R/descripSurv.R

In ZhonghuiGai/groutable: This is a wrapper function of compareGroups package

descripSurv <- function(x, y, timemax, surv) {
    tt<-table(y)
    ll<-names(tt)[tt>0]

    nn<-by(!is.na(x[,1]),y,sum)
    nn[is.na(nn)]<-0
    oo<-by(x[,2]==1,y,sum,na.rm=TRUE)

    ss<-try(summary(survfit(x~y),times=timemax,extend=TRUE),silent=TRUE)

    Pmax.i<-Pmax.lower.i<-Pmax.upper.i<-rep(NaN,nlevels(y))
    names(Pmax.i)<-names(Pmax.lower.i)<-names(Pmax.upper.i)<-levels(y)
    if (!inherits(ss,"try-error")){
      # incid
      temp<-1-ss$surv
      names(temp)<-ll
      Pmax.i[ll]<-temp
      #lower
      temp<-1-ss$upper
      names(temp)<-ll
      Pmax.lower.i[ll]<-temp
      #upper
      temp<-1-ss$lower
      names(temp)<-ll
      Pmax.upper.i[ll]<-temp
    }

    nn.all<-sum(nn,na.rm=TRUE)

    ss.all<-try(summary(survfit(x~1),times=timemax,extend=TRUE),silent=TRUE)

    if (inherits(ss.all,"try-error")){
      Pmax.all<-Pmax.lower.all<-Pmax.upper.all<-NaN
    } else {
      Pmax.all<-1-ss.all$surv
      Pmax.lower.all<-1-ss.all$upper
      Pmax.upper.all<-1-ss.all$lower
    }
    ans<-cbind(c(nn.all,nn),c(Pmax.all,Pmax.i)*100,c(Pmax.lower.all,Pmax.lower.i)*100,c(Pmax.upper.all,Pmax.upper.i)*100)
    colnames(ans) <- c("n", "inc","lower","upper")
    if (surv){
      ans[,-1] <- 100-ans[,-1]
      ans[,3:4] <- ans[,4:3]
      colnames(ans) <- c("n", "surv","lower","upper")
    }
    rownames(ans) <- c("[ALL]",levels(y))
    ans

  }