R/label_variables.R

In EpidemiumOpenCancer/OpenCancer: Build statistical models to understand cancer causes

#' Use variables labels in a regression
#'
#' @param model An object of class \code{lm}
#' or \code{big.lm}
#' @return Same object with modified variable names

label_variables <- function(model){

  codes <- import_coding()
  if (class(model) %in% c("biglm","bigglm")){
    #During importation of wholedf R added "X" in front of colnames's FAO data
    codes$code[codes$source=="FAO"] <- paste0("X",codes$code[codes$source=="FAO"])
    colsub <- codes %>% filter(code %in% model$names)
    model$names <- plyr::mapvalues(model$names, from=colsub$code, to=colsub$label,
                                        warn_missing = FALSE)

  } else if (class(model) %in% c('lm','glm')){
    #names(model$coefficients) <- stringr::str_replace_all(names(model$coefficients),"X.","")
    colsub <- stringr::str_split(gsub("`","",names(model$coefficients)),"_",simplify = T)
    colsub[,1] <- plyr::mapvalues(colsub[,1],
                    from = colsub[colsub[,1] %in% codes$code,1],
                    to = codes$label[codes$code %in% colsub[,1]])
    colsub[!colsub[,2] == "",1] <-
      paste0(colsub[!colsub[,2] == "",1]," (",colsub[!colsub[,2] == "",2],
           ")")
    colsub <- as.character(colsub[,1])
    names(model$coefficients) <- colsub

  }
  return(model)
}