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* initial draft * now using exprs * added unit tests * added manual and namespace * lint and style * udpate manual * styler * update manual * fix select * fix example * update news.md * fix VSTEST * fix example * fix documentation * update filter * update manual * added keyword and family * update ad_advs.R template * updated functionality allows for specifyying by_vars * show recursive function * fix bug and improve documentation * updated tests * add warning for forgotten by_vars * style & lint * update manual * added helper documentation * update * half way there :) * clean up ad_adpc * UPDATE VIGNETTES * fix error * styler * Update vignettes/adsl.Rmd Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Update vignettes/bds_exposure.Rmd Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Update R/derive_vars_cat.R Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Update R/derive_vars_cat.R * Update NEWS.md * Update R/derive_vars_cat.R Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update inst/templates/ad_advs.R * update * Update vignettes/bds_finding.Rmd * update style of tibbles * update error message for definition * Simplify assertions. Update test formatting. * updated example * add alternative way * improve wording * Update R/derive_vars_cat.R Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update NEWS.md * Update vignettes/generic.Rmd * update man * remove reliance on assertthat * styler * Update vignettes/bds_finding.Rmd Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update vignettes/bds_exposure.Rmd Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update vignettes/adsl.Rmd Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update R/derive_vars_cat.R Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update R/derive_vars_cat.R Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update R/derive_vars_cat.R Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * update format * update format * format * Update R/derive_vars_cat.R * style & spelling * update tests to tibbles * fix template * switch function * fix alignment * tryout * add ::: to internal function * Update R/derive_vars_cat.R Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update R/derive_vars_cat.R Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * Update R/derive_vars_cat.R Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> * aligned again * update manual * Update R/derive_vars_cat.R Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Update R/derive_vars_cat.R Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Update R/derive_vars_cat.R Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Update R/derive_vars_cat.R Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * added test for error * lint * update to cli_warn * fix style --------- Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,258 @@ | ||
| #' Derive Categorization Variables Like `AVALCATy` and `AVALCAyN` | ||
| #' @param dataset | ||
| #' `r roxygen_param_dataset(expected_vars = c("by_vars", "definition"))` | ||
| #' @param definition List of expressions created by `exprs()`. | ||
| #' Must be in rectangular format and specified using the same syntax as when creating | ||
| #' a `tibble` using the `tribble()` function. | ||
| #' The `definition` object will be converted to a `tibble` using `tribble()` inside this function. | ||
| #' | ||
| #' Must contain: | ||
| #' - the column `condition` which will be converted to a logical expression and | ||
| #' will be used on the `dataset` input. | ||
| #' - at least one additional column with the new column name and | ||
| #' the category value(s) used by the logical expression. | ||
| #' - the column specified in `by_vars` (if `by_vars` is specified) | ||
| #' | ||
| #' e.g. if `by_vars` is not specified: | ||
| #' | ||
| #' ```{r} | ||
| #' #| eval: false | ||
| #' exprs(~condition, ~AVALCAT1, ~AVALCA1N, | ||
| #' AVAL >= 140, ">=140 cm", 1, | ||
| #' AVAL < 140, "<140 cm", 2) | ||
| #' ``` | ||
| #' | ||
| #' e.g. if `by_vars` is specified as `exprs(VSTEST)`: | ||
| #' | ||
| #' ```{r} | ||
| #' #| eval: false | ||
| #' exprs(~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, | ||
| #' "Height", AVAL >= 140, ">=140 cm", 1, | ||
| #' "Height", AVAL < 140, "<140 cm", 2) | ||
| #' ``` | ||
| #' | ||
| #' @param by_vars list of expressions with one element. `NULL` by default. | ||
| #' Allows for specifying by groups, e.g. `exprs(PARAMCD)`. | ||
| #' Variable must be present in both `dataset` and `definition`. | ||
| #' The conditions in `definition` are applied only to those records that match `by_vars`. | ||
| #' The categorization variables are set to `NA` for records | ||
| #' not matching any of the by groups in `definition`. | ||
| #' | ||
| #' | ||
| #' @details | ||
| #' If conditions are overlapping, the row order of `definitions` must be carefully considered. | ||
| #' The **first** match will determine the category. | ||
| #' i.e. if | ||
| #' | ||
| #' `AVAL = 155` | ||
| #' | ||
| #' and the `definition` is: | ||
| #' | ||
| #' ```{r} | ||
| #' #| eval: false | ||
| #' definition <- exprs( | ||
| #' ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, | ||
| #' "Height", AVAL > 170, ">170 cm", 1, | ||
| #' "Height", AVAL <= 170, "<=170 cm", 2, | ||
| #' "Height", AVAL <= 160, "<=160 cm", 3 | ||
| #' ) | ||
| #' ``` | ||
| #' then `AVALCAT1` will be `"<=170 cm"`, as this is the first match for `AVAL`. | ||
| #' If you specify: | ||
| #' | ||
| #' ```{r} | ||
| #' #| eval: false | ||
| #' definition <- exprs( | ||
| #' ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, | ||
| #' "Height", AVAL <= 160, "<=160 cm", 3, | ||
| #' "Height", AVAL <= 170, "<=170 cm", 2, | ||
| #' "Height", AVAL > 170, ">170 cm", 1 | ||
| #' ) | ||
| #' ``` | ||
| #' | ||
| #' Then `AVAL <= 160` will lead to `AVALCAT1 == "<=160 cm"`, | ||
| #' `AVAL` in-between `160` and `170` will lead to `AVALCAT1 == "<=170 cm"`, | ||
| #' and `AVAL <= 170` will lead to `AVALCAT1 == ">170 cm"`. | ||
| #' | ||
| #' However, we suggest to be more explicit when defining the `condition`, to avoid overlap. | ||
| #' In this case, the middle condition should be: | ||
| #' `AVAL <= 170 & AVAL > 160` | ||
| #' | ||
| #' @return The input dataset with the new variables defined in `definition` added | ||
| #' @family der_gen | ||
| #' @keywords der_gen | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' library(dplyr) | ||
| #' library(tibble) | ||
| #' | ||
| #' advs <- tibble::tribble( | ||
| #' ~USUBJID, ~VSTEST, ~AVAL, | ||
| #' "01-701-1015", "Height", 147.32, | ||
| #' "01-701-1015", "Weight", 53.98, | ||
| #' "01-701-1023", "Height", 162.56, | ||
| #' "01-701-1023", "Weight", NA, | ||
| #' "01-701-1028", "Height", NA, | ||
| #' "01-701-1028", "Weight", NA, | ||
| #' "01-701-1033", "Height", 175.26, | ||
| #' "01-701-1033", "Weight", 88.45 | ||
| #' ) | ||
| #' | ||
| #' definition <- exprs( | ||
| #' ~condition, ~AVALCAT1, ~AVALCA1N, ~NEWCOL, | ||
| #' VSTEST == "Height" & AVAL > 160, ">160 cm", 1, "extra1", | ||
| #' VSTEST == "Height" & AVAL <= 160, "<=160 cm", 2, "extra2" | ||
| #' ) | ||
| #' derive_vars_cat( | ||
| #' dataset = advs, | ||
| #' definition = definition | ||
| #' ) | ||
| #' | ||
| #' # Using by_vars: | ||
| #' definition2 <- exprs( | ||
| #' ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, | ||
| #' "Height", AVAL > 160, ">160 cm", 1, | ||
| #' "Height", AVAL <= 160, "<=160 cm", 2, | ||
| #' "Weight", AVAL > 70, ">70 kg", 1, | ||
| #' "Weight", AVAL <= 70, "<=70 kg", 2 | ||
| #' ) | ||
| #' | ||
| #' derive_vars_cat( | ||
| #' dataset = advs, | ||
| #' definition = definition2, | ||
| #' by_vars = exprs(VSTEST) | ||
| #' ) | ||
| #' | ||
| #' # With three conditions: | ||
| #' definition3 <- exprs( | ||
| #' ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, | ||
| #' "Height", AVAL > 170, ">170 cm", 1, | ||
| #' "Height", AVAL <= 170 & AVAL > 160, "<=170 cm", 2, | ||
| #' "Height", AVAL <= 160, "<=160 cm", 3 | ||
| #' ) | ||
| #' | ||
| #' derive_vars_cat( | ||
| #' dataset = advs, | ||
| #' definition = definition3, | ||
| #' by_vars = exprs(VSTEST) | ||
| #' ) | ||
| #' | ||
| #' # Let's derive both the MCRITyML and the MCRITyMN variables | ||
| #' adlb <- tibble::tribble( | ||
| #' ~USUBJID, ~PARAM, ~AVAL, ~AVALU, ~ANRHI, | ||
| #' "01-701-1015", "ALT", 150, "U/L", 40, | ||
| #' "01-701-1023", "ALT", 70, "U/L", 40, | ||
| #' "01-701-1036", "ALT", 130, "U/L", 40, | ||
| #' "01-701-1048", "ALT", 30, "U/L", 40, | ||
| #' "01-701-1015", "AST", 50, "U/L", 35 | ||
| #' ) | ||
| #' | ||
| #' definition_mcrit <- exprs( | ||
| #' ~PARAM, ~condition, ~MCRIT1ML, ~MCRIT1MN, | ||
| #' "ALT", AVAL <= ANRHI, "<=ANRHI", 1, | ||
| #' "ALT", ANRHI < AVAL & AVAL <= 3 * ANRHI, ">1-3*ANRHI", 2, | ||
| #' "ALT", 3 * ANRHI < AVAL, ">3*ANRHI", 3 | ||
| #' ) | ||
| #' | ||
| #' adlb %>% | ||
| #' derive_vars_cat( | ||
| #' definition = definition_mcrit, | ||
| #' by_vars = exprs(PARAM) | ||
| #' ) | ||
| derive_vars_cat <- function(dataset, | ||
| definition, | ||
| by_vars = NULL) { | ||
| assert_expr_list(definition) | ||
| assert_vars(by_vars, optional = TRUE) | ||
| if (length(by_vars) > 1) { | ||
| cli_abort("{.arg by_vars} must contain just one variable, e.g. {.code exprs(PARAMCD)}") | ||
| } | ||
|
|
||
| assert_data_frame(dataset, | ||
| required_vars = c( | ||
| admiraldev::extract_vars(definition) %>% unique(), | ||
| by_vars | ||
| ) | ||
| ) | ||
|
|
||
| # transform definition to tibble | ||
| names(definition) <- NULL | ||
| definition <- tryCatch( | ||
| { | ||
| tibble::tribble(!!!definition) | ||
| }, | ||
| error = function(e) { | ||
| # Catch the error and append your own message | ||
| cli_abort( | ||
| c( | ||
| paste( | ||
| "Failed to convert {.arg definition} to {.cls tibble}.", | ||
| "{.arg definition} should be specified similarly to how you would", | ||
| "specify a {.cls tibble} using the {.fun tibble::tribble} function so it", | ||
| "can be converted to {.cls tibble} using {.fun tibble::tribble}." | ||
| ), | ||
| e$message | ||
| ) | ||
| ) | ||
| } | ||
| ) | ||
| assert_data_frame(definition, required_vars = c(exprs(condition), by_vars)) | ||
| if (!is.null(by_vars)) { | ||
| # add condition | ||
| definition <- definition %>% | ||
| mutate( | ||
| condition = extend_condition(as.character(condition), | ||
| as.character(by_vars), | ||
| is = !!sym(as.character(by_vars)) | ||
| ) %>% | ||
| parse_exprs() | ||
| ) %>% | ||
| select(-by_vars[[1]]) | ||
| } | ||
|
|
||
| # extract new variable names and conditions | ||
| new_col_names <- names(definition)[!names(definition) == "condition"] | ||
| condition <- definition[["condition"]] | ||
|
|
||
| # warn if new variables already exist | ||
| if (any(new_col_names %in% names(dataset))) { | ||
| cli_warn(paste( | ||
| "Column(s) in {.arg definition} already exist in {.arg dataset}.", | ||
| "Did you forget to specify {.arg by_vars},", | ||
| "or are you rerunning your code?" | ||
| )) | ||
| } | ||
|
|
||
| # (re)apply the function for each new variable name and iteratively derive the categories | ||
| new_dataset <- reduce(new_col_names, function(.data, col_name) { | ||
| # extract conditions | ||
| values <- definition[[col_name]] | ||
|
|
||
| .data %>% | ||
| mutate(!!sym(col_name) := eval(rlang::call2( | ||
| "case_when", | ||
| !!!map2(condition, values, ~ expr(!!.x ~ !!.y)) | ||
| ))) | ||
| }, .init = dataset) | ||
|
|
||
| return(new_dataset) | ||
| } | ||
|
|
||
| #' Extend a condition string by adding a new condition based on a variable and its value | ||
| #' | ||
| #' This internal helper function extends a condition string by appending a new condition | ||
| #' that checks if a variable equals a specific value. | ||
| #' | ||
| #' @param cond A character string representing an existing condition. | ||
| #' @param var A character string representing the name of the variable to check. | ||
| #' @param is A character string representing the value the variable should be equal to. | ||
| #' | ||
| #' @return A character string representing the extended condition. | ||
| #' @examples | ||
| #' # Extend an existing condition to include a check for 'AGE == "30"' | ||
| #' admiral:::extend_condition("SEX == 'M'", "AGE", "30") | ||
| #' @keywords internal | ||
| extend_condition <- function(cond, var, is) { | ||
| paste(cond, " & ", var, " == '", is, "'", sep = "") | ||
| } |
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