mirror of
https://github.com/agdamsbo/daDoctoR.git
synced 2024-11-21 19:30:22 +01:00
adding pvals to strobe_diff_bygroup
This commit is contained in:
agdamsbo
parent
0f1c0cfe17
commit
0819d48953
@ -1,7 +1,7 @@
|
||||
Package: daDoctoR
|
||||
Type: Package
|
||||
Title: FUNCTIONS FOR HEALTH RESEARCH
|
||||
Version: 0.1.0.9019
|
||||
Version: 0.1.0.9020
|
||||
Author@R: c(person("Andreas", "Gammelgaard Damsbo", email = "agdamsbo@pm.me", role = c("cre", "aut")))
|
||||
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>
|
||||
Description: I am a Danish medical doctor involved in neuropsychiatric research.
|
||||
@ -15,4 +15,4 @@ Imports: broom,
|
||||
License: GPL (>= 2)
|
||||
Encoding: UTF-8
|
||||
LazyData: true
|
||||
RoxygenNote: 6.1.0.9000
|
||||
RoxygenNote: 6.1.1
|
||||
|
||||
@ -6,107 +6,137 @@
|
||||
#' @param groups groups to compare, as string.
|
||||
#' @param adj variables to adjust for, as string.
|
||||
#' @param data dataframe of data.
|
||||
#' @param dec decimals for results, standard is set to 2. Mean and sd is dec-1.
|
||||
#' @param dec decimals for results, standard is set to 2. Mean and sd is dec-1. pval has 3 decimals.
|
||||
#' @keywords strobe
|
||||
#' @export
|
||||
#' @examples
|
||||
#' strobe_diff_bygroup()
|
||||
|
||||
strobe_diff_bygroup<-function(meas,var,group,adj,data,dec=2){
|
||||
## Wishlist:
|
||||
## -fix confint()
|
||||
|
||||
|
||||
## meas: sdmt
|
||||
## var: rtreat
|
||||
## group: genotype
|
||||
## for dichotome exposure variable (var)
|
||||
|
||||
d<-data
|
||||
m<-d[,c(meas)]
|
||||
v<-d[,c(var)]
|
||||
g<-d[,c(group)]
|
||||
d <- data
|
||||
m <- d[, c(meas)]
|
||||
v <- d[, c(var)]
|
||||
g <- d[, c(group)]
|
||||
ads <- d[, c(adj)]
|
||||
dat <- data.frame(m, v, g, ads)
|
||||
df <- data.frame(matrix(ncol = 9))
|
||||
if (!is.factor(m)) {
|
||||
for (i in 1:length(levels(g))) {
|
||||
grp <- levels(dat$g)[i]
|
||||
di <- dat[dat$g == grp, ][, -3]
|
||||
mod <- lm(m ~ v, data = di)
|
||||
|
||||
ads<-d[,c(adj)]
|
||||
|
||||
dat<-data.frame(m,v,g,ads)
|
||||
|
||||
df<-data.frame(matrix(ncol=7))
|
||||
|
||||
if(!is.factor(m)){
|
||||
|
||||
for (i in 1:length(levels(g))){
|
||||
grp<-levels(dat$g)[i]
|
||||
di<-dat[dat$g==grp,][,-3]
|
||||
|
||||
mod<-lm(m~v,data=di)
|
||||
co<-round(coef(mod)[-1],dec)
|
||||
lo<-round(confint(mod)[-1,1],dec)
|
||||
up<-round(confint(mod)[-1,2],dec)
|
||||
p <- coef(summary(mod))[2,4]
|
||||
p<-ifelse(p<0.001,"<0.001",round(p,3))
|
||||
p <- ifelse(p<=0.05|p=="<0.001",paste0("*",p),
|
||||
ifelse(p>0.05&p<=0.1,paste0(".",p),p))
|
||||
pv<-p
|
||||
|
||||
co<-round(coef(mod),dec)[2]
|
||||
ci<-round(confint(mod),dec)[2,]
|
||||
lo<-ci[1]
|
||||
up<-ci[2]
|
||||
ci<-paste0(co," (",lo," to ",up,")")
|
||||
|
||||
amod<-lm(m~.,data=di)
|
||||
aco<-round(coef(amod)[2],dec)
|
||||
alo<-round(confint(amod)[2,1],dec)
|
||||
aup<-round(confint(amod)[2,2],dec)
|
||||
amod <- lm(m ~ ., data = di)
|
||||
pa <- coef(summary(amod))[2,4]
|
||||
pa<-ifelse(pa<0.001,"<0.001",round(pa,3))
|
||||
pa <- ifelse(pa<=0.05|pa=="<0.001",paste0("*",pa),
|
||||
ifelse(pa>0.05&pa<=0.1,paste0(".",pa),pa))
|
||||
apv<-pa
|
||||
|
||||
aco<-round(coef(amod),dec)[2]
|
||||
aci<-round(confint(amod),dec)[2,]
|
||||
alo<-aci[1]
|
||||
aup<-aci[2]
|
||||
aci<-paste0(aco," (",alo," to ",aup,")")
|
||||
|
||||
nr<-c()
|
||||
|
||||
for (r in 1:2){
|
||||
vr<-levels(di$v)[r]
|
||||
dr<-di[di$v==vr,]
|
||||
n<-as.numeric(nrow(dr[!is.na(dr$m),]))
|
||||
mean<-round(mean(dr$m,na.rm = TRUE),dec-1)
|
||||
sd<-round(sd(dr$m,na.rm = TRUE),dec-1)
|
||||
ms<-paste0(mean," (",sd,")")
|
||||
|
||||
nr<-c(nr,n,ms)
|
||||
nr <- c()
|
||||
for (r in 1:2) {
|
||||
vr <- levels(di$v)[r]
|
||||
dr <- di[di$v == vr, ]
|
||||
n <- as.numeric(nrow(dr[!is.na(dr$m), ]))
|
||||
mean <- round(mean(dr$m, na.rm = TRUE), dec -
|
||||
1)
|
||||
sd <- round(sd(dr$m, na.rm = TRUE), dec - 1)
|
||||
ms <- paste0(mean, " (", sd, ")")
|
||||
nr <- c(nr, n, ms)
|
||||
}
|
||||
irl<-c(grp,nr,ci,aci)
|
||||
df<-rbind(df,irl)
|
||||
names(df)<-c("grp",paste0("N.",substr(levels(v)[1],1,3)),paste0("M.",substr(levels(v)[1],1,3)),paste0("N.",substr(levels(v)[2],1,3)),paste0("M.",substr(levels(v)[2],1,3)),"diff","ad.diff")
|
||||
}}
|
||||
|
||||
if(is.factor(m)){
|
||||
|
||||
for (i in 1:length(levels(g))){
|
||||
grp<-levels(dat$g)[i]
|
||||
di<-dat[dat$g==grp,][,-3]
|
||||
|
||||
mod<-glm(m~v,family=binomial(),data=di)
|
||||
co<-round(exp(coef(mod)[-1]),dec)
|
||||
lo<-round(exp(confint(mod)[-1,1]),dec)
|
||||
up<-round(exp(confint(mod)[-1,2]),dec)
|
||||
|
||||
ci<-paste0(co," (",lo," to ",up,")")
|
||||
|
||||
amod<-glm(m~.,family=binomial(),data=di)
|
||||
aco<-round(exp(coef(amod)[2]),dec)
|
||||
alo<-suppressMessages(round(exp(confint(amod)[2,1]),dec))
|
||||
aup<-suppressMessages(round(exp(confint(amod)[2,2]),dec))
|
||||
|
||||
aci<-paste0(aco," (",alo," to ",aup,")")
|
||||
|
||||
nr<-c()
|
||||
|
||||
for (r in 1:2){
|
||||
vr<-levels(di$v)[r]
|
||||
dr<-di[di$v==vr,]
|
||||
n<-as.numeric(nrow(dr[!is.na(dr$m),]))
|
||||
nl<-levels(m)[2]
|
||||
out<-nrow(dr[dr$m==nl&!is.na(dr$m),])
|
||||
pro<-round(out/n*100,0)
|
||||
rt<-paste0(out," (",pro,"%)")
|
||||
|
||||
nr<-c(nr,n,rt)
|
||||
irl <- c(grp, nr, ci, pv, aci, apv)
|
||||
df <- rbind(df, irl)
|
||||
names(df) <- c("grp",
|
||||
paste0("N.", substr(levels(v)[1], 1, 3)),
|
||||
paste0("M.", substr(levels(v)[1], 1, 3)),
|
||||
paste0("N.", substr(levels(v)[2], 1, 3)),
|
||||
paste0("M.", substr(levels(v)[2], 1, 3)),
|
||||
"diff",
|
||||
"pval",
|
||||
"ad.diff",
|
||||
"ad.pval")
|
||||
}
|
||||
irl<-c(grp,nr,ci,aci)
|
||||
df<-rbind(df,irl)
|
||||
names(df)<-c("grp",paste0("N.",substr(levels(v)[1],1,3)),paste0(nl,".",substr(levels(v)[1],1,3)),paste0("N.",substr(levels(v)[2],1,3)),paste0(nl,".",substr(levels(v)[2],1,3)),"OR","ad.OR")
|
||||
}}
|
||||
}
|
||||
if (is.factor(m)) {
|
||||
for (i in 1:length(levels(g))) {
|
||||
grp <- levels(dat$g)[i]
|
||||
di <- dat[dat$g == grp, ][, -3]
|
||||
|
||||
mod <- glm(m ~ v, family = binomial(), data = di)
|
||||
|
||||
p <- coef(summary(mod))[2,4]
|
||||
p<-ifelse(p<0.001,"<0.001",round(p,3))
|
||||
p <- ifelse(p<=0.05|p=="<0.001",paste0("*",p),
|
||||
ifelse(p>0.05&p<=0.1,paste0(".",p),p))
|
||||
pv<-p
|
||||
|
||||
co <- round(exp(coef(mod)[-1]), dec)
|
||||
ci<-round(exp(confint(mod)),dec)[2,]
|
||||
lo<-ci[1]
|
||||
up<-ci[2]
|
||||
ci <- paste0(co, " (", lo, " to ", up, ")")
|
||||
|
||||
amod <- glm(m ~ ., family = binomial(), data = di)
|
||||
|
||||
pa <- coef(summary(amod))[2,4]
|
||||
pa<-ifelse(pa<0.001,"<0.001",round(pa,3))
|
||||
pa <- ifelse(pa<=0.05|pa=="<0.001",paste0("*",pa),
|
||||
ifelse(pa>0.05&pa<=0.1,paste0(".",pa),pa))
|
||||
apv<-pa
|
||||
|
||||
aco <- round(exp(coef(amod)[2]), dec)
|
||||
aci<-suppressMessages(round(exp(confint(amod)),dec))[2,]
|
||||
alo<-aci[1]
|
||||
aup<-aci[2]
|
||||
aci <- paste0(aco, " (", alo, " to ", aup, ")")
|
||||
nr <- c()
|
||||
|
||||
for (r in 1:2) {
|
||||
vr <- levels(di$v)[r]
|
||||
dr <- di[di$v == vr, ]
|
||||
n <- as.numeric(nrow(dr[!is.na(dr$m), ]))
|
||||
nl <- levels(m)[2]
|
||||
out <- nrow(dr[dr$m == nl & !is.na(dr$m), ])
|
||||
pro <- round(out/n * 100, 0)
|
||||
rt <- paste0(out, " (", pro, "%)")
|
||||
nr <- c(nr, n, rt)
|
||||
}
|
||||
irl <- c(grp, nr, ci, pv, aci, apv)
|
||||
df <- rbind(df, irl)
|
||||
names(df) <- c("grp",
|
||||
paste0("N.", substr(levels(v)[1], 1, 3)),
|
||||
paste0(nl, ".", substr(levels(v)[1], 1, 3)),
|
||||
paste0("N.", substr(levels(v)[2], 1, 3)),
|
||||
paste0(nl, ".", substr(levels(v)[2], 1, 3)),
|
||||
"OR",
|
||||
"pval",
|
||||
"ad.OR",
|
||||
"ad.pval")
|
||||
}
|
||||
}
|
||||
return(df)
|
||||
}
|
||||
}
|
||||
|
||||
@ -15,7 +15,7 @@ strobe_diff_bygroup(meas, var, group, adj, data, dec = 2)
|
||||
|
||||
\item{data}{dataframe of data.}
|
||||
|
||||
\item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1.}
|
||||
\item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1. pval has 3 decimals.}
|
||||
|
||||
\item{groups}{groups to compare, as string.}
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user