253 feature request deprecatesupersede derive vars crit #254
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federicobaratin
added
documentation
ahasoplakus
requested review from
ahasoplakus and
manciniedoardo
and removed request for
vikrams95
ahasoplakus
requested changes
Dec 12, 2024
R/derive_vars_crit.R
Outdated
Comment on lines
6
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13
| #' @export | ||
| #' @keywords der_var | ||
| #' @family der_var | ||
| #' | ||
| #' @examples | ||
| #' library(tibble) | ||
| #' library(admiral) | ||
| #' library(admiraldev) | ||
| #' library(dplyr) | ||
| #' | ||
| #' input <- tribble( | ||
| #' ~USUBJID, ~AVISITN, ~ISCAT, ~PARAMCD, ~AVAL, ~ISLLOQ, | ||
| #' "999999-000001", 10, "IMMUNOLOGY", "J0033VN", 2, 4, | ||
| #' "999999-000001", 10, "IMMUNOLOGY", "I0019NT", 3, 6, | ||
| #' "999999-000001", 10, "IMMUNOLOGY", "M0019LN", 4, 4, | ||
| #' "999999-000001", 10, "IMMUNOLOGY", "R0003MA", 3, 6, | ||
| #' "999999-000001", 30, "IMMUNOLOGY", "J0033VN", 60, 4, | ||
| #' "999999-000001", 30, "IMMUNOLOGY", "I0019NT", 567, 6, | ||
| #' "999999-000001", 30, "IMMUNOLOGY", "M0019LN", 659, 4, | ||
| #' "999999-000001", 30, "IMMUNOLOGY", "R0003MA", 250, 6, | ||
| #' "999999-000002", 10, "IMMUNOLOGY", "J0033VN", 2, 4, | ||
| #' "999999-000002", 10, "IMMUNOLOGY", "I0019NT", 7, 6, | ||
| #' "999999-000002", 10, "IMMUNOLOGY", "M0019LN", 5, 4, | ||
| #' "999999-000002", 10, "IMMUNOLOGY", "R0003MA", 3, 6, | ||
| #' "999999-000002", 30, "IMMUNOLOGY", "J0033VN", 55, 4, | ||
| #' "999999-000002", 30, "IMMUNOLOGY", "I0019NT", 89, 6, | ||
| #' "999999-000002", 30, "IMMUNOLOGY", "M0019LN", 990, 4, | ||
| #' "999999-000002", 30, "IMMUNOLOGY", "R0003MA", 340, 6, | ||
| #' "999999-000003", 10, "IMMUNOLOGY", "J0033VN", 3, 4, | ||
| #' "999999-000003", 10, "IMMUNOLOGY", "I0019NT", 6, 6, | ||
| #' "999999-000003", 10, "IMMUNOLOGY", "M0019LN", 2, 4, | ||
| #' "999999-000003", 10, "IMMUNOLOGY", "R0003MA", 2, 6, | ||
| #' "999999-000003", 30, "IMMUNOLOGY", "J0033VN", 45, 4, | ||
| #' "999999-000003", 30, "IMMUNOLOGY", "I0019NT", 381, 6, | ||
| #' "999999-000003", 30, "IMMUNOLOGY", "M0019LN", 542, 4, | ||
| #' "999999-000003", 30, "IMMUNOLOGY", "R0003MA", NA, 6 | ||
| #' ) | ||
| #' | ||
| #' | ||
| #' derive_vars_crit( | ||
| #' dataset = input, | ||
| #' prefix = "CRIT1", | ||
| #' crit_label = "Titer >= ISLLOQ", | ||
| #' condition = !is.na(AVAL) & !is.na(ISLLOQ), | ||
| #' criterion = AVAL >= ISLLOQ | ||
| #' ) | ||
| #' | ||
| derive_vars_crit <- function(dataset, prefix, crit_label, condition, criterion) { | ||
| condition <- assert_filter_cond(enquo(condition)) | ||
| criterion <- assert_filter_cond(enquo(criterion)) | ||
|
|
||
| var_char <- paste0(prefix, "FL") | ||
| var_num <- paste0(prefix, "FN") | ||
|
|
||
| if (grepl("CRIT", prefix)) { | ||
| data <- dataset %>% | ||
| mutate( | ||
| `:=`( | ||
| !!var_char, | ||
| case_when( | ||
| !(!!condition) ~ NA_character_, | ||
| !!criterion & !!condition ~ "Y", | ||
| !(!!criterion) & !!condition ~ "N" | ||
| ) | ||
| ), | ||
| `:=`( | ||
| !!var_num, | ||
| case_when( | ||
| !(!!condition) ~ NA_real_, | ||
| !!criterion & !!condition ~ 1, | ||
| !(!!criterion) & !!condition ~ 0 | ||
| ) | ||
| ), | ||
| `:=`( | ||
| !!prefix, | ||
| case_when( | ||
| !(!!condition) ~ NA_character_, | ||
| !!criterion & !!condition ~ crit_label, | ||
| !(!!criterion) & !!condition ~ crit_label | ||
| ) | ||
| ) | ||
| ) | ||
| } else { | ||
| data <- dataset %>% | ||
| mutate( | ||
| `:=`( | ||
| !!var_char, | ||
| case_when( | ||
| !(!!condition) ~ NA_character_, | ||
| !!criterion & !!condition ~ "Y", | ||
| !(!!criterion) & !!condition ~ "N" | ||
| ) | ||
| ) | ||
| ) | ||
| } | ||
|
|
||
| return(data) | ||
| } | ||
| #' @keywords deprecated | ||
| #' . |
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Hi @federicobaratin Thanks for making the changes. Instead of completely removing the function please adhere to the deprecation strategy for admiral packages as mentioned here https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation
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Hi Sukalpo, I have updated the function description.
I followed the strategy, by updating relative fields (function description, family and keywords) and removed examples, as suggested. Thanks!
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Hi @ahasoplakus, I have corrected most of the errors and now both ADIS template and vignette are fine. Same for the admiralvaccine function that need to be deprecated.
I think one link need to be updated in ADFACE. If you provide me the correct one, I can update it for you.
The other issue is that ADIS template does not recognize the new admiral function.
Please, let me know :)
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Thank you for your Pull Request! We have developed this task checklist from the Development Process Guide 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
develbranch until you have checked off each task.styler::style_file()to style R and Rmd filesdevtools::document()so all.Rdfiles in themanfolder and theNAMESPACEfile in the project root are updated appropriatelyNEWS.mdif the changes pertain to a user-facing function (i.e. it has an@exporttag) or documentation aimed at users (rather than developers)pkgdown::build_site()and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.lintr::lint_package()R CMD checklocally and address all errors and warnings -devtools::check()