 -2.990 0.003457 **
BMI 1.884e-01 2.478e-02 7.601 1.14e-11 ***
sleep_disorders2 -3.521e+00 4.906e-01 -7.178 9.44e-11 ***
sleep_disorders7 2.578e+01 5.924e+00 4.351 3.08e-05 ***
sleep_disorders9 -8.691e+00 1.111e+01 -0.782 0.435890
sleep_disordersNone -4.079e+00 7.252e-01 -5.625 1.47e-07 ***
Smoked_days 1.542e+00 6.087e-01 2.533 0.012748 *
now_smoke 2.403e+00 2.806e-01 8.563 8.39e-14 ***
quit_smoking 2.066e-04 2.881e-05 7.173 9.64e-11 ***
Avg_alcohol_drinks2 4.757e+00 4.732e-01 10.052 < 2e-16 ***
Avg_alcohol_drinks9 4.971e+00 5.943e+00 0.837 0.404681
Avg_alcohol_drinksNone -2.132e-01 5.747e-01 -0.371 0.711337
had_cancer2 -1.340e+01 5.452e-01 -24.570 < 2e-16 ***
had_cancer9 -6.369e+00 4.197e+00 -1.518 0.132030
had_cancerNone -4.885e+01 4.984e+00 -9.801 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 243.4841)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 4.866969e+01 5.544259e+01
ln(Perfluorohexane_sulfonic_acid) 9.377143e-01 1.964246e+00
Gender -2.227671e+00 -4.848634e-01
Race 7.122201e-01 1.283995e+00
Marital_Status2 1.468770e+01 1.775125e+01
Marital_Status3 -4.152113e+00 -1.312013e+00
Marital_Status4 -4.943942e+00 -1.006615e+00
Marital_Status5 -1.703658e+01 -1.507481e+01
Marital_Status6 -1.479508e+01 -1.172161e+01
Marital_Status77 -1.305766e+01 6.700152e+00
Marital_Status99 2.367587e+01 3.015924e+01
Marital_StatusNone -1.802881e+00 1.774486e+01
Ratio_income_poverty -6.457039e-01 -1.308644e-01
BMI 1.392669e-01 2.375231e-01
sleep_disorders2 -4.493391e+00 -2.548635e+00
sleep_disorders7 1.403328e+01 3.751731e+01
sleep_disorders9 -3.071748e+01 1.333621e+01
sleep_disordersNone -5.516646e+00 -2.641730e+00
Smoked_days 3.352220e-01 2.748148e+00
now_smoke 1.846845e+00 2.959428e+00
quit_smoking 1.495331e-04 2.637292e-04
Avg_alcohol_drinks2 3.818748e+00 5.694655e+00
Avg_alcohol_drinks9 -6.807792e+00 1.675051e+01
Avg_alcohol_drinksNone -1.352444e+00 9.259578e-01
had_cancer2 -1.447581e+01 -1.231452e+01
had_cancer9 -1.468743e+01 1.949527e+00
had_cancerNone -5.872693e+01 -3.896839e+01#“Perfluorononanoic_acid” “Perfluorononanoic_acid_comment”
Call:
svyglm(formula = Phenotypic_Age ~ Perfluorononanoic_acid_comment,
design = des, family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 45.5414 0.2615 174.168 <2e-16 ***
Perfluorononanoic_acid_comment 1.2082 2.5944 0.466 0.642
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 377.3081)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 45.024247 46.058640
Perfluorononanoic_acid_comment -3.923447 6.339837
Call:
svyglm(formula = Phenotypic_Age ~ Perfluorononanoic_acid_comment +
Gender + Race + Marital_Status + Ratio_income_poverty, design = des,
family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 49.4083 0.8867 55.720 < 2e-16 ***
Perfluorononanoic_acid_comment -0.2160 2.6031 -0.083 0.93401
Gender -1.9979 0.4018 -4.972 2.19e-06 ***
Race 1.0983 0.1606 6.840 3.38e-10 ***
Marital_Status2 19.0132 0.8261 23.016 < 2e-16 ***
Marital_Status3 -3.1164 0.7584 -4.109 7.23e-05 ***
Marital_Status4 -3.4432 1.0412 -3.307 0.00124 **
Marital_Status5 -18.6525 0.5232 -35.653 < 2e-16 ***
Marital_Status6 -15.0491 0.7634 -19.713 < 2e-16 ***
Marital_Status77 3.7791 6.7237 0.562 0.57511
Marital_Status99 24.5692 1.9554 12.565 < 2e-16 ***
Marital_StatusNone -31.7153 0.5324 -59.565 < 2e-16 ***
Ratio_income_poverty -0.3278 0.1318 -2.486 0.01426 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 270.3862)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 47.6529558 51.16367498
Perfluorononanoic_acid_comment -5.3691701 4.93718479
Gender -2.7933500 -1.20238269
Race 0.7804058 1.41614677
Marital_Status2 17.3778665 20.64854724
Marital_Status3 -4.6177951 -1.61501657
Marital_Status4 -5.5043023 -1.38211792
Marital_Status5 -19.6881718 -17.61685561
Marital_Status6 -16.5603238 -13.53780818
Marital_Status77 -9.5311433 17.08938908
Marital_Status99 20.6982854 28.44003952
Marital_StatusNone -32.7693283 -30.66126672
Ratio_income_poverty -0.5887259 -0.06679675
Call:
svyglm(formula = Phenotypic_Age ~ Perfluorononanoic_acid_comment +
Gender + Race + Marital_Status + Ratio_income_poverty + BMI +
sleep_disorders + Smoked_days + now_smoke + quit_smoking +
Avg_alcohol_drinks + had_cancer, design = des, family = "gaussian",
data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.371e+01 1.668e+00 32.196 < 2e-16 ***
Perfluorononanoic_acid_comment -1.468e-01 2.612e+00 -0.056 0.955287
Gender -2.146e+00 3.769e-01 -5.693 1.08e-07 ***
Race 1.037e+00 1.496e-01 6.933 3.15e-10 ***
Marital_Status2 1.658e+01 7.685e-01 21.576 < 2e-16 ***
Marital_Status3 -2.755e+00 7.419e-01 -3.714 0.000325 ***
Marital_Status4 -2.888e+00 9.757e-01 -2.960 0.003784 **
Marital_Status5 -1.600e+01 4.843e-01 -33.042 < 2e-16 ***
Marital_Status6 -1.325e+01 7.555e-01 -17.532 < 2e-16 ***
Marital_Status77 -2.384e+00 4.944e+00 -0.482 0.630627
Marital_Status99 2.852e+01 4.493e-01 63.483 < 2e-16 ***
Marital_StatusNone 8.011e+00 5.105e+00 1.569 0.119479
Ratio_income_poverty -3.077e-01 1.273e-01 -2.417 0.017322 *
BMI 1.824e-01 2.470e-02 7.385 3.37e-11 ***
sleep_disorders2 -3.485e+00 4.914e-01 -7.092 1.44e-10 ***
sleep_disorders7 2.534e+01 5.870e+00 4.317 3.52e-05 ***
sleep_disorders9 -6.549e+00 1.023e+01 -0.640 0.523540
sleep_disordersNone -3.714e+00 7.220e-01 -5.144 1.21e-06 ***
Smoked_days 1.483e+00 6.165e-01 2.406 0.017848 *
now_smoke 2.412e+00 2.862e-01 8.427 1.69e-13 ***
quit_smoking 2.102e-04 2.891e-05 7.269 6.01e-11 ***
Avg_alcohol_drinks2 4.747e+00 4.837e-01 9.814 < 2e-16 ***
Avg_alcohol_drinks9 6.022e+00 5.714e+00 1.054 0.294293
Avg_alcohol_drinksNone -3.523e-01 5.656e-01 -0.623 0.534651
had_cancer2 -1.356e+01 5.494e-01 -24.687 < 2e-16 ***
had_cancer9 -6.390e+00 4.164e+00 -1.535 0.127799
had_cancerNone -4.933e+01 5.148e+00 -9.582 4.16e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 245.1134)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 5.040380e+01 5.701736e+01
Perfluorononanoic_acid_comment -5.324830e+00 5.031212e+00
Gender -2.892928e+00 -1.398779e+00
Race 7.403662e-01 1.333261e+00
Marital_Status2 1.505775e+01 1.810425e+01
Marital_Status3 -4.225821e+00 -1.284569e+00
Marital_Status4 -4.821782e+00 -9.538893e-01
Marital_Status5 -1.696270e+01 -1.504270e+01
Marital_Status6 -1.474270e+01 -1.174774e+01
Marital_Status77 -1.218393e+01 7.415766e+00
Marital_Status99 2.763399e+01 2.941528e+01
Marital_StatusNone -2.107035e+00 1.812943e+01
Ratio_income_poverty -5.601056e-01 -5.536987e-02
BMI 1.334508e-01 2.313700e-01
sleep_disorders2 -4.458878e+00 -2.510945e+00
sleep_disorders7 1.370591e+01 3.697819e+01
sleep_disorders9 -2.683254e+01 1.373467e+01
sleep_disordersNone -5.145365e+00 -2.283136e+00
Smoked_days 2.610178e-01 2.705117e+00
now_smoke 1.844862e+00 2.979623e+00
quit_smoking 1.528584e-04 2.674856e-04
Avg_alcohol_drinks2 3.788423e+00 5.706087e+00
Avg_alcohol_drinks9 -5.304266e+00 1.734784e+01
Avg_alcohol_drinksNone -1.473485e+00 7.688174e-01
had_cancer2 -1.465125e+01 -1.247334e+01
had_cancer9 -1.464305e+01 1.863459e+00
had_cancerNone -5.953878e+01 -3.912861e+01
Call:
svyglm(formula = Phenotypic_Age ~ ln(Perfluorononanoic_acid),
design = des, family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 45.8115 0.2650 172.864 < 2e-16 ***
ln(Perfluorononanoic_acid) 1.1868 0.3181 3.731 0.000282 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 376.4274)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 45.2872993 46.335675
ln(Perfluorononanoic_acid) 0.5575797 1.816049
Call:
svyglm(formula = Phenotypic_Age ~ ln(Perfluorononanoic_acid) +
Gender + Race + Marital_Status + Ratio_income_poverty, design = des,
family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 49.8365 0.8777 56.784 < 2e-16 ***
ln(Perfluorononanoic_acid) 1.4919 0.3206 4.654 8.35e-06 ***
Gender -1.7424 0.4169 -4.180 5.52e-05 ***
Race 0.9944 0.1586 6.270 5.68e-09 ***
Marital_Status2 19.0601 0.8092 23.554 < 2e-16 ***
Marital_Status3 -2.9211 0.7363 -3.967 0.000123 ***
Marital_Status4 -3.5726 1.0594 -3.372 0.000999 ***
Marital_Status5 -18.7916 0.5329 -35.261 < 2e-16 ***
Marital_Status6 -15.2221 0.7684 -19.810 < 2e-16 ***
Marital_Status77 3.0795 6.5941 0.467 0.641324
Marital_Status99 24.7334 2.6459 9.348 5.42e-16 ***
Marital_StatusNone -31.4723 0.5533 -56.877 < 2e-16 ***
Ratio_income_poverty -0.3960 0.1341 -2.953 0.003773 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 269.0123)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 48.0990893 51.5739038
ln(Perfluorononanoic_acid) 0.8572949 2.1265535
Gender -2.5676015 -0.9171946
Race 0.6804731 1.3084225
Marital_Status2 17.4581706 20.6620056
Marital_Status3 -4.3785418 -1.4635644
Marital_Status4 -5.6697286 -1.4755199
Marital_Status5 -19.8465980 -17.7366468
Marital_Status6 -16.7432478 -13.7009814
Marital_Status77 -9.9741959 16.1332790
Marital_Status99 19.4954567 29.9712801
Marital_StatusNone -32.5677348 -30.3769613
Ratio_income_poverty -0.6614237 -0.1305526
Call:
svyglm(formula = Phenotypic_Age ~ ln(Perfluorononanoic_acid) +
Gender + Race + Marital_Status + Ratio_income_poverty + BMI +
sleep_disorders + Smoked_days + now_smoke + quit_smoking +
Avg_alcohol_drinks + had_cancer, design = des, family = "gaussian",
data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.414e+01 1.660e+00 32.610 < 2e-16 ***
ln(Perfluorononanoic_acid) 1.473e+00 3.279e-01 4.493 1.77e-05 ***
Gender -1.880e+00 3.926e-01 -4.787 5.40e-06 ***
Race 9.334e-01 1.492e-01 6.254 8.18e-09 ***
Marital_Status2 1.663e+01 7.572e-01 21.963 < 2e-16 ***
Marital_Status3 -2.581e+00 7.202e-01 -3.584 0.00051 ***
Marital_Status4 -3.013e+00 9.889e-01 -3.047 0.00291 **
Marital_Status5 -1.613e+01 4.937e-01 -32.673 < 2e-16 ***
Marital_Status6 -1.340e+01 7.593e-01 -17.646 < 2e-16 ***
Marital_Status77 -2.996e+00 4.896e+00 -0.612 0.54183
Marital_Status99 2.856e+01 9.085e-01 31.437 < 2e-16 ***
Marital_StatusNone 7.297e+00 5.308e+00 1.375 0.17210
Ratio_income_poverty -3.733e-01 1.295e-01 -2.883 0.00475 **
BMI 1.873e-01 2.477e-02 7.561 1.39e-11 ***
sleep_disorders2 -3.473e+00 4.865e-01 -7.139 1.14e-10 ***
sleep_disorders7 2.493e+01 5.830e+00 4.277 4.11e-05 ***
sleep_disorders9 -6.574e+00 1.003e+01 -0.655 0.51371
sleep_disordersNone -4.147e+00 7.147e-01 -5.802 6.62e-08 ***
Smoked_days 1.410e+00 6.166e-01 2.287 0.02417 *
now_smoke 2.371e+00 2.846e-01 8.331 2.77e-13 ***
quit_smoking 2.096e-04 2.894e-05 7.243 6.81e-11 ***
Avg_alcohol_drinks2 4.665e+00 4.753e-01 9.814 < 2e-16 ***
Avg_alcohol_drinks9 6.060e+00 5.505e+00 1.101 0.27344
Avg_alcohol_drinksNone -4.837e-01 5.651e-01 -0.856 0.39392
had_cancer2 -1.346e+01 5.537e-01 -24.303 < 2e-16 ***
had_cancer9 -6.241e+00 4.245e+00 -1.470 0.14443
had_cancerNone -4.781e+01 5.346e+00 -8.943 1.17e-14 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 243.7777)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 5.085168e+01 5.743378e+01
ln(Perfluorononanoic_acid) 8.233669e-01 2.123459e+00
Gender -2.657943e+00 -1.101408e+00
Race 6.376090e-01 1.229277e+00
Marital_Status2 1.512848e+01 1.813013e+01
Marital_Status3 -4.008573e+00 -1.153344e+00
Marital_Status4 -4.973168e+00 -1.052664e+00
Marital_Status5 -1.711076e+01 -1.515339e+01
Marital_Status6 -1.490352e+01 -1.189348e+01
Marital_Status77 -1.270038e+01 6.708115e+00
Marital_Status99 2.676008e+01 3.036174e+01
Marital_StatusNone -3.225155e+00 1.781874e+01
Ratio_income_poverty -6.300218e-01 -1.166713e-01
BMI 1.381673e-01 2.363476e-01
sleep_disorders2 -4.437358e+00 -2.508677e+00
sleep_disorders7 1.337698e+01 3.648874e+01
sleep_disorders9 -2.646322e+01 1.331427e+01
sleep_disordersNone -5.563410e+00 -2.730111e+00
Smoked_days 1.877602e-01 2.632309e+00
now_smoke 1.807140e+00 2.935562e+00
quit_smoking 1.522552e-04 2.669793e-04
Avg_alcohol_drinks2 3.722634e+00 5.607075e+00
Avg_alcohol_drinks9 -4.852176e+00 1.697205e+01
Avg_alcohol_drinksNone -1.603748e+00 6.364000e-01
had_cancer2 -1.455501e+01 -1.235985e+01
had_cancer9 -1.465538e+01 2.173593e+00
had_cancerNone -5.841045e+01 -3.721531e+01#“perfluorooctanoic_acid” “perfluorooctanoic_acid_comment”
Call:
svyglm(formula = Phenotypic_Age ~ perfluorooctanoic_acid_comment,
design = des, family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 43.4970 0.3398 127.989 < 2e-16 ***
perfluorooctanoic_acid_comment 4.8208 0.6522 7.391 2.29e-11 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 368.6468)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 42.824027 44.170014
perfluorooctanoic_acid_comment 3.529163 6.112411
Call:
svyglm(formula = Phenotypic_Age ~ perfluorooctanoic_acid_comment +
Gender + Race + Marital_Status + Ratio_income_poverty, design = des,
family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 48.6231 0.9517 51.091 < 2e-16 ***
perfluorooctanoic_acid_comment 1.0269 0.5881 1.746 0.083659 .
Gender -1.9816 0.4411 -4.492 1.79e-05 ***
Race 1.1316 0.1764 6.413 3.96e-09 ***
Marital_Status2 18.4843 0.8791 21.026 < 2e-16 ***
Marital_Status3 -4.0251 0.7837 -5.136 1.27e-06 ***
Marital_Status4 -4.3082 1.1254 -3.828 0.000218 ***
Marital_Status5 -18.4174 0.5604 -32.864 < 2e-16 ***
Marital_Status6 -14.8550 0.8167 -18.190 < 2e-16 ***
Marital_Status77 3.1743 7.8695 0.403 0.687484
Marital_Status99 24.2465 2.0403 11.884 < 2e-16 ***
Marital_StatusNone -31.7592 0.6082 -52.218 < 2e-16 ***
Ratio_income_poverty -0.3628 0.1416 -2.563 0.011777 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 268.6396)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 46.7365077 50.50977163
perfluorooctanoic_acid_comment -0.1389475 2.19283640
Gender -2.8560787 -1.10707493
Race 0.7818230 1.48140113
Marital_Status2 16.7415141 20.22702458
Marital_Status3 -5.5786397 -2.47155834
Marital_Status4 -6.5391902 -2.07716944
Marital_Status5 -19.5283399 -17.30642230
Marital_Status6 -16.4739221 -13.23606475
Marital_Status77 -12.4260398 18.77459054
Marital_Status99 20.2017921 28.29121053
Marital_StatusNone -32.9648792 -30.55349003
Ratio_income_poverty -0.6435140 -0.08216326
Call:
svyglm(formula = Phenotypic_Age ~ perfluorooctanoic_acid_comment +
Gender + Race + Marital_Status + Ratio_income_poverty + BMI +
sleep_disorders + Smoked_days + now_smoke + quit_smoking +
Avg_alcohol_drinks + had_cancer, design = des, family = "gaussian",
data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.296e+01 1.838e+00 28.815 < 2e-16 ***
perfluorooctanoic_acid_comment 1.112e+00 6.032e-01 1.844 0.068409 .
Gender -2.077e+00 4.164e-01 -4.988 2.82e-06 ***
Race 1.057e+00 1.640e-01 6.442 5.15e-09 ***
Marital_Status2 1.623e+01 8.193e-01 19.809 < 2e-16 ***
Marital_Status3 -3.554e+00 7.634e-01 -4.655 1.07e-05 ***
Marital_Status4 -3.570e+00 1.060e+00 -3.368 0.001104 **
Marital_Status5 -1.573e+01 5.173e-01 -30.410 < 2e-16 ***
Marital_Status6 -1.314e+01 8.275e-01 -15.882 < 2e-16 ***
Marital_Status77 -5.521e+00 4.164e+00 -1.326 0.188067
Marital_Status99 2.830e+01 6.412e-01 44.136 < 2e-16 ***
Marital_StatusNone 8.031e+00 5.051e+00 1.590 0.115236
Ratio_income_poverty -3.569e-01 1.345e-01 -2.654 0.009363 **
BMI 1.808e-01 2.704e-02 6.687 1.67e-09 ***
sleep_disorders2 -3.431e+00 5.495e-01 -6.243 1.27e-08 ***
sleep_disorders7 2.923e+01 5.282e+00 5.534 2.88e-07 ***
sleep_disorders9 -1.535e+01 4.720e+00 -3.252 0.001600 **
sleep_disordersNone -2.622e+00 7.605e-01 -3.447 0.000852 ***
Smoked_days 1.501e+00 6.899e-01 2.176 0.032102 *
now_smoke 2.415e+00 3.167e-01 7.623 2.06e-11 ***
quit_smoking 1.951e-04 3.204e-05 6.090 2.51e-08 ***
Avg_alcohol_drinks2 4.581e+00 4.817e-01 9.510 2.23e-15 ***
Avg_alcohol_drinks9 4.568e+00 6.797e+00 0.672 0.503185
Avg_alcohol_drinksNone -3.825e-01 6.088e-01 -0.628 0.531334
had_cancer2 -1.382e+01 5.773e-01 -23.943 < 2e-16 ***
had_cancer9 -5.711e+00 4.080e+00 -1.400 0.164900
had_cancerNone -4.957e+01 5.119e+00 -9.683 9.56e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 244.8431)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 4.931154e+01 5.661133e+01
perfluorooctanoic_acid_comment -8.569895e-02 2.309792e+00
Gender -2.903926e+00 -1.250193e+00
Race 7.308472e-01 1.382265e+00
Marital_Status2 1.460290e+01 1.785699e+01
Marital_Status3 -5.069810e+00 -2.037927e+00
Marital_Status4 -5.675450e+00 -1.465041e+00
Marital_Status5 -1.675687e+01 -1.470252e+01
Marital_Status6 -1.478649e+01 -1.149985e+01
Marital_Status77 -1.378947e+01 2.746940e+00
Marital_Status99 2.702719e+01 2.957383e+01
Marital_StatusNone -1.999356e+00 1.806129e+01
Ratio_income_poverty -6.239755e-01 -8.983096e-02
BMI 1.271258e-01 2.345281e-01
sleep_disorders2 -4.521899e+00 -2.339490e+00
sleep_disorders7 1.873945e+01 3.971794e+01
sleep_disorders9 -2.472120e+01 -5.974376e+00
sleep_disordersNone -4.132198e+00 -1.111631e+00
Smoked_days 1.311019e-01 2.871068e+00
now_smoke 1.785671e+00 3.043676e+00
quit_smoking 1.315034e-04 2.587553e-04
Avg_alcohol_drinks2 3.624314e+00 5.537489e+00
Avg_alcohol_drinks9 -8.929097e+00 1.806552e+01
Avg_alcohol_drinksNone -1.591526e+00 8.264603e-01
had_cancer2 -1.496865e+01 -1.267585e+01
had_cancer9 -1.381372e+01 2.390968e+00
had_cancerNone -5.973221e+01 -3.940254e+01
Call:
svyglm(formula = Phenotypic_Age ~ ln(perfluorooctanoic_acid),
design = des, family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 44.8316 0.4040 110.96 <2e-16 ***
ln(perfluorooctanoic_acid) 0.3687 0.2926 1.26 0.21
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 373.8409)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 44.0315522 45.6316902
ln(perfluorooctanoic_acid) -0.2107285 0.9482098
Call:
svyglm(formula = Phenotypic_Age ~ ln(perfluorooctanoic_acid) +
Gender + Race + Marital_Status + Ratio_income_poverty, design = des,
family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 47.9006 1.0881 44.022 < 2e-16 ***
ln(perfluorooctanoic_acid) 1.0906 0.3048 3.579 0.000521 ***
Gender -1.7227 0.4734 -3.639 0.000423 ***
Race 1.1234 0.1697 6.618 1.49e-09 ***
Marital_Status2 18.5885 0.8811 21.097 < 2e-16 ***
Marital_Status3 -3.9228 0.7731 -5.074 1.65e-06 ***
Marital_Status4 -4.6474 1.1495 -4.043 9.98e-05 ***
Marital_Status5 -18.8897 0.5717 -33.040 < 2e-16 ***
Marital_Status6 -15.2718 0.8330 -18.334 < 2e-16 ***
Marital_Status77 2.7362 7.6610 0.357 0.721681
Marital_Status99 25.1055 2.4386 10.295 < 2e-16 ***
Marital_StatusNone -31.5737 0.6294 -50.164 < 2e-16 ***
Ratio_income_poverty -0.4393 0.1474 -2.981 0.003555 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 268.1669)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 45.7435471 50.0576093
ln(perfluorooctanoic_acid) 0.4864688 1.6948291
Gender -2.6612329 -0.7842608
Race 0.7869198 1.4599153
Marital_Status2 16.8418376 20.3351974
Marital_Status3 -5.4553366 -2.3903074
Marital_Status4 -6.9261555 -2.3686236
Marital_Status5 -20.0230972 -17.7563525
Marital_Status6 -16.9230382 -13.6204864
Marital_Status77 -12.4509465 17.9232520
Marital_Status99 20.2712285 29.9397799
Marital_StatusNone -32.8213875 -30.3259242
Ratio_income_poverty -0.7315016 -0.1471948
Call:
svyglm(formula = Phenotypic_Age ~ ln(perfluorooctanoic_acid) +
Gender + Race + Marital_Status + Ratio_income_poverty + BMI +
sleep_disorders + Smoked_days + now_smoke + quit_smoking +
Avg_alcohol_drinks + had_cancer, design = des, family = "gaussian",
data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.208e+01 1.862e+00 27.972 < 2e-16 ***
ln(perfluorooctanoic_acid) 1.105e+00 3.127e-01 3.533 0.000643 ***
Gender -1.791e+00 4.351e-01 -4.116 8.34e-05 ***
Race 1.048e+00 1.597e-01 6.560 3.00e-09 ***
Marital_Status2 1.631e+01 8.234e-01 19.807 < 2e-16 ***
Marital_Status3 -3.482e+00 7.552e-01 -4.611 1.27e-05 ***
Marital_Status4 -3.856e+00 1.075e+00 -3.587 0.000536 ***
Marital_Status5 -1.615e+01 5.310e-01 -30.423 < 2e-16 ***
Marital_Status6 -1.347e+01 8.423e-01 -15.992 < 2e-16 ***
Marital_Status77 -5.917e+00 3.991e+00 -1.483 0.141577
Marital_Status99 2.885e+01 7.889e-01 36.576 < 2e-16 ***
Marital_StatusNone 7.781e+00 5.171e+00 1.505 0.135804
Ratio_income_poverty -4.330e-01 1.402e-01 -3.090 0.002642 **
BMI 1.889e-01 2.699e-02 6.998 3.94e-10 ***
sleep_disorders2 -3.449e+00 5.539e-01 -6.226 1.37e-08 ***
sleep_disorders7 2.772e+01 5.141e+00 5.391 5.28e-07 ***
sleep_disorders9 -1.493e+01 5.137e+00 -2.907 0.004557 **
sleep_disordersNone -3.748e+00 7.813e-01 -4.798 6.10e-06 ***
Smoked_days 1.579e+00 6.884e-01 2.294 0.024012 *
now_smoke 2.400e+00 3.134e-01 7.657 1.76e-11 ***
quit_smoking 2.024e-04 3.308e-05 6.117 2.23e-08 ***
Avg_alcohol_drinks2 4.379e+00 4.736e-01 9.247 8.00e-15 ***
Avg_alcohol_drinks9 4.691e+00 6.554e+00 0.716 0.475961
Avg_alcohol_drinksNone -5.088e-01 6.133e-01 -0.830 0.408931
had_cancer2 -1.369e+01 5.826e-01 -23.496 < 2e-16 ***
had_cancer9 -5.402e+00 4.309e+00 -1.254 0.213126
had_cancerNone -4.807e+01 5.242e+00 -9.170 1.17e-14 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 244.4102)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 4.838692e+01 5.578203e+01
ln(perfluorooctanoic_acid) 4.836300e-01 1.725405e+00
Gender -2.654762e+00 -9.267156e-01
Race 7.305456e-01 1.364857e+00
Marital_Status2 1.467382e+01 1.794399e+01
Marital_Status3 -4.982126e+00 -1.982805e+00
Marital_Status4 -5.991155e+00 -1.721224e+00
Marital_Status5 -1.720782e+01 -1.509904e+01
Marital_Status6 -1.514341e+01 -1.179805e+01
Marital_Status77 -1.384154e+01 2.008414e+00
Marital_Status99 2.728769e+01 3.042079e+01
Marital_StatusNone -2.488092e+00 1.804933e+01
Ratio_income_poverty -7.113428e-01 -1.547212e-01
BMI 1.352668e-01 2.424430e-01
sleep_disorders2 -4.548613e+00 -2.348750e+00
sleep_disorders7 1.750853e+01 3.792741e+01
sleep_disorders9 -2.513449e+01 -4.733652e+00
sleep_disordersNone -5.299727e+00 -2.196806e+00
Smoked_days 2.124947e-01 2.946469e+00
now_smoke 1.777479e+00 3.022344e+00
quit_smoking 1.366793e-04 2.680645e-04
Avg_alcohol_drinks2 3.438904e+00 5.319773e+00
Avg_alcohol_drinks9 -8.323861e+00 1.770511e+01
Avg_alcohol_drinksNone -1.726741e+00 7.091856e-01
had_cancer2 -1.484640e+01 -1.253245e+01
had_cancer9 -1.395908e+01 3.155119e+00
had_cancerNone -5.848372e+01 -3.766326e+01#“perfluorooctane_sulfonic_acid” “perfluorooctane_sulfonic_acid_comment”
Call:
svyglm(formula = Phenotypic_Age ~ perfluorooctane_sulfonic_acid_comment,
design = des, family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 45.1300 0.2921 154.485 <2e-16 ***
perfluorooctane_sulfonic_acid_comment 8.2645 4.1835 1.975 0.0505 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 373.6055)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 44.55146084 45.70846
perfluorooctane_sulfonic_acid_comment -0.02003231 16.54910
Call:
svyglm(formula = Phenotypic_Age ~ perfluorooctane_sulfonic_acid_comment +
Gender + Race + Marital_Status + Ratio_income_poverty, design = des,
family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 48.9900 0.9920 49.383 < 2e-16 ***
perfluorooctane_sulfonic_acid_comment 6.0391 4.7517 1.271 0.206513
Gender -2.0110 0.4441 -4.528 1.55e-05 ***
Race 1.1387 0.1740 6.545 2.11e-09 ***
Marital_Status2 18.6466 0.8916 20.914 < 2e-16 ***
Marital_Status3 -3.9369 0.7867 -5.004 2.22e-06 ***
Marital_Status4 -4.4218 1.1446 -3.863 0.000192 ***
Marital_Status5 -18.6068 0.5722 -32.516 < 2e-16 ***
Marital_Status6 -15.0727 0.8157 -18.478 < 2e-16 ***
Marital_Status77 3.0601 7.7856 0.393 0.695069
Marital_Status99 24.9361 2.0223 12.331 < 2e-16 ***
Marital_StatusNone -31.7364 0.6162 -51.507 < 2e-16 ***
Ratio_income_poverty -0.3624 0.1433 -2.529 0.012911 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 268.6965)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 47.0234501 50.95663964
perfluorooctane_sulfonic_acid_comment -3.3806965 15.45888283
Gender -2.8913930 -1.13055144
Race 0.7937839 1.48356267
Marital_Status2 16.8791331 20.41411782
Marital_Status3 -5.4964917 -2.37724892
Marital_Status4 -6.6909315 -2.15276546
Marital_Status5 -19.7412017 -17.47244445
Marital_Status6 -16.6897819 -13.45559537
Marital_Status77 -12.3740014 18.49419343
Marital_Status99 20.9271719 28.94496734
Marital_StatusNone -32.9579030 -30.51497045
Ratio_income_poverty -0.6465513 -0.07828686
Call:
svyglm(formula = Phenotypic_Age ~ perfluorooctane_sulfonic_acid_comment +
Gender + Race + Marital_Status + Ratio_income_poverty + BMI +
sleep_disorders + Smoked_days + now_smoke + quit_smoking +
Avg_alcohol_drinks + had_cancer, design = des, family = "gaussian",
data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.328e+01 1.856e+00 28.713 < 2e-16 ***
perfluorooctane_sulfonic_acid_comment 5.988e+00 4.621e+00 1.296 0.198248
Gender -2.092e+00 4.162e-01 -5.026 2.42e-06 ***
Race 1.067e+00 1.620e-01 6.586 2.67e-09 ***
Marital_Status2 1.638e+01 8.298e-01 19.744 < 2e-16 ***
Marital_Status3 -3.478e+00 7.660e-01 -4.540 1.68e-05 ***
Marital_Status4 -3.668e+00 1.074e+00 -3.415 0.000948 ***
Marital_Status5 -1.591e+01 5.289e-01 -30.074 < 2e-16 ***
Marital_Status6 -1.333e+01 8.290e-01 -16.082 < 2e-16 ***
Marital_Status77 -5.618e+00 4.134e+00 -1.359 0.177448
Marital_Status99 2.886e+01 5.300e-01 54.461 < 2e-16 ***
Marital_StatusNone 7.956e+00 4.993e+00 1.593 0.114447
Ratio_income_poverty -3.595e-01 1.360e-01 -2.643 0.009653 **
BMI 1.840e-01 2.682e-02 6.861 7.49e-10 ***
sleep_disorders2 -3.471e+00 5.513e-01 -6.297 9.95e-09 ***
sleep_disorders7 2.848e+01 5.253e+00 5.421 4.65e-07 ***
sleep_disorders9 -1.523e+01 5.058e+00 -3.011 0.003355 **
sleep_disordersNone -3.090e+00 7.597e-01 -4.067 9.96e-05 ***
Smoked_days 1.578e+00 6.898e-01 2.287 0.024473 *
now_smoke 2.417e+00 3.166e-01 7.636 1.94e-11 ***
quit_smoking 2.010e-04 3.261e-05 6.165 1.80e-08 ***
Avg_alcohol_drinks2 4.431e+00 4.832e-01 9.169 1.17e-14 ***
Avg_alcohol_drinks9 4.672e+00 6.711e+00 0.696 0.488117
Avg_alcohol_drinksNone -4.906e-01 6.146e-01 -0.798 0.426763
had_cancer2 -1.381e+01 5.788e-01 -23.858 < 2e-16 ***
had_cancer9 -5.813e+00 4.145e+00 -1.402 0.164146
had_cancerNone -4.897e+01 5.057e+00 -9.683 9.59e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 244.8899)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 4.959764e+01 5.696767e+01
perfluorooctane_sulfonic_acid_comment -3.188605e+00 1.516505e+01
Gender -2.918587e+00 -1.265543e+00
Race 7.451252e-01 1.388491e+00
Marital_Status2 1.473506e+01 1.803059e+01
Marital_Status3 -4.998726e+00 -1.956586e+00
Marital_Status4 -5.800657e+00 -1.534791e+00
Marital_Status5 -1.695634e+01 -1.485574e+01
Marital_Status6 -1.497856e+01 -1.168603e+01
Marital_Status77 -1.382801e+01 2.591541e+00
Marital_Status99 2.781024e+01 2.991506e+01
Marital_StatusNone -1.958724e+00 1.786992e+01
Ratio_income_poverty -6.295623e-01 -8.934096e-02
BMI 1.307222e-01 2.372250e-01
sleep_disorders2 -4.566216e+00 -2.376607e+00
sleep_disorders7 1.804657e+01 3.890945e+01
sleep_disorders9 -2.527290e+01 -5.184195e+00
sleep_disordersNone -4.598652e+00 -1.581262e+00
Smoked_days 2.076731e-01 2.947365e+00
now_smoke 1.788702e+00 3.045976e+00
quit_smoking 1.362674e-04 2.657666e-04
Avg_alcohol_drinks2 3.471371e+00 5.390625e+00
Avg_alcohol_drinks9 -8.655889e+00 1.799921e+01
Avg_alcohol_drinksNone -1.711016e+00 7.298495e-01
had_cancer2 -1.495956e+01 -1.266064e+01
had_cancer9 -1.404479e+01 2.418666e+00
had_cancerNone -5.900902e+01 -3.892452e+01
Call:
svyglm(formula = Phenotypic_Age ~ ln(perfluorooctane_sulfonic_acid),
design = des, family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 39.9300 0.6158 64.838 < 2e-16 ***
ln(perfluorooctane_sulfonic_acid) 2.4350 0.2560 9.513 2.86e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 368.1841)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 38.710501 41.14959
ln(perfluorooctane_sulfonic_acid) 1.928069 2.94185
Call:
svyglm(formula = Phenotypic_Age ~ ln(perfluorooctane_sulfonic_acid) +
Gender + Race + Marital_Status + Ratio_income_poverty, design = des,
family = "gaussian", data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 43.3600 1.2791 33.899 < 2e-16 ***
ln(perfluorooctane_sulfonic_acid) 2.3205 0.2942 7.887 2.81e-12 ***
Gender -1.0073 0.4800 -2.099 0.038203 *
Race 0.9607 0.1666 5.765 7.99e-08 ***
Marital_Status2 18.4688 0.8438 21.888 < 2e-16 ***
Marital_Status3 -3.5860 0.7324 -4.896 3.48e-06 ***
Marital_Status4 -4.6732 1.1741 -3.980 0.000126 ***
Marital_Status5 -18.8366 0.5794 -32.510 < 2e-16 ***
Marital_Status6 -15.2923 0.8444 -18.110 < 2e-16 ***
Marital_Status77 2.0856 7.6690 0.272 0.786179
Marital_Status99 24.5176 3.4097 7.191 9.17e-11 ***
Marital_StatusNone -30.5657 0.6580 -46.450 < 2e-16 ***
Ratio_income_poverty -0.4764 0.1441 -3.307 0.001284 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 264.0313)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 40.8243954 45.89566825
ln(perfluorooctane_sulfonic_acid) 1.7372956 2.90377872
Gender -1.9588334 -0.05579815
Race 0.6303138 1.29101713
Marital_Status2 16.7960761 20.14147095
Marital_Status3 -5.0379457 -2.13407188
Marital_Status4 -7.0006294 -2.34568695
Marital_Status5 -19.9852174 -17.68797215
Marital_Status6 -16.9662745 -13.61830960
Marital_Status77 -13.1172948 17.28858513
Marital_Status99 17.7583249 31.27687510
Marital_StatusNone -31.8701419 -29.26120375
Ratio_income_poverty -0.7619654 -0.19084041
Call:
svyglm(formula = Phenotypic_Age ~ ln(perfluorooctane_sulfonic_acid) +
Gender + Race + Marital_Status + Ratio_income_poverty + BMI +
sleep_disorders + Smoked_days + now_smoke + quit_smoking +
Avg_alcohol_drinks + had_cancer, design = des, family = "gaussian",
data = Fulldat_Pheno)
Survey design:
svydesign(id = ~psu, strata = ~Strata, weights = ~weight_2, nest = TRUE,
data = Fulldat_Pheno)
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 4.672e+01 2.020e+00 23.125 < 2e-16 ***
ln(perfluorooctane_sulfonic_acid) 2.865e+00 3.255e-01 8.800 7.05e-14 ***
Gender -7.650e-01 4.508e-01 -1.697 0.093046 .
Race 8.270e-01 1.584e-01 5.221 1.08e-06 ***
Marital_Status2 1.609e+01 7.839e-01 20.521 < 2e-16 ***
Marital_Status3 -3.158e+00 7.102e-01 -4.447 2.41e-05 ***
Marital_Status4 -3.818e+00 1.068e+00 -3.573 0.000561 ***
Marital_Status5 -1.599e+01 5.477e-01 -29.193 < 2e-16 ***
Marital_Status6 -1.338e+01 8.505e-01 -15.726 < 2e-16 ***
Marital_Status77 -6.997e+00 3.942e+00 -1.775 0.079221 .
Marital_Status99 2.753e+01 1.910e+00 14.411 < 2e-16 ***
Marital_StatusNone 7.836e+00 5.219e+00 1.501 0.136637
Ratio_income_poverty -4.761e-01 1.359e-01 -3.503 0.000709 ***
BMI 1.988e-01 2.646e-02 7.511 3.51e-11 ***
sleep_disorders2 -3.500e+00 5.234e-01 -6.687 1.68e-09 ***
sleep_disorders7 2.829e+01 5.103e+00 5.543 2.77e-07 ***
sleep_disorders9 -1.657e+01 6.938e+00 -2.388 0.018945 *
sleep_disordersNone -6.104e+00 7.617e-01 -8.014 3.17e-12 ***
Smoked_days 1.295e+00 6.896e-01 1.878 0.063507 .
now_smoke 2.294e+00 3.092e-01 7.417 5.50e-11 ***
quit_smoking 1.887e-04 3.223e-05 5.856 7.09e-08 ***
Avg_alcohol_drinks2 4.019e+00 4.594e-01 8.748 9.08e-14 ***
Avg_alcohol_drinks9 3.038e+00 6.340e+00 0.479 0.632995
Avg_alcohol_drinksNone -5.040e-01 6.075e-01 -0.830 0.408901
had_cancer2 -1.333e+01 5.835e-01 -22.842 < 2e-16 ***
had_cancer9 -5.592e+00 4.429e+00 -1.262 0.209964
had_cancerNone -4.596e+01 5.312e+00 -8.651 1.46e-13 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 239.2388)
Number of Fisher Scoring iterations: 2
2.5 % 97.5 %
(Intercept) 4.270468e+01 5.072798e+01
ln(perfluorooctane_sulfonic_acid) 2.218407e+00 3.511302e+00
Gender -1.660280e+00 1.302107e-01
Race 5.124869e-01 1.141597e+00
Marital_Status2 1.453000e+01 1.764346e+01
Marital_Status3 -4.567987e+00 -1.747507e+00
Marital_Status4 -5.939196e+00 -1.695836e+00
Marital_Status5 -1.707693e+01 -1.490167e+01
Marital_Status6 -1.506452e+01 -1.168658e+01
Marital_Status77 -1.482530e+01 8.322730e-01
Marital_Status99 2.373695e+01 3.132445e+01
Marital_StatusNone -2.528033e+00 1.819970e+01
Ratio_income_poverty -7.460465e-01 -2.062452e-01
BMI 1.462187e-01 2.513218e-01
sleep_disorders2 -4.539460e+00 -2.460557e+00
sleep_disorders7 1.815213e+01 3.842072e+01
sleep_disorders9 -3.034739e+01 -2.792865e+00
sleep_disordersNone -7.616321e+00 -4.591265e+00
Smoked_days -7.430420e-02 2.664651e+00
now_smoke 1.679440e+00 2.907593e+00
quit_smoking 1.247403e-04 2.527435e-04
Avg_alcohol_drinks2 3.106945e+00 4.931637e+00
Avg_alcohol_drinks9 -9.553174e+00 1.562854e+01
Avg_alcohol_drinksNone -1.710408e+00 7.024315e-01
had_cancer2 -1.448791e+01 -1.217030e+01
had_cancer9 -1.438753e+01 3.204257e+00
had_cancerNone -5.650865e+01 -3.540961e+01#Perfluorohexane_sulfonic_acid
library("rcssci")
Fulldat_Pheno <- Fulldat_Pheno %>% mutate(Ln_Perfluorohexane_sulfonic_acid = ln(Perfluorohexane_sulfonic_acid))
rcssci_linear(data = Fulldat_Pheno, y = "Phenotypic_Age", x = "Ln_Perfluorohexane_sulfonic_acid", covs=c("Gender", "Race", "BMI","had_cancer"), prob = 0.1,ref.zero=FALSE,
filepath = "C:/Users/HKUSCM/Documents")#Perfluorononanoic_acid
library("rcssci")
Fulldat_Pheno <- Fulldat_Pheno %>% mutate(Ln_Perfluorononanoic_acid = ln(Perfluorononanoic_acid))
rcssci_linear(data = Fulldat_Pheno, y = "Phenotypic_Age", x = "Perfluorononanoic_acid", covs=c("Gender", "Race", "BMI","had_cancer"), prob = 0.1,ref.zero=FALSE,
filepath = "C:/Users/HKUSCM/Documents")#perfluorooctanoic_acid
library("rcssci")
Fulldat_Pheno <- Fulldat_Pheno %>% mutate(Ln_perfluorooctanoic_acid = ln(perfluorooctanoic_acid))
rcssci_linear(data = Fulldat_Pheno, y = "Phenotypic_Age", x = "perfluorooctanoic_acid", covs=c("Gender", "Race", "BMI","had_cancer"), prob = 0.1,ref.zero=FALSE,
filepath = "C:/Users/HKUSCM/Documents")#perfluorooctane_sulfonic_acid
library("rcssci")
Fulldat_Pheno <- Fulldat_Pheno %>% mutate(Ln_perfluorooctane_sulfonic_acid = ln(perfluorooctane_sulfonic_acid))
rcssci_linear(data = Fulldat_Pheno, y = "Phenotypic_Age", x = "perfluorooctane_sulfonic_acid", covs=c("Gender", "Race", "BMI","had_cancer"), prob = 0.1,ref.zero=FALSE,
filepath = "C:/Users/HKUSCM/Documents")