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