r 此函数接受glm和geeglm / gee对象。它输出变量名称，变量级别，然后是比值比，置信度

Posted 2021-05-24

# please break this function so I know what to fix. Also recommend edits to the function. Thanks!
model_output <- function(mod_obj){
  # libraries
  require(geepack); require(tibble); require(dplyr)
  xvar <- names(lm_object$model)[-1]
  yvar <- names(lm_object$model)[1] # idky i need this but just in case
  data <- lm_object$data
  
  # xvar levels
  xvar_levels <- sapply(data[, xvar], levels)
  xvar_levels_unlist <- unlist(lapply(seq_along(xvar_levels), 
                                      function(x) paste(names(xvar_levels)[[x]], xvar_levels[[x]], sep = "")))
  xvar_levels_df <- data.frame(vec_levels = xvar_levels_unlist)
  
  # odds ratio, confidence interval, and pvalues
  # first, determine if object is geeglm/gee object or not
  if("geeglm" %in% class(lm_object) | "gee" %in% class(lm_object)){
    confint.geeglm <- function(object, parm, level = 0.95, ...) {
      cc <- coef(summary(object))
      mult <- qnorm((1+level)/2)
      citab <- with(as.data.frame(cc),
                    cbind(lwr=Estimate-mult*Std.err,
                          upr=Estimate+mult*Std.err))
      rownames(citab) <- rownames(cc)
      citab[parm,]
    }
    confint_obj <- confint.geeglm(lm_object)
  } else {
    confint_obj <- confint(lm_object)
    colnames(confint_obj) <- c("lwr", "upr")
  }
  or_ci_obj <- as.data.frame(round(cbind(exp(coef(lm_object)), exp(confint_obj)), 2))
  or_ci_obj1 <- rownames_to_column(or_ci_obj, var = "variable") # surprisingly, it works
  or_ci_obj1$ci <- sprintf("%.2f %s %.2f", or_ci_obj1$lwr, "-", or_ci_obj1$upr)
  
  pval_obj <- as.data.frame(round(summary(lm_object)$coef, 3))
  pval_obj1 <- rownames_to_column(pval_obj, var = "variable")
  colnames(pval_obj1)[5] <- "pvalue"
  
  mod_df <- data.frame(or_ci_obj1[, c("variable", "V1", "ci")], pval_obj1[, c("pvalue")])
  colnames(mod_df) <- c("variable", "or", "ci", "pvalue")
  
  # merge xvar_levels_df with mod_df to create REF categories
  # left_join doesn't need standard evaluation...strange...is it just 5 dplyr verbs? must be
  suppressWarnings(merged_df <- left_join(xvar_levels_df, mod_df, by = c("vec_levels" = "variable")))
  merged_df$pvalue1 <- sprintf("%.3f", merged_df$pvalue)
  
  merged_df1 <- replace(merged_df, is.na(merged_df) == TRUE | merged_df == "NA", "Ref")
  merged_df2 <- select_(merged_df1, ~vec_levels, ~or, ~ci, ~pvalue1) #standard evaluation
  
  # insert function
  insertRow <- function(existingDF, newrows) {
    new_idx <- as.integer(newrows[,1]) # get indices of the new rows
    new_idx <- sort(new_idx) + seq(0, length(new_idx) - 1) # adjust for rows shifting due to other insertions 
    old_idx <- seq(nrow(existingDF) + length(new_idx))[-new_idx] # ge indices for the old rows
    existingDF[old_idx,] <- existingDF # assign old rows
    existingDF[new_idx,] <- newrows[,-1] # assign new rows
    existingDF
  }
  # insert row names into model
  list_length <- unlist(lapply(seq_along(xvar_levels), function(x) length(xvar_levels[[x]])))
  merged_df3 <- insertRow(merged_df2, newrows = cbind(cumsum(list_length) - list_length + 1, 
                                                      xvar, "", "", "")) # ugly but gets the job done
  return(merged_df3)
}