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agdamsbo 2018-10-05 12:39:29 +02:00
parent 38928f53c1
commit a56f4d3a1d
2 changed files with 70 additions and 29 deletions
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45
R/strobe_print.R
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@ -1,7 +1,7 @@
#' Print regression results according to STROBE #' Print regression results according to STROBE
#' #'
#' Printable table of linear regression analysis of group vs var for meas. #' Printable table of linear regression analysis of group vs var for meas.
#' @param meas outcome meassure variable name in data-data.frame as a string. #' @param meas outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly.
#' @param var exposure variable to compare against (active vs placebo). As string. #' @param var exposure variable to compare against (active vs placebo). As string.
#' @param groups groups to compare, as string. #' @param groups groups to compare, as string.
#' @param adj variables to adjust for, as string. #' @param adj variables to adjust for, as string.
@ -28,7 +28,8 @@ strobe_print<-function(meas,var,group,adj,data,dec=2){
dat<-data.frame(m,v,g,ads) dat<-data.frame(m,v,g,ads)
df<-data.frame(matrix(ncol=7)) df<-data.frame(matrix(ncol=7))
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))){ for (i in 1:length(levels(g))){
grp<-levels(dat$g)[i] grp<-levels(dat$g)[i]
@ -62,6 +63,46 @@ strobe_print<-function(meas,var,group,adj,data,dec=2){
} }
irl<-c(grp,nr,ci,aci) irl<-c(grp,nr,ci,aci)
df<-rbind(df,irl) 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<-round(exp(confint(amod)[2,1]),dec)
aup<-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,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")
}}
return(df) return(df)
} }

2
man/strobe_print.Rd
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@ -7,7 +7,7 @@
strobe_print(meas, var, group, adj, data, dec = 2) strobe_print(meas, var, group, adj, data, dec = 2)
} }
\arguments{ \arguments{
\item{meas}{outcome meassure variable name in data-data.frame as a string.} \item{meas}{outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly.}
\item{var}{exposure variable to compare against (active vs placebo). As string.} \item{var}{exposure variable to compare against (active vs placebo). As string.}