daDoctoR/R/cie_test.R
agdamsbo 76dd8a4ce7 u
2018-10-04 12:05:14 +02:00

80 lines
2.1 KiB
R

#' A repeated regression function for change-in-estimate analysis
#'
#' For bivariate analyses. From "Modeling and variable selection in epidemiologic analysis." - S. Greenland, 1989.
#' @param y Effect meassure.
#' @param v1 Main variable in model
#' @param string String of columnnames from dataframe to include. Use dput().
#' @keywords change-in-estimate
#' @examples
#' l<-5
#' y<-factor(rep(c("a","b"),l))
#' x<-rnorm(length(y), mean=50, sd=10)
#' v1<-factor(rep(c("r","s"),length(y)/2))
#' v2<-as.numeric(sample(1:100, length(y), replace=FALSE))
#' v3<-as.numeric(1:length(y))
#' d<-data.frame(y,x,v1,v2,v3)
#' preds<-dput(names(d)[3:ncol(d)])
#' cie_test(meas="y",vars="x",string=preds,data=d,logistic = TRUE,cut = 0.1)
#' @export
cie_test<-function(meas,vars,string,data,logistic=FALSE,cut=0.1){
require(broom)
d<-data
x<-data.frame(d[,c(string)])
v<-data.frame(d[,c(vars)])
names(v)<-c(vars)
y<-d[,c(meas)]
dt<-cbind(y,v)
c<-as.numeric(cut)
if(logistic==FALSE){
if (is.factor(y)){stop("Logistic is flagged as FALSE, but the provided meassure is formatted as a factor!")}
e<-as.numeric(round(coef(lm(y~.,data = dt)),3))[1]
df<-data.frame(pred="base",b=e)
for(i in 1:ncol(x)){
dat<-cbind(dt,x[,i])
m<-lm(y~.,data=dat)
b<-as.numeric(round(coef(m),3))[1]
pred<-paste(names(x)[i])
df<-rbind(df,cbind(pred,b)) }
di<-as.vector(abs(e-as.numeric(df[-1,2]))/e)
dif<-c(NA,di)
t<-c(NA,ifelse(di>=c,"include","drop"))
r<-cbind(df,dif,t) }
if(logistic==TRUE){
if (!is.factor(y)){stop("Logistic is flagged as TRUE, but the provided meassure is NOT formatted as a factor!")}
e<-as.numeric(round(exp(coef(glm(y~.,family=binomial(),data=dt))),3))[1]
df<-data.frame(pred="base",b=e)
for(i in 1:ncol(x)){
dat<-cbind(dt,x[,i])
m<-glm(y~.,family=binomial(),data=dat)
b<-as.numeric(round(exp(coef(m)),3))[1]
pred<-paste(names(x)[i])
df<-rbind(df,cbind(pred,b)) }
di<-as.vector(abs(e-as.numeric(df[-1,2]))/e)
dif<-c(NA,di)
t<-c(NA,ifelse(di>=c,"include","drop"))
r<-cbind(df,dif,t)
}
return(r)
}