Merge pull request #186 from Merck/parepare-cran-release

Parepare cran release

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metalite.ae
 Title: Adverse Events Analysis Using 'metalite'
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: c(
     person("Yilong", "Zhang", role = c("aut")),
     person("Yujie", "Zhao", email = "[email protected]", role = c("aut", "cre")),
@@ -12,6 +12,8 @@ Authors@R: c(
     person("Ruchitbhai", "Patel", role = c("aut")),
     person("Brian", "Lang", role = c("aut")),
     person("Xuan", "Deng", role = c("aut")),
+    person("Hiroaki", "Fukuda", role = c("aut")),
+    person("Bing", "Liu", role = c("aut")),
     person("Merck Sharp & Dohme Corp", role = c("cph"))
     )
 Description: Analyzes adverse events in clinical trials using the 'metalite'

NEWS.md

@@ -1,7 +1,39 @@
 # metalite.ae 0.1.2
 
-- Updated `format_ae_specific` to avoid warning when no comparison variables are
-requested.
+## New features
+
+- `tlf_ae_summary()` now has a new argument `title` for a user-customized title (#133).
+- Add new functions: `extend_ae_specific_subgroup()`, `prepare_ae_specific_subgroup()`, `format_ae_specific_subgroup()`, `tlf_ae_specific_subgroup()`, `extend_ae_summary_eaer()`, 
+`format_ae_exp_adj()` and `tlf_ae_exp_adj()` (#150, #161, #174, #180).
+- Add `data/metalite_ae_adex.rda` (#164).
+- Add new vignettes: `vignette("ae-specific-subgroup")` and `vignette("exposure-adjusted-event-rate")` (#167, #169).
+- Add System Organ Classes (SOC) information to `outdata` in `prepare_ae_specific()` (#186).
+
+## Bug fixes
+
+- Fix bug to avoid warning messages when no comparison variables are requested in `format_ae_specific()` (#135).
+- Fix bug to align the row order of output data with the input one in `avg_event()` and `avg_duration()` (#136).
+- Fix bug to check missing grouping variable after a subset of input data in `prepare_ae_specific()` (#137).
+- Fix bug to display item if AE term has `NA` in `prepare_ae_specific()` (#166).
+- Fix bug to correctly assign treatment labels when a treatment variable has `NA` (#179).
+
+## Improvements
+
+- Update GitHub Actions workflow (#131, #163, #181).
+- Add styler workflow (#134).
+- Add CRAN download badge (#140).
+- Remove dependencies on `dplyr` and `tidyr` from `avg_event()`, `avg_duration()` and `fmt_val()` (#136).
+- Change the default value of the `title` argument in `tlf_ae_specific()` (#138).
+- Remove `R/n_subject.R` and change to use `metalite::n_subject()` in `prepare_ae_specific()` (#144).
+- Race values for adsl and adae are converted to title case in `meta_ae_exmple()` (#158).
+- Organize files for utility functions (#159)
+  - Rename `R/rtf_output.R` to `R/utility.R`.
+  - Remove `rate_compare_sum.R`, `R/to_mock.R` and `R/to_sentence.R`.
+  - Move `to_rate_compare_sum()` to `R/rate_compare.R`, and move `to_mock()` and `to_sentence()` to `R/utility.R`.
+- Remove library calls from tests (#183).
+- Add `R/outdata.R` to control `outdata` object (#161).
+- Add an installation section to `README.md` (#177).
+- Improve style and formatting for vignettes and code (#158, #168).
 
 # metalite.ae 0.1.1
 

R/extend_ae_specific.R

@@ -343,8 +343,6 @@ extend_ae_specific_events <- function(outdata) {
 #'
 #' @param outdata An `outdata` object created by [prepare_ae_specific()].
 #' @param subgroup_var a character string for subgroup variable name
-#' @param outdata  An `outdata` object created by [prepare_ae_specific()].
-#' @param subgroup A character string for subgroup variable name.
 #'
 #' @return A list of analysis raw datasets.
 #' @export

R/prepare_ae_specific.R

@@ -156,6 +156,7 @@ prepare_ae_specific <- function(meta,
     soc_n[[par_var]] <- soc_n$name
     soc_n$order <- 1e3 * seq_len(nrow(soc_n))
     soc_n$name <- to_sentence(soc_n$name)
+    soc_n$soc_name <- soc_n$name
   } else {
     soc_n <- NULL
   }
@@ -173,6 +174,7 @@ prepare_ae_specific <- function(meta,
     par_n$order <- 1e3 * as.numeric(factor(par_n[[par_soc]])) + seq_len(nrow(par_n))
     par_n$order[is.na(par_n$order)] <- (if (!all(is.na(soc_n$order))) max(soc_n$order, na.rm = TRUE) else -Inf) + 1
     par_n$name <- to_sentence(par_n$name)
+    par_n$soc_name <- par_n[[par_soc]]
   } else {
     par_n <- NULL
   }
@@ -183,8 +185,14 @@ prepare_ae_specific <- function(meta,
   names(blank_row) <- names(pop_n[, col])
 
   # Combine count values
-  tbl <- rbind(pop_n[, col], obs_n[, col], blank_row, par_n[, col], soc_n[, col])
+  tbl0 <- rbind(pop_n[, col], obs_n[, col], blank_row)
+  tbl0$soc_name <- NA
+  tbl <- rbind(par_n[, c(col, "soc_name")], soc_n[, c(col, "soc_name")])
+  tbl <- rbind(tbl0, tbl)
   tbl <- tbl[order(tbl$order), ]
+  soc_name <- tbl$soc_name
+  tbl <- tbl[, !(names(tbl) %in% "soc_name")]
+
 
   # Calculate Proportion
   tbl_num <- tbl[, u_group]
@@ -205,6 +213,7 @@ prepare_ae_specific <- function(meta,
     prop = tbl_rate, diff = tbl_diff,
     n_pop = tbl_num[1, ],
     name = tbl$name,
+    soc_name = soc_name,
     components = components,
     prepare_call = match.call()
   )

_pkgdown.yml

@@ -20,7 +20,7 @@ footer:
     left: [developed_by, built_with, legal]
     right: [blank]
   components:
-    legal: "<br>Copyright &copy; 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
+    legal: "<br>Copyright &copy; 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
     blank: "<span></span>"
 
 navbar:

vignettes/exposure-adjusted-event-rate.Rmd

@@ -97,7 +97,7 @@ $$
 library(metalite.ae)
 ```
 
-```{r}
+```{r, message = FALSE}
 meta <- meta_ae_example()
 
 x <- meta |>