generated from pharmaverse/admiraltemplate
-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* exploratory programs for read-out files * markdown practice * changes to markdown table layout * basic Rmarkdown file produced & exploratory scripts * draft completion of Read-out file version 1 * format complete of .Rmd for datacutr read-out file, modified process_cut() to enable auto-generation * changed .Rmd file location and combined custom functions within the markdown * read_out function added, exploratory work on updating functions within read_out_2.Rmd * remove .Rmd test scripts * update to the .Rmd text * draft testing files for read_out() function with minor updates to .Rmd * updates made to .Rmd file and function with testing * updates to the read_out() function along with modifications to the .Rmd messages * development of read_out() function and testing continued. * updates to process_cut() and read_out() functions, completion of test-read_out.R * remove excess .Rmd files * remove final_cut argument and section in .Rmd, update file path read_out() * Update read_out.Rmd with reactables package instead of datatables to allow for larger data inputs. * removed old datacutr read-out file .Rmd * Changes made to the documentation for read-out * update renv.lock files for R4.3.1 * resolving warnings in pull request checks * updates to resolve check errors * updates to read_out.Rmd & read_out.R to address feedback * update to renv.lock file CRAN version * updates to renv file, removed unused packages * revert renv.lock file * updates to renv.lock - include "admiraldev", upgrade "remotes" * update remotes version * troubleshooting - test * update stringi repo to "CRAN" * add author * updates to the read_out function and read_out.Rmd * updated the renv.lock for datacutr R4.3.1 * update the .Rprofile * add library(tibble) to read_out.Rmd * update R version in DESCRIPTION, remove lintr complexity check from process_cut.R * update to R version DESCRIPTION, common.yml & no lint process_cut.R * updates to resolve styler errors * resolve CICD check errors * resolve styler and roxygen2 errors * update the NEWS.md to reflect update in R version
- Loading branch information
1 parent
290d205
commit e3d41f1
Showing
17 changed files
with
2,213 additions
and
434 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1 @@ | ||
| if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) { | ||
| source("renv/activate.R") | ||
| } else { | ||
| options(repos = c(CRAN = "https://cran.rstudio.com")) | ||
| } | ||
| options(repos = c(CRAN = "https://cran.rstudio.com")) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| #' @title Function to generate datacut summary file | ||
| #' | ||
| #' @description Produces a .html file summarizing the changes applied to data during a data cut. | ||
| #' The file will contain an overview for the change in number of records for each dataset, the types | ||
| #' of cut applied and the opportunity to inspect the removed records. | ||
| #' | ||
| #' @param dcut The output datacut dataset (DCUT), created via the `create_dcut()` function, | ||
| #' containing the variable DCUTDTC. | ||
| #' @param patient_cut_data A list of quoted SDTMv domain names in which a patient cut has been. | ||
| #' applied (via the `pt_cut()` function). To be left blank if a patient cut has not been performed | ||
| #' on any domains. | ||
| #' @param date_cut_data A list of quoted SDTMv domain names in which a date cut has been applied. | ||
| #' (via the `date_cut()` function). To be left blank if a date cut has not been performed on any | ||
| #' domains. | ||
| #' @param dm_cut The output dataset, created via the `special_dm_cut()` function, containing | ||
| #' the variables DCUT_TEMP_REMOVE and DCUT_TEMP_DTHCHANGE. | ||
| #' @param no_cut_list List of of quoted SDTMv domain names in which no cut should be applied. To be | ||
| #' left blank if no domains are to remain exactly as source. | ||
| #' @param out_path A character vector of file save path for the summary file; | ||
| #' the default corresponds to the working directory, `getwd()`. | ||
| #' | ||
| #' @return Returns a .html file summarizing the changes made to data during a datacut. | ||
| #' | ||
| #' @export | ||
| #' | ||
| #' @keywords derive | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' dcut <- tibble::tribble( | ||
| #' ~USUBJID, ~DCUTDTM, ~DCUTDTC, | ||
| #' "subject1", lubridate::ymd_hms("2020-10-11T23:59:59"), "2020-10-11T23:59:59", | ||
| #' "subject2", lubridate::ymd_hms("2020-10-11T23:59:59"), "2020-10-11T23:59:59", | ||
| #' "subject4", lubridate::ymd_hms("2020-10-11T23:59:59"), "2020-10-11T23:59:59" | ||
| #' ) | ||
| #' | ||
| #' ae <- tibble::tribble( | ||
| #' ~USUBJID, ~AESEQ, ~AESTDTC, | ||
| #' "subject1", 1, "2020-01-02T00:00:00", | ||
| #' "subject1", 2, "2020-08-31T00:00:00", | ||
| #' "subject1", 3, "2020-10-10T00:00:00", | ||
| #' "subject2", 2, "2020-02-20T00:00:00", | ||
| #' "subject3", 1, "2020-03-02T00:00:00", | ||
| #' "subject4", 1, "2020-11-02T00:00:00", | ||
| #' "subject4", 2, "" | ||
| #' ) | ||
| #' | ||
| #' dm <- tibble::tribble( | ||
| #' ~USUBJID, ~DTHDTC, ~DTHFL, | ||
| #' "subject1", "2020-10-11", "Y", | ||
| #' "subject2", "2020-10-12", "Y", | ||
| #' ) | ||
| #' | ||
| #' dt_ae <- date_cut( | ||
| #' dataset_sdtm = ae, | ||
| #' sdtm_date_var = AESTDTC, | ||
| #' dataset_cut = dcut, | ||
| #' cut_var = DCUTDTM | ||
| #' ) | ||
| #' | ||
| #' pt_ae <- pt_cut( | ||
| #' dataset_sdtm = ae, | ||
| #' dataset_cut = dcut | ||
| #' ) | ||
| #' | ||
| #' dm_cut <- special_dm_cut( | ||
| #' dataset_dm = dm, | ||
| #' dataset_cut = dcut, | ||
| #' cut_var = DCUTDTM | ||
| #' ) | ||
| #' | ||
| #' read_out(dcut, patient_cut_data = list(ae = pt_ae), date_cut_data = list(ae = dt_ae), dm_cut) | ||
| #' } | ||
| read_out <- function(dcut = NULL, | ||
| patient_cut_data = NULL, | ||
| date_cut_data = NULL, | ||
| dm_cut = NULL, | ||
| no_cut_list = NULL, | ||
| out_path = ".") { | ||
| if (!is.null(dcut)) { | ||
| assert_data_frame(dcut, | ||
| required_vars = exprs(USUBJID, DCUTDTC) | ||
| ) | ||
| } | ||
| if (!is.null(patient_cut_data)) { | ||
| assert_that(is.list(patient_cut_data) & !is.data.frame(patient_cut_data), | ||
| msg = "patient_cut_data must be a list. \n | ||
| Note: If you have not used or do not with to view patient cut on any SDTMv domains, then | ||
| please leave patient_cut_data empty, in which case a default value of NULL will be used." | ||
| ) | ||
|
|
||
| for (i in seq_along(patient_cut_data)) { | ||
| assert_data_frame(patient_cut_data[[i]], | ||
| required_vars = exprs(USUBJID, DCUT_TEMP_REMOVE) | ||
| ) | ||
|
|
||
| assert_that(rlang::is_named(patient_cut_data[i]), | ||
| msg = "All elements patient_cut_data must be named with corresponding domain" | ||
| ) | ||
| } | ||
| } | ||
| if (!is.null(date_cut_data)) { | ||
| assert_that(is.list(date_cut_data) & !is.data.frame(date_cut_data), | ||
| msg = "date_cut_data must be a list. \n | ||
| Note: If you have not used or do not with to view date cut on any SDTMv domains, then please | ||
| leave date_cut_data empty, in which case a default value of NULL will be used." | ||
| ) | ||
| for (i in seq_along(date_cut_data)) { | ||
| assert_data_frame(date_cut_data[[i]], | ||
| required_vars = exprs(USUBJID, DCUT_TEMP_REMOVE) | ||
| ) | ||
|
|
||
| assert_that(rlang::is_named(date_cut_data[i]), | ||
| msg = "All elements in date_cut_data must be named with corresponding domain" | ||
| ) | ||
| } | ||
| } | ||
| if (!is.null(dm_cut)) { | ||
| assert_data_frame(dm_cut, | ||
| required_vars = exprs(USUBJID, DCUT_TEMP_REMOVE, DCUT_TEMP_DTHCHANGE) | ||
| ) | ||
| } | ||
| if (!is.null(no_cut_list)) { | ||
| assert_that(is.list(no_cut_list) & !is.data.frame(no_cut_list), | ||
| msg = "no_cut_list must be a list. \n | ||
| Note: If you have not used or do not with to view the SDTMv domains where no cut has been | ||
| applied, then please leave no_cut_list empty, in which case a default value of NULL will be | ||
| used." | ||
| ) | ||
| for (i in seq_along(no_cut_list)) { | ||
| assert_data_frame(no_cut_list[[i]]) | ||
|
|
||
| assert_that(rlang::is_named(no_cut_list[i]), | ||
| msg = "All elements in no_cut_list must be named with corresponding domain" | ||
| ) | ||
| } | ||
| } | ||
| rmarkdown::render( | ||
| paste0(system.file(package = "datacutr"), | ||
| path = "/read-out/read_out.Rmd" | ||
| ), | ||
| output_file = paste("datacut_", format(Sys.time(), "%Y-%m-%d_%H:%M:%S", ".html")), | ||
| output_dir = out_path | ||
| ) | ||
| } |
Oops, something went wrong.