change version to 0.9.0, [skip vbump] (insightsengineering#1052)

# Pull Request

<!--- Replace `#nnn` with your issue link for reference. -->

Fixes #nnn

---------

Co-authored-by: Melkiades <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.8.5.9020
+Version: 0.9.0
 Date: 2023-09-01
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),

NEWS.md

@@ -1,11 +1,12 @@
-# tern 0.8.5.9020
+# tern 0.9.0
+### New Features
+* Added `stat_propdiff_ci` function to calculate proportion/risk difference and CI.
+* Added risk difference column functionality via the `riskdiff` argument to functions `count_occurrences`, `count_occurrences_by_grade`, `count_patients_with_event`, `count_patients_with_flags`, `analyze_num_patients`, and `summarize_num_patients`.
 
 ### Enhancements
-* Refactored `a_summary` to no longer use helper function `create_afun_summary`. 
-* Refactored `summarize_vars` and `compare_vars` to use refactored `a_summary`.
+* Refactored the function `a_summary` to no longer use the helper function `create_afun_summary`.
+* Refactored functions `summarize_vars` and `compare_vars` to use the refactored `a_summary` function.
 * Created new internal helper functions `ungroup_stats` to ungroup statistics calculated for factor variables, and `a_summary_internal` to perform calculations for `a_summary`.
-* Added `stat_propdiff_ci` function to calculate proportion/risk difference and CI.
-* Added risk difference column functionality via the `riskdiff` argument to `count_occurrences`, `count_occurrences_by_grade`, `count_patients_with_event`, `count_patients_with_flags`, `analyze_num_patients`, and `summarize_num_patients`.
 
 ### Bug Fixes
 * Fixed bug in `s_count_occurrences_by_grade` so that "missing" grade always appears as the final level.

R/prop_diff_test.R

@@ -212,8 +212,7 @@ prop_cmh <- function(ary) {
 
 #' @describeIn h_prop_diff_test performs the Chi-Squared test with Schouten correction.
 #'
-#' @seealso For information on the Schouten correction (Schouten, 1980),
-#'   visit \url{https://onlinelibrary.wiley.com/doi/abs/10.1002/bimj.4710220305}.
+#' @seealso Schouten correction is based upon \insertCite{Schouten1980-kd;textual}{tern}.
 #'
 #'
 #' @keywords internal

R/summarize_glm_count.R

@@ -169,7 +169,7 @@ h_glm_count <- function(.var,
 #' @param .df_row (`data.frame`)\cr data set that includes all the variables that are called in `.var` and `variables`.
 #' @param conf_level (`numeric`)\cr value used to derive the confidence interval for the rate.
 #' @param obj (`glm.fit`)\cr fitted model object used to derive the mean rate estimates in each treatment arm.
-#' @param `arm` (`string`)\cr group variable, for which the covariate adjusted means of multiple groups will be
+#' @param arm (`string`)\cr group variable, for which the covariate adjusted means of multiple groups will be
 #'   summarized. Specifically, the first level of `arm` variable is taken as the reference group.
 #'
 #' @return

R/utils_checkmate.R

@@ -11,7 +11,6 @@
 #' @param na_level (`character`)\cr the string you have been using to represent NA or
 #'   missing data. For `NA` values please consider using directly [is.na()] or
 #'   similar approaches.
-#' @param ... a collection of objects to test.
 #'
 #' @return Nothing if assertion passes, otherwise prints the error message.
 #'

inst/REFERENCES.bib

@@ -25,3 +25,29 @@ @ARTICLE{Yan2010-jt
   month     =  aug,
   year      =  2010
 }
+
+
+% The entry below contains non-ASCII chars that could not be converted
+% to a LaTeX equivalent.
+@ARTICLE{Schouten1980-kd,
+  title     = "Comparing two independent binomial proportions by a modified chi
+               square test",
+  author    = "Schouten, H J A and Molenaar, I W and Van Strik, R and Boomsma,
+               A",
+  abstract  = "When using the chi square test to compare the proportions of
+               successes in two independent binomial samples, a new continuity
+               correction is proposed, which equals half the size of the
+               smaller sample. Exact computations of unconditional
+               tail‐probabilities, together with a theoretical argument, show
+               that this correction is more appropriate than the YATES
+               correction. This version of the chi square test is still
+               conservative, but less so, and as a consequence more powerful,
+               than the YATES corrected test.",
+  journal   = "Biom. J.",
+  publisher = "Wiley",
+  volume    =  22,
+  number    =  3,
+  pages     = "241--248",
+  year      =  1980,
+  language  = "en"
+}