Prepare chefStats for CRAN submission

.Rbuildignore

@@ -23,3 +23,5 @@ setImgSrc.js
 \.github
 RELEASE_BODY\.txt
 ^\.github$
+^cran-plan\.md$
+^tools$

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: chefStats
-Title: Provide methods for different statistics
+Title: Provide Methods for Different Statistics
 Version: 0.1.1
 Authors@R:
     c(person(given = "Matthew David Phelps",
@@ -22,14 +22,19 @@ Authors@R:
              email = "cino@novonordisk.com"),
       person(given = "Novo Nordisk A/S",
              role = "cph"))
-Maintainer: Christian Haargaard Olsen <cino@novonordisk.com>
-Description: Provide a library of methods that can be used to calculate different statistics.
+Description: Provides a library of statistical methods for use in clinical trial evidence
+    generation workflows. Functions cover subject counts, event rates, odds ratios,
+    relative risks, risk differences, p-values, and demographic summaries, all
+    formatted for use with the 'chef' pipeline framework. Designed to support
+    healthcare technology assessments such as AMNOG dossier submissions.
 License: MIT + file LICENSE
+BugReports: https://github.com/hta-pharma/chefStats/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
+Remotes:
+    hta-pharma/chef@feature/CRAN_submission
 Suggests:
-    testr,
     covr,
     pkgdown,
     testthat,
@@ -39,7 +44,8 @@ Suggests:
     pharmaverseadam,
     tidyr,
     purrr,
-    kableExtra
+    kableExtra,
+    withr
 Imports:
     Barnard,
     stats,
@@ -48,14 +54,9 @@ Imports:
     checkmate,
     cli,
     usethis,
-	DescTools
-Remotes:
-    hta-pharma/chef,
-    matthew-phelps/testr
+    DescTools
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 Config/testthat/parallel: true
-URL: 
-       https://hta-pharma.github.io/chefStats/,
-       https://github.com/hta-pharma/chefStats,
-       https://app.codecov.io/github/hta-pharma/chefStats
+URL: https://hta-pharma.github.io/chefStats/,
+    https://github.com/hta-pharma/chefStats

R/BreslowDayFunction.R

@@ -7,6 +7,7 @@
 #' @return A vector with three values statistic - Breslow and Day test
 #'   statistic pval - p value evtl. based on the Tarone test statistic using a
 #'    \eqn{\chi^2(K-1)} distribution
+#' @keywords internal
 breslowdaytest_ <- function(x, odds_ratio = NA, correct = FALSE) {
 
     # Call the BreslowDayTest from the DescTools package

R/across_strata_across_trt.R

@@ -14,6 +14,18 @@
 #'
 #' @return A data.table containing the statistics for p-value interaction tests.
 #' @export
+#' @examples
+#' dat <- data.table::data.table(
+#'   USUBJID = c("S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8"),
+#'   TRT     = c("Active", "Active", "Active", "Active",
+#'               "Placebo", "Placebo", "Placebo", "Placebo"),
+#'   STRATA  = c("M", "M", "F", "F", "M", "M", "F", "F")
+#' )
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' p_val_interaction(dat, event_index = c(1L, 3L, 5L, 7L),
+#'                   treatment_var = "TRT", treatment_refval = "Placebo",
+#'                   subjectid_var = "USUBJID", strata_var = "STRATA")
 p_val_interaction <- function(dat,
                               event_index,
                               treatment_var,
@@ -69,7 +81,13 @@ p_val_interaction <- function(dat,
 #' @param ... optional arguments to
 #' @return A list containing Hedges G statistics.
 #' @export
-#'
+#' @examples
+#' dat <- data.table::data.table(
+#'   treatment_val = c("Active", "Active", "Active", "Placebo", "Placebo", "Placebo"),
+#'   stat_var      = rep(c("N_sub", "mean_value", "sd_value"), 2),
+#'   stat_val      = c(50, 12.3, 2.1, 50, 10.1, 2.5)
+#' )
+#' hedges_g(dat, reference_val = "Placebo")
 hedges_g <-
   function(dat, reference_val, safe_mode = FALSE, ...) {
     n_trt <-

R/barnard_test.R

@@ -8,6 +8,7 @@
 #'   error (default), or return an NA (safe_mode = FALSE)
 #'
 #' @return 2-sided p-value for the Barnards Unconditional Exact test
+#' @keywords internal
 #' @importFrom Barnard barnard.test
 
 barnard_test_ <-

R/building_blocks.R

@@ -2,15 +2,22 @@
 #'
 #' @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
+#'   analyzed. See the "Endpoint Events" vignette in \pkg{ramnog} for more
 #'   information.
 #' @param subjectid_var character. Name of the subject identifier variable in
 #'   the data (default is "USUBJID").
 #' @param dat data.table. The analysis data set.
 #'
 #' @return An integer
 #' @export
-#' 
+#' @examples
+#' dat <- data.table::data.table(
+#'   USUBJID = c("S1", "S2", "S3"),
+#'   VALUE   = c(1.1, 2.2, 3.3)
+#' )
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' n_subj_(dat, cell_index = dat[["INDEX_"]], subjectid_var = "USUBJID")
 n_subj_ <-
   function(dat,
            cell_index,
@@ -28,7 +35,11 @@ n_subj_ <-
 #'
 #' @return an integer value
 #' @export
-#'
+#' @examples
+#' dat <- data.table::data.table(USUBJID = c("S1", "S2", "S3"))
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' n_event_(dat, intersect_index = c(1L, 2L))
 n_event_ <- function(dat, intersect_index) {
   dat[list(intersect_index)] |>
     NROW()
@@ -46,7 +57,11 @@ n_event_ <- function(dat, intersect_index) {
 #'
 #' @return an interger value
 #' @export
-#'
+#' @examples
+#' dat <- data.table::data.table(USUBJID = c("S1", "S2", "S3"))
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' n_subj_event_(dat, intersect_index = c(1L, 2L), subjectid_var = "USUBJID")
 n_subj_event_ <- function(dat, intersect_index, subjectid_var) {
   dat[list(intersect_index)] |>
     data.table::uniqueN(by = subjectid_var)
@@ -57,7 +72,7 @@ n_subj_event_ <- function(dat, intersect_index, subjectid_var) {
 #' @param dat data.table. The analysis data set.
 #' @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
+#'   analyzed. See the "Endpoint Events" vignette in \pkg{ramnog} for more
 #'   information.
 #' @param intersect_index A vector of intergers referencing the rows of `dat`
 #'   that match both (1) the population to be analyzed and (2) the defenition of
@@ -66,7 +81,13 @@ n_subj_event_ <- function(dat, intersect_index, subjectid_var) {
 #'   the data (default is "USUBJID").
 #'
 #' @return an integer value
-#' @export 
+#' @export
+#' @examples
+#' dat <- data.table::data.table(USUBJID = c("S1", "S2", "S3"))
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' p_subj_event_(dat, cell_index = 1:3, intersect_index = c(1L, 2L),
+#'               subjectid_var = "USUBJID")
 p_subj_event_ <-
   function(dat,
            cell_index,

R/by_strata_across_trt.R

@@ -9,7 +9,7 @@
 #'   `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}
+#'   analyzed. See the "Endpoint Events" vignette in \pkg{ramnog}
 #'   for more information.
 #' @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.
@@ -18,6 +18,16 @@
 #' 
 #' @return A data.table containing Relative Risk statistics.
 #' @export
+#' @examples
+#' dat <- data.table::data.table(
+#'   USUBJID = c("S1", "S2", "S3", "S4", "S5", "S6"),
+#'   TRT     = c("Active", "Active", "Active", "Placebo", "Placebo", "Placebo")
+#' )
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' RR(dat, event_index = c(1L, 2L, 4L), cell_index = dat[["INDEX_"]],
+#'    treatment_var = "TRT", treatment_refval = "Placebo",
+#'    subjectid_var = "USUBJID")
 RR <- function(dat,
                event_index,
                cell_index,
@@ -66,7 +76,7 @@ RR <- function(dat,
 #'   `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}
+#'   analyzed. See the "Endpoint Events" vignette in \pkg{ramnog}
 #'   for more information.
 #' @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.
@@ -75,6 +85,16 @@ RR <- function(dat,
 #'
 #' @return A data.table containing Odds Ratio statistics.
 #' @export
+#' @examples
+#' dat <- data.table::data.table(
+#'   USUBJID = c("S1", "S2", "S3", "S4", "S5", "S6"),
+#'   TRT     = c("Active", "Active", "Active", "Placebo", "Placebo", "Placebo")
+#' )
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' OR(dat, event_index = c(1L, 2L, 4L), cell_index = dat[["INDEX_"]],
+#'    treatment_var = "TRT", treatment_refval = "Placebo",
+#'    subjectid_var = "USUBJID")
 OR <- function(dat,
                event_index,
                cell_index,
@@ -124,7 +144,7 @@ OR <- function(dat,
 #'   `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}
+#'   analyzed. See the "Endpoint Events" vignette in \pkg{ramnog}
 #'   for more information.
 #' @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.
@@ -134,6 +154,16 @@ OR <- function(dat,
 #'
 #' @return A data.table containing Risk Difference statistics.
 #' @export
+#' @examples
+#' dat <- data.table::data.table(
+#'   USUBJID = c("S1", "S2", "S3", "S4", "S5", "S6"),
+#'   TRT     = c("Active", "Active", "Active", "Placebo", "Placebo", "Placebo")
+#' )
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' RD(dat, event_index = c(1L, 2L, 4L), cell_index = dat[["INDEX_"]],
+#'    treatment_var = "TRT", treatment_refval = "Placebo",
+#'    subjectid_var = "USUBJID")
 RD <- function(dat,
                event_index,
                cell_index,
@@ -184,7 +214,7 @@ RD <- function(dat,
 #'   `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}
+#'   analyzed. See the "Endpoint Events" vignette in \pkg{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 silently return a `NA` value (default).
@@ -196,6 +226,16 @@ RD <- function(dat,
 #' @param ... Optional parameters.  
 #' @return A data.table containing p-value statistics.
 #' @export
+#' @examples
+#' dat <- data.table::data.table(
+#'   USUBJID = c("S1", "S2", "S3", "S4", "S5", "S6"),
+#'   TRT     = c("Active", "Active", "Active", "Placebo", "Placebo", "Placebo")
+#' )
+#' dat[, INDEX_ := .I]
+#' data.table::setkey(dat, INDEX_)
+#' p_val(dat, event_index = c(1L, 2L, 4L), cell_index = dat[["INDEX_"]],
+#'       treatment_var = "TRT", treatment_refval = "Placebo",
+#'       subjectid_var = "USUBJID")
 p_val <-
   function(dat,
            event_index,