chore: response to CRAN checks

simpar1471 · Nov 21, 2024 · f3949bc · f3949bc
1 parent d43a03b
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@
 ^data-raw$
 ^vignettes/articles$
 ^cran-comments\.md$
+^CRAN-SUBMISSION$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,17 +1,19 @@
 Type: Package
 Package: matchedcc
 Title: 'Stata'-Like Matched Case-Control Analysis
-Version: 0.1.0
+Version: 0.1.1
 Date: 2024-11-19
 Authors@R:
-    person(c("Simon", "R"), "Parker", email = "simon.parker24@ucl.ac.uk",
+    person(c("Simon", "R"), "Parker", email = "simon.parker.24@ucl.ac.uk",
            role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0009-0003-8214-4496"))
-Maintainer: Simon R Parker <simon.parker24@ucl.ac.uk>
+Maintainer: Simon R Parker <simon.parker.24@ucl.ac.uk>
 Description: Calculate multiple statistics with confidence intervals for matched
     case-control data including risk difference, risk ratio, relative
     difference, and the odds ratio. Results are equivalent to those from
-    'Stata', and you can choose how to format your input data.
+    'Stata', and you can choose how to format your input data. Methods used are
+    those described on page 56 the 'Stata' documentation for "Epitab - Tables
+    for Epidemologists" <https://www.stata.com/manuals/repitab.pdf>.
 License: GPL (>= 3)
 Encoding: UTF-8
 RoxygenNote: 7.3.2
@@ -37,4 +39,3 @@ Suggests:
     RStata
 LazyData: true
 Config/Needs/website: rmarkdown
-VignetteBuilder: knitr
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# matchedcc 0.1.1
+
+* CRAN resubmission.
+
 # matchedcc 0.1.0
 
 * Added `mcc()` and `mcci()`, which facilitate Stata-like analysis of matched

diff --git a/R/data.R b/R/data.R
@@ -1,5 +1,5 @@
 # matchedcc: Stata-like matched case-control analysis
-# Copyright (C) 2024  Simon Parker
+# Copyright (C) 2024 Simon Parker
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/mcc.R b/R/mcc.R
@@ -1,5 +1,5 @@
 # matchedcc: Stata-like matched case-control analysis
-# Copyright (C) 2024  Simon Parker
+# Copyright (C) 2024 Simon Parker
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 [![R-CMD-check](https://github.com/simpar1471/matchedcc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/simpar1471/matchedcc/actions/workflows/R-CMD-check.yaml)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/matchedcc)](https://CRAN.R-project.org/package=matchedcc)
-[![codecov](https://codecov.io/gh/simpar1471/matchedcc/graph/badge.svg?token=OJSHMFFGXN)](https://codecov.io/gh/simpar1471/matchedcc)
+[![codecov](https://codecov.io/gh/simpar1471/matchedcc/graph/badge.svg?token=OJSHMFFGXN)](https://app.codecov.io/gh/simpar1471/matchedcc)
 <!-- badges: end -->
 
 The aim of **matchedcc** is to provide epidemiologists using R with

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,11 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Added link to DESCRIPTION for a description of the implemented methods.
+* Removed `installed.packages()` from code in `tests/testdata/run-stata-mcc.R`.
+* Removed installation of 'RStata' package in `tests/testdata/run-stata-mcc.R`.
+
+
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note

diff --git a/tests/testdata/run-stata-mcc.R b/tests/testdata/run-stata-mcc.R
@@ -2,17 +2,15 @@
 
 # The code does NOT work unless being run in interactive mode, as
 # `capture.output()` captures more than just the RStata call.
-
 if (interactive()) {
-  if (!"RStata" %in% installed.packages()) {
-    devtools::install_cran("RStata")
-  }
+  try({
+    testthat::skip_if_not_installed("RStata")
 
-  options("RStata.StataPath" = "\"C:\\Program Files\\Stata18\\StataSE-64\"")
-  options("RStata.StataVersion" = 18)
+    options("RStata.StataPath" = "\"C:\\Program Files\\Stata18\\StataSE-64\"")
+    options("RStata.StataVersion" = 18)
 
-  n_commands <- 1000
-  commands <- withr::with_seed(2800, {
+    n_commands <- 1000
+    commands <- withr::with_seed(2800, {
     idxs <- 1:4
     samples_vec <- 1L:1000L
     conf_level_vec <- seq(10, 99.99, 0.01)
@@ -25,14 +23,14 @@ if (interactive()) {
           FUN.VALUE = integer(length = 1)
         )
         conf_level <-  sample(conf_level_vec, size = 1, replace = FALSE)
-        glue::glue(
-          "mcci {paste(samples, collapse = \" \")}, level({conf_level})"
-        )
+        glue::glue("mcci {paste(samples, collapse = \" \")}, level({conf_level})")
       })
-  })
+    })
 
-  stata_testers <- utils::capture.output(
-    RStata::stata(commands, stata.echo = TRUE)
-  )
-  readr::write_lines(stata_testers, file = "tests/testdata/stata-output.log")
-}
+    stata_testers <- utils::capture.output(
+      RStata::stata(commands, stata.echo = TRUE)
+    )
+
+    readr::write_lines(stata_testers, file = "tests/testdata/stata-output.log")
+  })
+}