Feature/bugfix globals

DESCRIPTION

@@ -24,7 +24,7 @@ Description: Provide a library of methods that can be used to calculate differen
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
  covr,
  pkgdown,
@@ -41,6 +41,10 @@ Imports:
  stats,
  data.table (>= 1.14.2),
  magrittr,
- checkmate
+ checkmate,
+ cli,
+ usethis
+Remotes:
+ hta-pharma/chef
 Config/testthat/edition: 3
 VignetteBuilder: knitr

R/across_strata_across_trt.R

@@ -10,6 +10,7 @@
 #' @param strata_var character. Variable in the analysis data to stratify by specific for this call.
 #' @param odds_ratio numeric. Odds Ration (default = NA).
 #' @param correct logical. If TRUE Tarones correction is returned (default = FALSE).
+#' @param ... Optional parameters.
 #'
 #' @return A data.table containing the statistics for p-value interaction tests.
 #' @export

R/by_strata_across_trt.R

@@ -14,6 +14,7 @@
 #' @param treatment_var character. The name of the treatment variable in the data.
 #' @param treatment_refval character. The reference value of the treatment variable in the data.
 #' @param subjectid_var character. Name of the subject identifier variable in the data (default is "USUBJID").
+#' @param ... Optional parameters.
 #' 
 #' @return A data.table containing Relative Risk statistics.
 #' @export
@@ -70,6 +71,7 @@ RR <- function(dat,
 #' @param treatment_var character. The name of the treatment variable in the data.
 #' @param treatment_refval character. The reference value of the treatment variable in the data.
 #' @param subjectid_var character. Name of the subject identifier variable in the data (default is "USUBJID").
+#' @param ... Optional parameters.
 #'
 #' @return A data.table containing Odds Ratio statistics.
 #' @export
@@ -127,6 +129,8 @@ OR <- function(dat,
 #' @param treatment_var character. The name of the treatment variable in the data.
 #' @param treatment_refval character. The reference value of the treatment variable in the data.
 #' @param subjectid_var character. Name of the subject identifier variable in the data (default is "USUBJID").
+#' @param as_pct Boolean. 
+#' @param ... Optional parameters.
 #'
 #' @return A data.table containing Risk Difference statistics.
 #' @export
@@ -183,13 +187,13 @@ RD <- function(dat,
 #' analyzed. See the "Endpoint Events" vignette in {ramnog}
 #' for more information.
 #' @param safe_mode Boolean determing if the function should fail when given
-#' input that cannot be calculated (`safe_mode = TRUE`), or if it should
+#' input that cannot be calculated (`safe_mode = TRUE`), or if it should silently return a `NA` value (default).
 #' @param treatment_var character. The name of the treatment variable in the data.
 #' @param treatment_refval character. The reference value of the treatment variable in the data.
 #' @param subjectid_var character. Name of the subject identifier variable in the data (default is "USUBJID").
 #' @param threshold_lower numeric. Lower threshold limit for selecting Fischer vs. Barnard.
 #' @param threshold_upper numeric. Upper threshold limit for selecting Fischer vs. Barnard.
-#'  silently return a `NA` value (default).
+#' @param ... Optional parameters. 
 #' @return A data.table containing p-value statistics.
 #' @export
 p_val <-

R/by_strata_by_trt.R

@@ -301,7 +301,7 @@ total_missing_counts <- function(dat_cell, stratify_by) {
 #' analyzed. See the "Endpoint Events" vignette in {ramnog}
 #' for more information.
 #' @param subjectid_var character. Name of the subject identifier variable in the data (default is "USUBJID").
-#' @param treatment_var character. Name of the treatment variable in the data.
+#' @param var character. Name of the variable in the analysis data that is subject to the statistics.
 #' @param ... Optional parameters.
 #' 
 #' @return A data.table containing the percentage of subjects with events by treatment.
@@ -344,6 +344,8 @@ mean_value <- function(dat,
 #' for more information.
 #' @param subjectid_var character. Name of the subject identifier variable in the data (default is "USUBJID").
 #' @param treatment_var character. Name of the treatment variable in the data.
+#' @param treatment_value character. Value of the treatment variable in the data.
+#' @param ... Optional parameters.
 #' 
 #' @return A data.table containing the percentage of subjects with events by treatment.
 #' @export

R/globals.R

@@ -12,6 +12,6 @@ utils::globalVariables(
  "stat_var",
  "value",
  "N_sub",
- "N_no_event",
+ "N_no_event"
  )
 )

R/two_by_two_x.R

@@ -12,14 +12,18 @@
 #'
 #' Only observations that have a Treatment value recorded are returned.
 
-#'@param dat The ADaM table produced by baker
-#'@param treatment_var character. The name of the treatment variable
-#'@param treatment_refval character. The reference value of the treatment
-#'@param keepflg_var character. The name of the variable in the enriched ADaM
-#' data.table that contains the flag indicating whether each record fulfilled
-#' the criteria for being considered an event for the specific endpoint
-#'
-#' @return A matrix
+#' @param dat data.table. The analysis data set.
+#' @param event_index vector of integers that index the rows in `dat` that match
+#' the definition of an 'event'. Matching is done via the `INDEX_` column in
+#' `dat`.
+#' @param cell_index A vector of integers referencing the rows of `dat` (as
+#' specified by the `INDEX_` column in `dat`) that match the population to be
+#' analyzed. See the "Endpoint Events" vignette in {ramnog}
+#' for more information.
+#' @param treatment_var character. The name of the treatment variable in `dat`.
+#' @param treatment_refval character. The reference value of the treatment variable in `dat`.
+#' @param subjectid_var character. Name of the subject identifier variable in `dat` (default is "USUBJID").
+#'@return A matrix
 #' @export
 #'
 mk_two_by_two <-
@@ -120,16 +124,12 @@ ensure_complete_two_by_two <- function(two_by_two_long, treatment_var) {
 #' generalized
 #'
 #'
-#' @param dat data.table. An enriched ADaM table
-#' @param treatment_refval character. The treatment reference group
-#' @param treatment_var character. The name of the column containing the
-#' treatment value
-#' @param subjectid_var character. The name of the column in the enriched ADaM
-#' dataset containing the unique subject id (default = `USUBJID`).
-#' @param event_index
-#' @param cell_index
-#' @param strata_var
-#'
+#' @param dat data.table. The analysis data set.
+#' @param event_index vector of integers that index the rows in `dat` that match the definition of an 'event'. Matching is done via the `INDEX_` column in `dat`.
+#' @param strata_var character. Variable in `dat` to stratify by specific for this call.
+#' @param treatment_var character. The name of the treatment variable in `dat`.
+#' @param treatment_refval character. The reference value of the treatment variable in `dat`.
+#' @param subjectid_var character. Name of the subject identifier variable in `dat` (default is "USUBJID").
 #' @return A two-by-two-by-k array where k represents the number of subgroups
 #' (strata).
 #' @export

R/use_chefStats.R

@@ -10,7 +10,6 @@
 #' @return Nothing, run for side-effect (writes file to disk)
 #' @export
 #'
-#' @examples
 use_chefStats <-
  function(fn_name,
  fn_type = c(

tests/testthat/_snaps/demographics.md

@@ -4,6 +4,7 @@
  actual_total
  Output
  label qualifiers value description
+ <char> <fctr> <num> <char>
  1: n_non_missing AGEGR1 85 Demographics
  2: n_missing AGEGR1 1 Demographics
  3: n_non_missing SEX 82 Demographics
@@ -15,5 +16,6 @@
  actual_f
  Output
  label description qualifiers value
+ <char> <char> <char> <num>
  1: n_non_missing Demographics <NA> 52