diff --git a/.github/ISSUE_TEMPLATE/05_onboard.yml b/.github/ISSUE_TEMPLATE/05_onboard.yml deleted file mode 100644 index 9f6897a0..00000000 --- a/.github/ISSUE_TEMPLATE/05_onboard.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: Onboarding Tasks -description: Bringing a Core or non-Core member onto the admiral team [for admiral team only] -title: "Onboarding: " -labels: ["onboarding"] -assignees: - - octocat -body: - - type: markdown - attributes: - value: | - Welcome to the Team! We love contributors! - - type: checkboxes - id: core - attributes: - label: Onboarding tasks for Core (Roche-GSK) Team Members - description: - options: - - label: Given a tour of Github from a Core member - - label: Understand how to Create Issues and do a Pull Request - - label: Understand the Programming Strategy - - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiraldev/devel/articles/index.html) - - label: Invited to all relevant meetings - Stand Ups, Retrospective, Sprint Planning, Question/Comments, Backlog, Community Meeting - - label: Given access to Box and relevant documents - - label: Given write access to Github Repository - - label: Slack channel invites to admiral and admiralonco_dev - - label: Introduction to Teams ways of working - - type: checkboxes - id: non-core - attributes: - label: Onboarding tasks for non-Core Team Members - description: - options: - - label: Given a tour of Github from a Core member - - label: Understand how to Create Issues and do a Pull Request - - label: Understand the Programming Strategy - - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiraldev/devel/articles/index.html) - - label: Invited to all relevant meetings - Question/Comments, Community Meeting - - label: Given write access to Github Repository - - label: Slack channel invites to admiral - - label: Introduction to Teams ways of working diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 7564ba9d..e4d47349 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,13 +1,11 @@ -Please add "Closes #" to the title of the pull request. Then the -issue is closed automatically once it is merged to `main`. +Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html#detailed-development-process) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent. -Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent. - -Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `devel` branch until you have checked off each task. +Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `main` branch until you have checked off each task. +- [ ] Place Closes # into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update). Then the issue is closed automatically once it is merged to `main`. - [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files -- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html#writing-unit-tests-in-admiral) -- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html#deprecation)? +- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#writing-unit-tests-in-admiral) +- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)? - [ ] Update to all relevant roxygen headers and examples - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately - [ ] Address any updates needed for vignettes and/or templates diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index 8af3e029..e280e090 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -11,19 +11,17 @@ on: # 'push' events are triggered when commits # are pushed to one of these branches push: + tags: + - "v*" branches: - main - - devel - - pre-release - - test + - patch # 'pull_request' events are triggered when PRs are # created against one of these target branches. pull_request: branches: - main - - devel - - pre-release - - test + - patch # 'release' events are triggered when... # you guessed it - when releases are made. release: @@ -37,7 +35,7 @@ concurrency: env: R_VERSION: "4.1" - + jobs: get_r_version: name: Get R version @@ -86,19 +84,13 @@ jobs: docs: name: Documentation uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main - if: github.event_name == 'push' + if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/v') needs: get_r_version with: - r-version: "${{ needs.get_r_version.outputs.r-version }}" - # Whether to skip multiversion docs - # Note that if you have multiple versions of docs, - # your URL links are likely to break due to path changes - skip-multiversion-docs: false - latest-tag-alt-name: main - multiversion-docs-landing-page: main - branches-or-tags-to-list: >- - ^devel$|^main$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$ - + r-version: "4.3" + skip-multiversion-docs: true + secrets: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} linter: name: Lint uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main diff --git a/DESCRIPTION b/DESCRIPTION index e2fc77b5..980c7646 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -74,3 +74,4 @@ Suggests: DT VignetteBuilder: knitr Config/testthat/edition: 3 +Config/Needs/website: gert diff --git a/NAMESPACE b/NAMESPACE index 265b3115..4bdf6159 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -7,7 +7,6 @@ export(bor_non_crpd) export(bor_pd) export(bor_pr) export(bor_sd) -export(call_aval_fun) export(cb_y) export(cbor_cr) export(cbor_pr) diff --git a/NEWS.md b/NEWS.md index 94bb5da0..4228de27 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,33 @@ # admiralonco (development version) +## Updates of Existing Functions + +- The `bor_ne` event object was updated such that `CR` and `PR` are additionally +considered as event. This ensures that the confirmed best overall response for a +patient with a single `CR` or `PR` assessment is derived as `"NE"` instead of +`"MISSING"`. (#253) + +## Documentation + +- New vignette "Creating ADRS with iRECIST endpoints". (#233) + +- All vignettes and templates were updated to be in line with the changes in +`{admiral}` (see [Breaking +Changes](https://pharmaverse.github.io/admiral/news/index.html#breaking-changes-1-0-0) +for details)(#256). + +## Breaking Changes + +- The `derive_*()` functions were superseded in favor of +`derive_extreme_event()`. Any superseded functions can continue to be used as +demonstrated via the "Basic ADRS" vignette, as they will remain supported and +won't be deprecated in the near future. (#256) + +- The `filter_pd()` function was superseded in favor of `filter_relative()`. (#256) + +- The function `call_aval_fun()`, which was deprecated in admiralonco 0.4.0, +has been removed. (#256) + ## Various - Website now has button/links to Slack channel and GitHub Issues. (#262) diff --git a/R/check_crpr.R b/R/check_crpr.R index 931579be..45640ce8 100644 --- a/R/check_crpr.R +++ b/R/check_crpr.R @@ -61,21 +61,23 @@ signal_crpr <- function(dataset, crpr_data <- filter_joined( dataset, + dataset_add = dataset, by_vars = subject_keys, order = order, join_vars = exprs(AVALC), join_type = "after", - filter = AVALC == "CR" & AVALC.join == "PR" + filter_join = AVALC == "CR" & AVALC.join == "PR" ) if (nrow(crpr_data) > 0) { pr_data <- filter_joined( dataset, + dataset_add = dataset, by_vars = subject_keys, order = order, join_vars = exprs(AVALC), join_type = "before", - filter = AVALC == "PR" & AVALC.join == "CR" + filter_join = AVALC == "PR" & AVALC.join == "CR" ) crpr_data <- bind_rows(crpr_data, pr_data) %>% diff --git a/R/derive_param_bor.R b/R/derive_param_bor.R index 9932aefc..10911356 100644 --- a/R/derive_param_bor.R +++ b/R/derive_param_bor.R @@ -1,5 +1,9 @@ #' Adds a Parameter for Best Overall Response (without confirmation) #' +#' @description +#' `r lifecycle::badge("superseded")` The `derive_param_bor()` function has been +#' superseded in favor of `derive_extreme_event()`. +#' #' Adds a parameter for best overall response, without confirmation, optionally up to #' first progressive disease #' @@ -252,9 +256,8 @@ #' #' @author Stephen Gormley #' -#' @family der_prm_adrs -#' -#' @keywords der_prm_adrs +#' @family superseded +#' @keywords superseded #' #' @return The dataframe passed in the `dataset` argument with additional columns and/or #' rows as set in the `set_values_to` argument. diff --git a/R/derive_param_clinbenefit.R b/R/derive_param_clinbenefit.R index 96af16f9..b67d8e6b 100644 --- a/R/derive_param_clinbenefit.R +++ b/R/derive_param_clinbenefit.R @@ -1,5 +1,9 @@ #' Adds a Parameter for Clinical Benefit #' +#' @description +#' `r lifecycle::badge("superseded")` The `derive_param_clinbenefit()` function +#' has been superseded in favor of `derive_extreme_event()`. +#' #' Adds a parameter for clinical benefit/disease control #' #' @details @@ -114,9 +118,8 @@ #' #' @return The input dataset with a new parameter for clinical benefit #' -#' @family der_prm_adrs -#' -#' @keywords der_prm_adrs +#' @family superseded +#' @keywords superseded #' #' @export #' diff --git a/R/derive_param_confirmed_bor.R b/R/derive_param_confirmed_bor.R index 595d9780..bf1af99a 100644 --- a/R/derive_param_confirmed_bor.R +++ b/R/derive_param_confirmed_bor.R @@ -1,5 +1,9 @@ #' Adds a Parameter for Confirmed Best Overall Response #' +#' @description +#' `r lifecycle::badge("superseded")` The `derive_param_confirmed_bor()` +#' function has been superseded in favor of `derive_extreme_event()`. +#' #' Adds a parameter for confirmed best overall response (BOR) #' #' @param dataset Input dataset @@ -187,9 +191,8 @@ #' @return The input dataset with a new parameter for confirmed best overall #' response #' -#' @family der_prm_adrs -#' -#' @keywords der_prm_adrs +#' @family superseded +#' @keywords superseded #' #' @author Stefan Bundfuss #' @@ -410,15 +413,16 @@ derive_param_confirmed_bor <- function(dataset, # Create observations for potential responses cr_data <- filter_joined( source_data, + dataset_add = source_data, by_vars = subject_keys, join_vars = exprs(AVALC, ADT), join_type = "after", order = exprs(ADT), - first_cond = AVALC.join == "CR" & + first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + days(!!ref_confirm), - filter = AVALC == "CR" & + filter_join = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & - count_vals(var = AVALC.join, val = "NE") <= !!max_nr_ne + {{ count_vals }}(var = AVALC.join, val = "NE") <= !!max_nr_ne ) %>% mutate(tmp_order = 1) @@ -429,23 +433,24 @@ derive_param_confirmed_bor <- function(dataset, } pr_data <- filter_joined( source_data, + dataset_add = source_data, by_vars = subject_keys, join_vars = exprs(AVALC, ADT), join_type = "after", order = exprs(ADT), - first_cond = AVALC.join %in% c("CR", "PR") & + first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + days(!!ref_confirm), - filter = AVALC == "PR" & + filter_join = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "SD", "NE")) & - count_vals(var = AVALC.join, val = "NE") <= !!max_nr_ne & - count_vals(var = AVALC.join, val = "SD") <= !!max_nr_sd & + {{ count_vals }}(var = AVALC.join, val = "NE") <= !!max_nr_ne & + {{ count_vals }}(var = AVALC.join, val = "SD") <= !!max_nr_sd & ( - min_cond( + {{ min_cond }}( var = ADT.join, cond = AVALC.join == "CR" - ) > max_cond(var = ADT.join, cond = AVALC.join == "PR") | - count_vals(var = AVALC.join, val = "CR") == 0 | - count_vals(var = AVALC.join, val = "PR") == 0 + ) > {{ max_cond }}(var = ADT.join, cond = AVALC.join == "PR") | + {{ count_vals }}(var = AVALC.join, val = "CR") == 0 | + {{ count_vals }}(var = AVALC.join, val = "PR") == 0 ) ) %>% mutate(tmp_order = 2) diff --git a/R/derive_param_confirmed_resp.R b/R/derive_param_confirmed_resp.R index deb38621..26c0b6ee 100644 --- a/R/derive_param_confirmed_resp.R +++ b/R/derive_param_confirmed_resp.R @@ -1,5 +1,9 @@ #' Adds a Parameter for Confirmed Response #' +#' @description +#' `r lifecycle::badge("superseded")` The `derive_param_confirmed_resp()` +#' function has been superseded in favor of `derive_extreme_event()`. +#' #' Adds a parameter for confirmed response #' #' @param dataset Input dataset @@ -135,9 +139,8 @@ #' #' @return The input dataset with a new parameter for confirmed response #' -#' @family der_prm_adrs -#' -#' @keywords der_prm_adrs +#' @family superseded +#' @keywords superseded #' #' @author Stefan Bundfuss #' @@ -342,15 +345,16 @@ derive_param_confirmed_resp <- function(dataset, # Create observations for potential responses cr_data <- filter_joined( source_data, + dataset_add = source_data, by_vars = subject_keys, join_vars = exprs(AVALC, ADT), join_type = "after", order = exprs(ADT), - first_cond = AVALC.join == "CR" & + first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + days(!!ref_confirm), - filter = AVALC == "CR" & + filter_join = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & - count_vals(var = AVALC.join, val = "NE") <= !!max_nr_ne + {{ count_vals }}(var = AVALC.join, val = "NE") <= !!max_nr_ne ) %>% mutate( AVALC = "Y" @@ -363,23 +367,24 @@ derive_param_confirmed_resp <- function(dataset, } pr_data <- filter_joined( source_data, + dataset_add = source_data, by_vars = subject_keys, join_vars = exprs(AVALC, ADT), join_type = "after", order = exprs(ADT), - first_cond = AVALC.join %in% c("CR", "PR") & + first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + days(!!ref_confirm), - filter = AVALC == "PR" & + filter_join = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "SD", "NE")) & - count_vals(var = AVALC.join, val = "NE") <= !!max_nr_ne & - count_vals(var = AVALC.join, val = "SD") <= !!max_nr_sd & + {{ count_vals }}(var = AVALC.join, val = "NE") <= !!max_nr_ne & + {{ count_vals }}(var = AVALC.join, val = "SD") <= !!max_nr_sd & ( - min_cond( + {{ min_cond }}( var = ADT.join, cond = AVALC.join == "CR" - ) > max_cond(var = ADT.join, cond = AVALC.join == "PR") | - count_vals(var = AVALC.join, val = "CR") == 0 | - count_vals(var = AVALC.join, val = "PR") == 0 + ) > {{ max_cond }}(var = ADT.join, cond = AVALC.join == "PR") | + {{ count_vals }}(var = AVALC.join, val = "CR") == 0 | + {{ count_vals }}(var = AVALC.join, val = "PR") == 0 ) ) %>% mutate( diff --git a/R/derive_param_response.R b/R/derive_param_response.R index e5fe61b1..0cd7eeda 100644 --- a/R/derive_param_response.R +++ b/R/derive_param_response.R @@ -1,6 +1,10 @@ #' Adds a Parameter Indicating If a Subject Had a Response before Progressive #' Disease #' +#' @description +#' `r lifecycle::badge("superseded")` The `derive_param_response()` function has +#' been superseded in favor of `derive_extreme_event()`. +#' #' Adds a parameter indicating if a response has been observed. #' If a response has been observed, `AVALC` is set to "Y", `AVAL` to 1 and `ADT` #' is set to the @@ -104,9 +108,8 @@ #' @return The input dataset with a new parameter indicating if and when a #' response occurred #' -#' @family der_prm_adrs -#' -#' @keywords der_prm_adrs +#' @family superseded +#' @keywords superseded #' #' @export #' diff --git a/R/filter_pd.R b/R/filter_pd.R index 4a39c479..c788b4b0 100644 --- a/R/filter_pd.R +++ b/R/filter_pd.R @@ -1,5 +1,9 @@ #' Filter up to First PD (Progressive Disease) Date #' +#' @description +#' `r lifecycle::badge("superseded")` The `filter_pd()` function has been +#' superseded in favor of `filter_relative()`. +#' #' Filter a dataset to only include the source parameter records up to and #' including the first PD (progressive disease). These records are passed to #' downstream derivations regarding responses such as BOR (best overall @@ -45,8 +49,8 @@ #' #' @export #' -#' @keywords utils_fil -#' @family utils_fil +#' @family superseded +#' @keywords superseded #' #' @examples #' diff --git a/R/response_sources.R b/R/response_sources.R index bae3005e..f2fc4c9b 100644 --- a/R/response_sources.R +++ b/R/response_sources.R @@ -136,11 +136,11 @@ bor_pd <- event( #' @export bor_ne <- event( description = paste( - "Define not evaluable (NE) for best overall response (BOR) as SD, NON-CR/NON-PD,", - "or NE (should be specified after bor_sd and bor_non_crpd)" + "Define not evaluable (NE) for best overall response (BOR) as CR, PR, SD,", + "NON-CR/NON-PD, or NE (should be specified after bor_sd and bor_non_crpd)" ), dataset_name = "ovr", - condition = AVALC %in% c("SD", "NON-CR/NON-PD", "NE"), + condition = AVALC %in% c("CR", "PR", "SD", "NON-CR/NON-PD", "NE"), set_values_to = exprs(AVALC = "NE") ) @@ -172,7 +172,7 @@ crsp_y_cr <- event_joined( join_vars = exprs(AVALC, ADT), join_type = "after", order = exprs(ADT), - first_cond = AVALC.join == "CR" & + first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + days(28), condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & @@ -193,7 +193,7 @@ crsp_y_pr <- event_joined( join_vars = exprs(AVALC, ADT), join_type = "after", order = exprs(ADT), - first_cond = AVALC.join %in% c("CR", "PR") & + first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + days(28), condition = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & @@ -221,7 +221,7 @@ cbor_cr <- event_joined( dataset_name = "ovr", join_vars = exprs(AVALC, ADT), join_type = "after", - first_cond = AVALC.join == "CR" & + first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + 28, condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & @@ -242,7 +242,7 @@ cbor_pr <- event_joined( dataset_name = "ovr", join_vars = exprs(AVALC, ADT), join_type = "after", - first_cond = AVALC.join %in% c("CR", "PR") & + first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + 28, condition = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & diff --git a/R/utils.R b/R/utils.R deleted file mode 100644 index 5d73cb01..00000000 --- a/R/utils.R +++ /dev/null @@ -1,58 +0,0 @@ -#' Creates `AVAL` from `AVALC` by Calling User Function -#' -#' @description -#' `r lifecycle::badge("deprecated")` -#' -#' This function is *deprecated*, please use -#' `admiraldev::process_set_values_to()` instead. -#' -#' Create `AVAL` from `AVALC` by calling a function provided by the user. If -#' calling the function fails, the error is caught and a helpful error message -#' provided. -#' -#' @param dataset Input dataset -#' -#' The variable `AVALC` is expected. -#' -#' *Permitted Values*: a dataframe -#' -#' @param aval_fun Function returning the `AVALC` values -#' -#' The specified function must expect one argument expecting a character -#' vector and must return a numeric vector. -#' -#' *Permitted Values*: a function -#' -#' @details The new variable `AVAL` is set to `aval_fun(AVALC)`. -#' -#' @author Stefan Bundfuss -#' -#' @returns The input dataset with `AVAL` added -#' -#' @keywords deprecated -#' @family deprecated -#' -#' @export -call_aval_fun <- function(dataset, - aval_fun) { - assert_data_frame(dataset, required_vars = exprs(AVALC)) - assert_function(aval_fun) - - deprecate_warn("0.4.0", "call_aval_fun()", "admiraldev::process_set_values_to()") - - tryCatch( - mutate( - dataset, - AVAL = aval_fun(AVALC) - ), - error = function(cnd) { - abort( - paste0( - "Assigning new AVAL records with aval_fun (`AVAL = aval_fun(AVALC)`) has failed.\n", - "Error message:\n ", - cnd - ) - ) - } - ) -} diff --git a/README.Rmd b/README.Rmd index 9d952987..59c3ecf3 100644 --- a/README.Rmd +++ b/README.Rmd @@ -4,39 +4,7 @@ output: md_document date: '2022-10-04' --- -```{r setup, include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -link <- function(text, url) { - return( - paste0( - "[", text, "]", - "(", url, ")" - ) - ) -} -dyn_link <- function(text, - base_url, - relative_url = "", - # Change to TRUE when admiral adopts multiversion docs - is_multiversion = TRUE, - multiversion_default_ref = "main") { - url <- paste(base_url, relative_url, sep = "/") - if (is_multiversion) { - url <- paste( - base_url, - Sys.getenv("BRANCH_NAME", multiversion_default_ref), - relative_url, - sep = "/" - ) - } - return(link(text, url)) -} -# Other variables -admiral_homepage <- "https://pharmaverse.github.io/admiral" -``` - - # admiralonco diff --git a/README.md b/README.md index 289c1725..027bd8a2 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,4 @@ - # admiralonco diff --git a/_pkgdown.yml b/_pkgdown.yml index 2ec516ae..4a6b60fa 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -14,17 +14,14 @@ repo: user: https://github.com/ news: cran_dates: true -reference: - - title: Derivations for Adding Parameters - - subtitle: ADRS-specific - desc: Parameter Derivation Functions helpful for building the ADRS dataset - - contents: - - has_keyword("der_prm_adrs") +development: + mode: auto + +reference: - - title: Advanced Functions - - subtitle: Pre-Defined Objects - desc: 'Objects defined by {admiralonco} that can be used as input for derivations' + - title: Pre-Defined Objects + desc: 'Objects defined by `{admiralonco}` that can be used as input for derivations' - contents: - has_keyword("source_specifications") @@ -37,27 +34,25 @@ reference: - contents: - has_keyword('utils_ds_chk') - - subtitle: Utilities for Filtering Observations - - contents: - - has_keyword('utils_fil') - - title: Example Datasets desc: You can run `admiral::use_ad_template()` to produce additional datasets - contents: - has_keyword('datasets') - - title: Relocated/Deprecated - - subtitle: Functions moved to another admiraldev package - - contents: - - has_keyword("move_adm_dev") - - subtitle: Deprecated - - contents: - - has_keyword("deprecated") + - title: Superseded + desc: | + Superseded functions have been replaced with more flexible functions that + allow for construction of more diverse endpoints for a wider array of + oncology indications, beyond solid tumor/RECIST. However, we will not be + removing these functions from `{admiralonco}` in the near future and they + will continue to be supported. + contents: + - has_keyword("superseded") navbar: structure: left: [getstarted, reference, articles, news] - right: [search, slack, newissue, github] + right: [search, slack, history, newissue, github] components: getstarted: text: Get Started @@ -72,12 +67,18 @@ navbar: href: articles/adrs_basic.html - text: Creating ADRS (Including Non-standard Endpoints) href: articles/adrs.html + - text: Creating ADRS with iRECIST endpoints + href: articles/irecist.html - text: Creating ADTTE href: articles/adtte.html - text: Creating ADTR href: articles/adtr.html - text: Creating and Using New Anti-Cancer Start Date href: articles/nactdt.html + history: + icon: fa-history + href: articles/website-versions.html + aria-label: Previous Release Websites slack: icon: fa-slack href: https://app.slack.com/client/T028PB489D3/C02M8KN8269 diff --git a/inst/WORDLIST b/inst/WORDLIST index 20951a07..3bc9f86a 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -4,6 +4,7 @@ ADTR ADTTE ADaM ADaMs +BDS BICR BOR Biologics @@ -11,7 +12,12 @@ CDISC CRF GlaxoSmithKline Hoffmann +IBCP +ICBCP +ILSTA +IMDIS IMWG +IOVRB IRF LLC Myeloma @@ -20,22 +26,19 @@ Pre RECIST SDTM SDTMs -adrs censorings chk datetime -der ds durations evaluable -fil fmt funder +iCPD iRECIST myeloma pharmaverse pre -prm quosures radiological rda diff --git a/inst/templates/ad_adrs.R b/inst/templates/ad_adrs.R index e2c2f3a2..22449cd5 100644 --- a/inst/templates/ad_adrs.R +++ b/inst/templates/ad_adrs.R @@ -6,6 +6,9 @@ library(admiral) library(admiralonco) library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project +# pharmaverseadam contains example datasets generated from the CDISC pilot +# project SDTM ran through admiral templates +library(pharmaverseadam) library(dplyr) library(lubridate) library(stringr) @@ -16,11 +19,10 @@ library(stringr) # as needed and assign to the variables below. # For illustration purposes read in pharmaverse test data -data("admiral_adsl") +data("adsl") data("rs_onco_recist") data("tu_onco_recist") -adsl <- admiral_adsl rs <- rs_onco_recist tu <- tu_onco_recist @@ -51,7 +53,7 @@ adrs <- adrs %>% PARAM = "Overall Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1" + PARCAT3 = "RECIST 1.1" ) # Date imputations - here we impute missing day to last possible date @@ -75,12 +77,24 @@ adrs <- adrs %>% # parameter derivations - here only valid assessments and those occurring on or # after randomization date, if there is more than one assessment per date the # worst one is flagged +worst_resp <- function(arg) { + case_when( + arg == "NE" ~ 1, + arg == "CR" ~ 2, + arg == "PR" ~ 3, + arg == "SD" ~ 4, + arg == "NON-CR/NON-PD" ~ 5, + arg == "PD" ~ 6, + TRUE ~ 0 + ) +} + adrs <- adrs %>% restrict_derivation( derivation = derive_var_extreme_flag, args = params( by_vars = exprs(STUDYID, USUBJID, ADT), - order = exprs(AVAL, RSSEQ), + order = exprs(worst_resp(AVALC), RSSEQ), new_var = ANL01FL, mode = "last" ), @@ -134,12 +148,13 @@ adrs <- adrs %>% order = exprs(ADT, RSSEQ), mode = "first", exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "PD", PARAM = "Disease Progression by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -149,7 +164,8 @@ adrs <- adrs %>% adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(ADT), + order = exprs(event_nr, ADT), + tmp_event_nr_var = event_nr, mode = "first", events = list(rsp_y, no_data_n), source_datasets = list( @@ -161,7 +177,7 @@ adrs <- adrs %>% PARAM = "Response by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -171,20 +187,20 @@ adrs <- adrs %>% adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(desc(AVALC), ADT), + order = exprs(desc(AVALC), ADT, event_nr), + tmp_event_nr_var = event_nr, mode = "first", events = list(rsp_y, cb_y, no_data_n), source_datasets = list( ovr = ovr, adsl = adsl ), - ignore_event_order = TRUE, set_values_to = exprs( PARAMCD = "CB", PARAM = "Clinical Benefit by Investigator (confirmation for response not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ), @@ -199,7 +215,8 @@ adrs <- adrs %>% adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(ADT), + order = exprs(event_nr, ADT), + tmp_event_nr_var = event_nr, mode = "first", source_datasets = list( ovr = ovr, @@ -211,7 +228,7 @@ adrs <- adrs %>% PARAM = "Best Overall Response by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -225,12 +242,13 @@ adrs <- adrs %>% by_vars = exprs(STUDYID, USUBJID), filter_add = PARAMCD == "BOR" & AVALC %in% c("CR", "PR"), exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "BCP", PARAM = "Best Overall Response of CR/PR by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -240,20 +258,20 @@ adrs <- adrs %>% adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(desc(AVALC), ADT), + order = exprs(desc(AVALC), ADT, event_nr), + tmp_event_nr_var = event_nr, mode = "first", source_datasets = list( ovr = ovr, adsl = adsl ), events = list(crsp_y_cr, crsp_y_pr, no_data_n), - ignore_event_order = TRUE, set_values_to = exprs( PARAMCD = "CRSP", PARAM = "Confirmed Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -262,30 +280,30 @@ adrs <- adrs %>% adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(desc(AVALC), ADT), + order = exprs(desc(AVALC), ADT, event_nr), + tmp_event_nr_var = event_nr, mode = "first", events = list(crsp_y_cr, crsp_y_pr, cb_y, no_data_n), source_datasets = list( ovr = ovr, adsl = adsl ), - ignore_event_order = TRUE, set_values_to = exprs( PARAMCD = "CCB", PARAM = "Confirmed Clinical Benefit by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" - ), - check_type = "none" + ) ) adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(ADT), + order = exprs(event_nr, ADT), + tmp_event_nr_var = event_nr, mode = "first", events = list(cbor_cr, cbor_pr, bor_sd, bor_non_crpd, bor_pd, bor_ne, no_data_missing), source_datasets = list( @@ -297,7 +315,7 @@ adrs <- adrs %>% PARAM = "Best Confirmed Overall Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -308,12 +326,13 @@ adrs <- adrs %>% by_vars = exprs(STUDYID, USUBJID), filter_add = PARAMCD == "CBOR" & AVALC %in% c("CR", "PR"), exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "CBCP", PARAM = "Best Confirmed Overall Response of CR/PR by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -330,6 +349,7 @@ adrs <- adrs %>% by_vars = exprs(STUDYID, USUBJID), filter_add = !is.na(DTHDT), exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "DEATH", PARAM = "Death", @@ -355,7 +375,7 @@ adrs <- adrs %>% PARAM = "Last Disease Assessment by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", ANL01FL = "Y" ) ) @@ -375,7 +395,7 @@ adrs <- adrs %>% PARAMCD = "MDIS", PARAM = "Measurable Disease at Baseline by Investigator", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) diff --git a/inst/templates/ad_adrs_basic.R b/inst/templates/ad_adrs_basic.R index 87eb1b6b..387ff120 100644 --- a/inst/templates/ad_adrs_basic.R +++ b/inst/templates/ad_adrs_basic.R @@ -14,6 +14,9 @@ library(admiral) library(admiralonco) library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project +# pharmaverseadam contains example datasets generated from the CDISC pilot +# project SDTM ran through admiral templates +library(pharmaverseadam) library(dplyr) library(lubridate) library(stringr) @@ -24,11 +27,10 @@ library(stringr) # as needed and assign to the variables below. # For illustration purposes read in pharmaverse test data -data("admiral_adsl") +data("adsl") data("rs_onco_recist") data("tu_onco_recist") -adsl <- admiral_adsl rs <- rs_onco_recist tu <- tu_onco_recist @@ -59,7 +61,7 @@ adrs <- adrs %>% PARAM = "Overall Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1" + PARCAT3 = "RECIST 1.1" ) # Date imputations - here we impute missing day to last possible date @@ -83,12 +85,24 @@ adrs <- adrs %>% # parameter derivations - here only valid assessments and those occurring on or # after randomization date, if there is more than one assessment per date the # worst one is flagged +worst_resp <- function(arg) { + case_when( + arg == "NE" ~ 1, + arg == "CR" ~ 2, + arg == "PR" ~ 3, + arg == "SD" ~ 4, + arg == "NON-CR/NON-PD" ~ 5, + arg == "PD" ~ 6, + TRUE ~ 0 + ) +} + adrs <- adrs %>% restrict_derivation( derivation = derive_var_extreme_flag, args = params( by_vars = exprs(STUDYID, USUBJID, ADT), - order = exprs(AVAL, RSSEQ), + order = exprs(worst_resp(AVALC), RSSEQ), new_var = ANL01FL, mode = "last" ), @@ -107,12 +121,13 @@ adrs <- adrs %>% order = exprs(ADT, RSSEQ), mode = "first", exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "PD", PARAM = "Disease Progression by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -137,7 +152,7 @@ adrs <- adrs %>% PARAM = "Response by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -165,7 +180,7 @@ adrs <- adrs %>% PARAM = "Clinical Benefit by Investigator (confirmation for response not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -185,7 +200,7 @@ adrs <- adrs %>% PARAM = "Best Overall Response by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -201,12 +216,13 @@ adrs <- adrs %>% order = exprs(ADT, RSSEQ), mode = "first", exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "BCP", PARAM = "Best Overall Response of CR/PR by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -225,7 +241,7 @@ adrs <- adrs %>% PARAM = "Confirmed Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -251,7 +267,7 @@ adrs <- adrs %>% PARAM = "Confirmed Clinical Benefit by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -269,7 +285,7 @@ adrs <- adrs %>% PARAM = "Best Confirmed Overall Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -282,12 +298,13 @@ adrs <- adrs %>% order = exprs(ADT, RSSEQ), mode = "first", exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "CBCP", PARAM = "Best Confirmed Overall Response of CR/PR by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -304,6 +321,7 @@ adrs <- adrs %>% by_vars = exprs(STUDYID, USUBJID), filter_add = !is.na(DTHDT), exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "DEATH", PARAM = "Death", @@ -329,7 +347,7 @@ adrs <- adrs %>% PARAM = "Last Disease Assessment by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", ANL01FL = "Y" ) ) @@ -349,7 +367,7 @@ adrs <- adrs %>% PARAMCD = "MDIS", PARAM = "Measurable Disease at Baseline by Investigator", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) diff --git a/inst/templates/ad_adtr.R b/inst/templates/ad_adtr.R index 72668964..f3df56e6 100644 --- a/inst/templates/ad_adtr.R +++ b/inst/templates/ad_adtr.R @@ -6,6 +6,9 @@ library(admiral) library(admiralonco) library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project +# pharmaverseadam contains example datasets generated from the CDISC pilot +# project SDTM ran through admiral templates +library(pharmaverseadam) library(dplyr) library(lubridate) library(stringr) @@ -15,11 +18,10 @@ library(stringr) # Use e.g. haven::read_sas to read in .sas7bdat, or other suitable functions # as needed and assign to the variables below. # For illustration purposes read in pharmaverse test data -data("admiral_adsl") +data("adsl") data("rs_onco_recist") data("tu_onco_recist") data("tr_onco_recist") -adsl <- admiral_adsl tu <- tu_onco_recist tr <- tr_onco_recist rs <- rs_onco_recist @@ -107,26 +109,27 @@ adtr <- bind_rows( mutate( PARCAT1 = "Target Lesion(s)", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = TRSTRESN, ANL01FL = if_else(!is.na(AVAL), "Y", NA_character_) ) %>% select(-tmp_lesion_nr) # Derive parameter for sum of diameter (SDIAM) ---- -adtr_sum <- get_summary_records( - adtr, +adtr_sum <- derive_summary_records( + dataset_add = adtr, by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, AVISIT, AVISITN), - filter = (str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | + filter_add = (str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL"), - analysis_var = AVAL, - summary_fun = function(x) sum(x, na.rm = TRUE), set_values_to = exprs( + AVAL = sum(AVAL, na.rm = TRUE), + ADY = min(ADY, na.rm = TRUE), + ADT = min(ADT, na.rm = TRUE), PARAMCD = "SDIAM", PARAM = "Target Lesions Sum of Diameters by Investigator", PARCAT1 = "Target Lesion(s)", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1" + PARCAT3 = "RECIST 1.1" ) ) @@ -138,44 +141,19 @@ adtr_sum <- adtr_sum %>% filter_add = AVISIT == "BASELINE" & ((str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL")), - new_var = LSEXP, - analysis_var = TRLNKID, - summary_fun = function(x) paste(sort(x), collapse = ", ") + new_vars = exprs(LSEXP = paste(sort(TRLNKID), collapse = ", ")) ) %>% derive_var_merged_summary( dataset_add = adtr, by_vars = exprs(USUBJID, AVISIT), filter_add = ((str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL")) & ANL01FL == "Y", - new_var = LSASS, - analysis_var = TRLNKID, - summary_fun = function(x) paste(sort(x), collapse = ", ") + new_vars = exprs(LSASS = paste(sort(TRLNKID), collapse = ", ")) ) %>% mutate( ANL01FL = if_else(LSEXP == LSASS, "Y", NA_character_) ) -# Derive timing variables for sums (ADT, ADY) ---- -adtr_sum <- adtr_sum %>% - derive_var_merged_summary( - dataset_add = adtr, - by_vars = exprs(USUBJID, AVISIT), - filter_add = (str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | - (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL"), - new_var = ADY, - analysis_var = ADY, - summary_fun = function(x) min(x, na.rm = TRUE) - ) %>% - derive_var_merged_summary( - dataset_add = adtr, - by_vars = exprs(USUBJID, AVISIT), - filter_add = (str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | - (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL"), - new_var = ADT, - analysis_var = ADT, - summary_fun = function(x) min(x, na.rm = TRUE) - ) - # Derive baseline (ABLFL, BASE) ---- adtr_sum <- adtr_sum %>% restrict_derivation( @@ -200,6 +178,7 @@ adtr_sum <- adtr_sum %>% order = exprs(AVAL), new_vars = exprs(NADIR = AVAL), join_vars = exprs(ADY), + join_type = "all", filter_add = ANL01FL == "Y", filter_join = ADY.join < ADY, mode = "first", diff --git a/inst/templates/ad_adtte.R b/inst/templates/ad_adtte.R index 04e1a6c1..0b20b0ad 100644 --- a/inst/templates/ad_adtte.R +++ b/inst/templates/ad_adtte.R @@ -5,6 +5,9 @@ # Input: adsl, adrs, tte_source objects library(admiral) library(admiralonco) +# pharmaverseadam contains example datasets generated from the CDISC pilot +# project SDTM ran through admiral templates +library(pharmaverseadam) library(dplyr) library(lubridate) @@ -14,11 +17,10 @@ library(lubridate) # as needed and assign to the variables below. # For illustration purposes read in admiral test data -data("admiral_adsl") -data("admiral_adrs") +data("adsl") +data("adrs_onco") -adsl <- admiral_adsl -adrs <- admiral_adrs +adrs <- adrs_onco # Derivations ---- diff --git a/man/call_aval_fun.Rd b/man/call_aval_fun.Rd deleted file mode 100644 index d0c2f761..00000000 --- a/man/call_aval_fun.Rd +++ /dev/null @@ -1,43 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R -\name{call_aval_fun} -\alias{call_aval_fun} -\title{Creates \code{AVAL} from \code{AVALC} by Calling User Function} -\usage{ -call_aval_fun(dataset, aval_fun) -} -\arguments{ -\item{dataset}{Input dataset - -The variable \code{AVALC} is expected. - -\emph{Permitted Values}: a dataframe} - -\item{aval_fun}{Function returning the \code{AVALC} values - -The specified function must expect one argument expecting a character -vector and must return a numeric vector. - -\emph{Permitted Values}: a function} -} -\value{ -The input dataset with \code{AVAL} added -} -\description{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -This function is \emph{deprecated}, please use -\code{admiraldev::process_set_values_to()} instead. - -Create \code{AVAL} from \code{AVALC} by calling a function provided by the user. If -calling the function fails, the error is caught and a helpful error message -provided. -} -\details{ -The new variable \code{AVAL} is set to \code{aval_fun(AVALC)}. -} -\author{ -Stefan Bundfuss -} -\concept{deprecated} -\keyword{deprecated} diff --git a/man/derive_param_bor.Rd b/man/derive_param_bor.Rd index 73f36043..986d665e 100644 --- a/man/derive_param_bor.Rd +++ b/man/derive_param_bor.Rd @@ -119,6 +119,9 @@ The dataframe passed in the \code{dataset} argument with additional columns and/ rows as set in the \code{set_values_to} argument. } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} The \code{derive_param_bor()} function has been +superseded in favor of \code{derive_extreme_event()}. + Adds a parameter for best overall response, without confirmation, optionally up to first progressive disease } @@ -270,14 +273,15 @@ derive_param_bor( filter(PARAMCD == "BOR") } \seealso{ -ADRS Functions for adding Parameters: +Other superseded: \code{\link{derive_param_clinbenefit}()}, \code{\link{derive_param_confirmed_bor}()}, \code{\link{derive_param_confirmed_resp}()}, -\code{\link{derive_param_response}()} +\code{\link{derive_param_response}()}, +\code{\link{filter_pd}()} } \author{ Stephen Gormley } -\concept{der_prm_adrs} -\keyword{der_prm_adrs} +\concept{superseded} +\keyword{superseded} diff --git a/man/derive_param_clinbenefit.Rd b/man/derive_param_clinbenefit.Rd index 030a79d1..be7b0884 100644 --- a/man/derive_param_clinbenefit.Rd +++ b/man/derive_param_clinbenefit.Rd @@ -80,6 +80,9 @@ used to uniquely identify subjects.} The input dataset with a new parameter for clinical benefit } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} The \code{derive_param_clinbenefit()} function +has been superseded in favor of \code{derive_extreme_event()}. + Adds a parameter for clinical benefit/disease control } \details{ @@ -206,14 +209,15 @@ derive_param_clinbenefit( filter(PARAMCD == "CBR") } \seealso{ -ADRS Functions for adding Parameters: +Other superseded: \code{\link{derive_param_bor}()}, \code{\link{derive_param_confirmed_bor}()}, \code{\link{derive_param_confirmed_resp}()}, -\code{\link{derive_param_response}()} +\code{\link{derive_param_response}()}, +\code{\link{filter_pd}()} } \author{ Andrew Smith } -\concept{der_prm_adrs} -\keyword{der_prm_adrs} +\concept{superseded} +\keyword{superseded} diff --git a/man/derive_param_confirmed_bor.Rd b/man/derive_param_confirmed_bor.Rd index 7c375b8e..b9b6f5b4 100644 --- a/man/derive_param_confirmed_bor.Rd +++ b/man/derive_param_confirmed_bor.Rd @@ -132,6 +132,9 @@ The input dataset with a new parameter for confirmed best overall response } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} The \code{derive_param_confirmed_bor()} +function has been superseded in favor of \code{derive_extreme_event()}. + Adds a parameter for confirmed best overall response (BOR) } \details{ @@ -334,14 +337,15 @@ derive_param_confirmed_bor( filter(PARAMCD == "CBOR") } \seealso{ -ADRS Functions for adding Parameters: +Other superseded: \code{\link{derive_param_bor}()}, \code{\link{derive_param_clinbenefit}()}, \code{\link{derive_param_confirmed_resp}()}, -\code{\link{derive_param_response}()} +\code{\link{derive_param_response}()}, +\code{\link{filter_pd}()} } \author{ Stefan Bundfuss } -\concept{der_prm_adrs} -\keyword{der_prm_adrs} +\concept{superseded} +\keyword{superseded} diff --git a/man/derive_param_confirmed_resp.Rd b/man/derive_param_confirmed_resp.Rd index 55ff439a..313b9dfc 100644 --- a/man/derive_param_confirmed_resp.Rd +++ b/man/derive_param_confirmed_resp.Rd @@ -104,6 +104,9 @@ A list of symbols created using \code{exprs()} is expected.} The input dataset with a new parameter for confirmed response } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} The \code{derive_param_confirmed_resp()} +function has been superseded in favor of \code{derive_extreme_event()}. + Adds a parameter for confirmed response } \details{ @@ -268,14 +271,15 @@ derive_param_confirmed_resp( filter(PARAMCD == "CRSP") } \seealso{ -ADRS Functions for adding Parameters: +Other superseded: \code{\link{derive_param_bor}()}, \code{\link{derive_param_clinbenefit}()}, \code{\link{derive_param_confirmed_bor}()}, -\code{\link{derive_param_response}()} +\code{\link{derive_param_response}()}, +\code{\link{filter_pd}()} } \author{ Stefan Bundfuss } -\concept{der_prm_adrs} -\keyword{der_prm_adrs} +\concept{superseded} +\keyword{superseded} diff --git a/man/derive_param_response.Rd b/man/derive_param_response.Rd index 3ee56c42..c51e628a 100644 --- a/man/derive_param_response.Rd +++ b/man/derive_param_response.Rd @@ -88,6 +88,9 @@ The input dataset with a new parameter indicating if and when a response occurred } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} The \code{derive_param_response()} function has +been superseded in favor of \code{derive_extreme_event()}. + Adds a parameter indicating if a response has been observed. If a response has been observed, \code{AVALC} is set to "Y", \code{AVAL} to 1 and \code{ADT} is set to the @@ -179,14 +182,15 @@ derive_param_response( arrange(USUBJID, PARAMCD, ADT) } \seealso{ -ADRS Functions for adding Parameters: +Other superseded: \code{\link{derive_param_bor}()}, \code{\link{derive_param_clinbenefit}()}, \code{\link{derive_param_confirmed_bor}()}, -\code{\link{derive_param_confirmed_resp}()} +\code{\link{derive_param_confirmed_resp}()}, +\code{\link{filter_pd}()} } \author{ Samia Kabi } -\concept{der_prm_adrs} -\keyword{der_prm_adrs} +\concept{superseded} +\keyword{superseded} diff --git a/man/filter_pd.Rd b/man/filter_pd.Rd index 01584822..3f2e147d 100644 --- a/man/filter_pd.Rd +++ b/man/filter_pd.Rd @@ -38,6 +38,9 @@ A list of symbols created using \code{exprs()} is expected.} A subset of the input dataset } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} The \code{filter_pd()} function has been +superseded in favor of \code{filter_relative()}. + Filter a dataset to only include the source parameter records up to and including the first PD (progressive disease). These records are passed to downstream derivations regarding responses such as BOR (best overall @@ -187,8 +190,16 @@ filter_pd( source_datasets = list(adrs = adrs) ) } +\seealso{ +Other superseded: +\code{\link{derive_param_bor}()}, +\code{\link{derive_param_clinbenefit}()}, +\code{\link{derive_param_confirmed_bor}()}, +\code{\link{derive_param_confirmed_resp}()}, +\code{\link{derive_param_response}()} +} \author{ Teckla Akinyi, Stefan Bundfuss } -\concept{utils_fil} -\keyword{utils_fil} +\concept{superseded} +\keyword{superseded} diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R deleted file mode 100644 index 541b84c9..00000000 --- a/tests/testthat/test-utils.R +++ /dev/null @@ -1,53 +0,0 @@ -data <- tibble::tribble( - ~AVALC, - "YES", - "NO" -) - -# call_aval_fun ---- - -## Test 1: AVAL is created ---- -test_that("call_aval_fun Test 1: AVAL is created", { - yn_map <- function(x) { - case_when( - x == "YES" ~ 1, - x == "NO" ~ 0 - ) - } - - expect_warning( - actual <- call_aval_fun( - data, - yn_map - ), - class = "lifecycle_warning_deprecated" - ) - - expect_dfs_equal( - actual, - tibble::tribble( - ~AVALC, ~AVAL, - "YES", 1, - "NO", 0 - ), - keys = c("AVAL") - ) -}) - -## Test 2: Test error for invalid aval_fun ---- -test_that("call_aval_fun Test 2: Test error for invalid aval_fun", { - bad_fun <- function(x) { - abort("Function bad_fun failed!") - } - - expect_error( - suppress_warning( - call_aval_fun( - data, - aval_fun = bad_fun - ), - regexpr = "deprecated" - ), - regexp = "Assigning new AVAL records with aval_fun" - ) -}) diff --git a/vignettes/admiralonco.Rmd b/vignettes/admiralonco.Rmd index 33347b16..4c73029c 100644 --- a/vignettes/admiralonco.Rmd +++ b/vignettes/admiralonco.Rmd @@ -12,50 +12,18 @@ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) -link <- function(text, url) { - return( - paste0( - "[", text, "]", - "(", url, ")" - ) - ) -} -dyn_link <- function(text, - base_url, - relative_url = "", - # Change to TRUE when admiral adopts multiversion docs - is_multiversion = FALSE, - multiversion_default_ref = "main") { - url <- paste(base_url, relative_url, sep = "/") - if (is_multiversion) { - url <- paste( - base_url, - Sys.getenv("BRANCH_NAME", multiversion_default_ref), - relative_url, - sep = "/" - ) - } - return(link(text, url)) -} -# Other variables -admiral_homepage <- "https://pharmaverse.github.io/admiral/cran-release" ``` # Introduction -As this is a package extension, if you are new to `{admiral}` then the best place to first start -reading would be this `r dyn_link("Get Started", admiral_homepage, "articles/admiral.html")` -guide. This extension package follows the same main idea and conventions, and re-uses many -functions from `{admiral}`, so it is important to thoroughly understand these to be able to -use `{admiralonco}`. +As this is a package extension, if you are new to `{admiral}` then the best +place to first start reading would be the [Get +Started](https://pharmaverse.github.io/admiral/articles/admiral.html) page. This +extension package follows the same main idea and conventions, and re-uses many +functions from `{admiral}`, so it is important to thoroughly understand these to +be able to use `{admiralonco}`. -# Derivations - -The most important functions in `{admiralonco}` are the -[derivations](../reference/index.html#section-derivations). Again these follow the same -conventions as `{admiral}` but are focused to oncology-specific needs. - -# Starting a Script +# Creating Oncology ADaM Datasets For the oncology ADaM data structures, an overview of the flow and example function calls for the most common steps are provided by the following vignettes: @@ -66,7 +34,7 @@ for the most common steps are provided by the following vignettes: - [Creating ADTR](adtr.html) `{admiralonco}` also provides template R scripts as a starting point. They can be -created by calling `use_ad_template()` from {admiral}, e.g., +created by calling `use_ad_template()` from `{admiral}`, e.g., ```{r} library(admiral) @@ -81,7 +49,7 @@ use_ad_template( ``` A list of all available templates can be obtained by `list_all_templates()` -from {admiral}: +from `{admiral}`: ```{r} list_all_templates(package = "admiralonco") diff --git a/vignettes/adrs.Rmd b/vignettes/adrs.Rmd index 2dc5b14d..8f6593a3 100644 --- a/vignettes/adrs.Rmd +++ b/vignettes/adrs.Rmd @@ -14,36 +14,6 @@ knitr::opts_chunk$set( comment = "#>" ) -library(admiral) - -link <- function(text, url) { - return( - paste0( - "[", text, "]", - "(", url, ")" - ) - ) -} -dyn_link <- function(text, - base_url, - relative_url = "", - # Change to TRUE when admiral adopts multiversion docs - is_multiversion = FALSE, - multiversion_default_ref = "main") { - url <- paste(base_url, relative_url, sep = "/") - if (is_multiversion) { - url <- paste( - base_url, - Sys.getenv("BRANCH_NAME", multiversion_default_ref), - relative_url, - sep = "/" - ) - } - return(link(text, url)) -} -# Other variables -admiral_homepage <- "https://pharmaverse.github.io/admiral/cran-release" - library(admiraldev) ``` @@ -95,20 +65,21 @@ read into the environment. This will be a company specific process. Some of the data frames needed may be `ADSL`, `RS` and `TU`. For example purpose, the SDTM and ADaM datasets (based on CDISC Pilot -test data)---which are included in `{pharmaversesdtm}`---are used. +test data)---which are included in `{pharmaversesdtm}` and +`{pharmaverseadam}`---are used. ```{r message=FALSE} library(admiral) library(admiralonco) library(dplyr) library(pharmaversesdtm) +library(pharmaverseadam) library(lubridate) library(stringr) -data("admiral_adsl") +data("adsl") data("rs_onco_recist") data("tu_onco_recist") -adsl <- admiral_adsl rs <- rs_onco_recist tu <- tu_onco_recist @@ -193,7 +164,7 @@ adrs <- adrs %>% PARAM = "Overall Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1" + PARCAT3 = "RECIST 1.1" ) ``` @@ -259,12 +230,24 @@ those occurring on or after randomization date. If there is more than one assessment at a date, the worst one is flagged. ```{r} +worst_resp <- function(arg) { + case_when( + arg == "NE" ~ 1, + arg == "CR" ~ 2, + arg == "PR" ~ 3, + arg == "SD" ~ 4, + arg == "NON-CR/NON-PD" ~ 5, + arg == "PD" ~ 6, + TRUE ~ 0 + ) +} + adrs <- adrs %>% restrict_derivation( derivation = derive_var_extreme_flag, args = params( by_vars = exprs(STUDYID, USUBJID, ADT), - order = exprs(AVAL, RSSEQ), + order = exprs(worst_resp(AVALC), RSSEQ), new_var = ANL01FL, mode = "last" ), @@ -359,7 +342,7 @@ crsp_y_cr <- event_joined( join_vars = exprs(AVALC, ADT), join_type = "after", order = exprs(ADT), - first_cond = AVALC.join == "CR" & + first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + days(confirmation_period), condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & @@ -377,7 +360,7 @@ crsp_y_pr <- event_joined( join_vars = exprs(AVALC, ADT), join_type = "after", order = exprs(ADT), - first_cond = AVALC.join %in% c("CR", "PR") & + first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + days(confirmation_period), condition = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & @@ -403,7 +386,7 @@ cbor_cr <- event_joined( dataset_name = "ovr", join_vars = exprs(AVALC, ADT), join_type = "after", - first_cond = AVALC.join == "CR" & + first_cond_upper = AVALC.join == "CR" & ADT.join >= ADT + confirmation_period, condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & @@ -421,7 +404,7 @@ cbor_pr <- event_joined( dataset_name = "ovr", join_vars = exprs(AVALC, ADT), join_type = "after", - first_cond = AVALC.join %in% c("CR", "PR") & + first_cond_upper = AVALC.join %in% c("CR", "PR") & ADT.join >= ADT + confirmation_period, condition = AVALC == "PR" & all(AVALC.join %in% c("CR", "PR", "NE")) & @@ -478,12 +461,13 @@ adrs <- adrs %>% order = exprs(ADT, RSSEQ), mode = "first", exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "PD", PARAM = "Disease Progression by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -520,7 +504,8 @@ rsp_y adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(ADT), + order = exprs(event_nr, ADT), + tmp_event_nr_var = event_nr, mode = "first", events = list(rsp_y, no_data_n), source_datasets = list( @@ -532,7 +517,7 @@ adrs <- adrs %>% PARAM = "Response by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -569,24 +554,23 @@ list). Thus `ignore_event_order = TRUE` is specified. adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(desc(AVALC), ADT), + order = exprs(desc(AVALC), ADT, event_nr), + tmp_event_nr_var = event_nr, mode = "first", events = list(rsp_y, cb_y, no_data_n), source_datasets = list( ovr = ovr, adsl = adsl ), - ignore_event_order = TRUE, set_values_to = exprs( PARAMCD = "CB", PARAM = "Clinical Benefit by Investigator (confirmation for response not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" - ), - check_type = "none" + ) ) ``` @@ -615,7 +599,8 @@ response for this subject. adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(ADT), + order = exprs(event_nr, ADT), + tmp_event_nr_var = event_nr, mode = "first", source_datasets = list( ovr = ovr, @@ -627,7 +612,7 @@ adrs <- adrs %>% PARAM = "Best Overall Response by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -683,12 +668,13 @@ adrs <- adrs %>% by_vars = exprs(STUDYID, USUBJID), filter_add = PARAMCD == "BOR" & AVALC %in% c("CR", "PR"), exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "BCP", PARAM = "Best Overall Response of CR/PR by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -741,20 +727,20 @@ is specified. adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(desc(AVALC), ADT), + order = exprs(desc(AVALC), ADT, event_nr), + tmp_event_nr_var = event_nr, mode = "first", source_datasets = list( ovr = ovr, adsl = adsl ), events = list(crsp_y_cr, crsp_y_pr, no_data_n), - ignore_event_order = TRUE, set_values_to = exprs( PARAMCD = "CRSP", PARAM = "Confirmed Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -763,30 +749,30 @@ adrs <- adrs %>% adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(desc(AVALC), ADT), + order = exprs(desc(AVALC), ADT, event_nr), + tmp_event_nr_var = event_nr, mode = "first", events = list(crsp_y_cr, crsp_y_pr, cb_y, no_data_n), source_datasets = list( ovr = ovr, adsl = adsl ), - ignore_event_order = TRUE, set_values_to = exprs( PARAMCD = "CCB", PARAM = "Confirmed Clinical Benefit by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" - ), - check_type = "none" + ) ) adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(ADT), + order = exprs(event_nr, ADT), + tmp_event_nr_var = event_nr, mode = "first", events = list(cbor_cr, cbor_pr, bor_sd, bor_non_crpd, bor_pd, bor_ne, no_data_missing), source_datasets = list( @@ -798,7 +784,7 @@ adrs <- adrs %>% PARAM = "Best Confirmed Overall Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -809,12 +795,13 @@ adrs <- adrs %>% by_vars = exprs(STUDYID, USUBJID), filter_add = PARAMCD == "CBOR" & AVALC %in% c("CR", "PR"), exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "CBCP", PARAM = "Best Confirmed Overall Response of CR/PR by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -854,24 +841,23 @@ cb_y_pd <- event( adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(desc(AVALC), ADT), + order = exprs(desc(AVALC), ADT, event_nr), + tmp_event_nr_var = event_nr, mode = "first", events = list(crsp_y_cr, crsp_y_pr, cb_y, cb_y_pd, no_data_n), source_datasets = list( ovr = ovr, adsl = adsl ), - ignore_event_order = TRUE, set_values_to = exprs( PARAMCD = "ACCB", PARAM = "Alternative Confirmed Clinical Benefit by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" - ), - check_type = "none" + ) ) ``` @@ -896,7 +882,8 @@ bor_ned <- event( adrs <- adrs %>% derive_extreme_event( by_vars = exprs(STUDYID, USUBJID), - order = exprs(ADT), + order = exprs(event_nr, ADT), + tmp_event_nr_var = event_nr, mode = "first", source_datasets = list( ovr = ovr, @@ -907,11 +894,11 @@ adrs <- adrs %>% PARAMCD = "A1BOR", PARAM = paste( "Best Overall Response by Investigator (confirmation not required)", - "- Recist 1.1 adjusted for NED at Baseline" + "- RECIST 1.1 adjusted for NED at Baseline" ), PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1 adjusted for NED at Baseline", + PARCAT3 = "RECIST 1.1 adjusted for NED at Baseline", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -937,7 +924,7 @@ adrs_bicr <- rs %>% PARAM = "Overall Response by BICR", PARCAT1 = "Tumor Response", PARCAT2 = "Blinded Independent Central Review", - PARCAT3 = "Recist 1.1" + PARCAT3 = "RECIST 1.1" ) ``` @@ -970,6 +957,7 @@ adrs <- adrs %>% by_vars = exprs(STUDYID, USUBJID), filter_add = !is.na(DTHDT), exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "DEATH", PARAM = "Death", @@ -1009,7 +997,7 @@ adrs <- adrs %>% PARAM = "Last Disease Assessment by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", ANL01FL = "Y" ) ) @@ -1047,7 +1035,7 @@ adrs <- adrs %>% PARAMCD = "MDIS", PARAM = "Measurable Disease at Baseline by Investigator", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -1109,4 +1097,4 @@ dataset_vignette( ADaM | Sample Code ---- | -------------- -ADRS | `r dyn_link("ad_adrs.R", "https://github.com/pharmaverse/admiralonco/blob", "inst/templates/ad_adrs.R", is_multiversion = TRUE)` +ADRS | `admiral::use_ad_template("ADRS", package = "admiralonco")` diff --git a/vignettes/adrs_basic.Rmd b/vignettes/adrs_basic.Rmd index 973ceba2..3df21b59 100644 --- a/vignettes/adrs_basic.Rmd +++ b/vignettes/adrs_basic.Rmd @@ -14,36 +14,6 @@ knitr::opts_chunk$set( comment = "#>" ) -library(admiral) - -link <- function(text, url) { - return( - paste0( - "[", text, "]", - "(", url, ")" - ) - ) -} -dyn_link <- function(text, - base_url, - relative_url = "", - # Change to TRUE when admiral adopts multiversion docs - is_multiversion = FALSE, - multiversion_default_ref = "main") { - url <- paste(base_url, relative_url, sep = "/") - if (is_multiversion) { - url <- paste( - base_url, - Sys.getenv("BRANCH_NAME", multiversion_default_ref), - relative_url, - sep = "/" - ) - } - return(link(text, url)) -} -# Other variables -admiral_homepage <- "https://pharmaverse.github.io/admiral/cran-release" - library(admiraldev) ``` @@ -93,21 +63,22 @@ To start, all data frames needed for the creation of `ADRS` should be read into the environment. This will be a company specific process. Some of the data frames needed may be `ADSL`, `RS` and `TU`. -For example purpose, the SDTM and ADaM datasets (based on CDISC Pilot -test data)---which are included in `{pharmaversesdtm}`---are used. +For example purpose, the SDTM and ADaM datasets (based on CDISC Pilot test +data)---which are included in `{pharmaversesdtm}` and `{pharmaverseadam}`---are +used. ```{r message=FALSE} library(admiral) library(admiralonco) library(dplyr) library(pharmaversesdtm) +library(pharmaverseadam) library(lubridate) library(stringr) -data("admiral_adsl") +data("adsl") data("rs_onco_recist") data("tu_onco_recist") -adsl <- admiral_adsl rs <- rs_onco_recist tu <- tu_onco_recist @@ -192,7 +163,7 @@ adrs <- adrs %>% PARAM = "Overall Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1" + PARCAT3 = "RECIST 1.1" ) ``` @@ -258,12 +229,24 @@ those occurring on or after randomization date. If there is more than one assessment at a date, the worst one is flagged. ```{r} +worst_resp <- function(arg) { + case_when( + arg == "NE" ~ 1, + arg == "CR" ~ 2, + arg == "PR" ~ 3, + arg == "SD" ~ 4, + arg == "NON-CR/NON-PD" ~ 5, + arg == "PD" ~ 6, + TRUE ~ 0 + ) +} + adrs <- adrs %>% restrict_derivation( derivation = derive_var_extreme_flag, args = params( by_vars = exprs(STUDYID, USUBJID, ADT), - order = exprs(AVAL, RSSEQ), + order = exprs(worst_resp(AVALC), RSSEQ), new_var = ANL01FL, mode = "last" ), @@ -344,12 +327,13 @@ adrs <- adrs %>% order = exprs(ADT, RSSEQ), mode = "first", exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "PD", PARAM = "Disease Progression by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -414,7 +398,7 @@ adrs <- adrs %>% PARAM = "Response by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -464,7 +448,7 @@ adrs <- adrs %>% PARAM = "Clinical Benefit by Investigator (confirmation for response not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -501,7 +485,7 @@ adrs <- adrs %>% PARAM = "Best Overall Response by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -558,12 +542,13 @@ adrs <- adrs %>% order = exprs(ADT, RSSEQ), mode = "first", exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "BCP", PARAM = "Best Overall Response of CR/PR by Investigator (confirmation not required)", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -602,7 +587,7 @@ adrs <- adrs %>% PARAM = "Confirmed Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -628,7 +613,7 @@ adrs <- adrs %>% PARAM = "Confirmed Clinical Benefit by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -646,7 +631,7 @@ adrs <- adrs %>% PARAM = "Best Confirmed Overall Response by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = aval_resp(AVALC), ANL01FL = "Y" ) @@ -659,12 +644,13 @@ adrs <- adrs %>% order = exprs(ADT, RSSEQ), mode = "first", exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "CBCP", PARAM = "Best Confirmed Overall Response of CR/PR by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -700,7 +686,7 @@ adrs_bicr <- rs %>% PARAM = "Overall Response by BICR", PARCAT1 = "Tumor Response", PARCAT2 = "Blinded Independent Central Review", - PARCAT3 = "Recist 1.1" + PARCAT3 = "RECIST 1.1" ) ``` @@ -733,6 +719,7 @@ adrs <- adrs %>% by_vars = exprs(STUDYID, USUBJID), filter_add = !is.na(DTHDT), exist_flag = AVALC, + false_value = "N", set_values_to = exprs( PARAMCD = "DEATH", PARAM = "Death", @@ -772,7 +759,7 @@ adrs <- adrs %>% PARAM = "Last Disease Assessment by Investigator", PARCAT1 = "Tumor Response", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", ANL01FL = "Y" ) ) @@ -810,7 +797,7 @@ adrs <- adrs %>% PARAMCD = "MDIS", PARAM = "Measurable Disease at Baseline by Investigator", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = yn_to_numeric(AVALC), ANL01FL = "Y" ) @@ -872,4 +859,4 @@ dataset_vignette( ADaM | Sample Code ---- | -------------- -ADRS_BASIC | `r dyn_link("ad_adrs_basic.R", "https://github.com/pharmaverse/admiralonco/blob", "inst/templates/ad_adrs_basic.R", is_multiversion = TRUE)` +ADRS_BASIC | `admiral::use_ad_template("ADRS_BASIC", package = "admiralonco")` diff --git a/vignettes/adtr.Rmd b/vignettes/adtr.Rmd index 6f5be879..5bb8c01c 100644 --- a/vignettes/adtr.Rmd +++ b/vignettes/adtr.Rmd @@ -13,34 +13,6 @@ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) -library(admiral) -link <- function(text, url) { - return( - paste0( - "[", text, "]", - "(", url, ")" - ) - ) -} -dyn_link <- function(text, - base_url, - relative_url = "", - # Change to TRUE when admiral adopts multiversion docs - is_multiversion = FALSE, - multiversion_default_ref = "main") { - url <- paste(base_url, relative_url, sep = "/") - if (is_multiversion) { - url <- paste( - base_url, - Sys.getenv("BRANCH_NAME", multiversion_default_ref), - relative_url, - sep = "/" - ) - } - return(link(text, url)) -} -# Other variables -admiral_homepage <- "https://pharmaverse.github.io/admiral" library(admiraldev) ``` @@ -78,6 +50,7 @@ The examples of this vignette require the following packages. library(admiral) library(dplyr) library(pharmaversesdtm) +library(pharmaverseadam) library(lubridate) library(stringr) library(admiralonco) @@ -104,9 +77,9 @@ To start, all data frames needed for the creation of `ADTR` should be read into Some of the data frames needed may be `ADSL`, `ADRS` ,`RS`, `TU`, `TR`, `SUPPTU` `SUPPTR`. For example purposes, the SDTM and ADaM datasets (based on CDISC Pilot test -data)---which are included in `{pharmaversesdtm}`---are used. Also, see -[Handling of Missing -Values](https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values) +data)---which are included in `{pharmaversesdtm}` and `{pharmaverseadam}`---are +used. Also, see [Handling of Missing +Values](https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values) explains why we need to use the `convert_blanks_to_na()` function. On the `TR` domain we filter on where tumor assessment short name `TRTESTCD` is @@ -116,13 +89,12 @@ then the template code where we derive parameters for lesions diameters should be updated accordingly. ```{r} -data("admiral_adsl") -data("admiral_adrs") +data("adsl") +data("adrs_onco") data("rs_onco_recist") data("tu_onco_recist") data("tr_onco_recist") -adsl <- admiral_adsl -adrs <- admiral_adrs +adrs <- adrs_onco tu <- tu_onco_recist tr <- tr_onco_recist rs <- rs_onco_recist @@ -272,7 +244,7 @@ adtr <- bind_rows( mutate( PARCAT1 = "Target Lesion(s)", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1", + PARCAT3 = "RECIST 1.1", AVAL = TRSTRESN, ANL01FL = if_else(!is.na(AVAL), "Y", NA_character_) ) %>% @@ -302,21 +274,24 @@ flags therefore should be setup according to your company specifications. In the example below, the lesion sizes are counted and grouped according to the by variables specified, in this case we group by the visit (`AVISIT` and `AVISITN`) to ensure that the correct lesion measurements are summed together. +If there are different analysis day/dates (`ADY`/`ADT`) associated with a +particular visit, we take the minimum day/date. ```{r} -adtr_sum <- get_summary_records( - adtr, +adtr_sum <- derive_summary_records( + dataset_add = adtr, by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, AVISIT, AVISITN), - filter = (str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | + filter_add = (str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL"), - analysis_var = AVAL, - summary_fun = function(x) sum(x, na.rm = TRUE), set_values_to = exprs( + AVAL = sum(AVAL, na.rm = TRUE), + ADY = min(ADY, na.rm = TRUE), + ADT = min(ADT, na.rm = TRUE), PARAMCD = "SDIAM", PARAM = "Target Lesions Sum of Diameters by Investigator", PARCAT1 = "Target Lesion(s)", PARCAT2 = "Investigator", - PARCAT3 = "Recist 1.1" + PARCAT3 = "RECIST 1.1" ) ) ``` @@ -325,10 +300,10 @@ adtr_sum <- get_summary_records( dataset_vignette( adtr_sum %>% arrange(USUBJID, AVISITN) %>% - select(USUBJID, PARAMCD, PARAM, AVISIT, AVAL, everything()), - display_vars = exprs(USUBJID, PARAMCD, PARAM, AVISIT, AVAL) + select(USUBJID, PARAMCD, PARAM, AVISIT, AVAL, ADT, ADY, everything()), + display_vars = exprs(USUBJID, PARAMCD, PARAM, AVISIT, AVAL, ADT, ADY) ) -``` +``` The analysis flag `ANL01FL` flags the sum of diameters where the number of lesions assessed at baseline and at post-baseline match. To assess whether the number of lesions expected and assessed match, you could compare lesion identifiers (`TR.TRLNKID`) or use the previous variables set up earlier to compare lesion expected (`LSEXP`) vs lesion assessed (`LSASS`) or check for target lesion response (from `RS`) = `NE`. A target lesion response of `NE` means all lesions from baseline are not measured at that post-baseline visit. @@ -354,58 +329,20 @@ adtr_sum <- adtr_sum %>% filter_add = AVISIT == "BASELINE" & ((str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL")), - new_var = LSEXP, - analysis_var = TRLNKID, - summary_fun = function(x) paste(sort(x), collapse = ", ") + new_vars = exprs(LSEXP = paste(sort(TRLNKID), collapse = ", ")) ) %>% derive_var_merged_summary( dataset_add = adtr, by_vars = exprs(USUBJID, AVISIT), filter_add = ((str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL")) & ANL01FL == "Y", - new_var = LSASS, - analysis_var = TRLNKID, - summary_fun = function(x) paste(sort(x), collapse = ", ") + new_vars = exprs(LSASS = paste(sort(TRLNKID), collapse = ", ")) ) %>% mutate( ANL01FL = if_else(LSEXP == LSASS, "Y", NA_character_) ) ``` -In the next step we include the analysis day and date (`ADY`/`ADT`) variables to -the sum of diameter parameter dataset. If there are different analysis -day/dates associated with a particular visit, we take the minimum day/date. - -```{r} -adtr_sum <- adtr_sum %>% - derive_var_merged_summary( - dataset_add = adtr, - by_vars = exprs(USUBJID, AVISIT), - filter_add = (str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | - (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL"), - new_var = ADY, - analysis_var = ADY, - summary_fun = function(x) min(x, na.rm = TRUE) - ) %>% - derive_var_merged_summary( - dataset_add = adtr, - by_vars = exprs(USUBJID, AVISIT), - filter_add = (str_starts(PARAMCD, "LDIAM") & TULOCGR1 == "NON-NODAL") | - (str_starts(PARAMCD, "NLDIAM") & TULOCGR1 == "NODAL"), - new_var = ADT, - analysis_var = ADT, - summary_fun = function(x) min(x, na.rm = TRUE) - ) -``` - -```{r, echo=FALSE} -dataset_vignette( - arrange(adtr_sum, USUBJID, AVISITN), - display_vars = exprs(USUBJID, PARAMCD, AVISIT, LSEXP, LSASS, ANL01FL, ADT, ADY) -) -``` - - ## Derive Baseline (`ABLFL`, `BASE`) {#base} These functions are available in `admiral`, below examples show its usage for @@ -447,6 +384,7 @@ adtr_sum <- adtr_sum %>% order = exprs(AVAL), new_vars = exprs(NADIR = AVAL), join_vars = exprs(ADY), + join_type = "all", filter_add = ANL01FL == "Y", filter_join = ADY.join < ADY, mode = "first", @@ -745,8 +683,4 @@ dataset_vignette( ADaM | Sample Code ---- | -------------- -`ADTR` | `r dyn_link("ad_adtr.R", "https://github.com/pharmaverse/admiralonco/blob", "inst/templates/ad_adtr.R", is_multiversion = TRUE)` - - - - +`ADTR` | `admiral::use_ad_template("ADTR", package = "admiralonco")` diff --git a/vignettes/adtte.Rmd b/vignettes/adtte.Rmd index 34c26d54..cd481bdf 100644 --- a/vignettes/adtte.Rmd +++ b/vignettes/adtte.Rmd @@ -13,34 +13,6 @@ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) -link <- function(text, url) { - return( - paste0( - "[", text, "]", - "(", url, ")" - ) - ) -} -dyn_link <- function(text, - base_url, - relative_url = "", - # Change to TRUE when admiral adopts multiversion docs - is_multiversion = FALSE, - multiversion_default_ref = "main") { - url <- paste(base_url, relative_url, sep = "/") - if (is_multiversion) { - url <- paste( - base_url, - Sys.getenv("BRANCH_NAME", multiversion_default_ref), - relative_url, - sep = "/" - ) - } - return(link(text, url)) -} -# Other variables -admiral_homepage <- "https://pharmaverse.github.io/admiral/cran-release" - library(admiraldev) ``` @@ -70,6 +42,7 @@ The examples of this vignette require the following packages. ```{r, warning=FALSE, message=FALSE} library(admiral) library(admiralonco) +library(pharmaverseadam) library(dplyr) library(lubridate) ``` @@ -87,15 +60,14 @@ library(lubridate) To start, all datasets needed for the creation of the time-to-event dataset should be read into the environment. This will be a company specific process. -For example purpose, the ADaM datasets---which are included -in `{admiral}` and `{admiralonco}`---are used. An alternative might be to use -`ADEVENT` as input. +For example purpose, the ADaM datasets---which are included in +`{pharmaverseadam}`---are used. An alternative might be to use `ADEVENT` as +input. ```{r} -data("admiral_adsl") -data("admiral_adrs") -adsl <- admiral_adsl -adrs <- admiral_adrs +data("adsl") +data("adrs_onco") +adrs <- adrs_onco ``` ## Derive Parameters (`CNSR`, `ADT`, `STARTDT`) {#parameters} @@ -219,7 +191,7 @@ dataset_vignette( ### Creating Your Own Time-to-Event Source Objects {#tteobj} We advise you consult the `{admiral}` -`r dyn_link("Creating a BDS Time-to-Event ADaM vignette", admiral_homepage, "articles/bds_tte.html")` +[Creating a BDS Time-to-Event ADaM vignette](https://pharmaverse.github.io/admiral/articles/bds_tte.html) for further guidance on the different options available and more examples. One extra common oncology case we include here is around PFS when censoring @@ -375,4 +347,4 @@ dataset_vignette( ADaM | Sample Code ---- | -------------- -ADTTE | `r dyn_link("ad_adtte.R", "https://github.com/pharmaverse/admiralonco/blob", "inst/templates/ad_adtte.R", is_multiversion = TRUE)` +ADTTE | `admiral::use_ad_template("ADTTE", package = "admiralonco")` diff --git a/vignettes/articles/website-versions.Rmd b/vignettes/articles/website-versions.Rmd new file mode 100644 index 00000000..5143f6d2 --- /dev/null +++ b/vignettes/articles/website-versions.Rmd @@ -0,0 +1,82 @@ +--- +title: "Previous Versions of Website" +--- + +```{r, include = FALSE} +# TO USE THIS ARTICLE, THE DESCRIPTION FILE MUST INCLUDE +# Config/Needs/website: gert +# Make sure to copy the gh-pages branch to your local git + +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + +```{r setup, include=FALSE} +base_url <- + "https://pharmaverse.github.io/admiralonco/" # include the trailing backslash! + +# get list of all files in the `gh-pages` branch +df_all_files <- tryCatch(gert::git_ls(ref = "gh-pages"), error = function(x) FALSE) + +# if a local user (not on CI) does not have a copy of the `gh-pages` branch, exit silently +if (!isTRUE(as.logical(Sys.getenv("CI"))) && isFALSE(df_all_files)) { + knitr::knit_exit() +} +``` + +```{r include=FALSE} +# extract all folders in the root of the branch +all_folders <- + sub("/.*", "", df_all_files$path)[grepl( + x = df_all_files$path, + pattern = "/", + fixed = TRUE + )] |> + unique() + +# subset to all version folders +all_version_folders <- + all_folders[grep("^v[0-9]+|dev", x = all_folders)] |> + rev() +# more dev first if it appears +if ("dev" %in% all_version_folders) { + all_version_folders <- c("dev", all_version_folders) |> unique() +} + +# release dates of prior tags +df_tags <- gert::git_tag_list() +df_tags <- df_tags[df_tags$name %in% all_version_folders, ] +df_tags$date <- + lapply( + df_tags$commit, + FUN = function(x) { + tryCatch( + gert::git_commit_info(ref = x)$time |> as.Date() |> as.character(), + error = function(x) NA + ) + } + ) |> + unlist() +df_tags <- df_tags[!is.na(df_tags$date), ] + +lst_tag_dates <- + paste0(" (", df_tags$date, ")") |> + as.list() |> + setNames(df_tags$name) + +# string with all markdown links +str_website_links <- + lapply( + X = all_version_folders, + FUN = function(x) { + x_label <- ifelse(x %in% "dev", "Development Site", x) + paste0("[", x_label, lst_tag_dates[[x]], "](", paste0(base_url, x), ")") + } + ) |> + unlist() |> + paste(collapse = "\n\n") +``` + +`r str_website_links` diff --git a/vignettes/irecist.Rmd b/vignettes/irecist.Rmd new file mode 100644 index 00000000..f3d7812f --- /dev/null +++ b/vignettes/irecist.Rmd @@ -0,0 +1,884 @@ +--- +title: "Creating ADRS with iRECIST endpoints" +output: + rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Creating ADRS with iRECIST endpoints} + %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +--- + +```{r setup, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) + +library(admiraldev) +``` + +# Introduction + +This article describes creating an `ADRS` ADaM with oncology endpoint parameters +based on iRECIST. It shows a similar way of deriving the endpoints presented in +[Creating ADRS (Including Non-standard Endpoints)](adrs.html). Most of the endpoints +are derived by calling `admiral::derive_extreme_event()`. + +This vignette follows the iRECIST guidelines, for more information user may visit +https://recist.eortc.org/irecist/ + +Examples are currently presented and tested using `ADSL` (ADaM) and +`RS` (SDTM) inputs. However, other domains could be used. The `RS` test data +contains iRECIST response for target, non-target and overall response. Further +pre-processing and considerations may be needed if iRECIST are only collected +after RECIST 1.1 progression and input data contains multiple response criteria. +The functions and workflow could similarly be used to create an intermediary +`ADEVENT` ADaM. + +**Note**: *All examples assume CDISC SDTM and/or ADaM format as input +unless otherwise specified.* + +# Programming Workflow + +- [Read in Data](#readdata) +- [Pre-processing of Input Records](#input) +- [Derive Confirmed Progressive Disease Parameter](#pd) +- [Derive Response Parameter](#rsp) +- [Derive Clinical Benefit Parameter](#cb) +- [Derive Best Overall Response Parameter](#bor) +- [Derive Response Parameters requiring Confirmation](#confirm) +- [Other Endpoints](#Other) + +## Read in Data {#readdata} + +To start, all data frames needed for the creation of `ADRS` should be read into +the environment. This will be a company specific process. Some of the data +frames needed may be `ADSL`, `RS` and `TU`. For this vignette we assume that +`RS` provides the response values `"iCR"`, `"iPR"`, `"iSD"`, +`"NON-iCR/NON-iUPD"`, `"iUPD"`, `"iCPD"`, and `"NE"`. All examples can be easily +modified to consider other response values (see [Handling Different Input +Response Values](#different_resp_vals)). + +For example purpose, the SDTM and ADaM datasets (based on CDISC Pilot +test data)---which are included in `{pharmaversesdtm}` and `{pharmaverseadam}`---are used. + +```{r message=FALSE} +library(admiral) +library(admiralonco) +library(dplyr) +library(pharmaverseadam) +library(pharmaversesdtm) +library(lubridate) +library(stringr) +data("adsl") +# iRECIST oncology sdtm data +data("rs_onco_irecist") + +rs <- rs_onco_irecist + +rs <- convert_blanks_to_na(rs) +``` + +```{r echo=FALSE} +# select subjects from adsl such that there is one subject without RS data +rs_subjects <- unique(rs$USUBJID) +adsl_subjects <- unique(adsl$USUBJID) +adsl <- filter( + adsl, + USUBJID %in% union(rs_subjects, setdiff(adsl_subjects, rs_subjects)[1]) +) +``` + +At this step, it may be useful to join `ADSL` to your `RS` domain. Only +the `ADSL` variables used for derivations are selected at this step. The +rest of the relevant `ADSL` would be added later. + +```{r eval=TRUE} +adsl_vars <- exprs(RANDDT) +adrs <- derive_vars_merged( + rs, + dataset_add = adsl, + new_vars = adsl_vars, + by_vars = exprs(STUDYID, USUBJID) +) +``` + +```{r, eval=TRUE, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, RSTESTCD, RSDTC, VISIT, RANDDT), + filter = RSTESTCD == "OVRLRESP" +) +``` + +## Pre-processing of Input Records {#input} + +The first step involves company-specific pre-processing of records for +the required input to the downstream parameter functions. Note that this +could be needed multiple times (e.g. once for investigator and once for +Independent Review Facility (IRF)/Blinded Independent Central Review +(BICR) records). It could even involve merging input data from other +sources besides `RS`, such as `ADTR`. + +This step would include any required selection/derivation of `ADT` or applying +any necessary partial date imputations, updating `AVAL` (e.g. this should be +ordered from best to worst response), and setting analysis flag `ANL01FL`. +Common options for `ANL01FL` would be to set null for invalid assessments or +those occurring after new anti-cancer therapy, or to only flag assessments on or +after date of first treatment/randomization, or rules to cover the case when a +patient has multiple observations per visit (e.g. by selecting the worst value). +Another consideration could be extra potential protocol-specific sources of +Progressive Disease such as radiological assessments, which could be +pre-processed here to create a PD record to feed downstream derivations. + +For the derivation of the parameters it is expected that the subject +identifier variables (usually `STUDYID` and `USUBJID`) and `ADT` are a +unique key. This can be achieved by deriving an analysis flag +(`ANLzzFL`). See [Derive `ANL01FL`](#anl01fl) for an example. + +The below shows an example of a possible company-specific implementation +of this step. + +### Select Overall Response Records and Set Parameter Details + +In this case we use the overall response records from `RS` from the +investigator as our starting point. The parameter details such as +`PARAMCD`, `PARAM` etc will always be company-specific, but an example +is shown below so that you can trace through how these records feed into +the other parameter derivations. + +```{r} +adrs <- adrs %>% + filter(RSEVAL == "INVESTIGATOR" & RSTESTCD == "OVRLRESP") %>% + mutate( + PARAMCD = "OVR", + PARAM = "Overall Response by Investigator", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST" + ) +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, VISIT, RSTESTCD, RSEVAL, PARAMCD, PARAM, PARCAT1, PARCAT2, PARCAT3) +) +``` + +### Partial Date Imputation and Deriving `ADT`, `ADTF`, `AVISIT` etc + +If your data collection allows for partial dates, you could apply a +company-specific imputation rule at this stage when deriving `ADT`. For +this example, here we impute missing day to last possible date. + +```{r} +adrs <- adrs %>% + derive_vars_dt( + dtc = RSDTC, + new_vars_prefix = "A", + highest_imputation = "D", + date_imputation = "last" + ) %>% + mutate(AVISIT = VISIT) +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, PARAM, RSSTRESC, RSDTC, ADT, ADTF) +) +``` + +### Derive `AVALC` and `AVAL` + +Here we populate `AVALC` and create the numeric version as `AVAL` +(ordered from worst to best response, followed by `NE` and MISSING). The `AVAL` values are not considered in +the parameter derivations below, and so changing `AVAL` here would not change +the result of those derivations. However, please note that the ordering of `AVAL` +will be used to determine `ANL01FL` in the subsequent step, ensure that the appropriate +`mode` is being set in the `admiral::derive_var_extreme_flag()`. + +iRECIST ordering will be used or if you'd like to provide your own company-specific ordering here you +could do this as follows: + +```{r} +aval_resp_new <- function(arg) { + case_when( + arg == "NE" ~ 8, + arg == "MISSING" ~ 7, + arg == "iCR" ~ 6, + arg == "iPR" ~ 5, + arg == "iSD" ~ 4, + arg == "NON-iCR/NON-iUPD" ~ 3, + arg == "iUPD" ~ 2, + arg == "iCPD" ~ 1, + TRUE ~ NA_real_ + ) +} + +adrs <- adrs %>% + mutate( + AVALC = RSSTRESC, + AVAL = aval_resp_new(AVALC) + ) +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, PARAM, RSSTRESC, AVALC, AVAL) +) +``` + +### Flag Worst Assessment at Each Date (`ANL01FL`) {#anl01fl} + +When deriving `ANL01FL` this is an opportunity to exclude any records +that should not contribute to any downstream parameter derivations. In +the below example this includes only selecting valid assessments and +those occurring on or after randomization date. If there is more than +one assessment at a date, the worst one is flagged. + +```{r} +adrs <- adrs %>% + restrict_derivation( + derivation = derive_var_extreme_flag, + args = params( + by_vars = exprs(STUDYID, USUBJID, ADT), + order = exprs(AVAL, RSSEQ), + new_var = ANL01FL, + mode = "first" + ), + filter = !is.na(AVAL) & AVALC != "MISSING" & ADT >= RANDDT + ) +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, PARAM, AVALC, ADT, RANDDT, ANL01FL) +) +``` + +Here is an alternative example where those records occurring after new +anti-cancer therapy are additionally excluded (where `NACTDT` would be +pre-derived as first date of new anti-cancer therapy. See `{admiralonco}` +[Creating and Using New Anti-Cancer Start Date](nactdt.html) for deriving this +variable). + +```{r, eval=FALSE} +adrs <- adrs %>% + mutate( + ANL01FL = case_when( + !is.na(AVAL) & ADT >= RANDDT & ADT < NACTDT ~ "Y", + TRUE ~ NA_character_ + ) + ) +``` + +### Flag Assessments up to First iCPD (`ANL02FL`) {#anl02fl} + +To restrict response data up to and including first reported progressive disease +`ANL02FL` flag could be created by using `{admiral}` function +`admiral::derive_var_relative_flag()`. + +```{r} +adrs <- adrs %>% + derive_var_relative_flag( + by_vars = exprs(STUDYID, USUBJID), + order = exprs(ADT, RSSEQ), + new_var = ANL02FL, + condition = AVALC == "iCPD", + mode = "first", + selection = "before", + inclusive = TRUE + ) +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, AVALC, ADT, ANL01FL, ANL02FL) +) +``` + +### Select Source Assessments for Parameter derivations + +For most parameter derivations the post-baseline overall response assessments up +to and including first iCPD are considered. +```{r} +ovr <- filter(adrs, PARAMCD == "OVR" & ANL01FL == "Y" & ANL02FL == "Y") +``` + +```{r, echo=FALSE} +dataset_vignette( + ovr, + display_vars = exprs(USUBJID, AVISIT, AVALC, ADT, RANDDT) +) +``` + +## Define Events + +The building blocks for the events that contribute to deriving common endpoints +like what constitutes a responder, or a Best Overall Response of complete +response (CR), ... are predefined in admiralonco for RECIST 1.1 (see [Pre-Defined +Response Event Objects](../reference/event_objects.html)). New Response Event Objects +are needed for iRECIST and any study-specific needs. + +```{r} +icpd_y <- event_joined( + description = paste( + "Define confirmed progressive disease (iCPD) as", + "iUPD followed by iCPD with only other iUPD and NE responses in between" + ), + dataset_name = "ovr", + join_vars = exprs(AVALC, ADT), + join_type = "after", + first_cond_upper = AVALC.join == "iCPD", + condition = AVALC == "iUPD" & + all(AVALC.join %in% c("iCPD", "iUPD", "NE")), + set_values_to = exprs(AVALC = "Y") +) + +iupd_y <- event_joined( + description = paste( + "Define unconfirmed progressive disease (iUPD) as", + "iUPD followed only by other iUPD or NE responses" + ), + dataset_name = "ovr", + join_vars = exprs(AVALC, ADT), + join_type = "all", + condition = ADT <= ADT.join & AVALC == "iUPD" & all(AVALC.join %in% c("iUPD", "NE")), + set_values_to = exprs(AVALC = "Y") +) + +no_data_n <- event( + description = "Define no response for all patients in adsl (should be used as last event)", + dataset_name = "adsl", + condition = TRUE, + set_values_to = exprs(AVALC = "N"), + keep_source_vars = adsl_vars +) + +no_data_missing <- event( + description = paste( + "Define missing response (MISSING) for all patients in adsl (should be used", + "as last event)" + ), + dataset_name = "adsl", + condition = TRUE, + set_values_to = exprs(AVALC = "MISSING"), + keep_source_vars = adsl_vars +) +``` + +### Handling Different Input Response Values {#different_resp_vals} +If `RS` contains other response values than the iRECIST responses, the `event()` +and `event_joined()` can be adjusted to cover this scenario. For example, if +RECIST responses (`"CR"`, `"PR"`, `"SD"`, ...) are collected up to first PD and +iRECIST responses (`"iCR"`, `"iPR"`, `"iSD"`, ...) thereafter, the `event()` +object defining unconfirmed response can be adjusted in the following way. +``` +irsp_y <- event( + description = "Define CR, iCR, PR, or iPR as (unconfirmed) response", + dataset_name = "ovr", + condition = AVALC %in% c("CR", "iCR", "PR", "iPR"), + set_values_to = exprs(AVALC = "Y") +) + +``` + +## Derive Confirmed and Unconfirmed Progressive Disease Parameter {#pd} + +Now that we have the input records prepared above with any +company-specific requirements, we can start to derive new parameter +records. For the parameter derivations, all values except those +overwritten by `set_values_to` argument are kept from the earliest +occurring input record fulfilling the required criteria. + +When an `iCPD` occurs, the date of progression would be the first occurrence of `iUPD` in that block. +For example, when we have values of `iUPD`, `iUPD`, and `iCPD`, the iRECIST `PD` date would +be the first occurrence of `iUPD`. In cases where we have `SD`, `SD`, `iUPD`, `PR`, `PR`, `iUPD`, and `iCPD`, +the iRECIST `PD` date would be the second occurrence of `iUPD`. + +The function `admiral::derive_extreme_records()`, in conjunction with the event `icpd_y`, +could be used to find the date of the first `iUPD`. + +For the Unconfirmed Progressive Disease Parameter, it can be of interest to look at `iUPD` that has +never been confirmed and no subsequent `iSD`, `iPR` or `iCR` has been observed. + +```{r} +adrs <- adrs %>% + derive_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + order = exprs(ADT), + mode = "first", + source_datasets = list( + ovr = ovr, + adsl = adsl + ), + events = list(icpd_y, no_data_n), + set_values_to = exprs( + PARAMCD = "ICPD", + PARAM = "iRECIST Confirmation of Disease Progression by Investigator", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST", + AVAL = yn_to_numeric(AVALC), + ANL01FL = "Y" + ) + ) + +ovr_orig <- ovr +ovr <- ovr %>% + group_by(USUBJID) %>% + filter(ADT >= max_cond(var = ADT, cond = AVALC == "iUPD")) %>% + ungroup(USUBJID) + +adrs <- adrs %>% + derive_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + order = exprs(ADT), + mode = "first", + source_datasets = list( + ovr = ovr, + adsl = adsl + ), + events = list(iupd_y, no_data_n), + set_values_to = exprs( + PARAMCD = "IUPD", + PARAM = "iRECIST Unconfirmed Disease Progression by Investigator", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST", + AVAL = yn_to_numeric(AVALC), + ANL01FL = "Y" + ) + ) +ovr <- ovr_orig +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, PARAM, AVALC, ADT, ANL01FL), + filter = PARAMCD %in% c("ICPD", "IUPD") +) +``` + +For progressive disease and response shown in steps here and below, in our +examples we show these as `ADRS` parameters, but they could equally be +achieved via `ADSL` dates or `ADEVENT` parameters.If you prefer to store +as an ADSL date, then the function `admiral::derive_var_extreme_dt()` +could be used to find the date of first `iCPD` as a variable, rather than +as a new parameter record. + +## Derive Response Parameter {#rsp} + +The function `admiral::derive_extreme_event()` can then be used to find the date +of first response. In the below example, the response condition has been defined +as `iCR` or `iPR` via the event `irsp_y` that was created for iRECIST. + +```{r} +irsp_y <- event( + description = "Define iCR or iPR as (unconfirmed) response", + dataset_name = "ovr", + condition = AVALC %in% c("iCR", "iPR"), + set_values_to = exprs(AVALC = "Y") +) + +adrs <- adrs %>% + derive_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + order = exprs(ADT), + mode = "first", + events = list(irsp_y, no_data_n), + source_datasets = list( + ovr = ovr, + adsl = adsl + ), + set_values_to = exprs( + PARAMCD = "IRSP", + PARAM = "iRECIST Response by Investigator (confirmation not required)", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST", + AVAL = yn_to_numeric(AVALC), + ANL01FL = "Y" + ) + ) +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, PARAM, AVALC, ADT, ANL01FL), + filter = PARAMCD == "IRSP" +) +``` + +## Derive Clinical Benefit Parameter {#cb} + +The function `admiral::derive_extreme_event()` can then be used to derive the +clinical benefit parameter, which we define as a patient having had a response +or a sustained period of time before first `iUPD`. This could also be known as +disease control. In this example the "sustained period" has been defined as 42 +days after randomization date via the created `icb_y` event. + +```{r} +icb_y <- event( + description = paste( + "Define iCR, iPR, iSD, or NON-iCR/NON-iUPD occuring at least 42 days after", + "randomization as clinical benefit" + ), + dataset_name = "ovr", + condition = AVALC %in% c("iCR", "iPR", "iSD", "NON-iCR/NON-iUPD") & + ADT >= RANDDT + 42, + set_values_to = exprs(AVALC = "Y") +) +``` + +Please note that the result `AVALC = "Y"` is defined by the first _two_ events +specified for `events`. For subjects with observations fulfilling both events +the one with the earlier date should be selected (and not the first one in the +list). Thus `ignore_event_order` and `tmp_event_nr_var` are not specified. + +```{r} +adrs <- adrs %>% + derive_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + order = exprs(desc(AVALC), ADT), + mode = "first", + events = list(irsp_y, icb_y, no_data_n), + source_datasets = list( + ovr = ovr, + adsl = adsl + ), + set_values_to = exprs( + PARAMCD = "ICB", + PARAM = "iRECIST Clinical Benefit by Investigator (confirmation for response not required)", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST", + AVAL = yn_to_numeric(AVALC), + ANL01FL = "Y" + ), + check_type = "none" + ) +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, PARAM, AVALC, ADT, RANDDT, ANL01FL), + filter = PARAMCD == "ICB" +) +``` + +## Derive Best Overall Response Parameter {#bor} + +The function `admiral::derive_extreme_event()` can be used to derive the best +overall response (without confirmation required) parameter. Similar to the above +function you can optionally decide what period would you consider an `iSD` or +`NON-iCR/NON-iUPD` as being eligible from. In this example, 42 days after +randomization date has been used again. + +Please note that the order of the events specified for `events` is important. +For example, a subject with `iPR`, `iPR`, `iCR` qualifies for both `ibor_icr` and +`ibor_ipr`. As `ibor_icr` is listed before `ibor_ipr`, `iCR` is selected as best overall +response for this subject. + +```{r} +ibor_icr <- event( + description = "Define complete response (iCR) for best overall response (iBOR)", + dataset_name = "ovr", + condition = AVALC == "iCR", + set_values_to = exprs(AVALC = "iCR") +) + +ibor_ipr <- event( + description = "Define partial response (iPR) for best overall response (iBOR)", + dataset_name = "ovr", + condition = AVALC == "iPR", + set_values_to = exprs(AVALC = "iPR") +) + +ibor_isd <- event( + description = paste( + "Define stable disease (iSD) for best overall response (iBOR) as iCR, iPR, or iSD", + "occurring at least 42 days after randomization" + ), + dataset_name = "ovr", + condition = AVALC %in% c("iCR", "iPR", "iSD") & ADT >= RANDDT + 42, + set_values_to = exprs(AVALC = "iSD") +) + +ibor_non_icriupd <- event( + description = paste( + "Define NON-iCR/NON-iUPD for best overall response (iBOR) as NON-iCR/NON-iUPD", + "occuring at least 42 days after randomization" + ), + dataset_name = "ovr", + condition = AVALC == "NON-iCR/NON-iUPD" & ADT >= RANDDT + 42, + set_values_to = exprs(AVALC = "NON-iCR/NON-iUPD") +) + + +ibor_icpd <- event_joined( + description = paste( + "Define confirmed progressive disease (iCPD) for best overall response (iBOR) as", + "iUPD followed by iCPD with only other iUPD and NE responses in between" + ), + dataset_name = "ovr", + join_vars = exprs(AVALC, ADT), + join_type = "after", + first_cond_upper = AVALC.join == "iCPD", + condition = AVALC == "iUPD" & + all(AVALC.join %in% c("iCPD", "iUPD", "NE")), + set_values_to = exprs(AVALC = "iCPD") +) + + +ibor_iupd <- event( + description = "Define unconfirmed progressive disease (iUPD) for best overall response (iBOR)", + dataset_name = "ovr", + condition = AVALC == "iUPD", + set_values_to = exprs(AVALC = "iUPD") +) + +ibor_ne <- event( + description = paste( + "Define not evaluable (NE) for best overall response (iBOR) as iCR, iPR, iSD,", + "NON-iCR/NON-iUPD, or NE (should be specified after ibor_isd and ibor_non_icriupd)" + ), + dataset_name = "ovr", + condition = AVALC %in% c("iCR", "iPR", "iSD", "NON-iCR/NON-iUPD", "NE"), + set_values_to = exprs(AVALC = "NE") +) + +adrs <- adrs %>% + derive_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + tmp_event_nr_var = event_nr, + order = exprs(event_nr, ADT), + mode = "first", + source_datasets = list( + ovr = ovr, + adsl = adsl + ), + events = list(ibor_icr, ibor_ipr, ibor_isd, ibor_non_icriupd, ibor_icpd, ibor_iupd, ibor_ne, no_data_missing), + set_values_to = exprs( + PARAMCD = "IBOR", + PARAM = "iRECIST Best Overall Response by Investigator (confirmation not required)", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST", + AVAL = aval_resp_new(AVALC), + ANL01FL = "Y" + ) + ) +``` + +```{r, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, PARAM, AVALC, ADT, RANDDT, ANL01FL), + filter = PARAMCD == "IBOR" +) +``` + +## Derive Response Parameters requiring Confirmation {#confirm} + +Any of the above response parameters can be repeated for "confirmed" responses +only. For these the function `admiral::derive_extreme_event()` can be used with +different events. Some of the other functions from above can then be re-used +passing in these confirmed response records. See the examples below of derived +parameters requiring confirmation. The assessment and the confirmatory +assessment here need to occur at least 28 days apart *(without any +1 applied to +this calculation of days between visits)*, using the `icrsp_y_cr`, +`icrsp_y_ipr`, `icbor_icr`, and `icbor_ipr` event. Here the confirmation period +and the `keep_source_vars` argument is updated, as well as the `first_cond_upper` and +`condition` for the iRECIST values. + +```{r } +confirmation_period <- 28 + +icrsp_y_icr <- event_joined( + description = paste( + "Define confirmed response as iCR followed by iCR at least", + confirmation_period, + "days later and at most one NE in between" + ), + dataset_name = "ovr", + join_vars = exprs(AVALC, ADT), + join_type = "after", + order = exprs(ADT), + first_cond_upper = AVALC.join == "iCR" & + ADT.join >= ADT + days(confirmation_period), + condition = AVALC == "iCR" & + all(AVALC.join %in% c("iCR", "NE")) & + count_vals(var = AVALC.join, val = "NE") <= 1, + set_values_to = exprs(AVALC = "Y") +) + +icrsp_y_ipr <- event_joined( + description = paste( + "Define confirmed response as iPR followed by iCR or iPR at least", + confirmation_period, + "days later at most one NE in between, and no iPR after iCR" + ), + dataset_name = "ovr", + join_vars = exprs(AVALC, ADT), + join_type = "after", + order = exprs(ADT), + first_cond_upper = AVALC.join %in% c("iCR", "iPR") & + ADT.join >= ADT + days(confirmation_period), + condition = AVALC == "iPR" & + all(AVALC.join %in% c("iCR", "iPR", "NE")) & + count_vals(var = AVALC.join, val = "NE") <= 1 & + ( + min_cond( + var = ADT.join, + cond = AVALC.join == "iCR" + ) > max_cond(var = ADT.join, cond = AVALC.join == "iPR") | + count_vals(var = AVALC.join, val = "iCR") == 0 | + count_vals(var = AVALC.join, val = "iPR") == 0 + ), + set_values_to = exprs(AVALC = "Y") +) + +icbor_icr <- event_joined( + description = paste( + "Define complete response (iCR) for confirmed best overall response (iCBOR) as", + "iCR followed by iCR at least", + confirmation_period, + "days later and at most one NE in between" + ), + dataset_name = "ovr", + join_vars = exprs(AVALC, ADT), + join_type = "after", + first_cond_upper = AVALC.join == "iCR" & + ADT.join >= ADT + confirmation_period, + condition = AVALC == "iCR" & + all(AVALC.join %in% c("iCR", "NE")) & + count_vals(var = AVALC.join, val = "NE") <= 1, + set_values_to = exprs(AVALC = "iCR") +) + +icbor_ipr <- event_joined( + description = paste( + "Define partial response (iPR) for confirmed best overall response (iCBOR) as", + "iPR followed by iCR or iPR at least", + confirmation_period, + "days later, at most one NE in between and no iPR after iCR" + ), + dataset_name = "ovr", + join_vars = exprs(AVALC, ADT), + join_type = "after", + first_cond_upper = AVALC.join %in% c("iCR", "iPR") & + ADT.join >= ADT + confirmation_period, + condition = AVALC == "iPR" & + all(AVALC.join %in% c("iCR", "iPR", "NE")) & + count_vals(var = AVALC.join, val = "NE") <= 1 & + ( + min_cond( + var = ADT.join, + cond = AVALC.join == "iCR" + ) > max_cond(var = ADT.join, cond = AVALC.join == "iPR") | + count_vals(var = AVALC.join, val = "iCR") == 0 | + count_vals(var = AVALC.join, val = "iPR") == 0 + ), + set_values_to = exprs(AVALC = "iPR") +) +``` + +Please note that the result `AVALC = "Y"` for confirmed clinical benefit is +defined by the first _two_ events specified for `events`. For subjects with +observations fulfilling both events the one with the earlier date should be +selected (and not the first one in the list). + +```{r} +adrs <- adrs %>% + derive_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + order = exprs(desc(AVALC), ADT), + mode = "first", + source_datasets = list( + ovr = ovr, + adsl = adsl + ), + events = list(icrsp_y_icr, icrsp_y_ipr, no_data_n), + set_values_to = exprs( + PARAMCD = "ICRSP", + PARAM = "iRECIST Confirmed Response by Investigator", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST", + AVAL = yn_to_numeric(AVALC), + ANL01FL = "Y" + ) + ) + +adrs <- adrs %>% + derive_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + order = exprs(desc(AVALC), ADT), + mode = "first", + events = list(icrsp_y_icr, icrsp_y_ipr, icb_y, no_data_n), + source_datasets = list( + ovr = ovr, + adsl = adsl + ), + set_values_to = exprs( + PARAMCD = "ICCB", + PARAM = "iRECIST Confirmed Clinical Benefit by Investigator", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST", + AVAL = yn_to_numeric(AVALC), + ANL01FL = "Y" + ), + check_type = "none" + ) + +adrs <- adrs %>% + derive_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + tmp_event_nr_var = event_nr, + order = exprs(event_nr, ADT), + mode = "first", + events = list(icbor_icr, icbor_ipr, ibor_isd, ibor_non_icriupd, ibor_icpd, ibor_iupd, ibor_ne, no_data_missing), + source_datasets = list( + ovr = ovr, + adsl = adsl + ), + set_values_to = exprs( + PARAMCD = "ICBOR", + PARAM = "iRECIST Best Confirmed Overall Response by Investigator", + PARCAT1 = "Tumor Response", + PARCAT2 = "Investigator", + PARCAT3 = "iRECIST", + AVAL = aval_resp(AVALC), + ANL01FL = "Y" + ) + ) +``` + +```{r, eval=TRUE, echo=FALSE} +dataset_vignette( + adrs, + display_vars = exprs(USUBJID, AVISIT, PARAMCD, PARAM, AVALC, ADT, RANDDT, ANL01FL), + filter = PARAMCD %in% c("ICRSP", "ICCB", "ICBOR") +) +``` +## Other Endpoints {#other} + +The following parameters may also be added: + +IBCP - iRECIST Best Overall Response of CR/PR by Investigator (confirmation not required)
+ICBCP - iRECIST Best Confirmed Overall Response of CR/PR by Investigator
+IOVRB - iRECIST Overall Response by BICR
+ILSTA - iRECIST Last Disease Assessment by Investigator
+IMDIS - iRECIST Measurable Disease at Baseline by Investigator + +For examples on the additional endpoints, please see [Creating ADRS (Including Non-standard Endpoints)](adrs.html). diff --git a/vignettes/nactdt.Rmd b/vignettes/nactdt.Rmd index 94c5decf..6c5b0f46 100644 --- a/vignettes/nactdt.Rmd +++ b/vignettes/nactdt.Rmd @@ -13,35 +13,6 @@ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) -library(admiralonco) -link <- function(text, url) { - return( - paste0( - "[", text, "]", - "(", url, ")" - ) - ) -} -dyn_link <- function(text, - base_url, - relative_url = "", - # Change to TRUE when admiral adopts multiversion docs - is_multiversion = FALSE, - multiversion_default_ref = "main") { - url <- paste(base_url, relative_url, sep = "/") - if (is_multiversion) { - url <- paste( - base_url, - Sys.getenv("BRANCH_NAME", multiversion_default_ref), - relative_url, - sep = "/" - ) - } - return(link(text, url)) -} -# Other variables -admiral_homepage <- "https://pharmaverse.github.io/admiral/cran-release" - library(admiraldev) ``` @@ -72,7 +43,9 @@ library(admiral) library(pharmaverseadam) library(dplyr) +data("adsl") adsl_onco <- adsl +data("adrs_onco") cm <- tribble( ~STUDYID, ~USUBJID, ~CMCAT, ~CMSCAT, ~CMTRT, ~CMSTDTC, @@ -121,24 +94,29 @@ dataset_vignette( ## Multiple Sources - Prerequisite Steps {#multiinput} -To derive the New Anti-Cancer Therapy start date with data from multiple sources, the function `admiral::derive_var_extreme_dt()` can be used, or if time part is needed, `admiral::derive_var_extreme_dtm()` can be used. - +To derive the New Anti-Cancer Therapy start date with data from multiple +sources, the function `admiral::derive_vars_extreme_event()` can be used. ### Prerequisite -Prior to calling the function, an input `date_source` object must be created for each source dataset using `admiral::date_source()`. Within this function, any company-specific subsetting can be passed to the `filter` argument. If numeric version of the dates will be needed, `admiral::convert_dtc_to_dt()`, or if time part is needed, `admiral::convert_dtc_to_dtm()` can be used as part of an expression for the `new_vars` argument. +Prior to calling the function, an input `event` object must be created for each +source dataset using `admiral::event()`. Within this function, any +company-specific subsetting can be passed to the `condition` argument. If +numeric version of the dates will be needed, `admiral::convert_dtc_to_dt()`, or +if time part is needed, `admiral::convert_dtc_to_dtm()` can be used as part of +an expression for the `set_values_to` argument. ```{r message=FALSE} -cm_date <- date_source( +cm_date <- event( dataset_name = "cm", - filter = CMSCAT == "CHEMOTHERAPY" & CMCAT == "ON TREATMENT" & !is.na(CMSTDTC), - date = convert_dtc_to_dt(CMSTDTC) + condition = CMSCAT == "CHEMOTHERAPY" & CMCAT == "ON TREATMENT" & !is.na(CMSTDTC), + set_values_to = exprs(NACTDT = convert_dtc_to_dt(CMSTDTC)) ) -pr_date <- date_source( +pr_date <- event( dataset_name = "pr", - filter = PRCAT == "CANCER RELATED" & PRSCAT == "ON TREATMENT" & !is.na(PRSTDTC), - date = convert_dtc_to_dt(PRSTDTC) + condition = PRCAT == "CANCER RELATED" & PRSCAT == "ON TREATMENT" & !is.na(PRSTDTC), + set_values_to = exprs(NACTDT = convert_dtc_to_dt(PRSTDTC)) ) ``` @@ -148,9 +126,11 @@ After completion of the prerequisite step, the new anti-cancer date can be deriv ```{r message=FALSE} adsl <- adsl_onco %>% - derive_var_extreme_dt( - new_var = NACTDT, - cm_date, pr_date, + derive_vars_extreme_event( + by_vars = exprs(STUDYID, USUBJID), + order = exprs(NACTDT), + new_vars = exprs(NACTDT), + events = list(cm_date, pr_date), source_datasets = list( cm = cm, pr = pr @@ -173,28 +153,32 @@ Please refer to `{admiralonco}` [Derive `ANL01FL`](adrs.html#anl01fl) for an exa ## Derive Date Parameter {#par} -As of `{admiral}` version 0.11.0, `admiral::derive_param_extreme_record()` is recommended to be used for deriving parameter based on the first or last observation from single and multiple sources. +The `{admiral}` function `admiral::derive_extreme_event()` can be used for +deriving parameter based on the first or last observation from single and +multiple sources. -Based on individual company standards, this parameter may be added to an event or date dataset such as `ADEVENT` or `ADDATES`, which are generally intermediate datasets to `ADTTE`. For demonstration purpose, a new anti-cancer date parameter will be merged into `ADRS`. A list of `record_source()` objects is expected and this will contain the sources of the dates and any company specific filtering. +Based on individual company standards, this parameter may be added to an event +or date dataset such as `ADEVENT` or `ADDATES`, which are generally intermediate +datasets to `ADTTE`. For demonstration purpose, a new anti-cancer date parameter +will be merged into `ADRS`. A list of `event()` objects is expected and this +will contain the sources of the dates and any company specific filtering. ```{r, eval=TRUE, echo=TRUE} -library(admiralonco) - -adrs <- derive_param_extreme_record( +adrs <- derive_extreme_event( dataset = adrs_onco, - sources = list( - records_source( + events = list( + event( dataset_name = "cm", - filter = CMSCAT == "CHEMOTHERAPY" & CMCAT == "ON TREATMENT" & !is.na(CMSTDTC), - new_vars = exprs( + condition = CMSCAT == "CHEMOTHERAPY" & CMCAT == "ON TREATMENT" & !is.na(CMSTDTC), + set_values_to = exprs( ADT = convert_dtc_to_dt(CMSTDTC), AVALC = CMTRT ) ), - records_source( + event( dataset_name = "pr", - filter = PRCAT == "CANCER RELATED" & PRSCAT == "ON TREATMENT" & !is.na(PRSTDTC), - new_vars = exprs( + condition = PRCAT == "CANCER RELATED" & PRSCAT == "ON TREATMENT" & !is.na(PRSTDTC), + set_values_to = exprs( ADT = convert_dtc_to_dt(PRSTDTC), AVALC = PRTRT )