Match samples and plot Vegetarian effects
Mike Francis
2022-10-09 21:39:36
Load packages + functions
suppressMessages(silent <- lapply(
c("sandwich", "lmtest", "tidyverse", "MatchIt", "forestplot", "kableExtra"),
library, character.only=T))
table = function (..., useNA = 'always') base::table(..., useNA = useNA)Load phenotype file
tab=as_tibble(read.csv("../VegMarkdown/pheno/BioxVeg_pheno_09112022.csv"))
colnames(tab)%>%kbl()%>%
scroll_box(width = "200px", height = "200px")| x |
|---|
| FID |
| IID |
| Age |
| Sex |
| Townsend |
| Geno_batch |
| AlcoholFreq |
| Alanine_aminotransferase |
| Albumin |
| Alkaline_phosphatase |
| Apolipoprotein_A |
| Apolipoprotein_B |
| Aspartate_aminotransferase |
| C_reactive_protein |
| Calcium |
| Cholesterol |
| Creatinine |
| Cystatin_C |
| Direct_bilirubin |
| Gamma_glutamyltransferase |
| Glucose |
| HbA1c |
| HDL_cholesterol |
| IGF_1 |
| LDL_direct |
| Lipoprotein_A |
| Oestradiol |
| Phosphate |
| Rheumatoid_factor |
| SHBG |
| Testosterone |
| Total_bilirubin |
| Total_protein |
| Triglycerides |
| Urate |
| Urea |
| Vitamin_D |
| PCA1 |
| PCA2 |
| PCA3 |
| PCA4 |
| PCA5 |
| PCA6 |
| PCA7 |
| PCA8 |
| PCA9 |
| PCA10 |
| PCA11 |
| PCA12 |
| PCA13 |
| PCA14 |
| PCA15 |
| PCA16 |
| PCA17 |
| PCA18 |
| PCA19 |
| PCA20 |
| BMI |
| SmokeStatus |
| Veg5yr1 |
| Age2 |
| PreviousSmoker |
| CurrentSmoker |
| center1 |
| center2 |
| center3 |
| center4 |
| center5 |
| center6 |
| center7 |
| center8 |
| center9 |
| center10 |
| center11 |
| center12 |
| center13 |
| center14 |
| center15 |
| center16 |
| center17 |
| center18 |
| center19 |
| center20 |
| center21 |
| center22 |
| zblood |
| zTownsend |
| zAge |
| logSHBG |
| Scr |
| eGFR |
| bioavailableTest |
| freeTest |
| statins |
| Cholesterolold |
| LDL_directold |
| Apolipoprotein_Bold |
| tookMed |
| tookSSRI |
| Alanine_aminotransferase_rint |
| Albumin_rint |
| Alkaline_phosphatase_rint |
| Apolipoprotein_A_rint |
| Apolipoprotein_B_rint |
| Aspartate_aminotransferase_rint |
| C_reactive_protein_rint |
| Calcium_rint |
| Cholesterol_rint |
| Creatinine_rint |
| Cystatin_C_rint |
| Direct_bilirubin_rint |
| Gamma_glutamyltransferase_rint |
| Glucose_rint |
| HbA1c_rint |
| HDL_cholesterol_rint |
| IGF_1_rint |
| LDL_direct_rint |
| Lipoprotein_A_rint |
| Oestradiol_rint |
| Phosphate_rint |
| Rheumatoid_factor_rint |
| SHBG_rint |
| Testosterone_rint |
| Total_bilirubin_rint |
| Total_protein_rint |
| Triglycerides_rint |
| Urate_rint |
| Urea_rint |
| Vitamin_D_rint |
| eGFR_rint |
| bioavailableTest_rint |
| freeTest_rint |
tab2=tab%>%select(IID, Veg5yr1 ,Age , Sex , BMI,
PCA1:PCA10,
AlcoholFreq,
PreviousSmoker, CurrentSmoker,
zTownsend)
tab3=tab2[complete.cases(tab2),] #lose only 16 vegetarians from 2328 to 2312
table(tab3$Veg5yr1)%>%kbl()| Var1 | Freq |
|---|---|
| 0 | 151998 |
| 1 | 2312 |
| NA | 0 |
1:4 matching without replacement
match.nearest=matchit(Veg5yr1 ~ Age + Sex + BMI +
AlcoholFreq +PreviousSmoker+
CurrentSmoker + zTownsend+
PCA1 + PCA2 + PCA3 +
PCA4 + PCA5 ,
data=tab3, distance="glm",
method="nearest",
replace=FALSE,
ratio=4)
#Love plot
plot(summary(match.nearest))
summary(match.nearest)##
## Call:
## matchit(formula = Veg5yr1 ~ Age + Sex + BMI + AlcoholFreq + PreviousSmoker +
## CurrentSmoker + zTownsend + PCA1 + PCA2 + PCA3 + PCA4 + PCA5,
## data = tab3, method = "nearest", distance = "glm", replace = FALSE,
## ratio = 4)
##
## Summary of Balance for All Data:
## Means Treated Means Control Std. Mean Diff. Var. Ratio eCDF Mean
## distance 0.0241 0.0148 0.5500 2.1203 0.2010
## Age 52.6691 56.4053 -0.4819 0.9721 0.1168
## Sex 1.6600 1.5415 0.2502 0.9042 0.0593
## BMI 24.8177 26.9676 -0.5067 0.8378 0.1099
## AlcoholFreq 0.4416 0.4992 -0.1159 . 0.0576
## PreviousSmoker 0.3387 0.3595 -0.0441 . 0.0209
## CurrentSmoker 0.0662 0.0761 -0.0398 . 0.0099
## zTownsend 0.2204 -0.0044 0.2107 1.1439 0.0632
## PCA1 -12.1063 -12.1118 0.0026 1.0017 0.0029
## PCA2 3.6085 3.6753 -0.0361 1.1100 0.0094
## PCA3 -1.4092 -1.4400 0.0164 1.1058 0.0058
## PCA4 0.6801 0.8421 -0.0421 1.1349 0.0095
## PCA5 -0.9769 -1.0674 0.0140 0.9523 0.0098
## eCDF Max
## distance 0.3038
## Age 0.1935
## Sex 0.1185
## BMI 0.2201
## AlcoholFreq 0.0576
## PreviousSmoker 0.0209
## CurrentSmoker 0.0099
## zTownsend 0.1079
## PCA1 0.0131
## PCA2 0.0184
## PCA3 0.0172
## PCA4 0.0219
## PCA5 0.0297
##
##
## Summary of Balance for Matched Data:
## Means Treated Means Control Std. Mean Diff. Var. Ratio eCDF Mean
## distance 0.0241 0.0241 0.0018 1.0216 0.0000
## Age 52.6691 52.5763 0.0120 0.9406 0.0137
## Sex 1.6600 1.6581 0.0041 0.9976 0.0010
## BMI 24.8177 24.8616 -0.0104 1.2414 0.0123
## AlcoholFreq 0.4416 0.4513 -0.0196 . 0.0097
## PreviousSmoker 0.3387 0.3329 0.0121 . 0.0057
## CurrentSmoker 0.0662 0.0650 0.0048 . 0.0012
## zTownsend 0.2204 0.2329 -0.0117 0.9396 0.0078
## PCA1 -12.1063 -12.1356 0.0139 0.9735 0.0073
## PCA2 3.6085 3.6183 -0.0053 1.0615 0.0025
## PCA3 -1.4092 -1.3949 -0.0076 1.0434 0.0039
## PCA4 0.6801 0.6932 -0.0034 0.9681 0.0040
## PCA5 -0.9769 -0.8442 -0.0205 0.9282 0.0081
## eCDF Max Std. Pair Dist.
## distance 0.0013 0.0022
## Age 0.0308 0.8675
## Sex 0.0019 0.8408
## BMI 0.0300 0.7173
## AlcoholFreq 0.0097 0.9729
## PreviousSmoker 0.0057 0.9402
## CurrentSmoker 0.0012 0.4972
## zTownsend 0.0230 1.0571
## PCA1 0.0252 1.0133
## PCA2 0.0091 0.9927
## PCA3 0.0146 1.0668
## PCA4 0.0123 1.0203
## PCA5 0.0198 1.0846
##
## Sample Sizes:
## Control Treated
## All 151998 2312
## Matched 9248 2312
## Unmatched 142750 0
## Discarded 0 0Join matched participants back with full phenotype table.
md=match.data(match.nearest)
tab4=tab%>%select(IID, Alanine_aminotransferase_rint:freeTest_rint)%>%select(-c(Glucose_rint,Oestradiol_rint, Rheumatoid_factor_rint))
md=left_join(md, tab4)## Joining, by = "IID"md=as_tibble(md)
dim(md)## [1] 11560 52Run glm with same covariates as matching.
https://kosukeimai.github.io/MatchIt/articles/estimating-effects.html
Full cohort
Initialize for lm
#Fix shorthand names for derived variables from pheno step
md=md%>%rename("Bioavailable_testosterone_rint"="bioavailableTest_rint",
"Free_testosterone_rint"="freeTest_rint")
phe=md%>%select(Alanine_aminotransferase_rint:Free_testosterone_rint)%>%colnames()
#Arrange vars for plots by category
phe=c("Apolipoprotein_A_rint",
"Apolipoprotein_B_rint",
"HDL_cholesterol_rint","LDL_direct_rint",
"Lipoprotein_A_rint","Cholesterol_rint",
"Triglycerides_rint",
"IGF_1_rint","Vitamin_D_rint",
"Bioavailable_testosterone_rint","Free_testosterone_rint",
"Testosterone_rint","SHBG_rint",
"Alanine_aminotransferase_rint","Albumin_rint",
"Alkaline_phosphatase_rint","Aspartate_aminotransferase_rint",
"C_reactive_protein_rint",
"Gamma_glutamyltransferase_rint",
"Direct_bilirubin_rint","Total_bilirubin_rint","Total_protein_rint",
"Creatinine_rint",
"Cystatin_C_rint","eGFR_rint",
"HbA1c_rint",
"Urate_rint","Urea_rint",
"Calcium_rint",
"Phosphate_rint")
Category=c("Blood lipids", rep("",6),
"Hormones", rep("",5),
"Liver markers",rep("",8),
"Kidney markers",rep("",5),
"Minerals", "")
phe%>%kbl()%>%
scroll_box(width = "200px", height = "200px")| x |
|---|
| Apolipoprotein_A_rint |
| Apolipoprotein_B_rint |
| HDL_cholesterol_rint |
| LDL_direct_rint |
| Lipoprotein_A_rint |
| Cholesterol_rint |
| Triglycerides_rint |
| IGF_1_rint |
| Vitamin_D_rint |
| Bioavailable_testosterone_rint |
| Free_testosterone_rint |
| Testosterone_rint |
| SHBG_rint |
| Alanine_aminotransferase_rint |
| Albumin_rint |
| Alkaline_phosphatase_rint |
| Aspartate_aminotransferase_rint |
| C_reactive_protein_rint |
| Gamma_glutamyltransferase_rint |
| Direct_bilirubin_rint |
| Total_bilirubin_rint |
| Total_protein_rint |
| Creatinine_rint |
| Cystatin_C_rint |
| eGFR_rint |
| HbA1c_rint |
| Urate_rint |
| Urea_rint |
| Calcium_rint |
| Phosphate_rint |
#initialize
fit=list()
fitBMI=list()
out=matrix(NA, nrow=length(phe), ncol=4)
colnames(out)=c("Trait", "Estimate", "SE", "P")
outBMI=outRun lm full cohort, no adj-BMI
#----FULL COHORT, NO BMI--------------------------------------------
for (i in 1:length(phe)){
fit=lm(md[[phe[i]]] ~ Veg5yr1 + Age + Sex + AlcoholFreq +
PreviousSmoker +CurrentSmoker+
zTownsend+PCA1 + PCA2 + PCA3 +
PCA4 + PCA5, data = md, na.action = na.exclude)
out[i,1]=phe[i]
#Cluster-robust standard errors
co=coeftest(fit, vcov. = vcovCL, cluster = ~subclass)["Veg5yr1",,drop=FALSE]
out[i,2]=co[1]
out[i,3]=co[2]
out[i,4]=co[4]
}
out=as.data.frame(out)
out[2:4]=sapply(out[2:4], as.numeric)
out%>%kbl()%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P |
|---|---|---|---|
| Apolipoprotein_A_rint | -0.0678330 | 0.0207699 | 0.0010948 |
| Apolipoprotein_B_rint | -0.1817707 | 0.0225360 | 0.0000000 |
| HDL_cholesterol_rint | -0.1434914 | 0.0203234 | 0.0000000 |
| LDL_direct_rint | -0.1813523 | 0.0224368 | 0.0000000 |
| Lipoprotein_A_rint | -0.0624893 | 0.0259647 | 0.0161178 |
| Cholesterol_rint | -0.1917923 | 0.0224022 | 0.0000000 |
| Triglycerides_rint | 0.2139828 | 0.0221433 | 0.0000000 |
| IGF_1_rint | -0.2074448 | 0.0224744 | 0.0000000 |
| Vitamin_D_rint | -0.3838228 | 0.0262896 | 0.0000000 |
| Bioavailable_testosterone_rint | -0.0272579 | 0.0163224 | 0.0949612 |
| Free_testosterone_rint | -0.0198628 | 0.0160244 | 0.2151820 |
| Testosterone_rint | -0.0240502 | 0.0152004 | 0.1136363 |
| SHBG_rint | -0.0116386 | 0.0220862 | 0.5982308 |
| Alanine_aminotransferase_rint | -0.1505136 | 0.0216690 | 0.0000000 |
| Albumin_rint | -0.0671204 | 0.0242745 | 0.0057015 |
| Alkaline_phosphatase_rint | 0.1340596 | 0.0225922 | 0.0000000 |
| Aspartate_aminotransferase_rint | 0.0341174 | 0.0221578 | 0.1236501 |
| C_reactive_protein_rint | -0.0551381 | 0.0234842 | 0.0188979 |
| Gamma_glutamyltransferase_rint | -0.1553539 | 0.0216983 | 0.0000000 |
| Direct_bilirubin_rint | -0.0115609 | 0.0248624 | 0.6419465 |
| Total_bilirubin_rint | -0.0249462 | 0.0225235 | 0.2680742 |
| Total_protein_rint | -0.0705408 | 0.0247022 | 0.0043036 |
| Creatinine_rint | -0.4428694 | 0.0176538 | 0.0000000 |
| Cystatin_C_rint | 0.3319466 | 0.0201453 | 0.0000000 |
| eGFR_rint | -0.0208691 | 0.0199177 | 0.2947694 |
| HbA1c_rint | 0.0120977 | 0.0211105 | 0.5666120 |
| Urate_rint | -0.1709024 | 0.0184686 | 0.0000000 |
| Urea_rint | -0.6144779 | 0.0230717 | 0.0000000 |
| Calcium_rint | -0.0771083 | 0.0253304 | 0.0023397 |
| Phosphate_rint | 0.0131200 | 0.0252895 | 0.6039165 |
Add confidence intervals and round long decimals:
#CI range
out$upper=out$Estimate+1.96*out$SE
out$lower=out$Estimate-1.96*out$SE
#Round digits
out$Estimateround=format(round(out$Estimate, digits=3), digits=3)
out$SEround=format(round(out$SE, digits=3), digits=3)
out$Pround=ifelse(out$P < 0.001,
formatC(out$P, digits=1, format="e"),
formatC(out$P, digits=3, format="f"))Same exact thing as above but with adj-BMI
for (i in 1:length(phe)){
fit=lm(md[[phe[i]]] ~ Veg5yr1 + Age + Sex + BMI + AlcoholFreq +
PreviousSmoker +CurrentSmoker+
zTownsend+PCA1 + PCA2 + PCA3 +
PCA4 + PCA5, data = md, na.action = na.exclude)
outBMI[i,1]=phe[i]
#Cluster-robust standard errors
co=coeftest(fit, vcov. = vcovCL, cluster = ~subclass)["Veg5yr1",,drop=FALSE]
outBMI[i,2]=co[1]
outBMI[i,3]=co[2]
outBMI[i,4]=co[4]
}
outBMI=as.data.frame(outBMI)
outBMI[2:4]=sapply(outBMI[2:4], as.numeric)
#as_tibble(outBMI)
#95CI
outBMI$upper=outBMI$Estimate+1.96*outBMI$SE
outBMI$lower=outBMI$Estimate-1.96*outBMI$SE
#Round digits
outBMI$Estimateround=format(round(outBMI$Estimate, digits=3), digits=3)
outBMI$SEround=format(round(outBMI$SE, digits=3), digits=3)
outBMI$Pround=ifelse(outBMI$P < 0.001,
formatC(outBMI$P, digits=1, format="e"),
formatC(outBMI$P, digits=3, format="f"))Get sample sizes
ntot=sapply(md[phe], function(x) sum(!is.na(x)))
ncontr=md%>%filter(Veg5yr1==0)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
ncase=md%>%filter(Veg5yr1==1)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))Make Forest plots
https://cran.r-project.org/web/packages/forestplot/vignettes/forestplot.html
Forest plot: Full cohort, no BMI
# FULL, NO BMI --------------------------------------------------
xtik=c(-0.7,-0.6,-0.5,-0.4,-0.3,-0.2,-0.1,
0,0.1,0.2,0.3,0.4,0.5)
out$Trait=gsub(out$Trait, pattern = "_", replacement = " ")
out$Trait=gsub(out$Trait, pattern = " rint", replacement="")
out$samp=paste(ncase,ncontr, sep= "/")
out=out%>%select(Trait, Estimateround, Pround, samp,everything())
out=cbind(Category, out)
#Add header
header=tibble(Category="Category",
Trait="Biomarker",
Estimateround= "β Veg.",
Pround="P",
samp="N (Veg./Non-veg.)")
out2=bind_rows(header, out)
out2%>%kbl()%>%
scroll_box(width = "600px", height = "200px")| Category | Trait | Estimateround | Pround | samp | Estimate | SE | P | upper | lower | SEround |
|---|---|---|---|---|---|---|---|---|---|---|
| Category | Biomarker | β Veg. | P | N (Veg./Non-veg.) | NA | NA | NA | NA | NA | NA |
| Blood lipids | Apolipoprotein A | -0.068 | 0.001 | 2011/8021 | -0.0678330 | 0.0207699 | 0.0010948 | -0.0271239 | -0.1085421 | 0.021 |
| Apolipoprotein B | -0.182 | 8.0e-16 | 2197/8786 | -0.1817707 | 0.0225360 | 0.0000000 | -0.1376001 | -0.2259412 | 0.023 | |
| HDL cholesterol | -0.143 | 1.8e-12 | 2026/8075 | -0.1434914 | 0.0203234 | 0.0000000 | -0.1036575 | -0.1833253 | 0.020 | |
| LDL direct | -0.181 | 7.0e-16 | 2212/8808 | -0.1813523 | 0.0224368 | 0.0000000 | -0.1373761 | -0.2253284 | 0.022 | |
| Lipoprotein A | -0.062 | 0.016 | 1774/7068 | -0.0624893 | 0.0259647 | 0.0161178 | -0.0115984 | -0.1133801 | 0.026 | |
| Cholesterol | -0.192 | 1.3e-17 | 2215/8826 | -0.1917923 | 0.0224022 | 0.0000000 | -0.1478840 | -0.2357007 | 0.022 | |
| Triglycerides | 0.214 | 5.3e-22 | 2212/8819 | 0.2139828 | 0.0221433 | 0.0000000 | 0.2573838 | 0.1705818 | 0.022 | |
| Hormones | IGF 1 | -0.207 | 3.2e-20 | 2201/8785 | -0.2074448 | 0.0224744 | 0.0000000 | -0.1633950 | -0.2514947 | 0.022 |
| Vitamin D | -0.384 | 8.2e-48 | 2130/8521 | -0.3838228 | 0.0262896 | 0.0000000 | -0.3322952 | -0.4353504 | 0.026 | |
| Bioavailable testosterone | -0.027 | 0.095 | 1743/6981 | -0.0272579 | 0.0163224 | 0.0949612 | 0.0047340 | -0.0592498 | 0.016 | |
| Free testosterone | -0.020 | 0.215 | 1784/7220 | -0.0198628 | 0.0160244 | 0.2151820 | 0.0115451 | -0.0512707 | 0.016 | |
| Testosterone | -0.024 | 0.114 | 1919/7672 | -0.0240502 | 0.0152004 | 0.1136363 | 0.0057427 | -0.0538430 | 0.015 | |
| SHBG | -0.012 | 0.598 | 2005/7995 | -0.0116386 | 0.0220862 | 0.5982308 | 0.0316503 | -0.0549275 | 0.022 | |
| Liver markers | Alanine aminotransferase | -0.151 | 4.0e-12 | 2212/8827 | -0.1505136 | 0.0216690 | 0.0000000 | -0.1080423 | -0.1929850 | 0.022 |
| Albumin | -0.067 | 0.006 | 2026/8075 | -0.0671204 | 0.0242745 | 0.0057015 | -0.0195425 | -0.1146984 | 0.024 | |
| Alkaline phosphatase | 0.134 | 3.0e-09 | 2215/8826 | 0.1340596 | 0.0225922 | 0.0000000 | 0.1783404 | 0.0897789 | 0.023 | |
| Aspartate aminotransferase | 0.034 | 0.124 | 2206/8792 | 0.0341174 | 0.0221578 | 0.1236501 | 0.0775466 | -0.0093118 | 0.022 | |
| C reactive protein | -0.055 | 0.019 | 2202/8812 | -0.0551381 | 0.0234842 | 0.0188979 | -0.0091092 | -0.1011671 | 0.023 | |
| Gamma glutamyltransferase | -0.155 | 8.6e-13 | 2212/8819 | -0.1553539 | 0.0216983 | 0.0000000 | -0.1128252 | -0.1978826 | 0.022 | |
| Direct bilirubin | -0.012 | 0.642 | 1888/7560 | -0.0115609 | 0.0248624 | 0.6419465 | 0.0371694 | -0.0602912 | 0.025 | |
| Total bilirubin | -0.025 | 0.268 | 2206/8787 | -0.0249462 | 0.0225235 | 0.2680742 | 0.0191998 | -0.0690923 | 0.023 | |
| Total protein | -0.071 | 0.004 | 2026/8074 | -0.0705408 | 0.0247022 | 0.0043036 | -0.0221246 | -0.1189571 | 0.025 | |
| Kidney markers | Creatinine | -0.443 | 4.1e-135 | 2212/8822 | -0.4428694 | 0.0176538 | 0.0000000 | -0.4082680 | -0.4774709 | 0.018 |
| Cystatin C | 0.332 | 2.8e-60 | 2213/8830 | 0.3319466 | 0.0201453 | 0.0000000 | 0.3714314 | 0.2924619 | 0.020 | |
| eGFR | -0.021 | 0.295 | 2210/8820 | -0.0208691 | 0.0199177 | 0.2947694 | 0.0181696 | -0.0599077 | 0.020 | |
| HbA1c | 0.012 | 0.567 | 2198/8782 | 0.0120977 | 0.0211105 | 0.5666120 | 0.0534742 | -0.0292788 | 0.021 | |
| Urate | -0.171 | 2.6e-20 | 2209/8817 | -0.1709024 | 0.0184686 | 0.0000000 | -0.1347039 | -0.2071009 | 0.018 | |
| Urea | -0.614 | 1.6e-151 | 2212/8821 | -0.6144779 | 0.0230717 | 0.0000000 | -0.5692574 | -0.6596983 | 0.023 | |
| Minerals | Calcium | -0.077 | 0.002 | 2025/8072 | -0.0771083 | 0.0253304 | 0.0023397 | -0.0274608 | -0.1267559 | 0.025 |
| Phosphate | 0.013 | 0.604 | 2023/8055 | 0.0131200 | 0.0252895 | 0.6039165 | 0.0626873 | -0.0364473 | 0.025 |
#png("forest.fullnoBMI.png",width = 13, height = 8, units = 'in', res = 600)
forestplot(out2, mean="Estimate",
labeltext=c("Category", "Trait","Estimateround", "Pround", "samp"),
lower="lower", upper="upper",
boxsize = 0.4,
hrzl_lines = list("2" = gpar(lty = 2)),
col=fpColors(box = "black",
line = "black"),
vertices = TRUE,
grid=TRUE,
zero = 0,
xticks=xtik,
mar = unit(c(0,0.5,0,0.5), "in"),
xlab = "Standardized veg. effect ± 95% CI (no BMI covar.)",
txt_gp = fpTxtGp(xlab = gpar(cex = 1.),
ticks = gpar(fontfamily = "", cex = 1)
)
) %>% fp_set_zebra_style("#F7F7F7")
#dev.off()
outplot=out
outplot$Pround = cell_spec(outplot$Pround,
color=ifelse(as.double(outplot$Pround) <0.0017 , "#36E072", "grey"))
colnames(outplot)=c("Category", "Trait", "BetaVeg", "P", "N (veg/non-veg)","estimateexact", "SEexact","pexact", "upper", "lower", "SE")
outplot%>%select(Trait, BetaVeg,SE, P, `N (veg/non-veg)`)%>%
kbl(booktabs = T, linesep = "", escape=FALSE,align="l") %>%
kable_classic_2(full_width = F)| Trait | BetaVeg | SE | P | N (veg/non-veg) |
|---|---|---|---|---|
| Apolipoprotein A | -0.068 | 0.021 | 0.001 | 2011/8021 |
| Apolipoprotein B | -0.182 | 0.023 | 8.0e-16 | 2197/8786 |
| HDL cholesterol | -0.143 | 0.020 | 1.8e-12 | 2026/8075 |
| LDL direct | -0.181 | 0.022 | 7.0e-16 | 2212/8808 |
| Lipoprotein A | -0.062 | 0.026 | 0.016 | 1774/7068 |
| Cholesterol | -0.192 | 0.022 | 1.3e-17 | 2215/8826 |
| Triglycerides | 0.214 | 0.022 | 5.3e-22 | 2212/8819 |
| IGF 1 | -0.207 | 0.022 | 3.2e-20 | 2201/8785 |
| Vitamin D | -0.384 | 0.026 | 8.2e-48 | 2130/8521 |
| Bioavailable testosterone | -0.027 | 0.016 | 0.095 | 1743/6981 |
| Free testosterone | -0.020 | 0.016 | 0.215 | 1784/7220 |
| Testosterone | -0.024 | 0.015 | 0.114 | 1919/7672 |
| SHBG | -0.012 | 0.022 | 0.598 | 2005/7995 |
| Alanine aminotransferase | -0.151 | 0.022 | 4.0e-12 | 2212/8827 |
| Albumin | -0.067 | 0.024 | 0.006 | 2026/8075 |
| Alkaline phosphatase | 0.134 | 0.023 | 3.0e-09 | 2215/8826 |
| Aspartate aminotransferase | 0.034 | 0.022 | 0.124 | 2206/8792 |
| C reactive protein | -0.055 | 0.023 | 0.019 | 2202/8812 |
| Gamma glutamyltransferase | -0.155 | 0.022 | 8.6e-13 | 2212/8819 |
| Direct bilirubin | -0.012 | 0.025 | 0.642 | 1888/7560 |
| Total bilirubin | -0.025 | 0.023 | 0.268 | 2206/8787 |
| Total protein | -0.071 | 0.025 | 0.004 | 2026/8074 |
| Creatinine | -0.443 | 0.018 | 4.1e-135 | 2212/8822 |
| Cystatin C | 0.332 | 0.020 | 2.8e-60 | 2213/8830 |
| eGFR | -0.021 | 0.020 | 0.295 | 2210/8820 |
| HbA1c | 0.012 | 0.021 | 0.567 | 2198/8782 |
| Urate | -0.171 | 0.018 | 2.6e-20 | 2209/8817 |
| Urea | -0.614 | 0.023 | 1.6e-151 | 2212/8821 |
| Calcium | -0.077 | 0.025 | 0.002 | 2025/8072 |
| Phosphate | 0.013 | 0.025 | 0.604 | 2023/8055 |
Forest plot: Full cohort, adj-BMI
xtik=c(-0.7,-0.6,-0.5,-0.4,-0.3,-0.2,-0.1,
0,0.1,0.2,0.3,0.4,0.5)
outBMI$Trait=gsub(outBMI$Trait, pattern = "_", replacement = " ")
outBMI$Trait=gsub(outBMI$Trait, pattern = " rint", replacement="")
outBMI$samp=paste(ncase,ncontr, sep= "/")
outBMI=outBMI%>%select(Trait, Estimateround, Pround, samp,everything())
outBMI=cbind(Category, outBMI)
#Add header
header=tibble(Category="Category",
Trait="Biomarker",
Estimateround= "β Veg.",
Pround="P",
samp="N (Veg./Non-veg.)")
outBMI2=bind_rows(header, outBMI)
outBMI2%>%kbl()%>%
scroll_box(width = "600px", height = "200px")| Category | Trait | Estimateround | Pround | samp | Estimate | SE | P | upper | lower | SEround |
|---|---|---|---|---|---|---|---|---|---|---|
| Category | Biomarker | β Veg. | P | N (Veg./Non-veg.) | NA | NA | NA | NA | NA | NA |
| Blood lipids | Apolipoprotein A | -0.076 | 2.2e-04 | 2011/8021 | -0.0756386 | 0.0204772 | 0.0002221 | -0.0355033 | -0.1157739 | 0.020 |
| Apolipoprotein B | -0.175 | 1.0e-15 | 2197/8786 | -0.1754499 | 0.0218384 | 0.0000000 | -0.1326466 | -0.2182532 | 0.022 | |
| HDL cholesterol | -0.155 | 3.8e-15 | 2026/8075 | -0.1550842 | 0.0196969 | 0.0000000 | -0.1164783 | -0.1936901 | 0.020 | |
| LDL direct | -0.176 | 1.1e-15 | 2212/8808 | -0.1758329 | 0.0218950 | 0.0000000 | -0.1329188 | -0.2187470 | 0.022 | |
| Lipoprotein A | -0.062 | 0.016 | 1774/7068 | -0.0624393 | 0.0259677 | 0.0162150 | -0.0115426 | -0.1133359 | 0.026 | |
| Cholesterol | -0.188 | 1.9e-17 | 2215/8826 | -0.1882372 | 0.0221170 | 0.0000000 | -0.1448880 | -0.2315865 | 0.022 | |
| Triglycerides | 0.223 | 4.0e-26 | 2212/8819 | 0.2230082 | 0.0210410 | 0.0000000 | 0.2642486 | 0.1817678 | 0.021 | |
| Hormones | IGF 1 | -0.209 | 2.1e-20 | 2201/8785 | -0.2085186 | 0.0224777 | 0.0000000 | -0.1644622 | -0.2525750 | 0.022 |
| Vitamin D | -0.388 | 2.1e-49 | 2130/8521 | -0.3875943 | 0.0260985 | 0.0000000 | -0.3364412 | -0.4387474 | 0.026 | |
| Bioavailable testosterone | -0.026 | 0.107 | 1743/6981 | -0.0262846 | 0.0163052 | 0.1069897 | 0.0056736 | -0.0582427 | 0.016 | |
| Free testosterone | -0.016 | 0.314 | 1784/7220 | -0.0158583 | 0.0157441 | 0.3138386 | 0.0150001 | -0.0467168 | 0.016 | |
| Testosterone | -0.024 | 0.108 | 1919/7672 | -0.0244041 | 0.0151854 | 0.1080713 | 0.0053593 | -0.0541675 | 0.015 | |
| SHBG | -0.027 | 0.187 | 2005/7995 | -0.0272222 | 0.0206457 | 0.1873517 | 0.0132433 | -0.0676877 | 0.021 | |
| Liver markers | Alanine aminotransferase | -0.144 | 6.6e-12 | 2212/8827 | -0.1438391 | 0.0209243 | 0.0000000 | -0.1028275 | -0.1848506 | 0.021 |
| Albumin | -0.072 | 0.003 | 2026/8075 | -0.0723362 | 0.0241263 | 0.0027221 | -0.0250487 | -0.1196237 | 0.024 | |
| Alkaline phosphatase | 0.139 | 4.4e-10 | 2215/8826 | 0.1386650 | 0.0222002 | 0.0000000 | 0.1821775 | 0.0951525 | 0.022 | |
| Aspartate aminotransferase | 0.036 | 0.108 | 2206/8792 | 0.0355081 | 0.0220870 | 0.1079411 | 0.0787985 | -0.0077824 | 0.022 | |
| C reactive protein | -0.044 | 0.045 | 2202/8812 | -0.0437832 | 0.0218261 | 0.0448801 | -0.0010041 | -0.0865623 | 0.022 | |
| Gamma glutamyltransferase | -0.149 | 2.1e-12 | 2212/8819 | -0.1486769 | 0.0211324 | 0.0000000 | -0.1072574 | -0.1900965 | 0.021 | |
| Direct bilirubin | -0.015 | 0.534 | 1888/7560 | -0.0153855 | 0.0247425 | 0.5340727 | 0.0331099 | -0.0638809 | 0.025 | |
| Total bilirubin | -0.028 | 0.211 | 2206/8787 | -0.0280535 | 0.0224274 | 0.2110127 | 0.0159042 | -0.0720111 | 0.022 | |
| Total protein | -0.069 | 0.005 | 2026/8074 | -0.0692859 | 0.0247195 | 0.0050744 | -0.0208357 | -0.1177360 | 0.025 | |
| Kidney markers | Creatinine | -0.440 | 1.7e-135 | 2212/8822 | -0.4402147 | 0.0175224 | 0.0000000 | -0.4058707 | -0.4745586 | 0.018 |
| Cystatin C | 0.338 | 9.9e-66 | 2213/8830 | 0.3384178 | 0.0196317 | 0.0000000 | 0.3768959 | 0.2999397 | 0.020 | |
| eGFR | -0.027 | 0.172 | 2210/8820 | -0.0266182 | 0.0195047 | 0.1723731 | 0.0116110 | -0.0648475 | 0.020 | |
| HbA1c | 0.014 | 0.506 | 2198/8782 | 0.0139620 | 0.0210049 | 0.5062564 | 0.0551317 | -0.0272077 | 0.021 | |
| Urate | -0.162 | 1.8e-20 | 2209/8817 | -0.1621743 | 0.0174480 | 0.0000000 | -0.1279762 | -0.1963724 | 0.017 | |
| Urea | -0.613 | 2.3e-151 | 2212/8821 | -0.6126775 | 0.0230157 | 0.0000000 | -0.5675668 | -0.6577882 | 0.023 | |
| Minerals | Calcium | -0.078 | 0.002 | 2025/8072 | -0.0776592 | 0.0253446 | 0.0021888 | -0.0279838 | -0.1273346 | 0.025 |
| Phosphate | 0.010 | 0.688 | 2023/8055 | 0.0101137 | 0.0252014 | 0.6881971 | 0.0595085 | -0.0392811 | 0.025 |
# outBMI=rbind(colnames(outBMI),outBMI)
# outBMI=as.matrix(outBMI)
#tiff("forest.fullBMI.tiff",width = 13, height = 8, units = 'in', res = 600)
forestplot(outBMI2, mean="Estimate",
labeltext=c("Category", "Trait","Estimateround", "Pround", "samp"),
lower="lower", upper="upper",
boxsize = 0.4,
hrzl_lines = list("2" = gpar(lty = 2)),
col=fpColors(box = "#36E072",
line = "black"),
vertices = TRUE,
grid=TRUE,
zero = 0,
mar = unit(c(0,0.5,0,0.5), "in"),
xticks=xtik,
xlab = "Standardized veg. effect ± 95% CI",
txt_gp = fpTxtGp(xlab = gpar(cex = 1.),
ticks = gpar(fontfamily = "", cex = 1)
)
)%>% fp_set_zebra_style("#F7F7F7")
#dev.off()
outBMIplot=outBMI
outBMIplot$Pround = cell_spec(outBMIplot$Pround,
color=ifelse(as.double(outBMIplot$Pround) <(0.05/30), "#36E072", "grey"))
colnames(outBMIplot)=c("Category", "Trait", "BetaVeg", "P", "N (veg/non-veg)","estimateexact", "SEexact","pexact", "upper", "lower", "SE")
outBMIplot%>%select(Trait, BetaVeg,SE, P, `N (veg/non-veg)`)%>%
kbl(booktabs = T, linesep = "", escape=FALSE,align="l") %>%
kable_classic_2(full_width = F)| Trait | BetaVeg | SE | P | N (veg/non-veg) |
|---|---|---|---|---|
| Apolipoprotein A | -0.076 | 0.020 | 2.2e-04 | 2011/8021 |
| Apolipoprotein B | -0.175 | 0.022 | 1.0e-15 | 2197/8786 |
| HDL cholesterol | -0.155 | 0.020 | 3.8e-15 | 2026/8075 |
| LDL direct | -0.176 | 0.022 | 1.1e-15 | 2212/8808 |
| Lipoprotein A | -0.062 | 0.026 | 0.016 | 1774/7068 |
| Cholesterol | -0.188 | 0.022 | 1.9e-17 | 2215/8826 |
| Triglycerides | 0.223 | 0.021 | 4.0e-26 | 2212/8819 |
| IGF 1 | -0.209 | 0.022 | 2.1e-20 | 2201/8785 |
| Vitamin D | -0.388 | 0.026 | 2.1e-49 | 2130/8521 |
| Bioavailable testosterone | -0.026 | 0.016 | 0.107 | 1743/6981 |
| Free testosterone | -0.016 | 0.016 | 0.314 | 1784/7220 |
| Testosterone | -0.024 | 0.015 | 0.108 | 1919/7672 |
| SHBG | -0.027 | 0.021 | 0.187 | 2005/7995 |
| Alanine aminotransferase | -0.144 | 0.021 | 6.6e-12 | 2212/8827 |
| Albumin | -0.072 | 0.024 | 0.003 | 2026/8075 |
| Alkaline phosphatase | 0.139 | 0.022 | 4.4e-10 | 2215/8826 |
| Aspartate aminotransferase | 0.036 | 0.022 | 0.108 | 2206/8792 |
| C reactive protein | -0.044 | 0.022 | 0.045 | 2202/8812 |
| Gamma glutamyltransferase | -0.149 | 0.021 | 2.1e-12 | 2212/8819 |
| Direct bilirubin | -0.015 | 0.025 | 0.534 | 1888/7560 |
| Total bilirubin | -0.028 | 0.022 | 0.211 | 2206/8787 |
| Total protein | -0.069 | 0.025 | 0.005 | 2026/8074 |
| Creatinine | -0.440 | 0.018 | 1.7e-135 | 2212/8822 |
| Cystatin C | 0.338 | 0.020 | 9.9e-66 | 2213/8830 |
| eGFR | -0.027 | 0.020 | 0.172 | 2210/8820 |
| HbA1c | 0.014 | 0.021 | 0.506 | 2198/8782 |
| Urate | -0.162 | 0.017 | 1.8e-20 | 2209/8817 |
| Urea | -0.613 | 0.023 | 2.3e-151 | 2212/8821 |
| Calcium | -0.078 | 0.025 | 0.002 | 2025/8072 |
| Phosphate | 0.010 | 0.025 | 0.688 | 2023/8055 |
#%>%save_kable(file = "table.forest.fullBMI.png", zoom=5)Sex-stratified models
Initialize for lm
mdM=md%>%filter(Sex==1)
mdF=md%>%filter(Sex==2)
#Linear model with covariates
fitM=list()
fitcM=list()
fitF=list()
fitcF=list()
outM=matrix(NA, nrow=length(phe), ncol=4)
outF=matrix(NA, nrow=length(phe), ncol=4)
colnames(outM)=c("Trait", "Estimate", "SE", "P")
colnames(outF)=c("Trait", "Estimate", "SE", "P")Run lm sex-stratified
for (i in 1:length(phe)){
fitM[[i]] <- lm(mdM[[phe[i]]] ~ Veg5yr1 + Age + AlcoholFreq +
PreviousSmoker +CurrentSmoker+
zTownsend+PCA1 + PCA2 + PCA3 +
PCA4 + PCA5, data = mdM, na.action = na.exclude)
fitF[[i]] <- lm(mdF[[phe[i]]] ~ Veg5yr1 + Age + AlcoholFreq +
PreviousSmoker +CurrentSmoker+
zTownsend+PCA1 + PCA2 + PCA3 +
PCA4 + PCA5, data = mdF, na.action = na.exclude)
outM[i,1]=phe[i]
outF[i,1]=phe[i]
#Cluster-robust standard errors
coM=coeftest(fitM[[i]], vcov. = vcovCL, cluster = ~subclass)["Veg5yr1",,drop=FALSE]
coF=coeftest(fitF[[i]], vcov. = vcovCL, cluster = ~subclass)["Veg5yr1",,drop=FALSE]
outM[i,2]=coM[1]
outM[i,3]=coM[2]
outM[i,4]=coM[4]
outF[i,2]=coF[1]
outF[i,3]=coF[2]
outF[i,4]=coF[4]
}
outM=as.data.frame(outM)
outM[2:4]=sapply(outM[2:4], as.numeric)
as_tibble(outM)%>%kbl(caption="Male")%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P |
|---|---|---|---|
| Apolipoprotein_A_rint | -0.0952853 | 0.0364059 | 0.0089011 |
| Apolipoprotein_B_rint | -0.2207853 | 0.0392515 | 0.0000000 |
| HDL_cholesterol_rint | -0.1641141 | 0.0366923 | 0.0000080 |
| LDL_direct_rint | -0.2332525 | 0.0379934 | 0.0000000 |
| Lipoprotein_A_rint | 0.0328448 | 0.0437274 | 0.4526356 |
| Cholesterol_rint | -0.2397004 | 0.0385400 | 0.0000000 |
| Triglycerides_rint | 0.1819623 | 0.0423750 | 0.0000180 |
| IGF_1_rint | -0.1470875 | 0.0361661 | 0.0000486 |
| Vitamin_D_rint | -0.3399957 | 0.0445313 | 0.0000000 |
| Bioavailable_testosterone_rint | -0.0136650 | 0.0271881 | 0.6152724 |
| Free_testosterone_rint | -0.0271668 | 0.0256020 | 0.2887110 |
| Testosterone_rint | -0.0054171 | 0.0258406 | 0.8339647 |
| SHBG_rint | 0.0084908 | 0.0338931 | 0.8022022 |
| Alanine_aminotransferase_rint | -0.1786818 | 0.0380667 | 0.0000028 |
| Albumin_rint | -0.0725563 | 0.0392101 | 0.0643339 |
| Alkaline_phosphatase_rint | 0.0918610 | 0.0371810 | 0.0135309 |
| Aspartate_aminotransferase_rint | -0.0138357 | 0.0380193 | 0.7159433 |
| C_reactive_protein_rint | -0.0217979 | 0.0397824 | 0.5837734 |
| Gamma_glutamyltransferase_rint | -0.1839996 | 0.0335011 | 0.0000000 |
| Direct_bilirubin_rint | 0.0016235 | 0.0401377 | 0.9677389 |
| Total_bilirubin_rint | -0.0049710 | 0.0365885 | 0.8919374 |
| Total_protein_rint | -0.1212301 | 0.0407742 | 0.0029672 |
| Creatinine_rint | -0.5932464 | 0.0287057 | 0.0000000 |
| Cystatin_C_rint | 0.2584474 | 0.0326227 | 0.0000000 |
| eGFR_rint | 0.0270818 | 0.0333761 | 0.4171801 |
| HbA1c_rint | -0.0579008 | 0.0390234 | 0.1379605 |
| Urate_rint | -0.2125853 | 0.0301554 | 0.0000000 |
| Urea_rint | -0.6485103 | 0.0392898 | 0.0000000 |
| Calcium_rint | -0.1079126 | 0.0410376 | 0.0085861 |
| Phosphate_rint | -0.0043175 | 0.0457044 | 0.9247453 |
outF=as.data.frame(outF)
outF[2:4]=sapply(outF[2:4], as.numeric)
as_tibble(outF)%>%kbl(caption="Female")%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P |
|---|---|---|---|
| Apolipoprotein_A_rint | -0.0537930 | 0.0258712 | 0.0376326 |
| Apolipoprotein_B_rint | -0.1610183 | 0.0276138 | 0.0000000 |
| HDL_cholesterol_rint | -0.1338099 | 0.0252510 | 0.0000001 |
| LDL_direct_rint | -0.1533478 | 0.0278392 | 0.0000000 |
| Lipoprotein_A_rint | -0.1128965 | 0.0324002 | 0.0004968 |
| Cholesterol_rint | -0.1668960 | 0.0272094 | 0.0000000 |
| Triglycerides_rint | 0.2294534 | 0.0255783 | 0.0000000 |
| IGF_1_rint | -0.2393446 | 0.0284029 | 0.0000000 |
| Vitamin_D_rint | -0.4082598 | 0.0325304 | 0.0000000 |
| Bioavailable_testosterone_rint | -0.0362555 | 0.0204403 | 0.0761658 |
| Free_testosterone_rint | -0.0145430 | 0.0204022 | 0.4759896 |
| Testosterone_rint | -0.0361472 | 0.0188108 | 0.0547023 |
| SHBG_rint | -0.0249352 | 0.0282841 | 0.3780273 |
| Alanine_aminotransferase_rint | -0.1360117 | 0.0258480 | 0.0000001 |
| Albumin_rint | -0.0657714 | 0.0303187 | 0.0300928 |
| Alkaline_phosphatase_rint | 0.1533666 | 0.0280940 | 0.0000000 |
| Aspartate_aminotransferase_rint | 0.0583374 | 0.0267167 | 0.0290268 |
| C_reactive_protein_rint | -0.0729257 | 0.0297921 | 0.0143957 |
| Gamma_glutamyltransferase_rint | -0.1426310 | 0.0278650 | 0.0000003 |
| Direct_bilirubin_rint | -0.0185505 | 0.0316874 | 0.5582862 |
| Total_bilirubin_rint | -0.0356154 | 0.0288654 | 0.2173023 |
| Total_protein_rint | -0.0436369 | 0.0307202 | 0.1555203 |
| Creatinine_rint | -0.3648762 | 0.0221789 | 0.0000000 |
| Cystatin_C_rint | 0.3706779 | 0.0255587 | 0.0000000 |
| eGFR_rint | -0.0457096 | 0.0250802 | 0.0684152 |
| HbA1c_rint | 0.0489391 | 0.0247224 | 0.0477929 |
| Urate_rint | -0.1482158 | 0.0231485 | 0.0000000 |
| Urea_rint | -0.5982422 | 0.0280654 | 0.0000000 |
| Calcium_rint | -0.0598459 | 0.0313665 | 0.0564403 |
| Phosphate_rint | 0.0206362 | 0.0297469 | 0.4878791 |
outM$Sex="Male"
outF$Sex="Female"Add confidence intervals and round long decimals:
#95CI
outM$upper=outM$Estimate+1.96*outM$SE
outM$lower=outM$Estimate-1.96*outM$SE
outM$Estimateround=format(round(outM$Estimate, digits=3), digits=3)
outM$SEround=format(round(outM$SE, digits=3), digits=3)
outM$Pround=ifelse(outM$P < 0.001,
formatC(outM$P, digits=1, format="e"),
formatC(outM$P, digits=3, format="f"))
outF$upper=outF$Estimate+1.96*outF$SE
outF$lower=outF$Estimate-1.96*outF$SE
outF$Estimateround=format(round(outF$Estimate, digits=3), digits=3)
outF$SEround=format(round(outF$SE, digits=3), digits=3)
outF$Pround=ifelse(outF$P < 0.001,
formatC(outF$P, digits=1, format="e"),
formatC(outF$P, digits=3, format="f"))Get sample sizes
ncontrM=md%>%filter(Veg5yr1==0, Sex==1)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
ncaseM=md%>%filter(Veg5yr1==1, Sex==1)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
ncontrF=md%>%filter(Veg5yr1==0, Sex==2)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
ncaseF=md%>%filter(Veg5yr1==1, Sex==2)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
outM$samp=paste(ncaseM,ncontrM, sep= "/")
outF$samp=paste(ncaseF,ncontrF, sep= "/")
tot=rbind(outM, outF)Forest plots sex-stratified no-BMI
tot$Trait=gsub(out$Trait, pattern = "_", replacement = " ")
tot$Trait=gsub(out$Trait, pattern = " rint", replacement="")
tot%>%kbl()%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P | Sex | upper | lower | Estimateround | SEround | Pround | samp |
|---|---|---|---|---|---|---|---|---|---|---|
| Apolipoprotein A | -0.0952853 | 0.0364059 | 0.0089011 | Male | -0.0239298 | -0.1666409 | -0.095 | 0.036 | 0.009 | 687/2798 |
| Apolipoprotein B | -0.2207853 | 0.0392515 | 0.0000000 | Male | -0.1438524 | -0.2977183 | -0.221 | 0.039 | 2.0e-08 | 745/3014 |
| HDL cholesterol | -0.1641141 | 0.0366923 | 0.0000080 | Male | -0.0921972 | -0.2360310 | -0.164 | 0.037 | 8.0e-06 | 689/2800 |
| LDL direct | -0.2332525 | 0.0379934 | 0.0000000 | Male | -0.1587854 | -0.3077196 | -0.233 | 0.038 | 9.1e-10 | 757/3025 |
| Lipoprotein A | 0.0328448 | 0.0437274 | 0.4526356 | Male | 0.1185506 | -0.0528610 | 0.033 | 0.044 | 0.453 | 608/2415 |
| Cholesterol | -0.2397004 | 0.0385400 | 0.0000000 | Male | -0.1641620 | -0.3152388 | -0.240 | 0.039 | 5.5e-10 | 758/3030 |
| Triglycerides | 0.1819623 | 0.0423750 | 0.0000180 | Male | 0.2650173 | 0.0989073 | 0.182 | 0.042 | 1.8e-05 | 756/3027 |
| IGF 1 | -0.1470875 | 0.0361661 | 0.0000486 | Male | -0.0762020 | -0.2179730 | -0.147 | 0.036 | 4.9e-05 | 752/3013 |
| Vitamin D | -0.3399957 | 0.0445313 | 0.0000000 | Male | -0.2527144 | -0.4272770 | -0.340 | 0.045 | 2.9e-14 | 738/2956 |
| Bioavailable testosterone | -0.0136650 | 0.0271881 | 0.6152724 | Male | 0.0396238 | -0.0669537 | -0.014 | 0.027 | 0.615 | 679/2761 |
| Free testosterone | -0.0271668 | 0.0256020 | 0.2887110 | Male | 0.0230132 | -0.0773468 | -0.027 | 0.026 | 0.289 | 678/2767 |
| Testosterone | -0.0054171 | 0.0258406 | 0.8339647 | Male | 0.0452305 | -0.0560646 | -0.005 | 0.026 | 0.834 | 751/2994 |
| SHBG | 0.0084908 | 0.0338931 | 0.8022022 | Male | 0.0749213 | -0.0579397 | 0.008 | 0.034 | 0.802 | 682/2783 |
| Alanine aminotransferase | -0.1786818 | 0.0380667 | 0.0000028 | Male | -0.1040710 | -0.2532925 | -0.179 | 0.038 | 2.8e-06 | 755/3029 |
| Albumin | -0.0725563 | 0.0392101 | 0.0643339 | Male | 0.0042956 | -0.1494082 | -0.073 | 0.039 | 0.064 | 688/2800 |
| Alkaline phosphatase | 0.0918610 | 0.0371810 | 0.0135309 | Male | 0.1647358 | 0.0189862 | 0.092 | 0.037 | 0.014 | 758/3030 |
| Aspartate aminotransferase | -0.0138357 | 0.0380193 | 0.7159433 | Male | 0.0606821 | -0.0883536 | -0.014 | 0.038 | 0.716 | 754/3020 |
| C reactive protein | -0.0217979 | 0.0397824 | 0.5837734 | Male | 0.0561756 | -0.0997715 | -0.022 | 0.040 | 0.584 | 750/3023 |
| Gamma glutamyltransferase | -0.1839996 | 0.0335011 | 0.0000000 | Male | -0.1183374 | -0.2496618 | -0.184 | 0.034 | 4.2e-08 | 757/3026 |
| Direct bilirubin | 0.0016235 | 0.0401377 | 0.9677389 | Male | 0.0802933 | -0.0770464 | 0.002 | 0.040 | 0.968 | 704/2844 |
| Total bilirubin | -0.0049710 | 0.0365885 | 0.8919374 | Male | 0.0667425 | -0.0766845 | -0.005 | 0.037 | 0.892 | 755/3018 |
| Total protein | -0.1212301 | 0.0407742 | 0.0029672 | Male | -0.0413128 | -0.2011475 | -0.121 | 0.041 | 0.003 | 689/2802 |
| Creatinine | -0.5932464 | 0.0287057 | 0.0000000 | Male | -0.5369832 | -0.6495095 | -0.593 | 0.029 | 5.6e-90 | 756/3029 |
| Cystatin C | 0.2584474 | 0.0326227 | 0.0000000 | Male | 0.3223879 | 0.1945069 | 0.258 | 0.033 | 3.0e-15 | 757/3029 |
| eGFR | 0.0270818 | 0.0333761 | 0.4171801 | Male | 0.0924989 | -0.0383353 | 0.027 | 0.033 | 0.417 | 755/3028 |
| HbA1c | -0.0579008 | 0.0390234 | 0.1379605 | Male | 0.0185850 | -0.1343866 | -0.058 | 0.039 | 0.138 | 748/3008 |
| Urate | -0.2125853 | 0.0301554 | 0.0000000 | Male | -0.1534806 | -0.2716900 | -0.213 | 0.030 | 2.1e-12 | 757/3026 |
| Urea | -0.6485103 | 0.0392898 | 0.0000000 | Male | -0.5715022 | -0.7255184 | -0.649 | 0.039 | 3.8e-59 | 757/3029 |
| Calcium | -0.1079126 | 0.0410376 | 0.0085861 | Male | -0.0274790 | -0.1883462 | -0.108 | 0.041 | 0.009 | 687/2802 |
| Phosphate | -0.0043175 | 0.0457044 | 0.9247453 | Male | 0.0852632 | -0.0938982 | -0.004 | 0.046 | 0.925 | 688/2791 |
| Apolipoprotein A | -0.0537930 | 0.0258712 | 0.0376326 | Female | -0.0030853 | -0.1045006 | -0.054 | 0.026 | 0.038 | 1324/5223 |
| Apolipoprotein B | -0.1610183 | 0.0276138 | 0.0000000 | Female | -0.1068953 | -0.2151413 | -0.161 | 0.028 | 5.7e-09 | 1452/5772 |
| HDL cholesterol | -0.1338099 | 0.0252510 | 0.0000001 | Female | -0.0843179 | -0.1833018 | -0.134 | 0.025 | 1.2e-07 | 1337/5275 |
| LDL direct | -0.1533478 | 0.0278392 | 0.0000000 | Female | -0.0987829 | -0.2079128 | -0.153 | 0.028 | 3.7e-08 | 1455/5783 |
| Lipoprotein A | -0.1128965 | 0.0324002 | 0.0004968 | Female | -0.0493921 | -0.1764010 | -0.113 | 0.032 | 5.0e-04 | 1166/4653 |
| Cholesterol | -0.1668960 | 0.0272094 | 0.0000000 | Female | -0.1135655 | -0.2202265 | -0.167 | 0.027 | 9.0e-10 | 1457/5796 |
| Triglycerides | 0.2294534 | 0.0255783 | 0.0000000 | Female | 0.2795868 | 0.1793200 | 0.229 | 0.026 | 3.7e-19 | 1456/5792 |
| IGF 1 | -0.2393446 | 0.0284029 | 0.0000000 | Female | -0.1836750 | -0.2950142 | -0.239 | 0.028 | 4.2e-17 | 1449/5772 |
| Vitamin D | -0.4082598 | 0.0325304 | 0.0000000 | Female | -0.3445001 | -0.4720194 | -0.408 | 0.033 | 9.7e-36 | 1392/5565 |
| Bioavailable testosterone | -0.0362555 | 0.0204403 | 0.0761658 | Female | 0.0038074 | -0.0763184 | -0.036 | 0.020 | 0.076 | 1064/4220 |
| Free testosterone | -0.0145430 | 0.0204022 | 0.4759896 | Female | 0.0254453 | -0.0545312 | -0.015 | 0.020 | 0.476 | 1106/4453 |
| Testosterone | -0.0361472 | 0.0188108 | 0.0547023 | Female | 0.0007220 | -0.0730163 | -0.036 | 0.019 | 0.055 | 1168/4678 |
| SHBG | -0.0249352 | 0.0282841 | 0.3780273 | Female | 0.0305016 | -0.0803720 | -0.025 | 0.028 | 0.378 | 1323/5212 |
| Alanine aminotransferase | -0.1360117 | 0.0258480 | 0.0000001 | Female | -0.0853497 | -0.1866737 | -0.136 | 0.026 | 1.5e-07 | 1457/5798 |
| Albumin | -0.0657714 | 0.0303187 | 0.0300928 | Female | -0.0063468 | -0.1251960 | -0.066 | 0.030 | 0.030 | 1338/5275 |
| Alkaline phosphatase | 0.1533666 | 0.0280940 | 0.0000000 | Female | 0.2084309 | 0.0983023 | 0.153 | 0.028 | 4.9e-08 | 1457/5796 |
| Aspartate aminotransferase | 0.0583374 | 0.0267167 | 0.0290268 | Female | 0.1107021 | 0.0059728 | 0.058 | 0.027 | 0.029 | 1452/5772 |
| C reactive protein | -0.0729257 | 0.0297921 | 0.0143957 | Female | -0.0145333 | -0.1313182 | -0.073 | 0.030 | 0.014 | 1452/5789 |
| Gamma glutamyltransferase | -0.1426310 | 0.0278650 | 0.0000003 | Female | -0.0880156 | -0.1972464 | -0.143 | 0.028 | 3.2e-07 | 1455/5793 |
| Direct bilirubin | -0.0185505 | 0.0316874 | 0.5582862 | Female | 0.0435568 | -0.0806577 | -0.019 | 0.032 | 0.558 | 1184/4716 |
| Total bilirubin | -0.0356154 | 0.0288654 | 0.2173023 | Female | 0.0209609 | -0.0921916 | -0.036 | 0.029 | 0.217 | 1451/5769 |
| Total protein | -0.0436369 | 0.0307202 | 0.1555203 | Female | 0.0165747 | -0.1038486 | -0.044 | 0.031 | 0.156 | 1337/5272 |
| Creatinine | -0.3648762 | 0.0221789 | 0.0000000 | Female | -0.3214055 | -0.4083469 | -0.365 | 0.022 | 9.8e-60 | 1456/5793 |
| Cystatin C | 0.3706779 | 0.0255587 | 0.0000000 | Female | 0.4207729 | 0.3205828 | 0.371 | 0.026 | 5.3e-47 | 1456/5801 |
| eGFR | -0.0457096 | 0.0250802 | 0.0684152 | Female | 0.0034477 | -0.0948668 | -0.046 | 0.025 | 0.068 | 1455/5792 |
| HbA1c | 0.0489391 | 0.0247224 | 0.0477929 | Female | 0.0973950 | 0.0004831 | 0.049 | 0.025 | 0.048 | 1450/5774 |
| Urate | -0.1482158 | 0.0231485 | 0.0000000 | Female | -0.1028448 | -0.1935869 | -0.148 | 0.023 | 1.6e-10 | 1452/5791 |
| Urea | -0.5982422 | 0.0280654 | 0.0000000 | Female | -0.5432340 | -0.6532504 | -0.598 | 0.028 | 7.8e-98 | 1455/5792 |
| Calcium | -0.0598459 | 0.0313665 | 0.0564403 | Female | 0.0016324 | -0.1213241 | -0.060 | 0.031 | 0.056 | 1338/5270 |
| Phosphate | 0.0206362 | 0.0297469 | 0.4878791 | Female | 0.0789402 | -0.0376678 | 0.021 | 0.030 | 0.488 | 1335/5264 |
tot$EstimateroundM=tot$Estimateround[tot$Sex=="Male"]
tot$EstimateroundF=tot$Estimateround[tot$Sex=="Female"]
tot$SEroundM=tot$SEround[tot$Sex=="Male"]
tot$SEroundF=tot$SEround[tot$Sex=="Female"]
tot$ProundM=tot$Pround[tot$Sex=="Male"]
tot$ProundF=tot$Pround[tot$Sex=="Female"]
tot$sampM=tot$samp[tot$Sex=="Male"]
tot$sampF=tot$samp[tot$Sex=="Female"]
tot%>%kbl()%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P | Sex | upper | lower | Estimateround | SEround | Pround | samp | EstimateroundM | EstimateroundF | SEroundM | SEroundF | ProundM | ProundF | sampM | sampF |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Apolipoprotein A | -0.0952853 | 0.0364059 | 0.0089011 | Male | -0.0239298 | -0.1666409 | -0.095 | 0.036 | 0.009 | 687/2798 | -0.095 | -0.054 | 0.036 | 0.026 | 0.009 | 0.038 | 687/2798 | 1324/5223 |
| Apolipoprotein B | -0.2207853 | 0.0392515 | 0.0000000 | Male | -0.1438524 | -0.2977183 | -0.221 | 0.039 | 2.0e-08 | 745/3014 | -0.221 | -0.161 | 0.039 | 0.028 | 2.0e-08 | 5.7e-09 | 745/3014 | 1452/5772 |
| HDL cholesterol | -0.1641141 | 0.0366923 | 0.0000080 | Male | -0.0921972 | -0.2360310 | -0.164 | 0.037 | 8.0e-06 | 689/2800 | -0.164 | -0.134 | 0.037 | 0.025 | 8.0e-06 | 1.2e-07 | 689/2800 | 1337/5275 |
| LDL direct | -0.2332525 | 0.0379934 | 0.0000000 | Male | -0.1587854 | -0.3077196 | -0.233 | 0.038 | 9.1e-10 | 757/3025 | -0.233 | -0.153 | 0.038 | 0.028 | 9.1e-10 | 3.7e-08 | 757/3025 | 1455/5783 |
| Lipoprotein A | 0.0328448 | 0.0437274 | 0.4526356 | Male | 0.1185506 | -0.0528610 | 0.033 | 0.044 | 0.453 | 608/2415 | 0.033 | -0.113 | 0.044 | 0.032 | 0.453 | 5.0e-04 | 608/2415 | 1166/4653 |
| Cholesterol | -0.2397004 | 0.0385400 | 0.0000000 | Male | -0.1641620 | -0.3152388 | -0.240 | 0.039 | 5.5e-10 | 758/3030 | -0.240 | -0.167 | 0.039 | 0.027 | 5.5e-10 | 9.0e-10 | 758/3030 | 1457/5796 |
| Triglycerides | 0.1819623 | 0.0423750 | 0.0000180 | Male | 0.2650173 | 0.0989073 | 0.182 | 0.042 | 1.8e-05 | 756/3027 | 0.182 | 0.229 | 0.042 | 0.026 | 1.8e-05 | 3.7e-19 | 756/3027 | 1456/5792 |
| IGF 1 | -0.1470875 | 0.0361661 | 0.0000486 | Male | -0.0762020 | -0.2179730 | -0.147 | 0.036 | 4.9e-05 | 752/3013 | -0.147 | -0.239 | 0.036 | 0.028 | 4.9e-05 | 4.2e-17 | 752/3013 | 1449/5772 |
| Vitamin D | -0.3399957 | 0.0445313 | 0.0000000 | Male | -0.2527144 | -0.4272770 | -0.340 | 0.045 | 2.9e-14 | 738/2956 | -0.340 | -0.408 | 0.045 | 0.033 | 2.9e-14 | 9.7e-36 | 738/2956 | 1392/5565 |
| Bioavailable testosterone | -0.0136650 | 0.0271881 | 0.6152724 | Male | 0.0396238 | -0.0669537 | -0.014 | 0.027 | 0.615 | 679/2761 | -0.014 | -0.036 | 0.027 | 0.020 | 0.615 | 0.076 | 679/2761 | 1064/4220 |
| Free testosterone | -0.0271668 | 0.0256020 | 0.2887110 | Male | 0.0230132 | -0.0773468 | -0.027 | 0.026 | 0.289 | 678/2767 | -0.027 | -0.015 | 0.026 | 0.020 | 0.289 | 0.476 | 678/2767 | 1106/4453 |
| Testosterone | -0.0054171 | 0.0258406 | 0.8339647 | Male | 0.0452305 | -0.0560646 | -0.005 | 0.026 | 0.834 | 751/2994 | -0.005 | -0.036 | 0.026 | 0.019 | 0.834 | 0.055 | 751/2994 | 1168/4678 |
| SHBG | 0.0084908 | 0.0338931 | 0.8022022 | Male | 0.0749213 | -0.0579397 | 0.008 | 0.034 | 0.802 | 682/2783 | 0.008 | -0.025 | 0.034 | 0.028 | 0.802 | 0.378 | 682/2783 | 1323/5212 |
| Alanine aminotransferase | -0.1786818 | 0.0380667 | 0.0000028 | Male | -0.1040710 | -0.2532925 | -0.179 | 0.038 | 2.8e-06 | 755/3029 | -0.179 | -0.136 | 0.038 | 0.026 | 2.8e-06 | 1.5e-07 | 755/3029 | 1457/5798 |
| Albumin | -0.0725563 | 0.0392101 | 0.0643339 | Male | 0.0042956 | -0.1494082 | -0.073 | 0.039 | 0.064 | 688/2800 | -0.073 | -0.066 | 0.039 | 0.030 | 0.064 | 0.030 | 688/2800 | 1338/5275 |
| Alkaline phosphatase | 0.0918610 | 0.0371810 | 0.0135309 | Male | 0.1647358 | 0.0189862 | 0.092 | 0.037 | 0.014 | 758/3030 | 0.092 | 0.153 | 0.037 | 0.028 | 0.014 | 4.9e-08 | 758/3030 | 1457/5796 |
| Aspartate aminotransferase | -0.0138357 | 0.0380193 | 0.7159433 | Male | 0.0606821 | -0.0883536 | -0.014 | 0.038 | 0.716 | 754/3020 | -0.014 | 0.058 | 0.038 | 0.027 | 0.716 | 0.029 | 754/3020 | 1452/5772 |
| C reactive protein | -0.0217979 | 0.0397824 | 0.5837734 | Male | 0.0561756 | -0.0997715 | -0.022 | 0.040 | 0.584 | 750/3023 | -0.022 | -0.073 | 0.040 | 0.030 | 0.584 | 0.014 | 750/3023 | 1452/5789 |
| Gamma glutamyltransferase | -0.1839996 | 0.0335011 | 0.0000000 | Male | -0.1183374 | -0.2496618 | -0.184 | 0.034 | 4.2e-08 | 757/3026 | -0.184 | -0.143 | 0.034 | 0.028 | 4.2e-08 | 3.2e-07 | 757/3026 | 1455/5793 |
| Direct bilirubin | 0.0016235 | 0.0401377 | 0.9677389 | Male | 0.0802933 | -0.0770464 | 0.002 | 0.040 | 0.968 | 704/2844 | 0.002 | -0.019 | 0.040 | 0.032 | 0.968 | 0.558 | 704/2844 | 1184/4716 |
| Total bilirubin | -0.0049710 | 0.0365885 | 0.8919374 | Male | 0.0667425 | -0.0766845 | -0.005 | 0.037 | 0.892 | 755/3018 | -0.005 | -0.036 | 0.037 | 0.029 | 0.892 | 0.217 | 755/3018 | 1451/5769 |
| Total protein | -0.1212301 | 0.0407742 | 0.0029672 | Male | -0.0413128 | -0.2011475 | -0.121 | 0.041 | 0.003 | 689/2802 | -0.121 | -0.044 | 0.041 | 0.031 | 0.003 | 0.156 | 689/2802 | 1337/5272 |
| Creatinine | -0.5932464 | 0.0287057 | 0.0000000 | Male | -0.5369832 | -0.6495095 | -0.593 | 0.029 | 5.6e-90 | 756/3029 | -0.593 | -0.365 | 0.029 | 0.022 | 5.6e-90 | 9.8e-60 | 756/3029 | 1456/5793 |
| Cystatin C | 0.2584474 | 0.0326227 | 0.0000000 | Male | 0.3223879 | 0.1945069 | 0.258 | 0.033 | 3.0e-15 | 757/3029 | 0.258 | 0.371 | 0.033 | 0.026 | 3.0e-15 | 5.3e-47 | 757/3029 | 1456/5801 |
| eGFR | 0.0270818 | 0.0333761 | 0.4171801 | Male | 0.0924989 | -0.0383353 | 0.027 | 0.033 | 0.417 | 755/3028 | 0.027 | -0.046 | 0.033 | 0.025 | 0.417 | 0.068 | 755/3028 | 1455/5792 |
| HbA1c | -0.0579008 | 0.0390234 | 0.1379605 | Male | 0.0185850 | -0.1343866 | -0.058 | 0.039 | 0.138 | 748/3008 | -0.058 | 0.049 | 0.039 | 0.025 | 0.138 | 0.048 | 748/3008 | 1450/5774 |
| Urate | -0.2125853 | 0.0301554 | 0.0000000 | Male | -0.1534806 | -0.2716900 | -0.213 | 0.030 | 2.1e-12 | 757/3026 | -0.213 | -0.148 | 0.030 | 0.023 | 2.1e-12 | 1.6e-10 | 757/3026 | 1452/5791 |
| Urea | -0.6485103 | 0.0392898 | 0.0000000 | Male | -0.5715022 | -0.7255184 | -0.649 | 0.039 | 3.8e-59 | 757/3029 | -0.649 | -0.598 | 0.039 | 0.028 | 3.8e-59 | 7.8e-98 | 757/3029 | 1455/5792 |
| Calcium | -0.1079126 | 0.0410376 | 0.0085861 | Male | -0.0274790 | -0.1883462 | -0.108 | 0.041 | 0.009 | 687/2802 | -0.108 | -0.060 | 0.041 | 0.031 | 0.009 | 0.056 | 687/2802 | 1338/5270 |
| Phosphate | -0.0043175 | 0.0457044 | 0.9247453 | Male | 0.0852632 | -0.0938982 | -0.004 | 0.046 | 0.925 | 688/2791 | -0.004 | 0.021 | 0.046 | 0.030 | 0.925 | 0.488 | 688/2791 | 1335/5264 |
| Apolipoprotein A | -0.0537930 | 0.0258712 | 0.0376326 | Female | -0.0030853 | -0.1045006 | -0.054 | 0.026 | 0.038 | 1324/5223 | -0.095 | -0.054 | 0.036 | 0.026 | 0.009 | 0.038 | 687/2798 | 1324/5223 |
| Apolipoprotein B | -0.1610183 | 0.0276138 | 0.0000000 | Female | -0.1068953 | -0.2151413 | -0.161 | 0.028 | 5.7e-09 | 1452/5772 | -0.221 | -0.161 | 0.039 | 0.028 | 2.0e-08 | 5.7e-09 | 745/3014 | 1452/5772 |
| HDL cholesterol | -0.1338099 | 0.0252510 | 0.0000001 | Female | -0.0843179 | -0.1833018 | -0.134 | 0.025 | 1.2e-07 | 1337/5275 | -0.164 | -0.134 | 0.037 | 0.025 | 8.0e-06 | 1.2e-07 | 689/2800 | 1337/5275 |
| LDL direct | -0.1533478 | 0.0278392 | 0.0000000 | Female | -0.0987829 | -0.2079128 | -0.153 | 0.028 | 3.7e-08 | 1455/5783 | -0.233 | -0.153 | 0.038 | 0.028 | 9.1e-10 | 3.7e-08 | 757/3025 | 1455/5783 |
| Lipoprotein A | -0.1128965 | 0.0324002 | 0.0004968 | Female | -0.0493921 | -0.1764010 | -0.113 | 0.032 | 5.0e-04 | 1166/4653 | 0.033 | -0.113 | 0.044 | 0.032 | 0.453 | 5.0e-04 | 608/2415 | 1166/4653 |
| Cholesterol | -0.1668960 | 0.0272094 | 0.0000000 | Female | -0.1135655 | -0.2202265 | -0.167 | 0.027 | 9.0e-10 | 1457/5796 | -0.240 | -0.167 | 0.039 | 0.027 | 5.5e-10 | 9.0e-10 | 758/3030 | 1457/5796 |
| Triglycerides | 0.2294534 | 0.0255783 | 0.0000000 | Female | 0.2795868 | 0.1793200 | 0.229 | 0.026 | 3.7e-19 | 1456/5792 | 0.182 | 0.229 | 0.042 | 0.026 | 1.8e-05 | 3.7e-19 | 756/3027 | 1456/5792 |
| IGF 1 | -0.2393446 | 0.0284029 | 0.0000000 | Female | -0.1836750 | -0.2950142 | -0.239 | 0.028 | 4.2e-17 | 1449/5772 | -0.147 | -0.239 | 0.036 | 0.028 | 4.9e-05 | 4.2e-17 | 752/3013 | 1449/5772 |
| Vitamin D | -0.4082598 | 0.0325304 | 0.0000000 | Female | -0.3445001 | -0.4720194 | -0.408 | 0.033 | 9.7e-36 | 1392/5565 | -0.340 | -0.408 | 0.045 | 0.033 | 2.9e-14 | 9.7e-36 | 738/2956 | 1392/5565 |
| Bioavailable testosterone | -0.0362555 | 0.0204403 | 0.0761658 | Female | 0.0038074 | -0.0763184 | -0.036 | 0.020 | 0.076 | 1064/4220 | -0.014 | -0.036 | 0.027 | 0.020 | 0.615 | 0.076 | 679/2761 | 1064/4220 |
| Free testosterone | -0.0145430 | 0.0204022 | 0.4759896 | Female | 0.0254453 | -0.0545312 | -0.015 | 0.020 | 0.476 | 1106/4453 | -0.027 | -0.015 | 0.026 | 0.020 | 0.289 | 0.476 | 678/2767 | 1106/4453 |
| Testosterone | -0.0361472 | 0.0188108 | 0.0547023 | Female | 0.0007220 | -0.0730163 | -0.036 | 0.019 | 0.055 | 1168/4678 | -0.005 | -0.036 | 0.026 | 0.019 | 0.834 | 0.055 | 751/2994 | 1168/4678 |
| SHBG | -0.0249352 | 0.0282841 | 0.3780273 | Female | 0.0305016 | -0.0803720 | -0.025 | 0.028 | 0.378 | 1323/5212 | 0.008 | -0.025 | 0.034 | 0.028 | 0.802 | 0.378 | 682/2783 | 1323/5212 |
| Alanine aminotransferase | -0.1360117 | 0.0258480 | 0.0000001 | Female | -0.0853497 | -0.1866737 | -0.136 | 0.026 | 1.5e-07 | 1457/5798 | -0.179 | -0.136 | 0.038 | 0.026 | 2.8e-06 | 1.5e-07 | 755/3029 | 1457/5798 |
| Albumin | -0.0657714 | 0.0303187 | 0.0300928 | Female | -0.0063468 | -0.1251960 | -0.066 | 0.030 | 0.030 | 1338/5275 | -0.073 | -0.066 | 0.039 | 0.030 | 0.064 | 0.030 | 688/2800 | 1338/5275 |
| Alkaline phosphatase | 0.1533666 | 0.0280940 | 0.0000000 | Female | 0.2084309 | 0.0983023 | 0.153 | 0.028 | 4.9e-08 | 1457/5796 | 0.092 | 0.153 | 0.037 | 0.028 | 0.014 | 4.9e-08 | 758/3030 | 1457/5796 |
| Aspartate aminotransferase | 0.0583374 | 0.0267167 | 0.0290268 | Female | 0.1107021 | 0.0059728 | 0.058 | 0.027 | 0.029 | 1452/5772 | -0.014 | 0.058 | 0.038 | 0.027 | 0.716 | 0.029 | 754/3020 | 1452/5772 |
| C reactive protein | -0.0729257 | 0.0297921 | 0.0143957 | Female | -0.0145333 | -0.1313182 | -0.073 | 0.030 | 0.014 | 1452/5789 | -0.022 | -0.073 | 0.040 | 0.030 | 0.584 | 0.014 | 750/3023 | 1452/5789 |
| Gamma glutamyltransferase | -0.1426310 | 0.0278650 | 0.0000003 | Female | -0.0880156 | -0.1972464 | -0.143 | 0.028 | 3.2e-07 | 1455/5793 | -0.184 | -0.143 | 0.034 | 0.028 | 4.2e-08 | 3.2e-07 | 757/3026 | 1455/5793 |
| Direct bilirubin | -0.0185505 | 0.0316874 | 0.5582862 | Female | 0.0435568 | -0.0806577 | -0.019 | 0.032 | 0.558 | 1184/4716 | 0.002 | -0.019 | 0.040 | 0.032 | 0.968 | 0.558 | 704/2844 | 1184/4716 |
| Total bilirubin | -0.0356154 | 0.0288654 | 0.2173023 | Female | 0.0209609 | -0.0921916 | -0.036 | 0.029 | 0.217 | 1451/5769 | -0.005 | -0.036 | 0.037 | 0.029 | 0.892 | 0.217 | 755/3018 | 1451/5769 |
| Total protein | -0.0436369 | 0.0307202 | 0.1555203 | Female | 0.0165747 | -0.1038486 | -0.044 | 0.031 | 0.156 | 1337/5272 | -0.121 | -0.044 | 0.041 | 0.031 | 0.003 | 0.156 | 689/2802 | 1337/5272 |
| Creatinine | -0.3648762 | 0.0221789 | 0.0000000 | Female | -0.3214055 | -0.4083469 | -0.365 | 0.022 | 9.8e-60 | 1456/5793 | -0.593 | -0.365 | 0.029 | 0.022 | 5.6e-90 | 9.8e-60 | 756/3029 | 1456/5793 |
| Cystatin C | 0.3706779 | 0.0255587 | 0.0000000 | Female | 0.4207729 | 0.3205828 | 0.371 | 0.026 | 5.3e-47 | 1456/5801 | 0.258 | 0.371 | 0.033 | 0.026 | 3.0e-15 | 5.3e-47 | 757/3029 | 1456/5801 |
| eGFR | -0.0457096 | 0.0250802 | 0.0684152 | Female | 0.0034477 | -0.0948668 | -0.046 | 0.025 | 0.068 | 1455/5792 | 0.027 | -0.046 | 0.033 | 0.025 | 0.417 | 0.068 | 755/3028 | 1455/5792 |
| HbA1c | 0.0489391 | 0.0247224 | 0.0477929 | Female | 0.0973950 | 0.0004831 | 0.049 | 0.025 | 0.048 | 1450/5774 | -0.058 | 0.049 | 0.039 | 0.025 | 0.138 | 0.048 | 748/3008 | 1450/5774 |
| Urate | -0.1482158 | 0.0231485 | 0.0000000 | Female | -0.1028448 | -0.1935869 | -0.148 | 0.023 | 1.6e-10 | 1452/5791 | -0.213 | -0.148 | 0.030 | 0.023 | 2.1e-12 | 1.6e-10 | 757/3026 | 1452/5791 |
| Urea | -0.5982422 | 0.0280654 | 0.0000000 | Female | -0.5432340 | -0.6532504 | -0.598 | 0.028 | 7.8e-98 | 1455/5792 | -0.649 | -0.598 | 0.039 | 0.028 | 3.8e-59 | 7.8e-98 | 757/3029 | 1455/5792 |
| Calcium | -0.0598459 | 0.0313665 | 0.0564403 | Female | 0.0016324 | -0.1213241 | -0.060 | 0.031 | 0.056 | 1338/5270 | -0.108 | -0.060 | 0.041 | 0.031 | 0.009 | 0.056 | 687/2802 | 1338/5270 |
| Phosphate | 0.0206362 | 0.0297469 | 0.4878791 | Female | 0.0789402 | -0.0376678 | 0.021 | 0.030 | 0.488 | 1335/5264 | -0.004 | 0.021 | 0.046 | 0.030 | 0.925 | 0.488 | 688/2791 | 1335/5264 |
tot=tot%>%select(Trait, EstimateroundM, ProundM, sampM,
EstimateroundF, ProundF, sampF, everything())
tot=cbind(Category, tot)
headerM=tibble(Category="Category",
Trait="Trait",
Sex="Male")
headerF=tibble(Category="Category",
Trait="Trait",
Sex="Female")
tot2=bind_rows(headerM, tot)
tot3=bind_rows(headerF, tot2)
#
#png("forest.sexstrat.png",width = 10, height =8, units = 'in', res = 600)
tot3 %>%
group_by(Sex) %>%
forestplot(mean="Estimate",
labeltext=c("Category", "Trait"),
lower="lower", upper="upper",
boxsize = 0.2,
ci.vertices = TRUE,
ci.vertices.height = 0.05,
shapes_gp = fpShapesGp(box = c("darkred", "blue") %>%
lapply(function(x) gpar(fill = x, col = "#555555")),
default = gpar(vertices = TRUE)),
hrzl_lines = list("2" = gpar(lty = 2)),
grid=TRUE,
zero = 0,
xticks=xtik,
mar = unit(c(0,0.5,0.2,0.5), "in"),
xlab = "Standardized veg. effect ± 95% CI (no BMI covar.)",
txt_gp = fpTxtGp(xlab = gpar(cex = 1.2),
ticks = gpar(fontfamily = "", cex = 1)
),
fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI)
)%>% fp_set_zebra_style("#F7F7F7")
#dev.off()
outplot=tot%>%select(Trait, EstimateroundM, SEroundM, ProundM, sampM,
EstimateroundF, SEroundF, ProundF, sampF)
outplot$ProundM = cell_spec(outplot$ProundM,
color=ifelse(as.double(outplot$ProundM) <0.0017, "#36E072", "grey"))
outplot$ProundF = cell_spec(outplot$ProundF,
color=ifelse(as.double(outplot$ProundF) <0.0017, "#36E072", "grey"))
colnames(outplot)=c("Trait", "BetaVegm", "SEm", "Pm", "N (veg/non-veg)m","BetaVegf", "SEf", "Pf", "N (veg/non-veg)f")
outplot%>%
kbl(booktabs = T, linesep = "", escape=FALSE,align="l") %>%
kable_classic_2(full_width = F)| Trait | BetaVegm | SEm | Pm | N (veg/non-veg)m | BetaVegf | SEf | Pf | N (veg/non-veg)f |
|---|---|---|---|---|---|---|---|---|
| Apolipoprotein A | -0.095 | 0.036 | 0.009 | 687/2798 | -0.054 | 0.026 | 0.038 | 1324/5223 |
| Apolipoprotein B | -0.221 | 0.039 | 2.0e-08 | 745/3014 | -0.161 | 0.028 | 5.7e-09 | 1452/5772 |
| HDL cholesterol | -0.164 | 0.037 | 8.0e-06 | 689/2800 | -0.134 | 0.025 | 1.2e-07 | 1337/5275 |
| LDL direct | -0.233 | 0.038 | 9.1e-10 | 757/3025 | -0.153 | 0.028 | 3.7e-08 | 1455/5783 |
| Lipoprotein A | 0.033 | 0.044 | 0.453 | 608/2415 | -0.113 | 0.032 | 5.0e-04 | 1166/4653 |
| Cholesterol | -0.240 | 0.039 | 5.5e-10 | 758/3030 | -0.167 | 0.027 | 9.0e-10 | 1457/5796 |
| Triglycerides | 0.182 | 0.042 | 1.8e-05 | 756/3027 | 0.229 | 0.026 | 3.7e-19 | 1456/5792 |
| IGF 1 | -0.147 | 0.036 | 4.9e-05 | 752/3013 | -0.239 | 0.028 | 4.2e-17 | 1449/5772 |
| Vitamin D | -0.340 | 0.045 | 2.9e-14 | 738/2956 | -0.408 | 0.033 | 9.7e-36 | 1392/5565 |
| Bioavailable testosterone | -0.014 | 0.027 | 0.615 | 679/2761 | -0.036 | 0.020 | 0.076 | 1064/4220 |
| Free testosterone | -0.027 | 0.026 | 0.289 | 678/2767 | -0.015 | 0.020 | 0.476 | 1106/4453 |
| Testosterone | -0.005 | 0.026 | 0.834 | 751/2994 | -0.036 | 0.019 | 0.055 | 1168/4678 |
| SHBG | 0.008 | 0.034 | 0.802 | 682/2783 | -0.025 | 0.028 | 0.378 | 1323/5212 |
| Alanine aminotransferase | -0.179 | 0.038 | 2.8e-06 | 755/3029 | -0.136 | 0.026 | 1.5e-07 | 1457/5798 |
| Albumin | -0.073 | 0.039 | 0.064 | 688/2800 | -0.066 | 0.030 | 0.030 | 1338/5275 |
| Alkaline phosphatase | 0.092 | 0.037 | 0.014 | 758/3030 | 0.153 | 0.028 | 4.9e-08 | 1457/5796 |
| Aspartate aminotransferase | -0.014 | 0.038 | 0.716 | 754/3020 | 0.058 | 0.027 | 0.029 | 1452/5772 |
| C reactive protein | -0.022 | 0.040 | 0.584 | 750/3023 | -0.073 | 0.030 | 0.014 | 1452/5789 |
| Gamma glutamyltransferase | -0.184 | 0.034 | 4.2e-08 | 757/3026 | -0.143 | 0.028 | 3.2e-07 | 1455/5793 |
| Direct bilirubin | 0.002 | 0.040 | 0.968 | 704/2844 | -0.019 | 0.032 | 0.558 | 1184/4716 |
| Total bilirubin | -0.005 | 0.037 | 0.892 | 755/3018 | -0.036 | 0.029 | 0.217 | 1451/5769 |
| Total protein | -0.121 | 0.041 | 0.003 | 689/2802 | -0.044 | 0.031 | 0.156 | 1337/5272 |
| Creatinine | -0.593 | 0.029 | 5.6e-90 | 756/3029 | -0.365 | 0.022 | 9.8e-60 | 1456/5793 |
| Cystatin C | 0.258 | 0.033 | 3.0e-15 | 757/3029 | 0.371 | 0.026 | 5.3e-47 | 1456/5801 |
| eGFR | 0.027 | 0.033 | 0.417 | 755/3028 | -0.046 | 0.025 | 0.068 | 1455/5792 |
| HbA1c | -0.058 | 0.039 | 0.138 | 748/3008 | 0.049 | 0.025 | 0.048 | 1450/5774 |
| Urate | -0.213 | 0.030 | 2.1e-12 | 757/3026 | -0.148 | 0.023 | 1.6e-10 | 1452/5791 |
| Urea | -0.649 | 0.039 | 3.8e-59 | 757/3029 | -0.598 | 0.028 | 7.8e-98 | 1455/5792 |
| Calcium | -0.108 | 0.041 | 0.009 | 687/2802 | -0.060 | 0.031 | 0.056 | 1338/5270 |
| Phosphate | -0.004 | 0.046 | 0.925 | 688/2791 | 0.021 | 0.030 | 0.488 | 1335/5264 |
| Apolipoprotein A | -0.095 | 0.036 | 0.009 | 687/2798 | -0.054 | 0.026 | 0.038 | 1324/5223 |
| Apolipoprotein B | -0.221 | 0.039 | 2.0e-08 | 745/3014 | -0.161 | 0.028 | 5.7e-09 | 1452/5772 |
| HDL cholesterol | -0.164 | 0.037 | 8.0e-06 | 689/2800 | -0.134 | 0.025 | 1.2e-07 | 1337/5275 |
| LDL direct | -0.233 | 0.038 | 9.1e-10 | 757/3025 | -0.153 | 0.028 | 3.7e-08 | 1455/5783 |
| Lipoprotein A | 0.033 | 0.044 | 0.453 | 608/2415 | -0.113 | 0.032 | 5.0e-04 | 1166/4653 |
| Cholesterol | -0.240 | 0.039 | 5.5e-10 | 758/3030 | -0.167 | 0.027 | 9.0e-10 | 1457/5796 |
| Triglycerides | 0.182 | 0.042 | 1.8e-05 | 756/3027 | 0.229 | 0.026 | 3.7e-19 | 1456/5792 |
| IGF 1 | -0.147 | 0.036 | 4.9e-05 | 752/3013 | -0.239 | 0.028 | 4.2e-17 | 1449/5772 |
| Vitamin D | -0.340 | 0.045 | 2.9e-14 | 738/2956 | -0.408 | 0.033 | 9.7e-36 | 1392/5565 |
| Bioavailable testosterone | -0.014 | 0.027 | 0.615 | 679/2761 | -0.036 | 0.020 | 0.076 | 1064/4220 |
| Free testosterone | -0.027 | 0.026 | 0.289 | 678/2767 | -0.015 | 0.020 | 0.476 | 1106/4453 |
| Testosterone | -0.005 | 0.026 | 0.834 | 751/2994 | -0.036 | 0.019 | 0.055 | 1168/4678 |
| SHBG | 0.008 | 0.034 | 0.802 | 682/2783 | -0.025 | 0.028 | 0.378 | 1323/5212 |
| Alanine aminotransferase | -0.179 | 0.038 | 2.8e-06 | 755/3029 | -0.136 | 0.026 | 1.5e-07 | 1457/5798 |
| Albumin | -0.073 | 0.039 | 0.064 | 688/2800 | -0.066 | 0.030 | 0.030 | 1338/5275 |
| Alkaline phosphatase | 0.092 | 0.037 | 0.014 | 758/3030 | 0.153 | 0.028 | 4.9e-08 | 1457/5796 |
| Aspartate aminotransferase | -0.014 | 0.038 | 0.716 | 754/3020 | 0.058 | 0.027 | 0.029 | 1452/5772 |
| C reactive protein | -0.022 | 0.040 | 0.584 | 750/3023 | -0.073 | 0.030 | 0.014 | 1452/5789 |
| Gamma glutamyltransferase | -0.184 | 0.034 | 4.2e-08 | 757/3026 | -0.143 | 0.028 | 3.2e-07 | 1455/5793 |
| Direct bilirubin | 0.002 | 0.040 | 0.968 | 704/2844 | -0.019 | 0.032 | 0.558 | 1184/4716 |
| Total bilirubin | -0.005 | 0.037 | 0.892 | 755/3018 | -0.036 | 0.029 | 0.217 | 1451/5769 |
| Total protein | -0.121 | 0.041 | 0.003 | 689/2802 | -0.044 | 0.031 | 0.156 | 1337/5272 |
| Creatinine | -0.593 | 0.029 | 5.6e-90 | 756/3029 | -0.365 | 0.022 | 9.8e-60 | 1456/5793 |
| Cystatin C | 0.258 | 0.033 | 3.0e-15 | 757/3029 | 0.371 | 0.026 | 5.3e-47 | 1456/5801 |
| eGFR | 0.027 | 0.033 | 0.417 | 755/3028 | -0.046 | 0.025 | 0.068 | 1455/5792 |
| HbA1c | -0.058 | 0.039 | 0.138 | 748/3008 | 0.049 | 0.025 | 0.048 | 1450/5774 |
| Urate | -0.213 | 0.030 | 2.1e-12 | 757/3026 | -0.148 | 0.023 | 1.6e-10 | 1452/5791 |
| Urea | -0.649 | 0.039 | 3.8e-59 | 757/3029 | -0.598 | 0.028 | 7.8e-98 | 1455/5792 |
| Calcium | -0.108 | 0.041 | 0.009 | 687/2802 | -0.060 | 0.031 | 0.056 | 1338/5270 |
| Phosphate | -0.004 | 0.046 | 0.925 | 688/2791 | 0.021 | 0.030 | 0.488 | 1335/5264 |
Run lm sex-stratified adj-BMI
for (i in 1:length(phe)){
fitM[[i]] <- lm(mdM[[phe[i]]] ~ Veg5yr1 + Age + BMI + AlcoholFreq +
PreviousSmoker +CurrentSmoker+
zTownsend+PCA1 + PCA2 + PCA3 +
PCA4 + PCA5, data = mdM, na.action = na.exclude)
fitF[[i]] <- lm(mdF[[phe[i]]] ~ Veg5yr1 + Age + BMI + AlcoholFreq +
PreviousSmoker +CurrentSmoker+
zTownsend+PCA1 + PCA2 + PCA3 +
PCA4 + PCA5, data = mdF, na.action = na.exclude)
outM[i,1]=phe[i]
outF[i,1]=phe[i]
#Cluster-robust standard errors
coM=coeftest(fitM[[i]], vcov. = vcovCL, cluster = ~subclass)["Veg5yr1",,drop=FALSE]
coF=coeftest(fitF[[i]], vcov. = vcovCL, cluster = ~subclass)["Veg5yr1",,drop=FALSE]
outM[i,2]=coM[1]
outM[i,3]=coM[2]
outM[i,4]=coM[4]
outF[i,2]=coF[1]
outF[i,3]=coF[2]
outF[i,4]=coF[4]
}
outM=as.data.frame(outM)
outM[2:4]=sapply(outM[2:4], as.numeric)
as_tibble(outM)%>%kbl(caption="Male adj-BMI")%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P | Sex | upper | lower | Estimateround | SEround | Pround | samp |
|---|---|---|---|---|---|---|---|---|---|---|
| Apolipoprotein_A_rint | -0.1267279 | 0.0355128 | 0.0003639 | Male | -0.0239298 | -0.1666409 | -0.095 | 0.036 | 0.009 | 687/2798 |
| Apolipoprotein_B_rint | -0.1925021 | 0.0380941 | 0.0000005 | Male | -0.1438524 | -0.2977183 | -0.221 | 0.039 | 2.0e-08 | 745/3014 |
| HDL_cholesterol_rint | -0.2083215 | 0.0348524 | 0.0000000 | Male | -0.0921972 | -0.2360310 | -0.164 | 0.037 | 8.0e-06 | 689/2800 |
| LDL_direct_rint | -0.2112578 | 0.0372037 | 0.0000000 | Male | -0.1587854 | -0.3077196 | -0.233 | 0.038 | 9.1e-10 | 757/3025 |
| Lipoprotein_A_rint | 0.0316919 | 0.0438591 | 0.4699919 | Male | 0.1185506 | -0.0528610 | 0.033 | 0.044 | 0.453 | 608/2415 |
| Cholesterol_rint | -0.2238045 | 0.0381212 | 0.0000000 | Male | -0.1641620 | -0.3152388 | -0.240 | 0.039 | 5.5e-10 | 758/3030 |
| Triglycerides_rint | 0.2301472 | 0.0397995 | 0.0000000 | Male | 0.2650173 | 0.0989073 | 0.182 | 0.042 | 1.8e-05 | 756/3027 |
| IGF_1_rint | -0.1502783 | 0.0361740 | 0.0000334 | Male | -0.0762020 | -0.2179730 | -0.147 | 0.036 | 4.9e-05 | 752/3013 |
| Vitamin_D_rint | -0.3567426 | 0.0442040 | 0.0000000 | Male | -0.2527144 | -0.4272770 | -0.340 | 0.045 | 2.9e-14 | 738/2956 |
| Bioavailable_testosterone_rint | -0.0291545 | 0.0267282 | 0.2754473 | Male | 0.0396238 | -0.0669537 | -0.014 | 0.027 | 0.615 | 679/2761 |
| Free_testosterone_rint | -0.0259667 | 0.0256344 | 0.3111496 | Male | 0.0230132 | -0.0773468 | -0.027 | 0.026 | 0.289 | 678/2767 |
| Testosterone_rint | -0.0269085 | 0.0248827 | 0.2795819 | Male | 0.0452305 | -0.0560646 | -0.005 | 0.026 | 0.834 | 751/2994 |
| SHBG_rint | -0.0350940 | 0.0314007 | 0.2638066 | Male | 0.0749213 | -0.0579397 | 0.008 | 0.034 | 0.802 | 682/2783 |
| Alanine_aminotransferase_rint | -0.1384570 | 0.0361785 | 0.0001318 | Male | -0.1040710 | -0.2532925 | -0.179 | 0.038 | 2.8e-06 | 755/3029 |
| Albumin_rint | -0.0808145 | 0.0392909 | 0.0397775 | Male | 0.0042956 | -0.1494082 | -0.073 | 0.039 | 0.064 | 688/2800 |
| Alkaline_phosphatase_rint | 0.1032799 | 0.0370858 | 0.0053813 | Male | 0.1647358 | 0.0189862 | 0.092 | 0.037 | 0.014 | 758/3030 |
| Aspartate_aminotransferase_rint | 0.0002263 | 0.0378300 | 0.9952281 | Male | 0.0606821 | -0.0883536 | -0.014 | 0.038 | 0.716 | 754/3020 |
| C_reactive_protein_rint | 0.0211213 | 0.0375527 | 0.5738468 | Male | 0.0561756 | -0.0997715 | -0.022 | 0.040 | 0.584 | 750/3023 |
| Gamma_glutamyltransferase_rint | -0.1486263 | 0.0320317 | 0.0000036 | Male | -0.1183374 | -0.2496618 | -0.184 | 0.034 | 4.2e-08 | 757/3026 |
| Direct_bilirubin_rint | -0.0102032 | 0.0400712 | 0.7990270 | Male | 0.0802933 | -0.0770464 | 0.002 | 0.040 | 0.968 | 704/2844 |
| Total_bilirubin_rint | -0.0133426 | 0.0365542 | 0.7151251 | Male | 0.0667425 | -0.0766845 | -0.005 | 0.037 | 0.892 | 755/3018 |
| Total_protein_rint | -0.1152243 | 0.0409079 | 0.0048797 | Male | -0.0413128 | -0.2011475 | -0.121 | 0.041 | 0.003 | 689/2802 |
| Creatinine_rint | -0.5768706 | 0.0284864 | 0.0000000 | Male | -0.5369832 | -0.6495095 | -0.593 | 0.029 | 5.6e-90 | 756/3029 |
| Cystatin_C_rint | 0.2854492 | 0.0314230 | 0.0000000 | Male | 0.3223879 | 0.1945069 | 0.258 | 0.033 | 3.0e-15 | 757/3029 |
| eGFR_rint | -0.0019476 | 0.0322265 | 0.9518123 | Male | 0.0924989 | -0.0383353 | 0.027 | 0.033 | 0.417 | 755/3028 |
| HbA1c_rint | -0.0396035 | 0.0386380 | 0.3054344 | Male | 0.0185850 | -0.1343866 | -0.058 | 0.039 | 0.138 | 748/3008 |
| Urate_rint | -0.1764115 | 0.0286627 | 0.0000000 | Male | -0.1534806 | -0.2716900 | -0.213 | 0.030 | 2.1e-12 | 757/3026 |
| Urea_rint | -0.6424311 | 0.0392741 | 0.0000000 | Male | -0.5715022 | -0.7255184 | -0.649 | 0.039 | 3.8e-59 | 757/3029 |
| Calcium_rint | -0.1105072 | 0.0411100 | 0.0072205 | Male | -0.0274790 | -0.1883462 | -0.108 | 0.041 | 0.009 | 687/2802 |
| Phosphate_rint | -0.0088235 | 0.0457907 | 0.8472122 | Male | 0.0852632 | -0.0938982 | -0.004 | 0.046 | 0.925 | 688/2791 |
outF=as.data.frame(outF)
outF[2:4]=sapply(outF[2:4], as.numeric)
as_tibble(outF)%>%kbl(caption="Female adj-BMI")%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P | Sex | upper | lower | Estimateround | SEround | Pround | samp |
|---|---|---|---|---|---|---|---|---|---|---|
| Apolipoprotein_A_rint | -0.0507849 | 0.0254139 | 0.0457243 | Female | -0.0030853 | -0.1045006 | -0.054 | 0.026 | 0.038 | 1324/5223 |
| Apolipoprotein_B_rint | -0.1669199 | 0.0267955 | 0.0000000 | Female | -0.1068953 | -0.2151413 | -0.161 | 0.028 | 5.7e-09 | 1452/5772 |
| HDL_cholesterol_rint | -0.1312893 | 0.0243112 | 0.0000001 | Female | -0.0843179 | -0.1833018 | -0.134 | 0.025 | 1.2e-07 | 1337/5275 |
| LDL_direct_rint | -0.1578437 | 0.0272018 | 0.0000000 | Female | -0.0987829 | -0.2079128 | -0.153 | 0.028 | 3.7e-08 | 1455/5783 |
| Lipoprotein_A_rint | -0.1133998 | 0.0323857 | 0.0004661 | Female | -0.0493921 | -0.1764010 | -0.113 | 0.032 | 5.0e-04 | 1166/4653 |
| Cholesterol_rint | -0.1696707 | 0.0269326 | 0.0000000 | Female | -0.1135655 | -0.2202265 | -0.167 | 0.027 | 9.0e-10 | 1457/5796 |
| Triglycerides_rint | 0.2221814 | 0.0241788 | 0.0000000 | Female | 0.2795868 | 0.1793200 | 0.229 | 0.026 | 3.7e-19 | 1456/5792 |
| IGF_1_rint | -0.2383082 | 0.0283668 | 0.0000000 | Female | -0.1836750 | -0.2950142 | -0.239 | 0.028 | 4.2e-17 | 1449/5772 |
| Vitamin_D_rint | -0.4043642 | 0.0323105 | 0.0000000 | Female | -0.3445001 | -0.4720194 | -0.408 | 0.033 | 9.7e-36 | 1392/5565 |
| Bioavailable_testosterone_rint | -0.0409250 | 0.0200896 | 0.0416879 | Female | 0.0038074 | -0.0763184 | -0.036 | 0.020 | 0.076 | 1064/4220 |
| Free_testosterone_rint | -0.0205851 | 0.0195642 | 0.2927619 | Female | 0.0254453 | -0.0545312 | -0.015 | 0.020 | 0.476 | 1106/4453 |
| Testosterone_rint | -0.0396346 | 0.0187474 | 0.0345460 | Female | 0.0007220 | -0.0730163 | -0.036 | 0.019 | 0.055 | 1168/4678 |
| SHBG_rint | -0.0225707 | 0.0262092 | 0.3891722 | Female | 0.0305016 | -0.0803720 | -0.025 | 0.028 | 0.378 | 1323/5212 |
| Alanine_aminotransferase_rint | -0.1409599 | 0.0251099 | 0.0000000 | Female | -0.0853497 | -0.1866737 | -0.136 | 0.026 | 1.5e-07 | 1457/5798 |
| Albumin_rint | -0.0642046 | 0.0299417 | 0.0320438 | Female | -0.0063468 | -0.1251960 | -0.066 | 0.030 | 0.030 | 1338/5275 |
| Alkaline_phosphatase_rint | 0.1487686 | 0.0273806 | 0.0000001 | Female | 0.2084309 | 0.0983023 | 0.153 | 0.028 | 4.9e-08 | 1457/5796 |
| Aspartate_aminotransferase_rint | 0.0578253 | 0.0266927 | 0.0303181 | Female | 0.1107021 | 0.0059728 | 0.058 | 0.027 | 0.029 | 1452/5772 |
| C_reactive_protein_rint | -0.0839135 | 0.0267741 | 0.0017306 | Female | -0.0145333 | -0.1313182 | -0.073 | 0.030 | 0.014 | 1452/5789 |
| Gamma_glutamyltransferase_rint | -0.1478597 | 0.0270909 | 0.0000000 | Female | -0.0880156 | -0.1972464 | -0.143 | 0.028 | 3.2e-07 | 1455/5793 |
| Direct_bilirubin_rint | -0.0154163 | 0.0315130 | 0.6247159 | Female | 0.0435568 | -0.0806577 | -0.019 | 0.032 | 0.558 | 1184/4716 |
| Total_bilirubin_rint | -0.0321196 | 0.0287448 | 0.2638580 | Female | 0.0209609 | -0.0921916 | -0.036 | 0.029 | 0.217 | 1451/5769 |
| Total_protein_rint | -0.0438038 | 0.0307217 | 0.1539664 | Female | 0.0165747 | -0.1038486 | -0.044 | 0.031 | 0.156 | 1337/5272 |
| Creatinine_rint | -0.3668075 | 0.0220102 | 0.0000000 | Female | -0.3214055 | -0.4083469 | -0.365 | 0.022 | 9.8e-60 | 1456/5793 |
| Cystatin_C_rint | 0.3647104 | 0.0245915 | 0.0000000 | Female | 0.4207729 | 0.3205828 | 0.371 | 0.026 | 5.3e-47 | 1456/5801 |
| eGFR_rint | -0.0407539 | 0.0243187 | 0.0938163 | Female | 0.0034477 | -0.0948668 | -0.046 | 0.025 | 0.068 | 1455/5792 |
| HbA1c_rint | 0.0450948 | 0.0244823 | 0.0655259 | Female | 0.0973950 | 0.0004831 | 0.049 | 0.025 | 0.048 | 1450/5774 |
| Urate_rint | -0.1543325 | 0.0218372 | 0.0000000 | Female | -0.1028448 | -0.1935869 | -0.148 | 0.023 | 1.6e-10 | 1452/5791 |
| Urea_rint | -0.6000758 | 0.0280218 | 0.0000000 | Female | -0.5432340 | -0.6532504 | -0.598 | 0.028 | 7.8e-98 | 1455/5792 |
| Calcium_rint | -0.0596322 | 0.0313444 | 0.0571512 | Female | 0.0016324 | -0.1213241 | -0.060 | 0.031 | 0.056 | 1338/5270 |
| Phosphate_rint | 0.0214230 | 0.0295982 | 0.4692184 | Female | 0.0789402 | -0.0376678 | 0.021 | 0.030 | 0.488 | 1335/5264 |
outM$Sex="Male"
outF$Sex="Female"Add confidence intervals and round long decimals: sex-stratified adj-BMI
#95CI
outM$upper=outM$Estimate+1.96*outM$SE
outM$lower=outM$Estimate-1.96*outM$SE
outM$Estimateround=format(round(outM$Estimate, digits=3), digits=3)
outM$SEround=format(round(outM$SE, digits=3), digits=3)
outM$Pround=ifelse(outM$P < 0.001,
formatC(outM$P, digits=1, format="e"),
formatC(outM$P, digits=3, format="f"))
outF$upper=outF$Estimate+1.96*outF$SE
outF$lower=outF$Estimate-1.96*outF$SE
outF$Estimateround=format(round(outF$Estimate, digits=3), digits=3)
outM$SEround=format(round(outM$SE, digits=3), digits=3)
outF$Pround=ifelse(outF$P < 0.001,
formatC(outF$P, digits=1, format="e"),
formatC(outF$P, digits=3, format="f"))Get sample sizes sex-stratified adj-BMI
ncontrM=md%>%filter(Veg5yr1==0, Sex==1)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
ncaseM=md%>%filter(Veg5yr1==1, Sex==1)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
ncontrF=md%>%filter(Veg5yr1==0, Sex==2)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
ncaseF=md%>%filter(Veg5yr1==1, Sex==2)%>%select(all_of(phe))%>%sapply(function(x) sum(!is.na(x)))
outM$samp=paste(ncaseM,ncontrM, sep= "/")
outF$samp=paste(ncaseF,ncontrF, sep= "/")
tot=rbind(outM, outF)Forest plots sex-stratified adj-BMI
tot$Trait=gsub(out$Trait, pattern = "_", replacement =" ")
tot$Trait=gsub(out$Trait, pattern =" rint", replacement="")
tot%>%kbl()%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P | Sex | upper | lower | Estimateround | SEround | Pround | samp |
|---|---|---|---|---|---|---|---|---|---|---|
| Apolipoprotein A | -0.1267279 | 0.0355128 | 0.0003639 | Male | -0.0571227 | -0.1963331 | -0.127 | 0.036 | 3.6e-04 | 687/2798 |
| Apolipoprotein B | -0.1925021 | 0.0380941 | 0.0000005 | Male | -0.1178377 | -0.2671664 | -0.193 | 0.038 | 4.5e-07 | 745/3014 |
| HDL cholesterol | -0.2083215 | 0.0348524 | 0.0000000 | Male | -0.1400107 | -0.2766323 | -0.208 | 0.035 | 2.5e-09 | 689/2800 |
| LDL direct | -0.2112578 | 0.0372037 | 0.0000000 | Male | -0.1383386 | -0.2841771 | -0.211 | 0.037 | 1.5e-08 | 757/3025 |
| Lipoprotein A | 0.0316919 | 0.0438591 | 0.4699919 | Male | 0.1176557 | -0.0542720 | 0.032 | 0.044 | 0.470 | 608/2415 |
| Cholesterol | -0.2238045 | 0.0381212 | 0.0000000 | Male | -0.1490870 | -0.2985221 | -0.224 | 0.038 | 4.7e-09 | 758/3030 |
| Triglycerides | 0.2301472 | 0.0397995 | 0.0000000 | Male | 0.3081542 | 0.1521403 | 0.230 | 0.040 | 7.9e-09 | 756/3027 |
| IGF 1 | -0.1502783 | 0.0361740 | 0.0000334 | Male | -0.0793773 | -0.2211794 | -0.150 | 0.036 | 3.3e-05 | 752/3013 |
| Vitamin D | -0.3567426 | 0.0442040 | 0.0000000 | Male | -0.2701027 | -0.4433824 | -0.357 | 0.044 | 9.4e-16 | 738/2956 |
| Bioavailable testosterone | -0.0291545 | 0.0267282 | 0.2754473 | Male | 0.0232327 | -0.0815417 | -0.029 | 0.027 | 0.275 | 679/2761 |
| Free testosterone | -0.0259667 | 0.0256344 | 0.3111496 | Male | 0.0242768 | -0.0762102 | -0.026 | 0.026 | 0.311 | 678/2767 |
| Testosterone | -0.0269085 | 0.0248827 | 0.2795819 | Male | 0.0218615 | -0.0756785 | -0.027 | 0.025 | 0.280 | 751/2994 |
| SHBG | -0.0350940 | 0.0314007 | 0.2638066 | Male | 0.0264513 | -0.0966393 | -0.035 | 0.031 | 0.264 | 682/2783 |
| Alanine aminotransferase | -0.1384570 | 0.0361785 | 0.0001318 | Male | -0.0675471 | -0.2093669 | -0.138 | 0.036 | 1.3e-04 | 755/3029 |
| Albumin | -0.0808145 | 0.0392909 | 0.0397775 | Male | -0.0038044 | -0.1578245 | -0.081 | 0.039 | 0.040 | 688/2800 |
| Alkaline phosphatase | 0.1032799 | 0.0370858 | 0.0053813 | Male | 0.1759681 | 0.0305916 | 0.103 | 0.037 | 0.005 | 758/3030 |
| Aspartate aminotransferase | 0.0002263 | 0.0378300 | 0.9952281 | Male | 0.0743731 | -0.0739205 | 0.000 | 0.038 | 0.995 | 754/3020 |
| C reactive protein | 0.0211213 | 0.0375527 | 0.5738468 | Male | 0.0947246 | -0.0524820 | 0.021 | 0.038 | 0.574 | 750/3023 |
| Gamma glutamyltransferase | -0.1486263 | 0.0320317 | 0.0000036 | Male | -0.0858441 | -0.2114084 | -0.149 | 0.032 | 3.6e-06 | 757/3026 |
| Direct bilirubin | -0.0102032 | 0.0400712 | 0.7990270 | Male | 0.0683364 | -0.0887427 | -0.010 | 0.040 | 0.799 | 704/2844 |
| Total bilirubin | -0.0133426 | 0.0365542 | 0.7151251 | Male | 0.0583035 | -0.0849887 | -0.013 | 0.037 | 0.715 | 755/3018 |
| Total protein | -0.1152243 | 0.0409079 | 0.0048797 | Male | -0.0350449 | -0.1954037 | -0.115 | 0.041 | 0.005 | 689/2802 |
| Creatinine | -0.5768706 | 0.0284864 | 0.0000000 | Male | -0.5210372 | -0.6327040 | -0.577 | 0.028 | 1.2e-86 | 756/3029 |
| Cystatin C | 0.2854492 | 0.0314230 | 0.0000000 | Male | 0.3470384 | 0.2238601 | 0.285 | 0.031 | 1.6e-19 | 757/3029 |
| eGFR | -0.0019476 | 0.0322265 | 0.9518123 | Male | 0.0612163 | -0.0651116 | -0.002 | 0.032 | 0.952 | 755/3028 |
| HbA1c | -0.0396035 | 0.0386380 | 0.3054344 | Male | 0.0361269 | -0.1153340 | -0.040 | 0.039 | 0.305 | 748/3008 |
| Urate | -0.1764115 | 0.0286627 | 0.0000000 | Male | -0.1202326 | -0.2325903 | -0.176 | 0.029 | 8.3e-10 | 757/3026 |
| Urea | -0.6424311 | 0.0392741 | 0.0000000 | Male | -0.5654539 | -0.7194083 | -0.642 | 0.039 | 3.7e-58 | 757/3029 |
| Calcium | -0.1105072 | 0.0411100 | 0.0072205 | Male | -0.0299317 | -0.1910827 | -0.111 | 0.041 | 0.007 | 687/2802 |
| Phosphate | -0.0088235 | 0.0457907 | 0.8472122 | Male | 0.0809263 | -0.0985732 | -0.009 | 0.046 | 0.847 | 688/2791 |
| Apolipoprotein A | -0.0507849 | 0.0254139 | 0.0457243 | Female | -0.0009736 | -0.1005962 | -0.051 | 0.026 | 0.046 | 1324/5223 |
| Apolipoprotein B | -0.1669199 | 0.0267955 | 0.0000000 | Female | -0.1144007 | -0.2194391 | -0.167 | 0.028 | 4.9e-10 | 1452/5772 |
| HDL cholesterol | -0.1312893 | 0.0243112 | 0.0000001 | Female | -0.0836394 | -0.1789392 | -0.131 | 0.025 | 6.9e-08 | 1337/5275 |
| LDL direct | -0.1578437 | 0.0272018 | 0.0000000 | Female | -0.1045282 | -0.2111593 | -0.158 | 0.028 | 6.8e-09 | 1455/5783 |
| Lipoprotein A | -0.1133998 | 0.0323857 | 0.0004661 | Female | -0.0499237 | -0.1768758 | -0.113 | 0.032 | 4.7e-04 | 1166/4653 |
| Cholesterol | -0.1696707 | 0.0269326 | 0.0000000 | Female | -0.1168828 | -0.2224585 | -0.170 | 0.027 | 3.2e-10 | 1457/5796 |
| Triglycerides | 0.2221814 | 0.0241788 | 0.0000000 | Female | 0.2695719 | 0.1747909 | 0.222 | 0.026 | 5.1e-20 | 1456/5792 |
| IGF 1 | -0.2383082 | 0.0283668 | 0.0000000 | Female | -0.1827092 | -0.2939072 | -0.238 | 0.028 | 5.3e-17 | 1449/5772 |
| Vitamin D | -0.4043642 | 0.0323105 | 0.0000000 | Female | -0.3410358 | -0.4676927 | -0.404 | 0.033 | 1.5e-35 | 1392/5565 |
| Bioavailable testosterone | -0.0409250 | 0.0200896 | 0.0416879 | Female | -0.0015493 | -0.0803006 | -0.041 | 0.020 | 0.042 | 1064/4220 |
| Free testosterone | -0.0205851 | 0.0195642 | 0.2927619 | Female | 0.0177607 | -0.0589308 | -0.021 | 0.020 | 0.293 | 1106/4453 |
| Testosterone | -0.0396346 | 0.0187474 | 0.0345460 | Female | -0.0028896 | -0.0763795 | -0.040 | 0.019 | 0.035 | 1168/4678 |
| SHBG | -0.0225707 | 0.0262092 | 0.3891722 | Female | 0.0287992 | -0.0739407 | -0.023 | 0.028 | 0.389 | 1323/5212 |
| Alanine aminotransferase | -0.1409599 | 0.0251099 | 0.0000000 | Female | -0.0917446 | -0.1901753 | -0.141 | 0.026 | 2.1e-08 | 1457/5798 |
| Albumin | -0.0642046 | 0.0299417 | 0.0320438 | Female | -0.0055188 | -0.1228904 | -0.064 | 0.030 | 0.032 | 1338/5275 |
| Alkaline phosphatase | 0.1487686 | 0.0273806 | 0.0000001 | Female | 0.2024345 | 0.0951027 | 0.149 | 0.028 | 5.7e-08 | 1457/5796 |
| Aspartate aminotransferase | 0.0578253 | 0.0266927 | 0.0303181 | Female | 0.1101429 | 0.0055077 | 0.058 | 0.027 | 0.030 | 1452/5772 |
| C reactive protein | -0.0839135 | 0.0267741 | 0.0017306 | Female | -0.0314363 | -0.1363908 | -0.084 | 0.030 | 0.002 | 1452/5789 |
| Gamma glutamyltransferase | -0.1478597 | 0.0270909 | 0.0000000 | Female | -0.0947615 | -0.2009578 | -0.148 | 0.028 | 5.0e-08 | 1455/5793 |
| Direct bilirubin | -0.0154163 | 0.0315130 | 0.6247159 | Female | 0.0463492 | -0.0771817 | -0.015 | 0.032 | 0.625 | 1184/4716 |
| Total bilirubin | -0.0321196 | 0.0287448 | 0.2638580 | Female | 0.0242202 | -0.0884595 | -0.032 | 0.029 | 0.264 | 1451/5769 |
| Total protein | -0.0438038 | 0.0307217 | 0.1539664 | Female | 0.0164108 | -0.1040184 | -0.044 | 0.031 | 0.154 | 1337/5272 |
| Creatinine | -0.3668075 | 0.0220102 | 0.0000000 | Female | -0.3236674 | -0.4099476 | -0.367 | 0.022 | 3.2e-61 | 1456/5793 |
| Cystatin C | 0.3647104 | 0.0245915 | 0.0000000 | Female | 0.4129098 | 0.3165110 | 0.365 | 0.026 | 4.8e-49 | 1456/5801 |
| eGFR | -0.0407539 | 0.0243187 | 0.0938163 | Female | 0.0069109 | -0.0884186 | -0.041 | 0.025 | 0.094 | 1455/5792 |
| HbA1c | 0.0450948 | 0.0244823 | 0.0655259 | Female | 0.0930800 | -0.0028905 | 0.045 | 0.025 | 0.066 | 1450/5774 |
| Urate | -0.1543325 | 0.0218372 | 0.0000000 | Female | -0.1115317 | -0.1971334 | -0.154 | 0.023 | 1.7e-12 | 1452/5791 |
| Urea | -0.6000758 | 0.0280218 | 0.0000000 | Female | -0.5451531 | -0.6549985 | -0.600 | 0.028 | 1.1e-98 | 1455/5792 |
| Calcium | -0.0596322 | 0.0313444 | 0.0571512 | Female | 0.0018028 | -0.1210672 | -0.060 | 0.031 | 0.057 | 1338/5270 |
| Phosphate | 0.0214230 | 0.0295982 | 0.4692184 | Female | 0.0794355 | -0.0365895 | 0.021 | 0.030 | 0.469 | 1335/5264 |
tot$EstimateroundM=tot$Estimateround[tot$Sex=="Male"]
tot$EstimateroundF=tot$Estimateround[tot$Sex=="Female"]
tot$SEroundM=tot$SEround[tot$Sex=="Male"]
tot$SEroundF=tot$SEround[tot$Sex=="Female"]
tot$ProundM=tot$Pround[tot$Sex=="Male"]
tot$ProundF=tot$Pround[tot$Sex=="Female"]
tot$sampM=tot$samp[tot$Sex=="Male"]
tot$sampF=tot$samp[tot$Sex=="Female"]
tot%>%kbl()%>%
scroll_box(width = "600px", height = "200px")| Trait | Estimate | SE | P | Sex | upper | lower | Estimateround | SEround | Pround | samp | EstimateroundM | EstimateroundF | SEroundM | SEroundF | ProundM | ProundF | sampM | sampF |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Apolipoprotein A | -0.1267279 | 0.0355128 | 0.0003639 | Male | -0.0571227 | -0.1963331 | -0.127 | 0.036 | 3.6e-04 | 687/2798 | -0.127 | -0.051 | 0.036 | 0.026 | 3.6e-04 | 0.046 | 687/2798 | 1324/5223 |
| Apolipoprotein B | -0.1925021 | 0.0380941 | 0.0000005 | Male | -0.1178377 | -0.2671664 | -0.193 | 0.038 | 4.5e-07 | 745/3014 | -0.193 | -0.167 | 0.038 | 0.028 | 4.5e-07 | 4.9e-10 | 745/3014 | 1452/5772 |
| HDL cholesterol | -0.2083215 | 0.0348524 | 0.0000000 | Male | -0.1400107 | -0.2766323 | -0.208 | 0.035 | 2.5e-09 | 689/2800 | -0.208 | -0.131 | 0.035 | 0.025 | 2.5e-09 | 6.9e-08 | 689/2800 | 1337/5275 |
| LDL direct | -0.2112578 | 0.0372037 | 0.0000000 | Male | -0.1383386 | -0.2841771 | -0.211 | 0.037 | 1.5e-08 | 757/3025 | -0.211 | -0.158 | 0.037 | 0.028 | 1.5e-08 | 6.8e-09 | 757/3025 | 1455/5783 |
| Lipoprotein A | 0.0316919 | 0.0438591 | 0.4699919 | Male | 0.1176557 | -0.0542720 | 0.032 | 0.044 | 0.470 | 608/2415 | 0.032 | -0.113 | 0.044 | 0.032 | 0.470 | 4.7e-04 | 608/2415 | 1166/4653 |
| Cholesterol | -0.2238045 | 0.0381212 | 0.0000000 | Male | -0.1490870 | -0.2985221 | -0.224 | 0.038 | 4.7e-09 | 758/3030 | -0.224 | -0.170 | 0.038 | 0.027 | 4.7e-09 | 3.2e-10 | 758/3030 | 1457/5796 |
| Triglycerides | 0.2301472 | 0.0397995 | 0.0000000 | Male | 0.3081542 | 0.1521403 | 0.230 | 0.040 | 7.9e-09 | 756/3027 | 0.230 | 0.222 | 0.040 | 0.026 | 7.9e-09 | 5.1e-20 | 756/3027 | 1456/5792 |
| IGF 1 | -0.1502783 | 0.0361740 | 0.0000334 | Male | -0.0793773 | -0.2211794 | -0.150 | 0.036 | 3.3e-05 | 752/3013 | -0.150 | -0.238 | 0.036 | 0.028 | 3.3e-05 | 5.3e-17 | 752/3013 | 1449/5772 |
| Vitamin D | -0.3567426 | 0.0442040 | 0.0000000 | Male | -0.2701027 | -0.4433824 | -0.357 | 0.044 | 9.4e-16 | 738/2956 | -0.357 | -0.404 | 0.044 | 0.033 | 9.4e-16 | 1.5e-35 | 738/2956 | 1392/5565 |
| Bioavailable testosterone | -0.0291545 | 0.0267282 | 0.2754473 | Male | 0.0232327 | -0.0815417 | -0.029 | 0.027 | 0.275 | 679/2761 | -0.029 | -0.041 | 0.027 | 0.020 | 0.275 | 0.042 | 679/2761 | 1064/4220 |
| Free testosterone | -0.0259667 | 0.0256344 | 0.3111496 | Male | 0.0242768 | -0.0762102 | -0.026 | 0.026 | 0.311 | 678/2767 | -0.026 | -0.021 | 0.026 | 0.020 | 0.311 | 0.293 | 678/2767 | 1106/4453 |
| Testosterone | -0.0269085 | 0.0248827 | 0.2795819 | Male | 0.0218615 | -0.0756785 | -0.027 | 0.025 | 0.280 | 751/2994 | -0.027 | -0.040 | 0.025 | 0.019 | 0.280 | 0.035 | 751/2994 | 1168/4678 |
| SHBG | -0.0350940 | 0.0314007 | 0.2638066 | Male | 0.0264513 | -0.0966393 | -0.035 | 0.031 | 0.264 | 682/2783 | -0.035 | -0.023 | 0.031 | 0.028 | 0.264 | 0.389 | 682/2783 | 1323/5212 |
| Alanine aminotransferase | -0.1384570 | 0.0361785 | 0.0001318 | Male | -0.0675471 | -0.2093669 | -0.138 | 0.036 | 1.3e-04 | 755/3029 | -0.138 | -0.141 | 0.036 | 0.026 | 1.3e-04 | 2.1e-08 | 755/3029 | 1457/5798 |
| Albumin | -0.0808145 | 0.0392909 | 0.0397775 | Male | -0.0038044 | -0.1578245 | -0.081 | 0.039 | 0.040 | 688/2800 | -0.081 | -0.064 | 0.039 | 0.030 | 0.040 | 0.032 | 688/2800 | 1338/5275 |
| Alkaline phosphatase | 0.1032799 | 0.0370858 | 0.0053813 | Male | 0.1759681 | 0.0305916 | 0.103 | 0.037 | 0.005 | 758/3030 | 0.103 | 0.149 | 0.037 | 0.028 | 0.005 | 5.7e-08 | 758/3030 | 1457/5796 |
| Aspartate aminotransferase | 0.0002263 | 0.0378300 | 0.9952281 | Male | 0.0743731 | -0.0739205 | 0.000 | 0.038 | 0.995 | 754/3020 | 0.000 | 0.058 | 0.038 | 0.027 | 0.995 | 0.030 | 754/3020 | 1452/5772 |
| C reactive protein | 0.0211213 | 0.0375527 | 0.5738468 | Male | 0.0947246 | -0.0524820 | 0.021 | 0.038 | 0.574 | 750/3023 | 0.021 | -0.084 | 0.038 | 0.030 | 0.574 | 0.002 | 750/3023 | 1452/5789 |
| Gamma glutamyltransferase | -0.1486263 | 0.0320317 | 0.0000036 | Male | -0.0858441 | -0.2114084 | -0.149 | 0.032 | 3.6e-06 | 757/3026 | -0.149 | -0.148 | 0.032 | 0.028 | 3.6e-06 | 5.0e-08 | 757/3026 | 1455/5793 |
| Direct bilirubin | -0.0102032 | 0.0400712 | 0.7990270 | Male | 0.0683364 | -0.0887427 | -0.010 | 0.040 | 0.799 | 704/2844 | -0.010 | -0.015 | 0.040 | 0.032 | 0.799 | 0.625 | 704/2844 | 1184/4716 |
| Total bilirubin | -0.0133426 | 0.0365542 | 0.7151251 | Male | 0.0583035 | -0.0849887 | -0.013 | 0.037 | 0.715 | 755/3018 | -0.013 | -0.032 | 0.037 | 0.029 | 0.715 | 0.264 | 755/3018 | 1451/5769 |
| Total protein | -0.1152243 | 0.0409079 | 0.0048797 | Male | -0.0350449 | -0.1954037 | -0.115 | 0.041 | 0.005 | 689/2802 | -0.115 | -0.044 | 0.041 | 0.031 | 0.005 | 0.154 | 689/2802 | 1337/5272 |
| Creatinine | -0.5768706 | 0.0284864 | 0.0000000 | Male | -0.5210372 | -0.6327040 | -0.577 | 0.028 | 1.2e-86 | 756/3029 | -0.577 | -0.367 | 0.028 | 0.022 | 1.2e-86 | 3.2e-61 | 756/3029 | 1456/5793 |
| Cystatin C | 0.2854492 | 0.0314230 | 0.0000000 | Male | 0.3470384 | 0.2238601 | 0.285 | 0.031 | 1.6e-19 | 757/3029 | 0.285 | 0.365 | 0.031 | 0.026 | 1.6e-19 | 4.8e-49 | 757/3029 | 1456/5801 |
| eGFR | -0.0019476 | 0.0322265 | 0.9518123 | Male | 0.0612163 | -0.0651116 | -0.002 | 0.032 | 0.952 | 755/3028 | -0.002 | -0.041 | 0.032 | 0.025 | 0.952 | 0.094 | 755/3028 | 1455/5792 |
| HbA1c | -0.0396035 | 0.0386380 | 0.3054344 | Male | 0.0361269 | -0.1153340 | -0.040 | 0.039 | 0.305 | 748/3008 | -0.040 | 0.045 | 0.039 | 0.025 | 0.305 | 0.066 | 748/3008 | 1450/5774 |
| Urate | -0.1764115 | 0.0286627 | 0.0000000 | Male | -0.1202326 | -0.2325903 | -0.176 | 0.029 | 8.3e-10 | 757/3026 | -0.176 | -0.154 | 0.029 | 0.023 | 8.3e-10 | 1.7e-12 | 757/3026 | 1452/5791 |
| Urea | -0.6424311 | 0.0392741 | 0.0000000 | Male | -0.5654539 | -0.7194083 | -0.642 | 0.039 | 3.7e-58 | 757/3029 | -0.642 | -0.600 | 0.039 | 0.028 | 3.7e-58 | 1.1e-98 | 757/3029 | 1455/5792 |
| Calcium | -0.1105072 | 0.0411100 | 0.0072205 | Male | -0.0299317 | -0.1910827 | -0.111 | 0.041 | 0.007 | 687/2802 | -0.111 | -0.060 | 0.041 | 0.031 | 0.007 | 0.057 | 687/2802 | 1338/5270 |
| Phosphate | -0.0088235 | 0.0457907 | 0.8472122 | Male | 0.0809263 | -0.0985732 | -0.009 | 0.046 | 0.847 | 688/2791 | -0.009 | 0.021 | 0.046 | 0.030 | 0.847 | 0.469 | 688/2791 | 1335/5264 |
| Apolipoprotein A | -0.0507849 | 0.0254139 | 0.0457243 | Female | -0.0009736 | -0.1005962 | -0.051 | 0.026 | 0.046 | 1324/5223 | -0.127 | -0.051 | 0.036 | 0.026 | 3.6e-04 | 0.046 | 687/2798 | 1324/5223 |
| Apolipoprotein B | -0.1669199 | 0.0267955 | 0.0000000 | Female | -0.1144007 | -0.2194391 | -0.167 | 0.028 | 4.9e-10 | 1452/5772 | -0.193 | -0.167 | 0.038 | 0.028 | 4.5e-07 | 4.9e-10 | 745/3014 | 1452/5772 |
| HDL cholesterol | -0.1312893 | 0.0243112 | 0.0000001 | Female | -0.0836394 | -0.1789392 | -0.131 | 0.025 | 6.9e-08 | 1337/5275 | -0.208 | -0.131 | 0.035 | 0.025 | 2.5e-09 | 6.9e-08 | 689/2800 | 1337/5275 |
| LDL direct | -0.1578437 | 0.0272018 | 0.0000000 | Female | -0.1045282 | -0.2111593 | -0.158 | 0.028 | 6.8e-09 | 1455/5783 | -0.211 | -0.158 | 0.037 | 0.028 | 1.5e-08 | 6.8e-09 | 757/3025 | 1455/5783 |
| Lipoprotein A | -0.1133998 | 0.0323857 | 0.0004661 | Female | -0.0499237 | -0.1768758 | -0.113 | 0.032 | 4.7e-04 | 1166/4653 | 0.032 | -0.113 | 0.044 | 0.032 | 0.470 | 4.7e-04 | 608/2415 | 1166/4653 |
| Cholesterol | -0.1696707 | 0.0269326 | 0.0000000 | Female | -0.1168828 | -0.2224585 | -0.170 | 0.027 | 3.2e-10 | 1457/5796 | -0.224 | -0.170 | 0.038 | 0.027 | 4.7e-09 | 3.2e-10 | 758/3030 | 1457/5796 |
| Triglycerides | 0.2221814 | 0.0241788 | 0.0000000 | Female | 0.2695719 | 0.1747909 | 0.222 | 0.026 | 5.1e-20 | 1456/5792 | 0.230 | 0.222 | 0.040 | 0.026 | 7.9e-09 | 5.1e-20 | 756/3027 | 1456/5792 |
| IGF 1 | -0.2383082 | 0.0283668 | 0.0000000 | Female | -0.1827092 | -0.2939072 | -0.238 | 0.028 | 5.3e-17 | 1449/5772 | -0.150 | -0.238 | 0.036 | 0.028 | 3.3e-05 | 5.3e-17 | 752/3013 | 1449/5772 |
| Vitamin D | -0.4043642 | 0.0323105 | 0.0000000 | Female | -0.3410358 | -0.4676927 | -0.404 | 0.033 | 1.5e-35 | 1392/5565 | -0.357 | -0.404 | 0.044 | 0.033 | 9.4e-16 | 1.5e-35 | 738/2956 | 1392/5565 |
| Bioavailable testosterone | -0.0409250 | 0.0200896 | 0.0416879 | Female | -0.0015493 | -0.0803006 | -0.041 | 0.020 | 0.042 | 1064/4220 | -0.029 | -0.041 | 0.027 | 0.020 | 0.275 | 0.042 | 679/2761 | 1064/4220 |
| Free testosterone | -0.0205851 | 0.0195642 | 0.2927619 | Female | 0.0177607 | -0.0589308 | -0.021 | 0.020 | 0.293 | 1106/4453 | -0.026 | -0.021 | 0.026 | 0.020 | 0.311 | 0.293 | 678/2767 | 1106/4453 |
| Testosterone | -0.0396346 | 0.0187474 | 0.0345460 | Female | -0.0028896 | -0.0763795 | -0.040 | 0.019 | 0.035 | 1168/4678 | -0.027 | -0.040 | 0.025 | 0.019 | 0.280 | 0.035 | 751/2994 | 1168/4678 |
| SHBG | -0.0225707 | 0.0262092 | 0.3891722 | Female | 0.0287992 | -0.0739407 | -0.023 | 0.028 | 0.389 | 1323/5212 | -0.035 | -0.023 | 0.031 | 0.028 | 0.264 | 0.389 | 682/2783 | 1323/5212 |
| Alanine aminotransferase | -0.1409599 | 0.0251099 | 0.0000000 | Female | -0.0917446 | -0.1901753 | -0.141 | 0.026 | 2.1e-08 | 1457/5798 | -0.138 | -0.141 | 0.036 | 0.026 | 1.3e-04 | 2.1e-08 | 755/3029 | 1457/5798 |
| Albumin | -0.0642046 | 0.0299417 | 0.0320438 | Female | -0.0055188 | -0.1228904 | -0.064 | 0.030 | 0.032 | 1338/5275 | -0.081 | -0.064 | 0.039 | 0.030 | 0.040 | 0.032 | 688/2800 | 1338/5275 |
| Alkaline phosphatase | 0.1487686 | 0.0273806 | 0.0000001 | Female | 0.2024345 | 0.0951027 | 0.149 | 0.028 | 5.7e-08 | 1457/5796 | 0.103 | 0.149 | 0.037 | 0.028 | 0.005 | 5.7e-08 | 758/3030 | 1457/5796 |
| Aspartate aminotransferase | 0.0578253 | 0.0266927 | 0.0303181 | Female | 0.1101429 | 0.0055077 | 0.058 | 0.027 | 0.030 | 1452/5772 | 0.000 | 0.058 | 0.038 | 0.027 | 0.995 | 0.030 | 754/3020 | 1452/5772 |
| C reactive protein | -0.0839135 | 0.0267741 | 0.0017306 | Female | -0.0314363 | -0.1363908 | -0.084 | 0.030 | 0.002 | 1452/5789 | 0.021 | -0.084 | 0.038 | 0.030 | 0.574 | 0.002 | 750/3023 | 1452/5789 |
| Gamma glutamyltransferase | -0.1478597 | 0.0270909 | 0.0000000 | Female | -0.0947615 | -0.2009578 | -0.148 | 0.028 | 5.0e-08 | 1455/5793 | -0.149 | -0.148 | 0.032 | 0.028 | 3.6e-06 | 5.0e-08 | 757/3026 | 1455/5793 |
| Direct bilirubin | -0.0154163 | 0.0315130 | 0.6247159 | Female | 0.0463492 | -0.0771817 | -0.015 | 0.032 | 0.625 | 1184/4716 | -0.010 | -0.015 | 0.040 | 0.032 | 0.799 | 0.625 | 704/2844 | 1184/4716 |
| Total bilirubin | -0.0321196 | 0.0287448 | 0.2638580 | Female | 0.0242202 | -0.0884595 | -0.032 | 0.029 | 0.264 | 1451/5769 | -0.013 | -0.032 | 0.037 | 0.029 | 0.715 | 0.264 | 755/3018 | 1451/5769 |
| Total protein | -0.0438038 | 0.0307217 | 0.1539664 | Female | 0.0164108 | -0.1040184 | -0.044 | 0.031 | 0.154 | 1337/5272 | -0.115 | -0.044 | 0.041 | 0.031 | 0.005 | 0.154 | 689/2802 | 1337/5272 |
| Creatinine | -0.3668075 | 0.0220102 | 0.0000000 | Female | -0.3236674 | -0.4099476 | -0.367 | 0.022 | 3.2e-61 | 1456/5793 | -0.577 | -0.367 | 0.028 | 0.022 | 1.2e-86 | 3.2e-61 | 756/3029 | 1456/5793 |
| Cystatin C | 0.3647104 | 0.0245915 | 0.0000000 | Female | 0.4129098 | 0.3165110 | 0.365 | 0.026 | 4.8e-49 | 1456/5801 | 0.285 | 0.365 | 0.031 | 0.026 | 1.6e-19 | 4.8e-49 | 757/3029 | 1456/5801 |
| eGFR | -0.0407539 | 0.0243187 | 0.0938163 | Female | 0.0069109 | -0.0884186 | -0.041 | 0.025 | 0.094 | 1455/5792 | -0.002 | -0.041 | 0.032 | 0.025 | 0.952 | 0.094 | 755/3028 | 1455/5792 |
| HbA1c | 0.0450948 | 0.0244823 | 0.0655259 | Female | 0.0930800 | -0.0028905 | 0.045 | 0.025 | 0.066 | 1450/5774 | -0.040 | 0.045 | 0.039 | 0.025 | 0.305 | 0.066 | 748/3008 | 1450/5774 |
| Urate | -0.1543325 | 0.0218372 | 0.0000000 | Female | -0.1115317 | -0.1971334 | -0.154 | 0.023 | 1.7e-12 | 1452/5791 | -0.176 | -0.154 | 0.029 | 0.023 | 8.3e-10 | 1.7e-12 | 757/3026 | 1452/5791 |
| Urea | -0.6000758 | 0.0280218 | 0.0000000 | Female | -0.5451531 | -0.6549985 | -0.600 | 0.028 | 1.1e-98 | 1455/5792 | -0.642 | -0.600 | 0.039 | 0.028 | 3.7e-58 | 1.1e-98 | 757/3029 | 1455/5792 |
| Calcium | -0.0596322 | 0.0313444 | 0.0571512 | Female | 0.0018028 | -0.1210672 | -0.060 | 0.031 | 0.057 | 1338/5270 | -0.111 | -0.060 | 0.041 | 0.031 | 0.007 | 0.057 | 687/2802 | 1338/5270 |
| Phosphate | 0.0214230 | 0.0295982 | 0.4692184 | Female | 0.0794355 | -0.0365895 | 0.021 | 0.030 | 0.469 | 1335/5264 | -0.009 | 0.021 | 0.046 | 0.030 | 0.847 | 0.469 | 688/2791 | 1335/5264 |
tot=tot%>%select(Trait, EstimateroundM, ProundM,
sampM, EstimateroundF, ProundF, sampF, everything())
tot=cbind(Category, tot)
headerM=tibble(Category="Category",
Trait="Trait",
Sex="Male",
ProundM="P (male)",
ProundF="P (female)")
headerF=tibble(Category="Category",
Trait="Trait",
Sex="Female",
ProundM="P (male)",
ProundF="P (female)")
tot2=bind_rows(headerM, tot)
tot3=bind_rows(headerF, tot2)
#png("forest.sexstrat-BMI.png",width = 12, height =8, units = 'in', res = 600)
tot3 %>% group_by(Sex) %>%
forestplot(mean="Estimate", labeltext=c("Category", "Trait", "ProundM", "ProundF"),
lower="lower", upper="upper",
boxsize = 0.2,
ci.vertices = TRUE,
ci.vertices.height = 0.05,
shapes_gp = fpShapesGp(box = c("darkred", "blue") %>%
lapply(function(x) gpar(fill = x, col = "#555555")),
default = gpar(vertices = TRUE)),
hrzl_lines = list("2" = gpar(lty = 2)),
grid=TRUE,
zero = 0,
xticks=xtik,
mar = unit(c(0,0.5,0.2,0.5), "in"),
xlab = "Standardized veg. effect ± 95% CI",
txt_gp = fpTxtGp(xlab = gpar(cex = 1),
ticks = gpar(fontfamily = "", cex = 1)
),
fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI)
)%>% fp_set_zebra_style("#F7F7F7")
#dev.off()
outplot=tot%>%select(Trait, EstimateroundM, SEroundM, ProundM, sampM,
EstimateroundF, SEroundF, ProundF, sampF)
outplot$ProundM = cell_spec(outplot$ProundM,
color=ifelse(as.double(outplot$ProundM) <(0.05/30), "#36E072", "grey"))
outplot$ProundF = cell_spec(outplot$ProundF,
color=ifelse(as.double(outplot$ProundF) <(0.05/30), "#36E072", "grey"))
colnames(outplot)=c("Trait", "BetaVegm", "SEm", "Pm", "N (veg/non-veg)m","BetaVegf", "SEf", "Pf", "N (veg/non-veg)f")
outplot%>%
kbl(booktabs = T, linesep = "", escape=FALSE,align="l") %>%
kable_classic_2(full_width = F)| Trait | BetaVegm | SEm | Pm | N (veg/non-veg)m | BetaVegf | SEf | Pf | N (veg/non-veg)f |
|---|---|---|---|---|---|---|---|---|
| Apolipoprotein A | -0.127 | 0.036 | 3.6e-04 | 687/2798 | -0.051 | 0.026 | 0.046 | 1324/5223 |
| Apolipoprotein B | -0.193 | 0.038 | 4.5e-07 | 745/3014 | -0.167 | 0.028 | 4.9e-10 | 1452/5772 |
| HDL cholesterol | -0.208 | 0.035 | 2.5e-09 | 689/2800 | -0.131 | 0.025 | 6.9e-08 | 1337/5275 |
| LDL direct | -0.211 | 0.037 | 1.5e-08 | 757/3025 | -0.158 | 0.028 | 6.8e-09 | 1455/5783 |
| Lipoprotein A | 0.032 | 0.044 | 0.470 | 608/2415 | -0.113 | 0.032 | 4.7e-04 | 1166/4653 |
| Cholesterol | -0.224 | 0.038 | 4.7e-09 | 758/3030 | -0.170 | 0.027 | 3.2e-10 | 1457/5796 |
| Triglycerides | 0.230 | 0.040 | 7.9e-09 | 756/3027 | 0.222 | 0.026 | 5.1e-20 | 1456/5792 |
| IGF 1 | -0.150 | 0.036 | 3.3e-05 | 752/3013 | -0.238 | 0.028 | 5.3e-17 | 1449/5772 |
| Vitamin D | -0.357 | 0.044 | 9.4e-16 | 738/2956 | -0.404 | 0.033 | 1.5e-35 | 1392/5565 |
| Bioavailable testosterone | -0.029 | 0.027 | 0.275 | 679/2761 | -0.041 | 0.020 | 0.042 | 1064/4220 |
| Free testosterone | -0.026 | 0.026 | 0.311 | 678/2767 | -0.021 | 0.020 | 0.293 | 1106/4453 |
| Testosterone | -0.027 | 0.025 | 0.280 | 751/2994 | -0.040 | 0.019 | 0.035 | 1168/4678 |
| SHBG | -0.035 | 0.031 | 0.264 | 682/2783 | -0.023 | 0.028 | 0.389 | 1323/5212 |
| Alanine aminotransferase | -0.138 | 0.036 | 1.3e-04 | 755/3029 | -0.141 | 0.026 | 2.1e-08 | 1457/5798 |
| Albumin | -0.081 | 0.039 | 0.040 | 688/2800 | -0.064 | 0.030 | 0.032 | 1338/5275 |
| Alkaline phosphatase | 0.103 | 0.037 | 0.005 | 758/3030 | 0.149 | 0.028 | 5.7e-08 | 1457/5796 |
| Aspartate aminotransferase | 0.000 | 0.038 | 0.995 | 754/3020 | 0.058 | 0.027 | 0.030 | 1452/5772 |
| C reactive protein | 0.021 | 0.038 | 0.574 | 750/3023 | -0.084 | 0.030 | 0.002 | 1452/5789 |
| Gamma glutamyltransferase | -0.149 | 0.032 | 3.6e-06 | 757/3026 | -0.148 | 0.028 | 5.0e-08 | 1455/5793 |
| Direct bilirubin | -0.010 | 0.040 | 0.799 | 704/2844 | -0.015 | 0.032 | 0.625 | 1184/4716 |
| Total bilirubin | -0.013 | 0.037 | 0.715 | 755/3018 | -0.032 | 0.029 | 0.264 | 1451/5769 |
| Total protein | -0.115 | 0.041 | 0.005 | 689/2802 | -0.044 | 0.031 | 0.154 | 1337/5272 |
| Creatinine | -0.577 | 0.028 | 1.2e-86 | 756/3029 | -0.367 | 0.022 | 3.2e-61 | 1456/5793 |
| Cystatin C | 0.285 | 0.031 | 1.6e-19 | 757/3029 | 0.365 | 0.026 | 4.8e-49 | 1456/5801 |
| eGFR | -0.002 | 0.032 | 0.952 | 755/3028 | -0.041 | 0.025 | 0.094 | 1455/5792 |
| HbA1c | -0.040 | 0.039 | 0.305 | 748/3008 | 0.045 | 0.025 | 0.066 | 1450/5774 |
| Urate | -0.176 | 0.029 | 8.3e-10 | 757/3026 | -0.154 | 0.023 | 1.7e-12 | 1452/5791 |
| Urea | -0.642 | 0.039 | 3.7e-58 | 757/3029 | -0.600 | 0.028 | 1.1e-98 | 1455/5792 |
| Calcium | -0.111 | 0.041 | 0.007 | 687/2802 | -0.060 | 0.031 | 0.057 | 1338/5270 |
| Phosphate | -0.009 | 0.046 | 0.847 | 688/2791 | 0.021 | 0.030 | 0.469 | 1335/5264 |
| Apolipoprotein A | -0.127 | 0.036 | 3.6e-04 | 687/2798 | -0.051 | 0.026 | 0.046 | 1324/5223 |
| Apolipoprotein B | -0.193 | 0.038 | 4.5e-07 | 745/3014 | -0.167 | 0.028 | 4.9e-10 | 1452/5772 |
| HDL cholesterol | -0.208 | 0.035 | 2.5e-09 | 689/2800 | -0.131 | 0.025 | 6.9e-08 | 1337/5275 |
| LDL direct | -0.211 | 0.037 | 1.5e-08 | 757/3025 | -0.158 | 0.028 | 6.8e-09 | 1455/5783 |
| Lipoprotein A | 0.032 | 0.044 | 0.470 | 608/2415 | -0.113 | 0.032 | 4.7e-04 | 1166/4653 |
| Cholesterol | -0.224 | 0.038 | 4.7e-09 | 758/3030 | -0.170 | 0.027 | 3.2e-10 | 1457/5796 |
| Triglycerides | 0.230 | 0.040 | 7.9e-09 | 756/3027 | 0.222 | 0.026 | 5.1e-20 | 1456/5792 |
| IGF 1 | -0.150 | 0.036 | 3.3e-05 | 752/3013 | -0.238 | 0.028 | 5.3e-17 | 1449/5772 |
| Vitamin D | -0.357 | 0.044 | 9.4e-16 | 738/2956 | -0.404 | 0.033 | 1.5e-35 | 1392/5565 |
| Bioavailable testosterone | -0.029 | 0.027 | 0.275 | 679/2761 | -0.041 | 0.020 | 0.042 | 1064/4220 |
| Free testosterone | -0.026 | 0.026 | 0.311 | 678/2767 | -0.021 | 0.020 | 0.293 | 1106/4453 |
| Testosterone | -0.027 | 0.025 | 0.280 | 751/2994 | -0.040 | 0.019 | 0.035 | 1168/4678 |
| SHBG | -0.035 | 0.031 | 0.264 | 682/2783 | -0.023 | 0.028 | 0.389 | 1323/5212 |
| Alanine aminotransferase | -0.138 | 0.036 | 1.3e-04 | 755/3029 | -0.141 | 0.026 | 2.1e-08 | 1457/5798 |
| Albumin | -0.081 | 0.039 | 0.040 | 688/2800 | -0.064 | 0.030 | 0.032 | 1338/5275 |
| Alkaline phosphatase | 0.103 | 0.037 | 0.005 | 758/3030 | 0.149 | 0.028 | 5.7e-08 | 1457/5796 |
| Aspartate aminotransferase | 0.000 | 0.038 | 0.995 | 754/3020 | 0.058 | 0.027 | 0.030 | 1452/5772 |
| C reactive protein | 0.021 | 0.038 | 0.574 | 750/3023 | -0.084 | 0.030 | 0.002 | 1452/5789 |
| Gamma glutamyltransferase | -0.149 | 0.032 | 3.6e-06 | 757/3026 | -0.148 | 0.028 | 5.0e-08 | 1455/5793 |
| Direct bilirubin | -0.010 | 0.040 | 0.799 | 704/2844 | -0.015 | 0.032 | 0.625 | 1184/4716 |
| Total bilirubin | -0.013 | 0.037 | 0.715 | 755/3018 | -0.032 | 0.029 | 0.264 | 1451/5769 |
| Total protein | -0.115 | 0.041 | 0.005 | 689/2802 | -0.044 | 0.031 | 0.154 | 1337/5272 |
| Creatinine | -0.577 | 0.028 | 1.2e-86 | 756/3029 | -0.367 | 0.022 | 3.2e-61 | 1456/5793 |
| Cystatin C | 0.285 | 0.031 | 1.6e-19 | 757/3029 | 0.365 | 0.026 | 4.8e-49 | 1456/5801 |
| eGFR | -0.002 | 0.032 | 0.952 | 755/3028 | -0.041 | 0.025 | 0.094 | 1455/5792 |
| HbA1c | -0.040 | 0.039 | 0.305 | 748/3008 | 0.045 | 0.025 | 0.066 | 1450/5774 |
| Urate | -0.176 | 0.029 | 8.3e-10 | 757/3026 | -0.154 | 0.023 | 1.7e-12 | 1452/5791 |
| Urea | -0.642 | 0.039 | 3.7e-58 | 757/3029 | -0.600 | 0.028 | 1.1e-98 | 1455/5792 |
| Calcium | -0.111 | 0.041 | 0.007 | 687/2802 | -0.060 | 0.031 | 0.057 | 1338/5270 |
| Phosphate | -0.009 | 0.046 | 0.847 | 688/2791 | 0.021 | 0.030 | 0.469 | 1335/5264 |
#%>%save_kable(file = "table.forest.sexstrat-BMI.png", zoom=5)