R/format_tidy_gen.R

In Oromendia/oromendia: Clara Oromendia's suite of R functions

#' Print generic regression output with CI and P values
#'
#' This is a wrapper around broom:::tidy that adds formatted confidence intervals and p values
#' @param rslt Output from regression (lm, glm, or coxPH)
#' @param d Decimal places used for HR and confidence interval
#' @param d_pVal Decimal places used for p value.
#' @param sub_out String to from variable names to replace with sub_in
#' @param sub_in String to from variable names to replace instead of sub_out
#' @param exponentiate_here Select whether exponentiation should be done (CoxPH, Poisson, etc.). Default is FALSE
#' @param Beta Label for coefficient. Default is 'Beta'
#' @param reportIntercept Whether intercept should be reported. Default is FALSE. 
#' @keywords tidy
#' @export
#' @examples
#' dontrun{
#' format_tidy_gen()
#' }
format_tidy_gen <- function(rslt,d=2,d_pVal=3,sub_out = NULL,sub_in = NULL,exponentiate_here = FALSE,Beta = "Beta",
                            reportIntercept=FALSE){
  digi <- paste0("%.",d,"f")
  if(!is.null(sub_out)) {Variable = gsub(sub_out,sub_in,rslt$term)
  }else{Variable = rslt$term}
  rslt = cbind(
    Variable = Variable,
    Beta = if(exponentiate_here){
    	paste0(sprintf(digi,exp(rslt$estimate))," (",sprintf(digi,exp(rslt$conf.low)),",",sprintf(digi,exp(rslt$conf.high)),")")
    }else{paste0(sprintf(digi,rslt$estimate)," (",sprintf(digi,rslt$conf.low),",",sprintf(digi,rslt$conf.high),")")},
    Pvalue = format_pval(rslt$p.value,equal="",d=d_pVal)
  ) %>% as.data.frame()
  if(Beta != "Beta") colnames(rslt)[which(colnames(rslt) == "Beta")] = Beta
  if(!reportIntercept) rslt = rslt[-which(rslt$Variable == "(Intercept)"),]
  rslt
}