cat cont functions for baseline tables

cat_cont_examples.R

cat       <-function(catvar,colvar,label){
  denoms    <-  tapply(!is.na(catvar),colvar,sum)
  counts    <-  tapply(catvar,colvar,sum)
  percen    <-  round(100*(counts/denoms),digits=2)
  totals    <-  tapply(catvar,rep(1,length(catvar)),sum)
  totalsden <-  tapply(!is.na(catvar),rep(1,length(catvar)),sum)
  totper    <-  round(100*(totals/totalsden),digits=2)

  meatcols  <-  paste(counts,'/',denoms,'(',percen,'',')',sep="")
  totcol    <-  paste(totals,'/',totalsden,'(',totper,'',')',sep="")
  temp              <- table(catvar,colvar)
  if (sum(as.logical(temp < 15))==0){
    a <- chisq.test(temp)
  } else {
    a <- fisher.test(temp)
  }
  output    <-  c(label,totcol,meatcols,ifelse(a$p.value<0.0001,'<0.0001',round(a$p.value,3)),a$method)
return(output)
}


cont      <- function(contvar,colvar,label,dat){
meds      <-  tapply(contvar,colvar,median,na.rm=TRUE)
Q1        <-  tapply(contvar,colvar,quantile,probs=0.25,na.rm=TRUE)
Q3        <-  tapply(contvar,colvar,quantile,probs=0.75,na.rm=TRUE)

totals    <-  tapply(contvar,rep(1,length(contvar)),median,na.rm=TRUE)
totalQ1   <-  tapply(contvar,rep(1,length(contvar)),quantile,probs=0.25,na.rm=TRUE) 
totalQ3   <-  tapply(contvar,rep(1,length(contvar)),quantile,probs=0.75,na.rm=TRUE) 

meatcols  <-  paste(round(meds,2),' (',round(Q1,2),",",round(Q3,2),")",sep="")
totcol    <-  paste(round(totals,2),' (',round(totalQ1,2),",",round(totalQ3,2),")",sep="")
a         <-  kruskal.test(contvar~colvar,data=dat)
output    <-  c(label,totcol,meatcols,ifelse(a$p.value<0.0001,'<0.0001',round(a$p.value,3)),a$method)
return(output)
}

out1 <- cont(contvar=sanal$b_age,colvar=colvar,label='Baseline Age (visit 4,5, or 6)',dat=sanal)
out2 <- cat(catvar=sanal$b_female,colvar=colvar,'Female ()')
out3 <- cat(catvar=sanal$b_smoke,colvar=colvar,'Smoking ()')
out4 <- cat(catvar=sanal$b_newdiab,colvar=colvar,'Diabetes ()')
out5 <- cont(contvar=sanal$b_cbmi,colvar=colvar,'Body Mass Index',sanal)