From e177156660c5c04307384e788475ace724cb6bc6 Mon Sep 17 00:00:00 2001
From: agdamsbo <agdamsbo@protonmail.com>
Date: Thu, 4 Oct 2018 09:23:14 +0200
Subject: [PATCH] making function more universal

---
 R/rep_glm.R    | 102 +++++++++++++++++++++++++------------------------
 man/rep_glm.Rd |   8 ++--
 2 files changed, 58 insertions(+), 52 deletions(-)

diff --git a/R/rep_glm.R b/R/rep_glm.R
index 21304cc..f2f18fc 100644
--- a/R/rep_glm.R
+++ b/R/rep_glm.R
@@ -1,91 +1,95 @@
 #' A repeated logistic regression function
 #'
-#' For bivariate analyses.
+#' @description For bivariate analyses. The confint() function is rather slow, causing the whole function to hang when including many predictors and calculating the ORs with CI.
 #' @param y Effect meassure.
-#' @param v1 Main variable in model
+#' @param vars variables in model. Input as c() of columnnames, use dput().
+#' @param string variables to test. Input as c() of columnnames, use dput().
 #' @keywords logistic regression
 #' @export
 #' @examples
 #' rep_glm()
 
-rep_glm<-function(y,v1,string,ci=FALSE,data,v2=NULL,v3=NULL){
-## x is data.frame of predictors, y is vector of an aoutcome as a factor
-## output is returned as coefficient, or if or=TRUE as OR with 95 % CI.
-## The confint() function is rather slow, causing the whole function to hang when including many predictors and calculating the ORs with CI.
+rep_glm<-function(y,vars,string,ci=FALSE,data){
+  ## x is data.frame of predictors, y is vector of an aoutcome as a factor
+  ## output is returned as coefficient, or if or=TRUE as OR with 95 % CI.
+  ##
 
-  require(broom)
+  require(dplyr)
 
   d<-data
   x<-select(d,one_of(c(string)))
-  m1<-length(coef(glm(y~v1,family = binomial())))
+  v<-select(d,one_of(c(vars)))
+  dt<-cbind(y,v)
+  m1<-length(coef(glm(y~.,family = binomial(),data = dt)))
 
-if (!is.factor(y)){stop("Some kind of error message would be nice, but y should be a factor!")}
+  if (!is.factor(y)){stop("Some kind of error message would be nice, but y should be a factor!")}
 
-    if (ci==TRUE){
+  if (ci==TRUE){
 
-             df<-data.frame(matrix(ncol = 4))
-  names(df)<-c("pred","or_ci","pv","t")
+    df<-data.frame(matrix(ncol = 3))
+    names(df)<-c("pred","or_ci","pv")
 
-      for(i in 1:ncol(x)){
-     m<-glm(y~v1+x[,i],family = binomial())
+    for(i in 1:ncol(x)){
 
-     l<-suppressMessages(round(exp(confint(m))[-c(1:m1),1],2))
-     u<-suppressMessages(round(exp(confint(m))[-c(1:m1),2],2))
-     or<-round(exp(coef(m))[-c(1:m1)],2)
+      dat<-cbind(dt,x[,i])
 
-     or_ci<-paste0(or," (",l," to ",u,")")
+      m<-glm(y~.,family = binomial(),data=dat)
 
-     pv<-round(tidy(m)$p.value[-c(1:m1)],3)
-     pv<-ifelse(pv<0.001,"<0.001",pv)
+      l<-suppressMessages(round(exp(confint(m))[-c(1:m1),1],2))
+      u<-suppressMessages(round(exp(confint(m))[-c(1:m1),2],2))
+      or<-round(exp(coef(m))[-c(1:m1)],2)
 
-         t <- ifelse(pv<=0.1|pv=="<0.001","include","drop")
+      or_ci<-paste0(or," (",l," to ",u,")")
 
-     pv <- ifelse(pv<=0.05|pv=="<0.001",paste0("*",pv),
-                  ifelse(pv>0.05&pv<=0.1,paste0(".",pv),pv))
+      pv<-round(tidy(m)$p.value[-c(1:m1)],3)
 
+      x1<-x[,i]
 
-    v<-x[,i]
+      if (is.factor(x1)){
+        pred<-paste(names(x)[i],levels(x1)[-1],sep = "_")
+      }
 
-    if (is.factor(v)){
-       pred<-paste(names(x)[i],levels(v)[-1],sep = "_")
-    }
+      else {pred<-names(x)[i]}
 
-       else {pred<-names(x)[i]}
-
-      df<-rbind(df,cbind(pred,or_ci,pv,t))
+      df<-rbind(df,cbind(pred,or_ci,pv))
 
     }}
 
   if (ci==FALSE){
 
-       df<-data.frame(matrix(ncol = 4))
-  names(df)<-c("pred","b","pv","t")
+    df<-data.frame(matrix(ncol = 3))
+    names(df)<-c("pred","b","pv")
 
-  for(i in 1:ncol(x)){
-     m<-glm(y~v1+x[,i],family = binomial())
+    for(i in 1:ncol(x)){
+      dat<-cbind(dt,x[,i])
 
-     b<-round(coef(m)[-c(1:m1)],3)
+      m<-glm(y~.,family = binomial(),data=dat)
 
-     pv<-round(tidy(m)$p.value[-c(1:m1)],3)
-     pv<-ifelse(pv<0.001,"<0.001",pv)
+      b<-round(coef(m)[-c(1:m1)],3)
 
-    t <- ifelse(pv<=0.1|pv=="<0.001","include","drop")
+      pv<-round(tidy(m)$p.value[-c(1:m1)],3)
 
-     pv <- ifelse(pv<=0.05|pv=="<0.001",paste0("*",pv),
-                  ifelse(pv>0.05&pv<=0.1,paste0(".",pv),pv))
+      x1<-x[,i]
 
+      if (is.factor(x1)){
+        pred<-paste(names(x1)[i],levels(x1)[-1],sep = "_")
+      }
 
-     v<-x[,i]
+      else {pred<-names(x)[i]}
 
-     if (is.factor(v)){
-       pred<-paste(names(x)[i],levels(v)[-1],sep = "_")
-     }
+      df<-rbind(df,cbind(pred,b,pv))
 
-       else {pred<-names(x)[i]}
+    }}
 
-     df<-rbind(df,cbind(pred,b,pv,t))
+  pa<-as.numeric(df[,3])
+  pa<-ifelse(pa<0.001,"<0.001",pa)
 
-  }}
-  result<-df
-  return(df)
+  t <- ifelse(pa<=0.1|pa=="<0.001","include","drop")
+
+  pa <- ifelse(pa<=0.05|pa=="<0.001",paste0("*",pa),
+               ifelse(pa>0.05&pa<=0.1,paste0(".",pa),pa))
+
+  r<-data.frame(df[,1:2],pa,t)[-1,]
+
+  return(r)
 }
diff --git a/man/rep_glm.Rd b/man/rep_glm.Rd
index 2f5b786..291c196 100644
--- a/man/rep_glm.Rd
+++ b/man/rep_glm.Rd
@@ -4,15 +4,17 @@
 \alias{rep_glm}
 \title{A repeated logistic regression function}
 \usage{
-rep_glm(y, v1, string, ci = FALSE, data, v2 = NULL, v3 = NULL)
+rep_glm(y, vars, string, ci = FALSE, data)
 }
 \arguments{
 \item{y}{Effect meassure.}
 
-\item{v1}{Main variable in model}
+\item{vars}{variables in model. Input as c() of columnnames, use dput().}
+
+\item{string}{variables to test. Input as c() of columnnames, use dput().}
 }
 \description{
-For bivariate analyses.
+For bivariate analyses. The confint() function is rather slow, causing the whole function to hang when including many predictors and calculating the ORs with CI.
 }
 \examples{
 rep_glm()