R/sanity_checks.R

In vincentarelbundock/gtsummary: Summary Tables and Plots for Statistical Models and Data: Beautiful, Customizable, and Publication-Ready

#' check if dependency is installed
#'
#' @noRd
check_dependency <- function(library_name) {
  flag <- requireNamespace(library_name, quietly = TRUE)
  if (isFALSE(flag)) {
      msg <- sprintf("Please install the `%s` package.", library_name)
      return(msg)
  } else {
      return(TRUE)
  }
}
assert_dependency <- checkmate::makeAssertionFunction(check_dependency)


#' sanity check
#'
#' @noRd
sanitize_escape <- function(escape) {
  checkmate::assert_flag(escape, null.ok = FALSE)
  settings_set("escape", escape)
}


#' sanity check
#'
#' @noRd
sanity_group_map <- function(group_map) {
  if (!is.null(group_map)) {
    if (is.null(names(group_map))) {
      checkmate::assert_character(group_map, unique = TRUE)
    } else {
      checkmate::assert_character(names(group_map), null.ok = TRUE, unique = TRUE)
    }
  }
}


#' sanity check
#'
#' @noRd
sanity_ellipsis <- function(vcov, ...) {
  ellip <- list(...)

  if ("statistic_vertical" %in% names(ellip)) {
    warning("The `statistic_vertical` argument is deprecated and will be ignored. To display uncertainty estimates next to your coefficients, use a `glue` string in the `estimate` argument. See `?modelsummary`",
            call. = FALSE)
  }

}


#' sanity check
#'
#' @noRd
sanity_model_names <- function(modelnames) {
  if (any(modelnames == '')) {
    stop('Model names cannot include empty strings. Please make sure that every object in the `models` list has a unique, non-empty name. If the `models` list has no names at all (NULL), `modelsummary` will create some automatically.')
  }
}


#' sanity check
#'
#' @noRd
sanity_align <- function(align, estimate = NULL, statistic = NULL, stars = FALSE) {
    checkmate::assert_string(align, null.ok = TRUE)
    if (!is.null(align) && any(grepl("[^lcrd]", align))) {
        insight::format_error('The `align` argument must be a character string which only includes the letters l, c, r, or d. Example: "lcdd"')
    }

    # the d-column siunitx LaTeX preamble doesn't play well with stars, so we need to wrap them in \\mbox{}
    if (any(grepl("d", align))) {
      settings_set("dcolumn_stars_mbox", TRUE)
    }
}


#' sanity check
#'
#' @noRd
sanitize_exponentiate <- function(exponentiate, number_of_models) {
  checkmate::assert(
    checkmate::check_logical(exponentiate, len = 1),
    checkmate::check_logical(exponentiate, len = number_of_models))
  if (length(exponentiate) == 1) {
    out <- rep(exponentiate, number_of_models)
  } else {
    out <- exponentiate
  }
  return(out)
}


#' sanity check
#'
#' @noRd
sanitize_estimate <- function(estimate, number_of_models) {
  checkmate::assert(
    checkmate::check_character(estimate, len = 1),
    checkmate::check_character(estimate, len = number_of_models))

  if (length(estimate) == 1) {
    out <- rep(estimate, number_of_models)
    out <- as.list(out)
  } else {
    if (!is.null(names(estimate)) && length(unique(names(estimate))) > 1) {
      insight::format_error("The `estimate` vector must have no name or every element must be named the same.")
    }
    out <- as.list(estimate)
  }

  return(out)
}



# TODO: sanity tite

#' sanity check
#'
#' @noRd
sanity_title <- function(title, ...) {
  dots <- list(...)
  if (is.null(title) && "caption" %in% names(dots)) {
    insight::format_warning("The `caption` argument is not supported by `modelsummary`. Try `title` instead.")
  }
  return(TRUE)
  #checkmate::assert_character(title, len = 1, null.ok = TRUE)
}


#' sanity check
#'
#' @noRd
sanity_coef <- function(coef_map, coef_rename, coef_omit) {

  checkmate::assert(
    checkmate::check_string(coef_omit, null.ok = TRUE),
    checkmate::check_numeric(coef_omit)
  )

  if ((!isTRUE(checkmate::check_flag(coef_rename)) && !is.null(coef_rename)) && !is.null(coef_map)) {
    stop("coef_map and coef_rename cannot be used together.", call. = FALSE)
  }

  if (!is.null(coef_map)) {
    if (is.null(names(coef_map))) {
      checkmate::assert_character(coef_map, null.ok = TRUE, unique = TRUE)
    } else {
      checkmate::assert_character(names(coef_map), null.ok = TRUE, unique = TRUE)
    }
  }

  checkmate::assert(
    checkmate::check_flag(coef_rename),
    checkmate::check_function(coef_rename, null.ok = TRUE),
    checkmate::check_character(coef_rename, names = "unique"),
    checkmate::check_character(coef_rename, names = "unnamed"),
    combine = "or"
  )
}







#' sanity check
#'
#' @noRd
sanity_factory <- function(factory_dict) {
  check_option <- function(output_type, valid) {
    if (!factory_dict[output_type] %in% valid) {
      msg <- sprintf("`modelsummary` cannot write a table of type '%s' using the '%s' package. You must use one of the following as a global option: %s. Consider setting a global option such as: options(modelsummary_factory_%s='%s')",
        output_type,
        factory_dict[output_type],
        paste(valid, collapse = ', '),
        output_type,
        valid[1])
      stop(msg)
    }
  }
  check_option('html', c('gt', 'kableExtra', 'flextable', 'huxtable', 'tinytable'))
  check_option('rtf', c('gt', 'huxtable'))
  check_option('latex', c('gt', 'kableExtra', 'huxtable', 'tinytable'))
  check_option('markdown', c('kableExtra', 'modelsummary', 'tinytable'))
  check_option('word', c('flextable', 'huxtable', 'tinytable'))
  check_option('powerpoint', c('flextable', 'huxtable'))
  check_option('png', c('gt', 'flextable', 'kableExtra', 'tinytable'))
  check_option('jpg', c('flextable', 'kableExtra'))

  # check default
  modelsummary_default <- getOption("modelsummary_factory_default", default = "kableExtra")
  checkmate::assert_true(modelsummary_default %in% c("tinytable", "gt", "kableExtra",
                                                     "flextable", "huxtable",
                                                     "DT",
                                                     "jupyter", "markdown",
                                                     "html", "data.frame",
                                                     "dataframe", "latex",
                                                     "latex_tabular"))
}


#' sanity check
#'
#' @noRd
sanity_stars <- function(stars) {
  checkmate::assert(
    checkmate::check_flag(stars),
    checkmate::check_numeric(stars, lower = 0, upper = 1, names = 'unique')
  )
}


#' sanity check
#'
#' @noRd
sanity_notes <- function(notes) {
  checkmate::assert(
    checkmate::check_list(notes, null.ok = TRUE),
    checkmate::check_character(notes)
  )
  if ('list' %in% class(notes)) {
    for (note in notes) {
      checkmate::assert(
        checkmate::check_character(note),
        checkmate::check_class(note, 'from_markdown')
      )
    }
  }
}


#' sanity check
#'
#' @noRd
sanity_add_rows <- function(add_rows, models) {
  if (inherits(add_rows, 'list')) {
    for (i in seq_along(add_rows)) {
      checkmate::assert_character(add_rows[[i]], null.ok = FALSE, len = (length(models) + 1))
    }
  } else if (inherits(add_rows, 'data.frame')) {
    checkmate::assert_true(all(c('section', 'position') %in% colnames(add_rows)))
    checkmate::assert_true(all(
      colnames(add_rows) %in% c('term', 'section', 'position', names(models))))
  }
}

sanity_add_columns <- function(add_columns) {
    checkmate::assert_data_frame(add_columns, min.cols = 1, null.ok = TRUE)
}


#' sanity check
#'
#' @noRd
sanity_gof <- function(gof_output, gof_custom) {
  checkmate::assert_data_frame(gof_output, nrows = 1, null.ok = FALSE)
  checkmate::assert_data_frame(gof_custom, nrows = 1, null.ok = TRUE)
}

#' sanity check
#'
#' @noRd
sanity_tidy <- function(tidy_output, tidy_custom, estimate, statistic, modelclass) {

  # tidy model
  checkmate::assert_data_frame(tidy_output, min.rows = 1, min.cols = 3)
  checkmate::assert_true('term' %in% colnames(tidy_output))

  # tidy_custom model
  if (!is.null(tidy_custom)) {
    checkmate::assert_data_frame(tidy_custom,
      min.rows = 1, min.cols = 2)
    checkmate::assert_true('term' %in% colnames(tidy_custom))
  }
}


sanity_ds_data <- function(formula, data, internal_call = FALSE) {
  checkmate::assert_data_frame(data)
}

  
#' sanity check: datasummary
#'
#' @noRd
sanity_ds_nesting_factor <- function(formula, data) {
  idx <- sapply(data, function(x) is.character(x) | is.logical(x))
  idx <- names(idx)[idx]
  idx <- c(paste0('^', idx, ':'), paste0(':', idx, '$'))
  termlabs <- labels(stats::terms(formula))
  warn <- any(sapply(idx, function(x) any(grepl(x, termlabs))))
  if (warn) {
    msg <- format_msg(
    'You are trying to create a nested table by applying the * operator to a
    character or a logical variable. It is usually a good idea to convert such
    variables to a factor before calling datasummary: dat$y<-as.factor(dat$y).
    Alternatively, you could wrap your categorical variable inside Factor() in
    the datasummary call itself: datasummary(x ~ Factor(y) * z, data)')
    warning(msg, call. = FALSE)
  }
}

#' sanity check: datasummary_balance
#'
#' right-handed formulae only
#' @noRd
sanity_ds_right_handed_formula <- function(formula) {
  termlabels <- labels(stats::terms(formula))
  if (length(termlabels) > 1) {
    stop("The 'datasummary_table' function only accepts a single right-hand side variable of type factor, character, or logical. If you do not want to transform your variable in the original data, you can wrap it in a Factor() call: datasummary_balance(~Factor(x), data). the name of your variablePlease visit the `modelsummary` website to learn how to build your own, more complex, Table 1. It's easy, I promise! https://modelsummary.com/datasummary.html")
  }
}


#' sanity dots
#' @noRd
sanity_dots <- function(model, ...) {
  dots <- list(...)

  # R2 can be misleading when standardizing without an intercept
  if (identical(dots[["standardize"]], "refit") && identical(class(model), "lm")) {
    if (!"(Intercept)" %in% names(stats::coef(model))) {
      msg <- "The goodness-of-fit statistics were calculated using the original model rather than the standardized model." 
      insight::format_warning(msg)
    }
  }
}