Merge pull request #39 from R4EPI/cran_manual_review

Cran manual review

Author: aspina7

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 0.1.0
-Date: 2025-11-05 17:14:19 UTC
-SHA: bd9b2707d6ba19bcf84d99ae7450e73339c028c5
+Date: 2025-11-09 18:56:31 UTC
+SHA: 68c8bacd319e6762dea8c219dc19e210bf6787ff

DESCRIPTION

@@ -2,56 +2,48 @@ Package: epitabulate
 Title: Tables for Epidemiological Analysis
 Version: 0.1.0
 Authors@R: c(
-    person(given = "Alexander",
-           family = "Spina",
-           email = "[email protected]", 
-           comment = c(ORCID = "0000-0001-8425-1867"),
-           role = c("aut", "cre")),
-    person(given = "Zhian N.",
-           family = "Kamvar",
-           role = c("aut"),
-           email = "[email protected]",
+    person("Alexander", "Spina", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-8425-1867")),
+    person("Zhian N.", "Kamvar", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0003-1458-7108")),
-    person(given = "Amy",
-           family = "Gimma",
-           role = "aut"),
-    person(given = "Kate",
-           family = "Doyle",
-           role = "ctb"), 
-    person("Applied Epi Incorporated", 
-           role = "cph"), 
-    person("Medecins Sans Frontieres Operational Centre Amsterdam", 
-           role = "fnd"))
-Description: Produces tables for descriptive epidemiological analysis. These
-    tables include attack rates, case fatality ratios and mortality rates
-    (with appropriate confidence intervals), with additional functionality to
-    calculate Mantel-Haenszel odds, risk, and incidence rate ratios. 
+    person("Amy", "Gimma", role = "aut"),
+    person("Kate", "Doyle", role = "ctb"),
+    person("Applied Epi Incorporated", role = "cph"),
+    person("Medecins Sans Frontieres Operational Centre Amsterdam", role = "fnd")
+  )
+Description: Produces tables for descriptive epidemiological analysis.
+    These tables include attack rates, case fatality ratios, and mortality
+    rates (with appropriate confidence intervals), with additional
+    functionality to calculate Mantel-Haenszel odds, risk, and incidence
+    rate ratios. The methods implemented follow standard epidemiological
+    approaches described in Rothman et al. (2008, ISBN:978-0-19-513554-2).
     This package is part of the 'R4EPIs' project <https://R4EPI.github.io/sitrep/>.
 License: GPL-3
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-URL: https://R4EPI.github.io/epitabulate/, https://github.com/R4EPI/epitabulate/
+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,
     glue,
-    gtsummary, 
+    gtsummary,
     MASS,
     purrr,
     rlang (>= 0.4.0),
-    scales, 
+    scales,
     stats,
     tibble (>= 3.0.0),
     tidyr (>= 1.0.0),
     tidyselect (>= 1.0.0)
 Suggests: 
-    broom.helpers, 
-    cardx, 
-    testthat,
+    broom.helpers,
+    cardx,
+    covr,
     matchmaker (>= 0.1.0),
-    covr
+    testthat
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

R/gt_univariate_crosstabs.R

@@ -15,6 +15,16 @@ utils::globalVariables(c("n_obs", "n_event", "n_nonevent", "estimate",
 #'This is only works for dichotomous variables (yes/no, TRUE/FALSE,
 #'male/female), others will be dropped with a warning message. (Default is FALSE)
 #'
+#'@return A modified `gtsummary` table object (same class as input — e.g.
+#'   `"tbl_uvregression"` or `"tbl_cmh"`) containing additional cross-tabulated
+#'   counts of outcomes and exposures. The structure depends on regression type:
+#'   \itemize{
+#'     \item For logistic models: adds case and control counts.
+#'     \item For Poisson models without offsets: adds total and case counts per exposure group (risk ratios).
+#'     \item For Poisson models with offsets: adds total person-time and case counts per exposure group (incidence rate ratios).
+#'     \item When `wide = TRUE`, dichotomous variables are reshaped to wide format with separate columns for exposed/unexposed counts.
+#'   }
+#'
 #'@importFrom gtsummary modify_table_styling modify_table_body modify_header modify_fmt_fun style_number modify_footnote
 #'@importFrom dplyr mutate relocate
 #'@importFrom rlang enquo as_label quo_get_expr

R/gt_univariate_stratified.R

@@ -30,6 +30,15 @@ utils::globalVariables(c("n_obs", "n_event", "n_nonevent", "estimate",
 #'
 #' @param conf.level Confidence level for confidence intervals (default 0.95)
 #'
+#' @return A gtsummary table of class `"tbl_cmh"` (and `"gtsummary"`, `"tbl_stack"`)
+#'   containing:
+#'   \itemize{
+#'     \item Crude estimates of association (odds ratios, risk ratios, or rate ratios)
+#'     \item Stratified estimates for each level of the stratification variable
+#'     \item Cochran–Mantel–Haenszel (CMH) adjusted estimates with 95\% confidence intervals
+#'     \item Woolf test p-values for assessing homogeneity across strata (when applicable)
+#'   }
+#'
 #' @importFrom tidyselect vars_select
 #' @importFrom dplyr mutate relocate filter
 #' @importFrom rlang enquo as_label