R/tidytlg-package.R

In tidytlg: Create TLGs using the 'tidyverse'

#' `tidytlg`: A package for producing tables, listings,
#'  and graphs (`TLGs`) using `tidyverse` packages.
#'
#' The `tidytlg` package provide a set of function allowing you to produce TLGs
#' using table metadata.
#'
#' @section `tidytlg` Options:
#'
#' \itemize{ \item{`tidytlg.row_type.levels` - The values of row_type and their
#' respective levels. Default: c("TABLE_BY_HEADER", "BY_HEADER1", "BY_HEADER2",
#' "BY_HEADER3", "BY_HEADER4", "BY_HEADER5", "HEADER", "N", "VALUE", "NESTED")}
#' \item{`tidytlg.fontsize.title` - Font size for titles in points. Default: 10}
#' \item{`tidytlg.fontsize.table.footnote` - Font size for footnotes in points.
#' For tables. Default: 9} \item{`tidytlg.fontsize.listing.footnote` - Font size
#' for footnotes in points. For listings. Default: 8}
#' \item{`tidytlg.fontsize.graph.footnote` - Font size for footnotes in points.
#' For graphs. Default: 8} \item{`tidytlg.fontsize.table` - Font size for tables
#' in points. Default: 9} \item{`tidytlg.fontsize.graph` - Font size for graphs in
#' points. Default: 10} \item{`tidytlg.fontsize.listing` - Font size for listings
#' in points. Default: 8} \item{`tidytlg.right.padding` - Amount of right padding
#' for cells in points. Default: 1} \item{`tidytlg.left.padding` - Amount of left
#' padding for cells in points. Default: 1}
#' \item{`tidytlg.stat_labels` - Labels
#' to be used for each summary statistic in the output table.  Will need to have
#' all available statistics if this option is changed!}
#' \item{`tidytlg.precision.extra` - Value to be added on for each summary
#' statistic when calculating precision.  This will be used to make different
#' statistics have different precision as needed}
#' \item{`tidytlg.nested_freq.statlist.default` - Default `statlist` object for
#' nested_freq tables. Default: `statlist("n (x.x)")`}
#' \item{`tidytlg.univar.statlist.default` - Default `statlist` object
#' for `univar` tables.
#' Default: `statlist(c("N", "MEANSD", "MEDIAN", "RANGE", "IQRANGE"))`}
#' \item{`tidytlg.freq.statlist.default` - Default `statlist` object
#' for frequency tables. Default: `statlist("n (x.x)")`}
#' \item{`tidytlg.stat_labels` - A `data.frame` controlling how the stats
#' are labeled in a `univar` table. See 'Default Stat Labels' section
#' for defaults.}
#' \item{`tidytlg.denoms.message` - A `boolean`, should a message print
#' detailing what the denominators are?}
#' }
#'
#' @section Default Stat Labels:
#'
#' | **stat** | **label** |
#' | --- | --- |
#' | `N` | N |
#' | `SUM` | Sum |
#' | `MEAN` | Mean |
#' | `GeoMEAN` | Geometric Mean |
#' | `SD` | Std. Deviation |
#' | `SE` | Std. Error |
#' | `GSD` | Geometric Std. Deviation |
#' | `GSE` | Geometric Std. Error |
#' | `CV` | CV |
#' | `MEANSD` | Mean (SD) |
#' | `MEANSE` | Mean (SE) |
#' | `MEDIAN` | Median |
#' | `MIN` | Minimum |
#' | `MAX` | Maximum |
#' | `RANGE` | Range |
#' | `Q1` | First quartile |
#' | `Q3` | Third quartile |
#' | `IQRANGE` | IQ range |
#' | `MEDRANGE` | Median (Range) |
#' | `MEDIQRANGE` | Median (Q1; Q3) |
#' | `MEAN_CI` | Mean (95% C.I.) |
#' | `GeoMEAN_CI` | Geometric Mean (95% C.I.) |
#'
#' @section Default Precision Extra:
#'
#' | **stat** | **extra** |
#' | --- | --- |
#' |`N` | 0 |
#' |`SUM`| 0 |
#' |`MEAN`| 1 |
#' |`GeoMEAN`| 1 |
#' |`SD`| 2 |
#' |`SE`| 2 |
#' |`GSD`| 2 |
#' |`GSE`| 2 |
#' |`CV`| 1 |
#' |`MEDIAN`| 1 |
#' |`MIN`| 0 |
#' |`MAX`| 0 |
#' |`Q1`| 1 |
#' |`Q3`| 1 |
#' |`LCL_MEAN`| 2 |
#' |`UCL_MEAN`| 2 |
#' |`LCL_GeoMEAN`| 2 |
#' |`UCL_GeoMEAN`| 2 |
#'
#' @section Updating Options:
#' \itemize{
#'   \item{For a single session, an option can be changed by
#'   `option(<optionToChange> = <NewValue>)`}
#'   \item{To change an option for a single projects across sessions in that
#'   projects, place the options update in the `.Rprofile` in that project
#'   directory.}
#'   \item{To change an option for a user across all sessions, place the options
#'   update in the `.Rprofile` file in the users home directory.}
#'   \item{To change an option for all users in an R environment, place the
#'   options update in the `.Rprofile.site` file in the R home directory.}
#' }
#'
#'
#'
#' @name tidytlg
#' @keywords internal
"_PACKAGE"

utils::globalVariables(c(
  "anbr", "label", "rowvar", "rowcondition", "row_type",
  "rowtext", "tableby", "by", "func", "colvar", "header_order",
  "df", "filter_to_df", "statlist", "denom_df", "precision",
  "tbltype", "dotdotdot",
  ".", "name", "alpha", "value", "N", "pct", "denom", "results",
  "n_ord", "n_ord2", "n_ord3", "data_nest", "nested_treatment",
  "nested_level", "nest_treatment", "stat", "extra", "prec",
  "IDENTIFIER", "TABLE ID", "decode", "colnbr", "newrows", "el",
  "sorter", "coldef", "V1"
))

## usethis namespace: start
#' @importFrom rlang enexprs is_call expr sym %||% exprs syms as_string is_named
#'   eval_tidy enexpr as_name .data :=
#' @importFrom tidyr pivot_wider pivot_longer complete nesting nest unnest
#'   replace_na crossing fill
#' @importFrom dplyr select bind_rows ungroup mutate rowwise filter summarise
#'   bind_cols
#' @importFrom dplyr group_by distinct n left_join rename relocate across
#'   if_else
#' @importFrom dplyr arrange case_when desc cur_group_id inner_join rename_with
#'   row_number
#' @importFrom dplyr group_by_at slice mutate_if
#' @importFrom stringr str_detect str_remove str_replace str_split regex
#'   str_to_lower
#' @importFrom dplyr all_of any_of everything starts_with ends_with
#' @importFrom forcats fct_expand fct_recode fct_relevel
#' @importFrom magrittr %>% extract2
#' @importFrom purrr map walk map_dfr pmap discard compact map_lgl imap map_chr
#' @importFrom tibble tibble tribble add_row tibble_row
#' @importFrom methods formalArgs
#' @importFrom stats setNames lag
#' @importFrom utils head modifyList tail
#' @importFrom huxtable everywhere
#' @importFrom crayon bold underline
#' @importFrom readxl read_excel
#' @importFrom cellranger cell_cols
#' @importFrom png readPNG
#' @importFrom ggplot2 ggsave
#' @importFrom grDevices dev.cur dev.off pdf
#' @importFrom rstudioapi getSourceEditorContext isAvailable
## usethis namespace: end
NULL


.onLoad <- function(libname, pkgname) {
  op <- options()
  op_tidytlg <- list(
    tidytlg.row_type.levels =
      c(
        "TABLE_BY_HEADER",
        "BY_HEADER1", "BY_HEADER2", "BY_HEADER3", "BY_HEADER4", "BY_HEADER5",
        "HEADER",
        "N", "VALUE", "NESTED"
      ),
    tidytlg.fontsize.title = 10,
    tidytlg.fontsize.table.footnote = 9,
    tidytlg.fontsize.listing.footnote = 8,
    tidytlg.fontsize.graph.footnote = 8,
    tidytlg.fontsize.table = 9,
    tidytlg.fontsize.graph = 10,
    tidytlg.fontsize.listing = 8,
    tidytlg.right.padding = 1,
    tidytlg.left.padding = 1,
    tidytlg.stat_labels = tibble::tribble(
      ~stat,           ~label,
      "N",             "N",
      "SUM",           "Sum",
      "MEAN",          "Mean",
      "GeoMEAN",       "Geometric Mean",
      "SD",            "Std. Dev.",
      "SE",            "Std. Error",
      "GSD",           "Geometric Std. Dev.",
      "GSE",           "Geometric Std. Error",
      "CV",            "CV (%)",
      "MEANSD",        "Mean (SD)",
      "MEANSE",        "Mean (SE)",
      "MEDIAN",        "Median",
      "MIN",           "Minimum",
      "MAX",           "Maximum",
      "RANGE",         "Range",
      "Q1",            "First quartile",
      "Q3",            "Third quartile",
      "IQRANGE",       "IQ range",
      "MEDRANGE",      "Median (Range)",
      "MEDIQRANGE",    "Median (Q1; Q3)",
      "MEAN_CI",       "Mean (95% C.I.)",
      "GeoMEAN_CI",    "Geometric Mean (95% C.I.)"
    ),
    tidytlg.precision.extra = tibble::tribble(
      ~stat,           ~extra,
      "N",             0,
      "SUM",           0,
      "MEAN",          1,
      "GeoMEAN",       1,
      "SD",            2,
      "SE",            2,
      "GSD",           2,
      "GSE",           2,
      "CV",            1,
      "MEDIAN",        1,
      "MIN",           0,
      "MAX",           0,
      "Q1",            1,
      "Q3",            1,
      "LCL_MEAN",      2,
      "UCL_MEAN",      2,
      "LCL_GeoMEAN",   2,
      "UCL_GeoMEAN",   2
    ),
    tidytlg.univar.statlist.default =
      statlist(c("N", "MEANSD", "MEDIAN", "RANGE", "IQRANGE")),
    tidytlg.freq.statlist.default = statlist(c("n (x.x)")),
    tidytlg.nested_freq.statlist.default = statlist(c("n (x.x)")),
    tidytlg.denoms.message = FALSE,
    # Do not document. This is just used for testing
    tidytlg.add_datetime = TRUE
  )

  toset <- !(names(op_tidytlg) %in% names(op))
  if (any(toset)) options(op_tidytlg[toset])

  invisible()
}