R/cross_numeric.R

In crosstable: Crosstables for Descriptive Analyses

#' @keywords internal
#' @importFrom checkmate assert assert_numeric
#' @importFrom dplyr everything mutate rename select
#' @importFrom tibble as_tibble
#' @noRd
cross_numeric = function(data_x, data_y, funs, funs_arg, showNA, total,
                         label, cor_digits, cor_method,  test, test_args, effect, effect_args) {
  assert(ncol(data_x)==1)
  assert(is.null(data_y) || ncol(data_y)==1)
  assert_numeric(data_x[[1]])

  if(label){
    x_name = get_label(data_x)
    y_name = get_label(data_y)
  } else {
    x_name = names(data_x)
    y_name = names(data_y)
  }

  if(is.null(data_y)){
    rtn = summarize_numeric_single(data_x[[1]], funs, funs_arg)
  } else if(is.character.or.factor(data_y[[1]])) {
    rtn = summarize_numeric_factor(data_x[[1]], data_y[[1]], funs, funs_arg, showNA, total,
                                   cor_digits, cor_method,  test, test_args,
                                   effect, effect_args)
  } else if(!is.date(data_x[[1]]) && is.numeric.and.not.surv(data_y[[1]])){
    rtn = summarize_numeric_numeric(data_x[[1]], data_y[[1]], method=cor_method,
                                    digits=cor_digits, test=test, test_args) %>%
      rename(!!y_name:="value")
  } else {
    return(NULL)
  }

  rtn = rtn %>%
    mutate(.id=names(data_x), label=unname(x_name)) %>%
    select(".id", "label", everything()) %>%
    as_tibble()

  rtn
}


#' Summarize numeric variables
#' @importFrom cli cli_abort
#' @importFrom dplyr across mutate where
#' @importFrom methods formalArgs
#' @importFrom purrr discard imap list_rbind
#' @keywords internal
#' @noRd
summarize_numeric_single = function(x, funs, funs_arg){
  imap(funs, ~{
    funs_arg2 = funs_arg
    if(!"..." %in% formalArgs(.x)){
      funs_arg2 = funs_arg[formalArgs(.x)] %>% discard(is.null)
    }
    v = do.call(.x, c(list(x), funs_arg2))
    if(length(v)<2){
      variable = .y
    } else {
      variable=names(v)
      if(.y!=" "){
        variable = paste(.y, variable)
      }
    }
    if(length(variable)!=length(v)){
      cli_abort("Summary functions should return a single value",
                class="crosstable_summary_not_scalar")
    }

    data.frame(variable=variable, value=v) %>%
      mutate(across(where(~is.numeric(.x)||is.date(.x)),
                    ~format_fixed(.x, !!!funs_arg)))
  }) %>% list_rbind()
}


#' Summarize numeric by categorical
#' @importFrom checkmate assert_numeric assert_scalar
#' @importFrom dplyr across everything mutate ungroup
#' @importFrom forcats fct_na_value_to_level
#' @importFrom purrr imap list_rbind
#' @importFrom tidyr pivot_wider
#' @keywords internal
#' @noRd
summarize_numeric_factor = function(x, by, funs, funs_arg, showNA, total,
                                    cor_digits, cor_method, test, test_args,
                                    effect, effect_args){
  assert_numeric(x)
  assert_scalar(showNA)
  .na=.effect=.test=.total=NULL
  .showNA = showNA == "always" | (showNA == "ifany" && anyNA(by))

  if(effect){
    .effect = effect_args$effect_display(effect_args$effect_summarize(x, by, effect_args$conf_level),
                                         digits = cor_digits)
  }
  if(test){
    .test = test_args$test_display(test_args$test_summarize(x, by), digits = test_args$plim,
                                   method = test_args$show_method)
  }
  if(identical(total, 1) | identical(total, 1:2) | identical(total, TRUE)){
    .total = summarize_numeric_single(x, funs=funs, funs_arg=funs_arg)[["value"]]
  }

  if(.showNA==TRUE) {
    if(!anyNA(by)) .na="no NA"
    by_filter=TRUE
    by = fct_na_value_to_level(by, "NA")
  } else{
    by_filter = !is.na(by)
  }

  by(x[by_filter], by[by_filter], summarize_numeric_single, funs=funs, funs_arg=funs_arg) %>%
    imap(~{
      if(is.null(.x)) .x=summarize_numeric_single(numeric(0), funs=funs, funs_arg=funs_arg)
      mutate(.x, by=.y, .before=1)
    }) %>%
    list_rbind() %>%
    pivot_wider(names_from = "by") %>%
    {if(!is.null(.na)){mutate(.,"NA"=.na)} else .} %>%
    mutate(Total=.total, effect=.effect, test=.test,
           across(everything(), as.character)) %>%
    ungroup()
}



#' Summarize numeric by numeric (correlation)
#' @importFrom checkmate assert_count assert_list assert_logical assert_numeric assert_string
#' @importFrom dplyr mutate
#' @importFrom glue glue
#' @importFrom tibble tibble
#' @keywords internal
#' @noRd
summarize_numeric_numeric = function(x, by, method, digits, test, test_args){
  assert_numeric(x)
  assert_numeric(by)
  assert_string(method)
  assert_count(digits)
  assert_logical(test)
  assert_list(test_args)

  ct=test_args$test_correlation(x, by, method=method)

  cor=round(ct$estimate, digits=digits)
  if(!is.null(ct$conf.int)){
    ci=round(ct$conf.int, digits=digits)
    value=glue("{cor} \n95%CI [{ci[1]};{ci[2]}]")
  } else {
    value=glue("{cor}")
  }

  if(test) .test=test_args$test_display(ct) else .test=NULL

  tibble(variable=method, value=as.character(value)) %>% mutate(test=.test)
}