R/myft.R

In autoReg: Automatic Linear and Logistic Regression and Survival Analysis

#' Convert data.frame into flextable
#' @param x A data.frame
#' @param vanilla logical
#' @param  fontsize Numeric
#' @param digits integer indicating the position of decimal place
#' @param showid logical if TRUE, show id
#' @param ... Further arguments to be passed to df2flextable()
#' @importFrom flextable align autofit hline hline_top add_footer_lines as_paragraph merge_at
#' @importFrom officer fp_border
#' @importFrom purrr map_chr
#' @examples
#' data(acs,package="moonBook")
#' library(dplyr)
#' gaze(acs) %>% myft()
#' gaze(sex~.,acs) %>% myft()
#' fit=lm(mpg~hp*wt,data=mtcars)
#' gaze(fit) %>% myft()
#' library(survival)
#' fit=coxph(Surv(time,status) ~rx,data=anderson1)
#' gaze(fit) %>% myft()
#' \donttest{
#' gaze(sex+Dx~.,data=acs,show.p=TRUE,show.total=TRUE,show.n=TRUE,shiw.missing=TRUE) %>% myft()
#' gaze(Dx+sex~cardiogenicShock,data=acs,show.p=TRUE) %>% myft()
#' gaze(Dx+sex+HBP~cardiogenicShock,data=acs,show.p=TRUE) %>% myft()
#' }
#' @return An object of class \code{\link[flextable]{flextable}}
#' @export
myft=function(x,vanilla=TRUE,fontsize=10,digits,showid=FALSE,...){
     #  vanilla=TRUE;fontsize=10;digits=2;showid=FALSE
     if("imputedReg" %in% class(x)){
          if(missing(digits)) digits=c(1,4,4,4,2,4,4,4,4,4,4,1)
     } else if("autoReg" %in% class(x)) {

          if(missing(digits)) digits=2
          if(is.null(attr(x,"summary"))){
               if(showid==FALSE) x$id=NULL
               names(x)[1]=paste0("Dependent: ",attr(x,"yvars"))
               names(x)[2]=" "
               if(attr(x,"model")=="coxph") names(x)[3]="all"

          }
          # else if(attr(x,"model") %in% c("coxph","glm")){
          #      names(x)[1]=" "
          #      for(i in 2:4){
          #           x[[i]]=sprintf("%.03f",x[[i]])
          #      }
          #      x[[5]]=p2character2(x[[5]],add.p=FALSE)
          #      for(i in 6:8){
          #           x[[i]]=sprintf("%.02f",x[[i]])
          #      }
          # } else{
          #      names(x)[1]=" "
          #      for(i in 2:4){
          #           x[[i]]=sprintf("%.03f",x[[i]])
          #      }
          #      x[[5]]=p2character2(x[[5]],add.p=FALSE)
          #      for(i in 6:7){
          #           x[[i]]=sprintf("%.03f",x[[i]])
          #      }
          # }


     } else if(("gaze" %in% class(x))&(showid==FALSE)) {
          x$id=NULL
          names(x)[2]="levels"
          if(missing(digits)) digits=2
     }
     yvars=attr(x,"yvars")
     yvars
     if(length(yvars)>0){
          if(!is.null(attr(x,"missing"))) {
               yname=str_remove(attr(x,"yvars"),"Missing")
               names(x)[1]=paste0("Dependent:",yname)
          }

     }
     vanilla=TRUE
     ft<-x %>% df2flextable(vanilla=vanilla,fontsize=fontsize,digits=digits,...)
     #ft<-x %>% df2flextable(vanilla=vanilla,fontsize=fontsize,digits=digits)


     if(length(yvars)>1){
          small_border = fp_border(color="gray", width = 1)
          df=attr(x,"groups")
          if(length(yvars)==2) {
               collapse=" "
          } else {
               collapse="\n"
          }
          groupvar=paste0(c(yvars[-length(yvars)],"(N)"),collapse=collapse)
          header=c(groupvar,map_chr(1:nrow(df),function(i){paste0(df[i,],collapse=collapse)}))
          length=nrow(df)
          no=(ncol(x)-2)%/%length
          widths=c(2,rep(no,length))

          ft<-ft %>%
               flextable::add_header_row(values=header,colwidths=widths) %>%
               hline(i=1,border=fp_border(color="gray", width = 0),part="header") %>%
               hline(i=1,border=fp_border(color="gray", width = 1),part="header") %>%
               hline_top(border=fp_border(color="black", width = 2),part="header")


     }
     if("autoReg" %in% class(x)){
             temp=c(attr(x,"lik"),attr(x,"dev"),attr(x,"add"))
             temp=paste(temp,collapse="\n")

          # ft=footnote(ft,i=1,j=1:2,value=as_paragraph(temp),ref_symbols="",part="body")
          # footnote(ft,i=1,j=1:2,value=as_paragraph(temp),ref_symbols="",part="body")
          ft=add_footer_lines(ft,values=as_paragraph(temp))
          if(!is.null(attr(x,"model"))){
                 if(attr(x,"model")=="coxph") {
                      if(is.null(attr(x,"summary"))) ft=merge_at(ft,i=1,j=1:2,part="header")
                 }
          }
     }
     ft<- ft %>%
          flextable::align(align="center",part="header")
     if(is.null(attr(x,"mode"))){
          ft=ft %>%flextable::align(j=1:2,align="left",part="body")
     } else{
          ft=ft %>%flextable::align(j=1,align="left",part="body")
     }

     ft %>% flextable::autofit()
}