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2 | 2 | #' |
3 | 3 | #' This documentation lists all the arguments in `falcon` that are used repeatedly by functions to output tables. |
4 | 4 | #' |
| 5 | +#' @param show_colcounts (`flag`)\cr Whether column counts should be printed. Boolean. |
| 6 | +#' @param arm_var (`character`)\cr Name of the treatment arm variable used to split table into columns. |
| 7 | +#' @param id_var (`character`)\cr Name of the unique subject identifiers variable. |
| 8 | +#' @param saffl_var (`character`)\cr Name of the safety flag variable which must contain at least "Y" for "Yes". |
| 9 | +#' @param ser_var (`character`)\cr Name of the serious adverse event flag variable which must contain at least |
| 10 | +#' "Y" for "Yes". |
| 11 | +#' @param lbl_overall (`character`)\cr Optional. If specified, an overall column will be added to the table with |
| 12 | +#' the given value as the column label. |
| 13 | +#' @param vars (`vector` of `character`)\cr Variables from `df` to include in the table. |
| 14 | +#' @param lbl_vars (`vector` of `character`)\cr Labels corresponding to variables in `vars` to print |
| 15 | +#' in the table. Labels should be ordered according to the order of variables in `vars`. |
| 16 | +#' @param pref_var (`character`)\cr Name of the preferred term variable from `adae` to include in the table. |
| 17 | +#' @param soc_var (`character`)\cr Name of the system organ class variable from `adae` to include in the table. |
| 18 | +#' @param lbl_pref_var (`character`)\cr Label corresponding to preferred term variable `pref_var` to print in the table. |
| 19 | +#' @param lbl_soc_var (`character`)\cr Label corresponding to system organ class variable `soc_var` to print in the |
| 20 | +#' table. |
| 21 | +#' @param .stats (`character`)\cr Statistics to include in the table. Includes statistics for all variable |
| 22 | +#' types (only the statistics that are valid for a given variable's type will be printed). |
| 23 | +#' See [`tern::analyze_vars()`] for options. |
| 24 | +#' @param .formats (named `list` of `character`)\cr List of formats corresponding to each value in `.stats`. |
| 25 | +#' Each name is a value in `.stats` and the corresponding value is the format that should be applied to |
| 26 | +#' that statistic. See [`formatters::list_valid_format_labels()`] for a list of valid formats. |
| 27 | +#' @param na_rm (`flag`)\cr Whether `NA` levels should be removed from the table. |
| 28 | +#' @param prune_0 (`flag`)\cr Whether all-zero rows should be removed from the table. Boolean. |
| 29 | +#' @param annotations (named `list` of `character`)\cr List of annotations to add to the table. Valid |
| 30 | +#' annotation types are `title`, `subtitles`, `main_footer`, and `prov_footer`. Each name-value pair should |
| 31 | +#' use the annotation type as name and the desired string as value. |
| 32 | +#' @param na_level (`character`)\cr String to represent missing values. |
5 | 33 | #' @param adae (`data.frame`)\cr dataset (typically ADAE) required to build table. |
6 | 34 | #' @param adex (`data.frame`)\cr dataset (typically ADEX) required to build table. |
7 | 35 | #' @param advs (`data.frame`)\cr dataset (typically ADVS) required to build table. |
|
10 | 38 | #' @param annotations (named `list` of `character`)\cr list of annotations to add to the table. Valid |
11 | 39 | #' annotation types are `title`, `subtitles`, `main_footer`, and `prov_footer`. Each name-value pair should |
12 | 40 | #' use the annotation type as name and the desired string as value. |
13 | | -#' @param arm_var (`character`)\cr arm variable used to split table into columns. |
14 | 41 | #' @param df (`data.frame`)\cr dataset required to build table. |
15 | 42 | #' @param eosdy_var (`character`)\cr variable denoting last recorded (relative) study day. |
16 | 43 | #' @param fmqsc_var (`character`)\cr FMQ scope variable to use in table. |
|
27 | 54 | #' in the table. Labels should be ordered according to the order of variables in `vars`. |
28 | 55 | #' @param na_level (`character`)\cr string to represent missing values. |
29 | 56 | #' @param na_rm (`flag`)\cr whether `NA` levels should be removed from the table. |
30 | | -#' @param pref_var (`character`)\cr preferred term variable from `adae` to include in the table. |
31 | | -#' @param prune_0 (`flag`)\cr whether all-zero rows should be removed from the table. |
32 | 57 | #' @param risk_diff (named `list`)\cr list of settings to apply to add one or more risk difference columns to the table. |
33 | 58 | #' Defaults to `NULL` (no risk difference column added). See [tern::add_riskdiff()] for more details. List should |
34 | 59 | #' contain the following elements: |
|
41 | 66 | #' * `pct`: (optional) whether the output should be returned as percentages. Defaults to `TRUE`. |
42 | 67 | #' @param saffl_var (`character`)\cr flag variable used to indicate inclusion in safety population. |
43 | 68 | #' @param sex_scope (`character`)\cr Level of `SEX` to output in table. |
44 | | -#' @param soc_var (`character`)\cr flag variable used to indicate system organ class. |
45 | | -#' @param show_colcounts (`flag`)\cr whether column counts should be printed. |
46 | | -#' @param trtsdtm_var (`character`)\cr treatment start datetime variable. |
47 | 69 | #' @param trtedtm_var (`character`)\cr treatment end datetime variable. |
| 70 | +#' @param trtemfl_var (`character`)\cr flag variable used to identify Treatment-emergent AE. |
| 71 | +#' @param trtsdtm_var (`character`)\cr treatment start datetime variable. |
48 | 72 | #' @param u_trtdur (`character`)\cr unit for duration of treatment. Options are `"days"`, `"weeks"`, `"months"`, |
49 | 73 | #' and `"years"`. |
50 | | -#' @param vars (`vector` of `character`)\cr variables from `df` to include in the table. |
51 | 74 | #' @param xticks (`vector` of `numeric`)\cr x-axis tick positions. If `NA` (default), tick mark positions are |
52 | 75 | #' automatically calculated. |
53 | 76 | #' @param x_lab (`character`)\cr x-axis label. |
| 77 | +#' @param yticks (`vector` of `numeric`)\cr y-axis tick positions. If `NA` (default), tick mark positions are |
| 78 | +#' automatically calculated. |
54 | 79 | #' @param y_lab (`character`)\cr y-axis label. |
55 | 80 | #' |
56 | 81 | #' @name argument_convention |
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