Merge pull request #231 from pharmaverse/devel

admiralonco 0.4.0
pharmaverse · Jun 12, 2023 · f11db28 · f11db28
2 parents 4b7d86c + ffa0c11
commit f11db28
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diff --git a/.Rprofile b/.Rprofile
@@ -1,4 +1,14 @@
-if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) {
+# Set renv profile base on R version.
+if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) {
+  renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
+  if (file.exists("./renv/profile")) {
+    message("Using renv profile from `renv/profile` file.")
+  } else if (renv_profile %in% c("4.1", "4.2", "4.3")) {
+    message("Set renv profile to `", renv_profile, "`")
+    Sys.setenv("RENV_PROFILE" = renv_profile)
+  } else {
+    message("This repository do not contains the renv profile for your R version.")
+  }
   source("renv/activate.R")
 } else {
   options(repos = c(CRAN = "https://cran.rstudio.com"))

diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml
@@ -41,25 +41,25 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   readme:
     name: Render README
     uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
     if: github.event_name == 'push'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
@@ -69,7 +69,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
       # Whether to skip multiversion docs
       # Note that if you have multiple versions of docs,
       # your URL links are likely to break due to path changes
@@ -79,7 +79,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -91,7 +91,7 @@ jobs:
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
@@ -102,10 +102,10 @@ jobs:
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   man-pages:
     name: Man Pages
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
diff --git a/.lintr b/.lintr
@@ -1,2 +1,14 @@
-linters: with_defaults(line_length_linter(100), object_usage_linter=NULL)
-exclusions: list("renv/activate.R")
+linters: linters_with_defaults(
+    any_duplicated_linter(),
+    any_is_na_linter(),
+    line_length_linter(100),
+    object_usage_linter=NULL,
+    cyclocomp_linter(complexity_limit = 20),
+    undesirable_function_linter = undesirable_function_linter()
+  )
+exclusions: list(
+    "R/data.R" = Inf,
+    "inst" = list(undesirable_function_linter = Inf),
+    "vignettes" = list(undesirable_function_linter = Inf),
+    "tests/testthat" = list(undesirable_function_linter = Inf)
+  )
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: admiralonco
 Type: Package
 Title: Oncology Extension Package for ADaM in 'R' Asset Library
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person("Stefan", "Bundfuss", email = "[email protected]", role = c("aut", "cre")),
     person("Ross", "Farrugia", role = "aut"),
@@ -11,6 +11,7 @@ Authors@R: c(
     person("Samia", "Kabi", role = "aut"),
     person("Stephen", "Gormley", role = "aut"),
     person("Hinal", "Patel", role = "aut"),
+    person("Vinh", "Nguyen", role = "aut"),
     person("Karl", "Kennedy", role = "ctb"),
     person("Matt", "Marino", role = "ctb"),
     person("Gopi", "Vegesna", role = "ctb"),    
@@ -35,14 +36,16 @@ Description: Programming oncology specific Clinical Data Interchange Standards C
     The package is an extension package of the 'admiral' package.
 Language: en-US
 License: Apache License (>= 2)
+BugReports: https://github.com/pharmaverse/admiralonco/issues
+URL: https://pharmaverse.github.io/admiralonco/, https://github.com/pharmaverse/admiralonco
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Depends: R (>= 3.5)
 Imports:
-    admiral (>= 0.10.0),
-    admiraldev (>= 0.3.0),
+    admiral (>= 0.11.0),
+    admiraldev (>= 0.4.0),
     dplyr (>= 0.8.4),
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),
@@ -63,7 +66,6 @@ Suggests:
     roxygen2,
     spelling,
     stringr,
-    styler,
     tibble,
     usethis,
     covr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -7,7 +7,6 @@ export(derive_param_bor)
 export(derive_param_clinbenefit)
 export(derive_param_confirmed_bor)
 export(derive_param_confirmed_resp)
-export(derive_param_lasta)
 export(derive_param_response)
 export(filter_pd)
 export(get_crpr_dataset)
@@ -19,7 +18,7 @@ export(signal_crpr)
 export(trts_censor)
 importFrom(admiral,censor_source)
 importFrom(admiral,count_vals)
-importFrom(admiral,derive_param_extreme_event)
+importFrom(admiral,derive_extreme_records)
 importFrom(admiral,derive_var_obs_number)
 importFrom(admiral,derive_vars_merged)
 importFrom(admiral,event_source)
@@ -53,6 +52,7 @@ importFrom(admiraldev,expect_dfs_equal)
 importFrom(admiraldev,expr_c)
 importFrom(admiraldev,extract_vars)
 importFrom(admiraldev,filter_if)
+importFrom(admiraldev,process_set_values_to)
 importFrom(admiraldev,squote)
 importFrom(admiraldev,suppress_warning)
 importFrom(admiraldev,vars2chr)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,40 @@
+# admiralonco 0.4.0
+
+## Documentation
+
+- New vignette "Creating and Using New Anti-Cancer Start Date" (#17)
+- "Create `ADRS`" and "Create `ADTTE`" vignette has been updated to include a link to "Creating and Using New Anti-Cancer Start Date" vignette
+
+## New Features
+
+- Added a "Report a bug" link to `{admiralonco}` website (#211)
+
+- Added a section regarding dependencies to the `{admiralonco}` website (#223)
+
+- Vignettes and templates were updated due to changes in admiral and
+admiralonco: (#216)
+    - The `AVAL` variable is now populated via the `set_values_to` argument as
+    the `aval_fun` argument was deprecated.
+    - `admiral::derive_param_extreme_event()` calls were replaced by
+    `admiral::derive_extreme_records()` calls due to deprecation of
+    `admiral::derive_param_extreme_event()`.
+    - `admiral::derive_param_exist_flag()` calls were updated as the
+    `dataset_adsl` argument was renamed to `dataset_ref`.
+
+## Breaking Changes
+
+- Function `derive_param_lasta()`, which was deprecated in admiralonco 0.2.0,
+has been removed. (#216)
+
+- The `aval_fun` argument of `derive_param_bor()`, `derive_param_clinbenefit()`,
+`derive_param_confirmed_bor()`, `derive_param_confirmed_resp()`,
+`derive_param_response()` was deprecated in favor of the `set_values_to`
+argument. (#216)
+
+- The `call_aval_fun()` function was deprecated in favor or
+`admiraldev::process_set_values_to()`. (#216)
+
+
 # admiralonco 0.3.0
 
 ## Breaking Changes

diff --git a/R/admiralonco-package.R b/R/admiralonco-package.R
@@ -1,6 +1,6 @@
 #' @keywords internal
 #' @family internal
-#' @importFrom admiral censor_source count_vals derive_param_extreme_event
+#' @importFrom admiral censor_source count_vals derive_extreme_records
 #'   derive_var_obs_number derive_vars_merged event_source filter_joined
 #'   filter_extreme filter_relative get_admiral_option list_tte_source_objects
 #'   max_cond min_cond params restrict_derivation set_admiral_options yn_to_numeric
@@ -9,7 +9,7 @@
 #'   assert_integer_scalar assert_list_of assert_logical_scalar
 #'   assert_order_vars assert_param_does_not_exist assert_s3_class assert_symbol
 #'   assert_vars assert_varval_list enumerate expect_dfs_equal extract_vars
-#'   filter_if expr_c squote suppress_warning vars2chr
+#'   filter_if expr_c process_set_values_to squote suppress_warning vars2chr
 #' @importFrom dplyr arrange bind_rows case_when filter group_by if_else
 #'   left_join mutate rename right_join select slice ungroup
 #' @importFrom lifecycle deprecate_warn deprecated deprecate_stop

diff --git a/R/derive_param_bor.R b/R/derive_param_bor.R
@@ -113,8 +113,10 @@
 #'
 #'   *Permitted Values:* a logical scalar
 #'
-#' @param aval_fun Function to map character analysis value (`AVALC`) to numeric
-#'                 analysis value (`AVAL`)
+#' @param aval_fun *Deprecated*, please use `set_values_to` instead.
+#'
+#'   Function to map character analysis value (`AVALC`) to numeric analysis
+#'   value (`AVAL`)
 #'
 #'   The (first) argument of the function must expect a character vector and the
 #'   function must return a numeric vector.
@@ -265,7 +267,7 @@ derive_param_bor <- function(dataset,
                              reference_date,
                              ref_start_window,
                              missing_as_ne = FALSE,
-                             aval_fun = aval_resp,
+                             aval_fun,
                              set_values_to,
                              subject_keys = get_admiral_option("subject_keys")) {
   #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
@@ -309,6 +311,11 @@ derive_param_bor <- function(dataset,
     param   = set_values_to$PARAMCD
   )
 
+  if (!missing(aval_fun)) {
+    deprecate_warn("0.4.0", "derive_param_bor(aval_fun = )", "derive_param_bor(set_values_to = )")
+    set_values_to <- exprs(!!!set_values_to, AVAL = {{ aval_fun }}(AVALC))
+  }
+
   #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   # filter_pd and filter_source: Filter source dataset using filter_source----
   # argument and also filter data after progressive disease with filter_pd
@@ -411,51 +418,15 @@ derive_param_bor <- function(dataset,
       order = exprs(tmp_order, ADT),
       mode = "first"
     ) %>%
-    select(-tmp_order)
-
-  #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-  # set_values_to: Execute set_values_to ----
-  #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
-  tryCatch(
-    param_bor_values_set <- param_bor %>%
-      mutate(
-        !!!set_values_to
-      ),
-    error = function(cnd) {
-      abort(
-        paste0(
-          "Assigning new columns with set_values_to has failed:\n",
-          "set_values_to = (\n",
-          paste(
-            " ",
-            names(set_values_to),
-            "=",
-            set_values_to,
-            collapse = "\n"
-          ),
-          "\n)\nError message:\n  ",
-          cnd
-        )
-      )
-    }
-  )
-
-  #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-  # aval_fun(AVALC): Execute aval_fun ----
-  #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
-  param_bor_aval_fun <- call_aval_fun(
-    param_bor_values_set,
-    aval_fun
-  )
+    select(-tmp_order) %>%
+    process_set_values_to(set_values_to)
 
   #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   # Bind back to passed dataframe in dataset argument and return ----
   #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
   bind_rows(
     dataset,
-    param_bor_aval_fun
+    param_bor
   )
 }
diff --git a/R/derive_param_clinbenefit.R b/R/derive_param_clinbenefit.R
@@ -94,8 +94,10 @@
 #' that must elapse before an evaluable non-PD assessment counts toward determining
 #' clinical benefit.
 #'
-#' @param aval_fun Function to map character analysis value (`AVALC`) to numeric
-#' analysis value (`AVAL`)
+#' @param aval_fun *Deprecated*, please use `set_values_to` instead.
+#'
+#' Function to map character analysis value (`AVALC`) to numeric analysis value
+#' (`AVAL`)
 #'
 #' The (first) argument of the function must expect a character vector and the
 #' function must return a numeric vector.
@@ -195,7 +197,7 @@ derive_param_clinbenefit <- function(dataset,
                                      source_datasets,
                                      reference_date,
                                      ref_start_window,
-                                     aval_fun = yn_to_numeric,
+                                     aval_fun,
                                      clinben_vals = c("CR", "PR", "SD", "NON-CR/NON-PD"),
                                      set_values_to,
                                      subject_keys = get_admiral_option("subject_keys")) {
@@ -216,12 +218,21 @@ derive_param_clinbenefit <- function(dataset,
     optional = FALSE
   )
 
-  assert_function(aval_fun)
   assert_s3_class(source_resp, "date_source")
   assert_s3_class(source_pd, "date_source", optional = TRUE)
   assert_list_of(source_datasets, "data.frame")
   assert_character_vector(clinben_vals)
 
+  if (!missing(aval_fun)) {
+    deprecate_warn(
+      "0.4.0",
+      "derive_param_clinbenefit(aval_fun = )",
+      "derive_param_clinbenefit(set_values_to = )"
+    )
+    assert_function(aval_fun)
+    set_values_to <- exprs(!!!set_values_to, AVAL = {{ aval_fun }}(AVALC))
+  }
+
   source_names <- names(source_datasets)
 
   if (!is.null(source_pd)) {
@@ -313,9 +324,6 @@ derive_param_clinbenefit <- function(dataset,
     mutate(
       AVALC = if_else(!is.na(ADT), "Y", "N"),
       !!!set_values_to
-    ) %>%
-    call_aval_fun(
-      aval_fun
     )
 
   bind_rows(dataset, new_param)