Merge pull request #203 from Merck/prepare-for-v0.1.3-release

Prepare for v0.1.3 release

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metalite.ae
 Title: Adverse Events Analysis Using 'metalite'
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: c(
     person("Yilong", "Zhang", role = c("aut")),
     person("Yujie", "Zhao", email = "[email protected]", role = c("aut", "cre")),
@@ -14,6 +14,8 @@ Authors@R: c(
     person("Xuan", "Deng", role = c("aut")),
     person("Hiroaki", "Fukuda", role = c("aut")),
     person("Bing", "Liu", role = c("aut")),
+    person("Jeetender", "Chauhan", role = c("aut")),
+    person("Li", "Ma", role = c("ctb")),
     person("Merck Sharp & Dohme Corp", role = c("cph"))
     )
 Description: Analyzes adverse events in clinical trials using the 'metalite'

NEWS.md

@@ -1,46 +1,65 @@
+# metalite.ae 0.1.3
+
+## New features
+
+-   `format_ae_specific()` now has new arguments `filter_method` and `filter_criteria` to control displayed rows in a table, `sort_order` and `sort_column` to sort an output table, and `hide_soc_stats` to control display of statistics for SOC rows (#191, #192, #203).
+-   Add `data/metalite_ae_adesxum.rda` (#189).
+-   Add event counts to `avg_count()` and `extend_ae_specific_events()` (#194).
+-   Add `empty_table()` to return an empty table object when data has no population (#200).
+
+## Bug fixes
+
+-   Fix bug to correctly display the order of means of duration and means of event count in `extend_ae_specific_events()` and `extend_ae_specific_duration()`(#194, #199).
+-   Fix bug to avoid an error when a treatment group has no observation to calculate event counts and duration in `avg_event()` and `avg_duration()` (#199).
+-   Fix bug to avoid an error when there is no observation to summarize event counts and duration in `avg_event()`, `avg_duration()`, `extend_ae_specific_events()` and `extend_ae_specific_duration()` (#200).
+
+## Improvements
+
+-   Update `fmt_est()` to change display of missing values from a character string of "NA" to a blank in an output table (#194).
+-   Update `extend_ae_specific_inference()` to pass additional arguments to `rate_compare_sum()` (#197).
+
 # metalite.ae 0.1.2
 
 ## 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).
+-   `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).
+-   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).
+-   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
 
-- Updated the `DESCRIPTION` file to reformat the reference.
-- Uncommented the previously commented code example.
+-   Updated the `DESCRIPTION` file to reformat the reference.
+-   Uncommented the previously commented code example.
 
 # metalite.ae 0.1.0
 
-- Initial submission to CRAN.
-- Added a `NEWS.md` file to track changes to the package.
+-   Initial submission to CRAN.
+-   Added a `NEWS.md` file to track changes to the package.

R/format_ae_specific.R

@@ -19,6 +19,7 @@
 #' Format AE specific analysis
 #'
 #' @inheritParams extend_ae_specific_inference
+#' @param hide_soc_stats A boolean value to hide stats for SOC rows.
 #' @param digits_prop A numeric value of number of digits for proportion value.
 #' @param digits_ci A numeric value of number of digits for confidence interval.
 #' @param digits_p A numeric value of number of digits for p-value.
@@ -84,6 +85,7 @@
 #' head(tbl$tbl)
 format_ae_specific <- function(outdata,
                                display = c("n", "prop", "total"),
+                               hide_soc_stats = FALSE,
                                digits_prop = 1,
                                digits_ci = 1,
                                digits_p = 3,
@@ -333,6 +335,11 @@ format_ae_specific <- function(outdata,
     }
   }
 
+  # Control SOC stats
+  if (hide_soc_stats) {
+    res[outdata$order %% 1000 == 0, names(res)[!names(res) == "name"]] <- NA
+  }
+
   # Transfer to Mock
   if (mock) {
     n_mock <- min(20, nrow(res), na.rm = TRUE)

vignettes/ae-specific.Rmd

@@ -172,12 +172,12 @@ tbl <- outdata |>
 head(tbl$tbl)
 ```
 
-We can use `extend_ae_specific_events()` to add average number of AE per subject.
+We can use `extend_ae_specific_events()` to add number of AE and/or average of it per subject.
 
 ```{r}
 tbl <- outdata |>
   extend_ae_specific_events() |>
-  format_ae_specific(display = c("n", "prop", "events"))
+  format_ae_specific(display = c("n", "prop", "events_count", "events_avg"))
 
 head(tbl$tbl)
 ```