R/combine_log.R

In dacarras/erce: An `R` wrapper to dowload ERCE 2019 data and few functions

#' combine_log() combine estimates from mitools like objects, intended for logit models
#'
#' @param mi_estimates is an object generated by mitools::mitools::MIcombine or survey::withPV()
#'
#' @return a tidy table with estimates, estandard errors, p value, and confidence intervals
#'
#' @examples
#' library(dplyr)
#' library(erce)
#' ## add example besides combine_log()
#'
#'
#' @export
# function
combine_log <- function(mi_estimates) {


  # require libraries
  require(dplyr)
  require(mitools)

  # function to avoid text output from mitools
  quiet <- function(x) {
    sink(tempfile())
    on.exit(sink())
    invisible(force(x))
  }

  # get cpmbined estimates and summary
  mi_results <- quiet(mitools::MIcombine(mi_estimates))
  summary    <- quiet(summary(mi_results))

  # create tidy table
  tidy_results <- summary %>%
    tibble::rownames_to_column("term") %>%
    dplyr::rename(e = results,
                  se = se,
                  lo = `(lower`,
                  hi = `upper)`) %>%
    cbind(miss_info = mi_results$missinfo) %>%
    cbind(df = mi_results$df) %>%
    dplyr::mutate(p_val = 2 * (1 - pt(abs(e / se), df))) %>%
    dplyr::mutate(
      e = as.numeric(e),
      se = as.numeric(se),
      p_val = as.numeric(p_val),
      lo = as.numeric(lo),
      hi = as.numeric(hi),
      miss_info = as.numeric(miss_info)
    ) %>%
    # for logit estimates
    mutate(or = exp(e)) %>%
    mutate(or_lo = exp(lo)) %>%
    mutate(or_hi = exp(hi)) %>%
    dplyr::select(term, e, se, p_val, lo, hi, or, or_lo, or_hi) %>%
    tibble::as_tibble()

  # give output
  return(tidy_results)

  # Source: https://github.com/wepelham3/sack2/blob/master/R/tidy_MIcombine.R
}