Trying to fix combined function without much luck

R/cie_test.R

@@ -10,53 +10,53 @@
 #' cie_test()
 
 cie_test<-function(y,v1,string,data,logistic=FALSE,cut=0.1,v2=NULL,v3=NULL){
-## Calculating variables, that should be included for a change in estimate analysis. 
+## Calculating variables, that should be included for a change in estimate analysis.
-## v1-3 are possible locked variables, y is the outcome vector. 
+## v1-3 are possible locked variables, y is the outcome vector.
 ## String defines variables to test, and is provided as vector of variable names. Use dput().
 ## From "Modeling and variable selection in epidemiologic analysis." - S. Greenland, 1989.
-  
+
   require(broom)
-  
+
   d<-data
   x<-select(d,one_of(c(string)))
   if(logistic==FALSE){
 if (is.factor(y)){stop("Some kind of error message would be nice, but y should not be a factor!")}
 
-if (is.null(v2)&is.null(v3)){     
+if (is.null(v2)&is.null(v3)){
-  
+
   e<-as.numeric(round(coef(lm(y~v1)),3))[1]
-     
+
-  
+
        df<-data.frame(pred="base",b=e)
-  
+
   for(i in 1:ncol(x)){
 
      m<-lm(y~v1+x[,i])
-     
+
      b<-as.numeric(round(coef(m),3))[1]
-  
+
      v<-x[,i]
-     
+
    pred<-paste(names(x)[i])
 
      df<-rbind(df,cbind(pred,b))
   }
        t<-c(NA,ifelse(abs(e-as.numeric(df[-1,2]))>=(e*cut),"include","drop"))
-df<-cbind(df,t)  
+df<-cbind(df,t)
        }
 
-       if (!is.null(v2)&is.null(v3)){   
+       if (!is.null(v2)&is.null(v3)){
-         
+
            e<-as.numeric(round(coef(lm(y~v1+v2)),3))[1]
-     
+
        df<-data.frame(pred="base",b=e)
-       
+
   for(i in 1:ncol(x)){
 
      m<-lm(y~v1+v2+x[,i])
-     
+
      b<-as.numeric(round(coef(m),3))[1]
-  
+
      v<-x[,i]
 
        pred<-paste(names(x)[i])
@@ -64,70 +64,70 @@ df<-cbind(df,t)
      df<-rbind(df,cbind(pred,b))
   }
        t<-c(NA,ifelse(abs(e-as.numeric(df[-1,2]))>=(e*cut),"include","drop"))
-df<-cbind(df,t)  
+df<-cbind(df,t)
        }
-       
+
-       if (!is.null(v2)&!is.null(v3)){   
+       if (!is.null(v2)&!is.null(v3)){
-         
+
            e<-as.numeric(round(coef(lm(y~v1+v2+v3)),3))[1]
-     
+
        df<-data.frame(pred="base",b=e)
-       
+
   for(i in 1:ncol(x)){
 
      m<-lm(y~v1+v2+v3+x[,i])
-     
+
      b<-as.numeric(round(coef(m),3))[1]
-     
+
      v<-x[,i]
-    
+
        pred<-paste(names(x)[i])
-     
+
      df<-rbind(df,cbind(pred,b))
-     
+
   }
        t<-c(NA,ifelse(abs(e-as.numeric(df[-1,2]))>=(e*cut),"include","drop"))
-df<-cbind(df,t)  
+df<-cbind(df,t)
 }}
 
 if(logistic==TRUE){
 
 if (!is.factor(y)){stop("Some kind of error message would be nice, but y should be a factor!")}
 
-if (is.null(v2)&is.null(v3)){     
+if (is.null(v2)&is.null(v3)){
-  
+
   e<-as.numeric(round(exp(coef(glm(y~v1,family=binomial()))),3))[1]
-     
+
        df<-data.frame(pred="base",b=e)
-  
+
   for(i in 1:ncol(x)){
 
      m<-glm(y~v1+x[,i],family=binomial())
-     
+
      b<-as.numeric(round(exp(coef(m)),3))[1]
-  
+
      v<-x[,i]
-     
+
    pred<-paste(names(x)[i])
 
      df<-rbind(df,cbind(pred,b))
   }
        t<-c(NA,ifelse(abs(e-as.numeric(df[-1,2]))>=(e*cut),"include","drop"))
-df<-cbind(df,t)  
+df<-cbind(df,t)
        }
 
-       if (!is.null(v2)&is.null(v3)){   
+       if (!is.null(v2)&is.null(v3)){
-         
+
            e<-as.numeric(round(exp(coef(glm(y~v1+v2,family=binomial()))),3))[1]
-     
+
        df<-data.frame(pred="base",b=e)
-       
+
   for(i in 1:ncol(x)){
 
      m<-glm(y~v1+v2+x[,i],family=binomial())
-     
+
      b<-as.numeric(round(exp(coef(m)),3))[1]
-  
+
      v<-x[,i]
 
        pred<-paste(names(x)[i])
@@ -135,30 +135,30 @@ df<-cbind(df,t)
      df<-rbind(df,cbind(pred,b))
   }
        t<-c(NA,ifelse(abs(e-as.numeric(df[-1,2]))>=(e*cut),"include","drop"))
-df<-cbind(df,t)  
+df<-cbind(df,t)
        }
-       
+
-       if (!is.null(v2)&!is.null(v3)){   
+       if (!is.null(v2)&!is.null(v3)){
-         
+
            e<-as.numeric(round(exp(coef(glm(y~v1+v2+v3,family=binomial()))),3))[1]
-     
+
        df<-data.frame(pred="base",b=e)
-       
+
   for(i in 1:ncol(x)){
 
      m<-glm(y~v1+v2+v3+x[,i],family=binomial())
-     
+
      b<-as.numeric(round(exp(coef(m)),3))[1]
-     
+
      v<-x[,i]
-    
+
        pred<-paste(names(x)[i])
-     
+
      df<-rbind(df,cbind(pred,b))
-     
+
   }
        t<-c(NA,ifelse(abs(e-as.numeric(df[-1,2]))>=(e*cut),"include","drop"))
-df<-cbind(df,t)  
+df<-cbind(df,t)
 }}
 
     return(df)

R/rep_biv.R

@@ -14,18 +14,23 @@
 
 rep_biv<-function(y,v1,string,data,method="pval",logistic=FALSE,ci=FALSE,cut=0.1,v2=NULL,v3=NULL){
 
-require(rep_lm)
+  a<-y
-  require(rep_glm)
+  b<-v1
-  require(cie_test)
+  s<-string
+  dat<-data
+  me<-method
+  log<-logistic
+  CI<-ci
+  ct<-cut
 
-if (method=="pval"&logistic==FALSE){
+if (me=="pval"&log==FALSE){
-rep_lm(y=y,v1=v1,string=string,data=data,ci=ci)
+daDoctoR::rep_lm(y=a,v1=b,string=s,data=dat,ci=CI)
 }
-if (method=="pval"&logistic==TRUE){
+if (me=="pval"&log==TRUE){
-rep_lm(y=y,v1=v1,string=string,data=data,ci=ci)
+  daDoctoR::rep_lm(y=a,v1=b,string=s,data=dat,ci=CI)
 }
 if (method=="cie"){
-cie_test(y=y,v1=v1,string=string,data=data,logistic=logistic,cut=cut,v2=v2,v3=v3)
+  daDoctoR::cie_test(y=a,v1=b,string=s,data=dat,logistic=log,cut=ct)
 }
 return(df)
 }