Merge pull request #34 from R4EPI/fix_checks

Fix checks and tests

Author: aspina7

DESCRIPTION

@@ -31,6 +31,7 @@ RoxygenNote: 7.3.2
 URL: https://R4EPI.github.io/epitabulate/, https://github.com/R4EPI/epitabulate/
 BugReports: https://github.com/R4EPI/epitabulate/issues
 Imports: 
+    binom,
     dplyr (>= 1.0.2),
     epikit (>= 0.1.2),
     forcats,
@@ -39,11 +40,14 @@ Imports:
     MASS,
     purrr,
     rlang (>= 0.4.0),
+    scales, 
     stats,
     tibble (>= 3.0.0),
     tidyr (>= 1.0.0),
     tidyselect (>= 1.0.0)
 Suggests: 
+    broom.helpers, 
+    cardx, 
     testthat,
     matchmaker (>= 0.1.0),
     epidict,

NAMESPACE

@@ -12,6 +12,7 @@ export(mortality_rate)
 export(tbl_cmh)
 import(dplyr)
 importFrom(MASS,glm.nb)
+importFrom(binom,binom.wilson)
 importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
 importFrom(dplyr,relocate)
@@ -27,9 +28,14 @@ importFrom(gtsummary,style_pvalue)
 importFrom(gtsummary,style_ratio)
 importFrom(gtsummary,tbl_stack)
 importFrom(gtsummary,tbl_uvregression)
+importFrom(rlang,":=")
 importFrom(rlang,as_label)
 importFrom(rlang,enquo)
 importFrom(rlang,quo_get_expr)
+importFrom(scales,number)
+importFrom(stats,binomial)
 importFrom(stats,glm)
+importFrom(stats,poisson)
+importFrom(stats,setNames)
 importFrom(tidyr,drop_na)
 importFrom(tidyselect,vars_select)

R/cfr.R

@@ -39,32 +39,6 @@
 #' @export
 #'
 #' @rdname attack_rate
-#'
-#' @examples
-#' # Attack rates can be calculated with just two numbers
-#' print(ar <- attack_rate(10, 50), digits = 4) # 20% attack rate
-#'
-#' # print them inline using `fmt_ci_df()`
-#' epikit::fmt_ci_df(ar)
-#'
-#' # Alternatively, if you want one column for the CI, use `mergeCI = TRUE`
-#' attack_rate(10, 50, mergeCI = TRUE, digits = 2) # 20% attack rate
-#'
-#' print(cfr <- case_fatality_rate(1, 100), digits = 2) # CFR of 1%
-#' epikit::fmt_ci_df(cfr)
-#'
-#' # using a data frame
-#' if (require("outbreaks")) {
-#'   withAutoprint({
-#'   e <- outbreaks::ebola_sim$linelist
-#'   case_fatality_rate_df(e,
-#'     outcome == "Death",
-#'     group = gender,
-#'     add_total = TRUE,
-#'     mergeCI = TRUE
-#'   )
-#'   })
-#' }
 attack_rate <- function(cases, population, conf_level = 0.95,
                         multiplier = 100, mergeCI = FALSE, digits = 2) {
   res <- proportion(cases, population, multiplier = multiplier, conf_level = conf_level)
@@ -89,6 +63,7 @@ case_fatality_rate <- function(deaths, population, conf_level = 0.95,
 
 #' @rdname attack_rate
 #' @importFrom forcats fct_explicit_na
+#' @importFrom rlang :=
 #' @export
 case_fatality_rate_df <- function(x, deaths, group = NULL, conf_level = 0.95,
                                   multiplier = 100, mergeCI = FALSE, digits = 2,
@@ -100,7 +75,7 @@ case_fatality_rate_df <- function(x, deaths, group = NULL, conf_level = 0.95,
 
   # Group the data if needed
   if (wants_grouping) {
-    x <- dplyr::mutate(x, !!qgroup := forcats::fct_explicit_na(!!qgroup, "(Missing)"))
+    x <- dplyr::mutate(x, !!qgroup := forcats::fct_na_value_to_level(!!qgroup, "(Missing)"))
     x <- dplyr::group_by(x, !!qgroup, .drop = FALSE)
   }
 
@@ -160,6 +135,7 @@ case_fatality_rate_df <- function(x, deaths, group = NULL, conf_level = 0.95,
 }
 
 #' @rdname attack_rate
+#' @importFrom scales number
 #' @export
 mortality_rate <- function(deaths, population, conf_level = 0.95,
                            multiplier = 10^4, mergeCI = FALSE, digits = 2) {
@@ -182,6 +158,7 @@ mortality_rate <- function(deaths, population, conf_level = 0.95,
 #' @param conf_level confidence level for the confidence interval
 #' @param multiplier multiplier for the proportion
 #'
+#' @importFrom binom binom.wilson
 #' @return a data frame with five columns: x, n, prop, lower, and upper
 #' @noRd
 #'

R/gt_cfr.R

@@ -1,27 +1,37 @@
+# Suppress CMD check notes for NSE variables and base functions used across gtsummary wrapper functions
+utils::globalVariables(c(
+  "case_n",           # column name created in dplyr operations
+  "deaths_n",         # column name created in dplyr operations
+  "Cases",            # column name in gtsummary table_body
+  "Deaths",           # column name in gtsummary table_body
+  "mortality per 10 000"  # column name created by mortality_rate function
+))
 
-#' A mortality rate wrapper function (using the gtsummary package)that takes
-#' a gtsummary object and returns a gtsummary object with attack rate (per given
-#'  multiple) with 95% confidence interval
-#'
-#' @param gts_object A data frame, passed by the gtsummary::add_stat function.
-#'
-#' @param deaths_var logical variable name that indicates deaths
-#'
-#' @param variable Name of a variable as the outcome of interest, passed by the
-#' gtsummary::add_stat function (e.g. illness)
-#'
-#' @param by Name of a variable for stratifying, passed by the gtsummary::add_stat
-#' function (e.g. illness).
+
+
+#' Add mortality rate statistics to a gtsummary table
 #'
-#'#'@param population the number of individuals in the population, passed to
-#'`epitabulate::mortality_rate`
+#' This function wraps `gtsummary::add_stat()` to calculate and display
+#' **mortality rates** (deaths per given population multiplier) with 95%
+#' confidence intervals, using the `epitabulate::mortality_rate()` function
+#' internally.
 #'
-#' @param ... additional params that may be passed from gtsummary functions.
+#' @param gts_object A gtsummary object created with functions such as
+#'   `gtsummary::tbl_summary()` or `gtsummary::tbl_cross()`.
+#' @param deaths_var A logical variable name in the data indicating death
+#'   status (e.g. `TRUE` for death).
+#' @param population Optional numeric vector giving the population size for
+#'   the denominator. If `NULL`, the population is inferred from the data.
+#' @param multiplier Numeric multiplier used to scale the mortality rate
+#'   (e.g. `1` = proportion, `100` = percent, `10^4` = per 10,000).
+#' @param drop_tblsummary_stat Logical; if `TRUE`, removes the original
+#'   `tbl_summary` statistic column (default = `FALSE`).
 #'
-#' @return a single-row gtsummary object with attack rate results cases,
-#' population, attack rate, and 95% confidence interval.
+#' @return A modified gtsummary object with additional columns showing
+#'   the number of deaths, population, mortality rate, and 95% confidence
+#'   interval.
 #'
-#' @rdname gt_attackrate
+#' @rdname add_mr
 #'
 #' @export
 add_mr <- function(gts_object,
@@ -89,32 +99,32 @@ add_mr <- function(gts_object,
   return(gts_object)
 }
 
-#' An attack rate wrapper function (using the gtsummary package)that takes
-#' a gtsummary object and returns a gtsummary object withattack rate (per given
-#'  multiple) with 95% confidence interval
+#' Add attack rate statistics to a gtsummary table
 #'
-#' @param gts_object A data frame, passed by the gtsummary::add_stat function.
+#' This function wraps `gtsummary::add_stat()` to calculate and display
+#' **attack rates** (cases per given population multiplier) with 95% confidence
+#' intervals, using the `epitabulate::attack_rate()` function internally.
 #'
-#' @param variable Name of a variable as the outcome of interest, passed by the
-#' gtsummary::add_stat function (e.g. illness)
+#' @param gts_object A gtsummary object created with functions such as
+#'   `gtsummary::tbl_summary()`
 #'
-#' @param by Name of a variable for stratifying, passed by the gtsummary::add_stat
-#' function (e.g. illness).
+#' @param case_var A logical variable name in the data indicating case status
+#'   (e.g. `TRUE` for cases).
 #'
-#'#'@param population the number of individuals in the population, passed to
-#'`epitabulate::attack_rate`
 #'
-#'@param multiplier The base by which to multiply the output:
-# '1: multiplier = 1: ratio between 0 and 1;
-# '2: multiplier = 100:proportion;
-# '3: multiplier = 10^4: x per 10,000 people; passed to `epitabulate::attack_rate`
+#' @param population Optional numeric vector giving the population size for
+#'   the denominator. If `NULL`, the population is inferred from the data.
 #'
-#' @param ... additional params that may be passed from gtsummary functions.
+#' @param multiplier Numeric multiplier used to scale the attack rate
+#'   (e.g. `1` = proportion, `100` = percent, `10^4` = per 10,000).
 #'
-#' @return a single-row gtsummary object with attack rate results cases,
-#' population, attack rate, and 95% confidence interval.
+#' @param drop_tblsummary_stat Logical; if `TRUE`, removes the original
+#'   `tbl_summary` statistic column (default = `FALSE`).
+#'
+#' @return A modified gtsummary object with additional columns showing
+#'   the number of cases, population, attack rate, and 95% confidence interval.
 #'
-#' @rdname gt_attackrate
+#' @rdname add_ar
 #'
 #' @export
 #'
@@ -183,27 +193,21 @@ add_ar <- function(gts_object,
 
 
 
-#' An case fatality rate wrapper function (using the gtsummary package)
-#' that takes a gtsummary object and returns a gtsummary object with number
-#' of deaths, case fatality rate, and 95% confidence interval.
-#'
-#' @param data A data frame, passed by the gtsummary::add_stat function.
-#'
-#' @param variable Name of a variable as the outcome of interest, passed by the
-#' gtsummary::add_stat function (e.g. illness).
-#'
-#' @param by Name of a variable for stratifying, passed by the gtsummary::add_stat function
-#'   (e.g. illness).
+#' Add case fatality rate (CFR) statistics to a gtsummary table
 #'
-#' @param deaths_var the name of a logical column in the data that indicates that the case died,
-#' is passed as the first argument to `epitabulate::case_fatality_rate_df`
-#'
-#' @param ... additional params that may be passed from gtsummary functions.
+#' This function wraps `gtsummary::add_stat()` to calculate and display
+#' **case fatality rates** (deaths among cases) with 95% confidence intervals,
+#' using the `epitabulate::case_fatality_rate_df()` function internally.
 #'
-#' @return a single row gtsummary object with case fatality rate results for
-#' deaths, cases, cfr, and 95% confidence interval.
+#' @param gts_object A gtsummary object created with functions such as
+#'   `gtsummary::tbl_summary()` or `gtsummary::tbl_cross()`.
+#' @param deaths_var A logical variable name in the data indicating death
+#'   status (e.g. `TRUE` for death).
+#' @return A modified gtsummary object with additional columns showing
+#'   the number of deaths, number of cases, case fatality rate, and 95%
+#'   confidence interval.
 #'
-#' @rdname gt_attackrate
+#' @rdname add_cfr
 #' @import dplyr
 #' @export
 #'
@@ -247,7 +251,7 @@ add_cfr <- function(gts_object, deaths_var) {
 
 #' @return a gtsummary object without the named column
 #'
-#' @rdname gtsummary_wrappers
+#' @rdname gt_remove_stat
 #' @export
 #'
 gt_remove_stat <- function(gts_object, col_name = "stat_0") {
@@ -382,6 +386,8 @@ add_gt_cfr_stat_level <- function(data, variable, by, deaths_var, ...) {
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
+#' @importFrom stats setNames
+#'
 #' @return a single row gtsummary object with with attack rate results with
 #' cases, attack rate, and 95% confidence interval.
 #'
@@ -459,6 +465,9 @@ add_gt_attack_rate_stat_label <-
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
+#' @importFrom rlang :=
+#' @importFrom stats setNames
+#'
 #' @return a single-row gtsummary object with attack rate results cases,
 #' population, attack rate, and 95% confidence interval.
 #'
@@ -552,6 +561,9 @@ add_gt_attack_rate_level <-
     return(ar)
   }
 
+
+#' @importFrom stats setNames
+#' @noRd
 add_gt_mortality_rate_stat_label <-
   function(data, variable, by=NULL, deaths_var, population = NULL,
            multiplier = 10^4, drop_total = TRUE, drop_deaths = TRUE, ...) {
@@ -629,6 +641,9 @@ add_gt_mortality_rate_stat_label <-
 #'
 #' @param ... additional params that may be passed from gtsummary functions.
 #'
+#' @importFrom rlang :=
+#' @importFrom stats setNames
+#'
 #' @return a single-row gtsummary object with attack rate results cases,
 #' population, attack rate, and 95% confidence interval.
 #'

R/gt_univariate_crosstabs.R

@@ -1,5 +1,10 @@
+# Suppress CMD check notes for variables used in NSE (column names from gtsummary)
+utils::globalVariables(c("n_obs", "n_event", "n_nonevent", "estimate",
+                         "var_type", "variable", "stratifier",
+                         "reference_row", "var_label"))
 
-#' A {gtsummary} wrapper function that takes a gtsummary univariate regression
+
+#' A \{gtsummary\} wrapper function that takes a gtsummary univariate regression
 #' table and adds appropriate cross tabs by exposure and outcome
 #'
 #'@param x Object with class `tbl_uvregression` from the gtsummary