Merge pull request #1937 from pharmaverse/devel

admiral 0.11.0

.Rprofile

@@ -1,4 +1,14 @@
-if (Sys.getenv("GITHUB_ACTIONS") == "") {
+# 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"))

.github/pull_request_template.md

@@ -14,5 +14,5 @@ Please check off each taskbox as an acknowledgment that you completed the task o
 - [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`
 - [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`
 - [ ] Link the issue in the Development Section on the right hand side.
-- [ ] Address all merge conflicts and resolve appropriately 
+- [ ] Address all merge conflicts and resolve appropriately
 - [ ] Pat yourself on the back for a job well done! Much love to your accomplishment!

.github/workflows/common.yml

@@ -43,25 +43,25 @@ 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
@@ -71,7 +71,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/v')
     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
@@ -85,7 +85,7 @@ 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
@@ -96,7 +96,7 @@ jobs:
     if: >
       github.event_name != 'release'
     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
@@ -106,4 +106,4 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"

.github/workflows/templates.yml

@@ -12,4 +12,4 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
     if: github.event.review.state == 'approved'
     with:
-      r-version: "4.0"
+      r-version: "4.1"

.lintr

@@ -1,2 +1,12 @@
-linters: with_defaults(line_length_linter(100), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20))
-exclusions: list("R/data.R")
+linters: linters_with_defaults(
+    line_length_linter(100),
+    object_usage_linter=NULL,
+    cyclocomp_linter(complexity_limit = 22),
+    undesirable_function_linter = undesirable_function_linter()
+  )
+exclusions: list(
+    "R/data.R" = Inf,
+    "inst" = list(undesirable_function_linter = Inf),
+    "vignettes" = list(undesirable_function_linter = Inf),
+    "R/admiral_options.R" = list(line_length_linter = 8)
+  )

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: admiral
 Type: Package
 Title: ADaM in R Asset Library
-Version: 0.10.2
+Version: 0.11.0
 Authors@R: c(
     person("Ben", "Straub", email = "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),
@@ -32,6 +32,8 @@ Authors@R: c(
     person("Kangjie", "Zhang", role = "aut"),
     person("Daphne", "Grasselly", role = "aut"),
     person("Adam", "Forys", role = "aut"),
+    person("Edoardo", "Mancini", role = "aut"),
+    person("Stefan", "Thoma", role = "aut"),
     person("Michael", "Thorpe", role = "ctb"),
     person("Declan", "Hodges", role = "ctb"),
     person("Jaxon", "Abercrombie", role = "ctb"),
@@ -69,14 +71,15 @@ Description: A toolbox for programming Clinical Data Interchange Standards Conso
     (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
 Language: en-US
 License: Apache License (>= 2)
+BugReports: https://github.com/pharmaverse/admiral/issues
 URL: https://pharmaverse.github.io/admiral/, https://github.com/pharmaverse/admiral
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Depends: R (>= 3.5)
 Imports:
-    admiraldev (>= 0.3.0),
+    admiraldev (>= 0.4.0),
     dplyr (>= 0.8.4),
     hms (>= 0.5.3),
     lifecycle (>= 0.1.0),
@@ -101,7 +104,6 @@ Suggests:
     rmarkdown,
     roxygen2,
     spelling,
-    styler,
     testthat (>= 3.0.0),
     tibble,
     usethis

NAMESPACE

@@ -10,6 +10,7 @@ S3method(convert_na_to_blanks,default)
 S3method(convert_na_to_blanks,list)
 S3method(format,basket_select)
 S3method(print,adam_templates)
+S3method(print,duplicates)
 S3method(print,source)
 export("%>%")
 export(ae_event)
@@ -29,10 +30,12 @@ export(call_derivation)
 export(call_user_fun)
 export(censor_source)
 export(chr2vars)
+export(compute_age_years)
 export(compute_bmi)
 export(compute_bsa)
 export(compute_dtf)
 export(compute_duration)
+export(compute_egfr)
 export(compute_framingham)
 export(compute_map)
 export(compute_qtc)
@@ -55,7 +58,7 @@ export(date_source)
 export(death_event)
 export(default_qtc_paramcd)
 export(derivation_slice)
-export(derive_derived_param)
+export(derive_basetype_records)
 export(derive_expected_records)
 export(derive_extreme_event)
 export(derive_extreme_records)
@@ -67,7 +70,7 @@ export(derive_param_doseint)
 export(derive_param_exist_flag)
 export(derive_param_exposure)
 export(derive_param_extreme_event)
-export(derive_param_first_event)
+export(derive_param_extreme_record)
 export(derive_param_framingham)
 export(derive_param_map)
 export(derive_param_qtc)
@@ -76,8 +79,6 @@ export(derive_param_tte)
 export(derive_param_wbc_abs)
 export(derive_summary_records)
 export(derive_var_age_years)
-export(derive_var_agegr_ema)
-export(derive_var_agegr_fda)
 export(derive_var_analysis_ratio)
 export(derive_var_anrind)
 export(derive_var_atoxgr)
@@ -119,8 +120,6 @@ export(derive_vars_dy)
 export(derive_vars_joined)
 export(derive_vars_last_dose)
 export(derive_vars_merged)
-export(derive_vars_merged_dt)
-export(derive_vars_merged_dtm)
 export(derive_vars_merged_lookup)
 export(derive_vars_period)
 export(derive_vars_query)
@@ -134,10 +133,11 @@ export(exprs)
 export(extend_source_datasets)
 export(extract_duplicate_records)
 export(extract_unit)
-export(filter_confirmation)
 export(filter_date_sources)
+export(filter_exist)
 export(filter_extreme)
 export(filter_joined)
+export(filter_not_exist)
 export(filter_relative)
 export(format_eoxxstt_default)
 export(format_reason_default)
@@ -158,14 +158,14 @@ export(negate_vars)
 export(params)
 export(print_named_list)
 export(query)
+export(records_source)
 export(restrict_derivation)
 export(set_admiral_options)
 export(signal_duplicate_records)
 export(slice_derivation)
 export(use_ad_template)
 export(validate_basket_select)
 export(validate_query)
-export(vars)
 export(yn_to_numeric)
 import(admiraldev)
 importFrom(dplyr,across)
@@ -179,8 +179,10 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,ends_with)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
+importFrom(dplyr,first)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
+importFrom(dplyr,group_by_at)
 importFrom(dplyr,if_else)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
@@ -195,8 +197,10 @@ importFrom(dplyr,semi_join)
 importFrom(dplyr,slice)
 importFrom(dplyr,starts_with)
 importFrom(dplyr,summarise)
+importFrom(dplyr,summarise_all)
 importFrom(dplyr,tibble)
 importFrom(dplyr,transmute)
+importFrom(dplyr,tribble)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,union)
 importFrom(hms,as_hms)
@@ -212,6 +216,7 @@ importFrom(lubridate,duration)
 importFrom(lubridate,floor_date)
 importFrom(lubridate,hours)
 importFrom(lubridate,is.Date)
+importFrom(lubridate,is.POSIXct)
 importFrom(lubridate,is.instant)
 importFrom(lubridate,minutes)
 importFrom(lubridate,rollback)
@@ -232,13 +237,15 @@ importFrom(purrr,map_if)
 importFrom(purrr,map_lgl)
 importFrom(purrr,modify_at)
 importFrom(purrr,modify_if)
+importFrom(purrr,pmap)
 importFrom(purrr,reduce)
 importFrom(purrr,transpose)
 importFrom(purrr,walk)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,abort)
 importFrom(rlang,arg_match)
+importFrom(rlang,as_data_mask)
 importFrom(rlang,as_function)
 importFrom(rlang,as_label)
 importFrom(rlang,as_name)
@@ -257,8 +264,10 @@ importFrom(rlang,exprs)
 importFrom(rlang,f_lhs)
 importFrom(rlang,f_rhs)
 importFrom(rlang,inform)
+importFrom(rlang,is_call)
 importFrom(rlang,is_expression)
 importFrom(rlang,is_missing)
+importFrom(rlang,list2)
 importFrom(rlang,new_formula)
 importFrom(rlang,parse_expr)
 importFrom(rlang,parse_exprs)
@@ -268,16 +277,20 @@ importFrom(rlang,syms)
 importFrom(rlang,type_of)
 importFrom(rlang,warn)
 importFrom(stringr,str_c)
+importFrom(stringr,str_count)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_glue)
 importFrom(stringr,str_length)
 importFrom(stringr,str_locate)
+importFrom(stringr,str_locate_all)
 importFrom(stringr,str_match)
 importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
+importFrom(stringr,str_split)
+importFrom(stringr,str_starts)
 importFrom(stringr,str_sub)
 importFrom(stringr,str_subset)
 importFrom(stringr,str_to_lower)
@@ -292,8 +305,10 @@ importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,all_of)
+importFrom(tidyselect,any_of)
 importFrom(tidyselect,contains)
 importFrom(tidyselect,matches)
 importFrom(tidyselect,vars_select)
 importFrom(utils,capture.output)
+importFrom(utils,file.edit)
 importFrom(utils,str)