From 963decf9c0ae5c928948656cec15e81d524bc1b5 Mon Sep 17 00:00:00 2001 From: CarlosEpiStats Date: Wed, 10 Jun 2026 14:50:51 +0000 Subject: [PATCH 1/3] * Add loggers and display error if wrong date variable * Add RFSTDT as default study start date --- DESCRIPTION | 1 + R/mod_calculate_fct_data.R | 34 ++++++++ R/mod_upload.R | 4 +- renv.lock | 160 +++++++++++++++++++++++++------------ 4 files changed, 146 insertions(+), 53 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 46525da..03aa7bd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -21,6 +21,7 @@ Imports: DT, golem, haven, + logger, metafor, pkgload, plotly, diff --git a/R/mod_calculate_fct_data.R b/R/mod_calculate_fct_data.R index 2ed89ad..6cdd8b7 100644 --- a/R/mod_calculate_fct_data.R +++ b/R/mod_calculate_fct_data.R @@ -50,6 +50,7 @@ calculate_results <- function( exposure_end_variable = NULL, ae_start_variable = NULL ) { + logger::log_info("calculate_results started") variable <- match.arg(variable) effect_measure <- match.arg(effect_measure) adjustment <- match.arg(adjustment) @@ -60,6 +61,7 @@ calculate_results <- function( assert_columns(joint_data, req_columns = variable) # Filter out empty or NA variable values comb_data <- filter_empty_variable(joint_data, variable) + logger::log_info("filter_empty_variable executed") # Get big N denominators for verum and comparison big_n <- get_big_n( adsl_filtered_data, @@ -69,6 +71,7 @@ calculate_results <- function( exposure_start_variable = exposure_start_variable, exposure_end_variable = exposure_end_variable ) + logger::log_info("big_n executed") # Calculation of RR / RD and p-values based on the condition of variable proportions_data <- comb_data |> get_count_proportions( @@ -82,6 +85,7 @@ calculate_results <- function( exposure_end_variable = exposure_end_variable, ae_start_variable = ae_start_variable ) + logger::log_info("get_count_proportions executed") # Add filters of minimum count of AEs filtered_data <- proportions_data |> filter_minimum_aes( @@ -91,6 +95,7 @@ calculate_results <- function( alternative = alternative, alpha = alpha ) + logger::log_info("fiter_minimum_aes executed") # Check that we still have rows left if (nrow(filtered_data) == 0) { # Early return of an empty tibble @@ -106,6 +111,7 @@ calculate_results <- function( alpha = alpha, variable = variable ) + logger::log_info("get_fisher_rr_proportions executed") } else { effect_data <- filtered_data |> get_fisher_rr_rates( @@ -113,6 +119,7 @@ calculate_results <- function( alpha = alpha, variable = variable ) + logger::log_info("get_fisher_rr_rates executed") } } else if (study_strat != "None") { effect_data <- comb_data |> @@ -123,6 +130,7 @@ calculate_results <- function( stratify_variable = study_strat ) |> dplyr::filter(.data[[variable]] %in% filtered_data[[variable]]) + logger::log_info("get_stratified_rr_rd executed") } checkmate::assert_data_frame(effect_data, min.rows = 1) # Benjamini-Hochberg FDR procedure adjusted p-values ---- @@ -133,6 +141,8 @@ calculate_results <- function( adjustment = "FDR", effect_measure = effect_measure ) + logger::log_info("get_fdr_p_values executed") + logger::log_info("flag_significant executed") # Join p-values with count data by treatment results_fdr_data <- filtered_data |> dplyr::left_join(effect_fdr_data, by = variable) @@ -379,6 +389,30 @@ get_count_proportions <- function( ) + 1 ) + # Catch if there is an error with dates (submitting relative day instead of date, for example) + # It results in all duration values being negative + negative_exposure <- sum(comb_data$exposure_duration < 0, na.rm = TRUE) + if (negative_exposure > 0) { + logger::log_error( + "Negative values in exposure duration (n: {negative_exposure}). + Please check study start and study end variables, they should be dates." + ) + rlang::abort( + "Negative values in exposure duration. + Please check study start and study end variables, they should be dates." + ) + } + negative_time_to_ae <- sum(comb_data$ae_duration < 0, na.rm = TRUE) + if (negative_time_to_ae > 0) { + logger::log_error( + "Negative values in time to Advere Event onset (n: {negative_time_to_ae}). + Please check AE start and study start variables, they should be dates." + ) + rlang::abort( + "Negative values in time to Advere Event onset. + Please check AE start and study start variables, they should be dates." + ) + } exposure_duration_variable <- "exposure_duration" ae_duration_variable <- "ae_duration" } diff --git a/R/mod_upload.R b/R/mod_upload.R index f99a5be..4b4a95a 100644 --- a/R/mod_upload.R +++ b/R/mod_upload.R @@ -650,7 +650,7 @@ mod_upload_server <- function(id, r) { update_variables_input( data_req = adsl_data_prepared(), var_names = adsl_variable_names(), - name_pattern = "ACTARM|TRT01AN|TREATMGR", + name_pattern = "ACTARM|TRT01[AP]|TREATMGR", input_id = "treatment_variable", session = session ) @@ -776,7 +776,7 @@ mod_upload_server <- function(id, r) { update_variables_input( data_req = adsl_data_prepared(), var_names = adsl_variable_names(), - name_pattern = "RANDDT", + name_pattern = "RFSTDT|RANDDT", input_id = "exposure_start_variable", session = session ) diff --git a/renv.lock b/renv.lock index 16cf5da..e6b1f60 100644 --- a/renv.lock +++ b/renv.lock @@ -238,7 +238,7 @@ "SystemRequirements": "OpenSSL library and headers (openssl-dev or similar)", "NeedsCompilation": "yes", "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.nz, ORCID: )", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest", + "Repository": "RSPM", "Encoding": "UTF-8" }, "R6": { @@ -342,7 +342,7 @@ "NeedsCompilation": "yes", "Author": "Dirk Eddelbuettel [aut, cre] (), Mark Gillard [aut] (Author of 'toml++' header library)", "Maintainer": "Dirk Eddelbuettel ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest", + "Repository": "RSPM", "Encoding": "UTF-8" }, "S7": { @@ -407,7 +407,7 @@ "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] ()", "Maintainer": "Jeroen Ooms ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "assertthat": { "Package": "assertthat", @@ -500,7 +500,7 @@ "URL": "https://www.rforge.net/base64enc", "BugReports": "https://github.com/s-u/base64enc/issues", "NeedsCompilation": "yes", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest", + "Repository": "CRAN", "Encoding": "UTF-8" }, "bit": { @@ -613,7 +613,7 @@ ], "Config/testthat/edition": "3", "Encoding": "UTF-8", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest", + "Repository": "CRAN", "NeedsCompilation": "no", "Author": "Jeffrey Horner [aut, cph], Greg Hunt [aut, cre, cph]", "Maintainer": "Greg Hunt " @@ -642,7 +642,7 @@ "NeedsCompilation": "yes", "Author": "Jim Hester [aut] (), Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "bslib": { "Package": "bslib", @@ -703,7 +703,7 @@ "NeedsCompilation": "no", "Author": "Carson Sievert [aut, cre] (ORCID: ), Joe Cheng [aut], Garrick Aden-Buie [aut] (ORCID: ), Posit Software, PBC [cph, fnd], Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Javi Aguilar [ctb, cph] (Bootstrap colorpicker library), Thomas Park [ctb, cph] (Bootswatch library), PayPal [ctb, cph] (Bootstrap accessibility plugin)", "Maintainer": "Carson Sievert ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "c212": { "Package": "c212", @@ -967,7 +967,7 @@ "NeedsCompilation": "no", "Author": "Matthew Lincoln [aut, cre] (), Louis Maddox [ctb], Steve Simpson [ctb], Jennifer Bryan [ctb]", "Maintainer": "Matthew Lincoln ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "coda": { "Package": "coda", @@ -1121,7 +1121,7 @@ "NeedsCompilation": "no", "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "credentials": { "Package": "credentials", @@ -1220,7 +1220,7 @@ "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Hadley Wickham [ctb], Posit Software, PBC [cph]", "Maintainer": "Jeroen Ooms ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "data.table": { "Package": "data.table", @@ -1397,7 +1397,7 @@ "NeedsCompilation": "yes", "Author": "Brodie Gaslam [aut, cre], Michael B. Allen [ctb, cph] (Original C implementation of Myers Diff Algorithm)", "Maintainer": "Brodie Gaslam ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "digest": { "Package": "digest", @@ -1426,7 +1426,7 @@ "NeedsCompilation": "yes", "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Antoine Lucas [ctb] (ORCID: ), Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (ORCID: ), Simon Urbanek [ctb] (ORCID: ), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb] (ORCID: ), Duncan Murdoch [ctb], Jim Hester [ctb] (ORCID: ), Wush Wu [ctb] (ORCID: ), Qiang Kou [ctb] (ORCID: ), Thierry Onkelinx [ctb] (ORCID: ), Michel Lang [ctb] (ORCID: ), Viliam Simko [ctb], Kurt Hornik [ctb] (ORCID: ), Radford Neal [ctb] (ORCID: ), Kendon Bell [ctb] (ORCID: ), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb] (ORCID: ), Ion Suruceanu [ctb] (ORCID: ), Bill Denney [ctb] (ORCID: ), Dirk Schumacher [ctb], András Svraka [ctb] (ORCID: ), Sergey Fedorov [ctb] (ORCID: ), Will Landau [ctb] (ORCID: ), Floris Vanderhaeghe [ctb] (ORCID: ), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (ORCID: ), Mark van der Loo [ctb] (ORCID: ), Chris Muir [ctb] (ORCID: ), Moritz Beller [ctb] (ORCID: ), Sebastian Campbell [ctb] (ORCID: ), Winston Chang [ctb] (ORCID: ), Dean Attali [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Kevin Ushey [ctb] (ORCID: ), Carl Pearson [ctb] (ORCID: )", "Maintainer": "Dirk Eddelbuettel ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "downlit": { "Package": "downlit", @@ -1597,7 +1597,7 @@ "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre], RStudio [cph]", "Maintainer": "Hadley Wickham ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "evaluate": { "Package": "evaluate", @@ -1858,7 +1858,7 @@ "NeedsCompilation": "yes", "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut], Jeroen Ooms [cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Jeroen Ooms ", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "generics": { "Package": "generics", @@ -2042,7 +2042,7 @@ "NeedsCompilation": "no", "Author": "Gábor Csárdi [cre, ctb], Jennifer Bryan [aut], Hadley Wickham [aut], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Gábor Csárdi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "gitcreds": { "Package": "gitcreds", @@ -2076,7 +2076,7 @@ "NeedsCompilation": "no", "Author": "Gábor Csárdi [aut, cre], RStudio [cph, fnd]", "Maintainer": "Gábor Csárdi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "gld": { "Package": "gld", @@ -2556,7 +2556,7 @@ "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "httr2": { "Package": "httr2", @@ -2650,7 +2650,7 @@ "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre], Authors of libhunspell [cph] (see AUTHORS file)", "Maintainer": "Jeroen Ooms ", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "ini": { "Package": "ini", @@ -2671,7 +2671,7 @@ "testthat" ], "NeedsCompilation": "no", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest", + "Repository": "CRAN", "Encoding": "UTF-8" }, "isoband": { @@ -2740,7 +2740,7 @@ "NeedsCompilation": "no", "Author": "Jeroen Ooms [aut, cre] ()", "Maintainer": "Jeroen Ooms ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "jquerylib": { "Package": "jquerylib", @@ -2857,7 +2857,7 @@ "NeedsCompilation": "no", "Author": "Yihui Xie [aut, cre] (ORCID: , URL: https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (ORCID: ), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (ORCID: ), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (ORCID: ), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Yihui Xie ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "labeling": { "Package": "labeling", @@ -3017,7 +3017,7 @@ "NeedsCompilation": "no", "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Lionel Henry ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "lmom": { "Package": "lmom", @@ -3041,6 +3041,64 @@ "Repository": "RSPM", "Encoding": "UTF-8" }, + "logger": { + "Package": "logger", + "Version": "0.4.2", + "Source": "Repository", + "Type": "Package", + "Title": "A Lightweight, Modern and Flexible Logging Utility", + "Date": "2026-05-08", + "Authors@R": "c( person(\"Gergely\", \"Daróczi\", , \"daroczig@rapporter.net\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3149-8537\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jonathan\", \"Carroll\", , \"rpkg@jcarroll.com.au\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1404-5264\")), person(\"Spare Cores\", role = \"fnd\"), person(\"System1\", role = \"fnd\") )", + "Description": "Inspired by the the 'futile.logger' R package and 'logging' Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.", + "License": "MIT + file LICENSE", + "URL": "https://daroczig.github.io/logger/", + "BugReports": "https://github.com/daroczig/logger/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "botor", + "cli", + "covr", + "crayon", + "devtools", + "glue", + "jsonlite", + "knitr", + "mirai (>= 1.3.0)", + "ntfy", + "pander", + "parallel", + "R.utils", + "rmarkdown", + "roxygen2", + "RPushbullet", + "rsyslog", + "shiny", + "slackr (>= 1.4.1)", + "syslognet", + "telegram", + "testthat (>= 3.0.0)", + "withr" + ], + "Enhances": [ + "futile.logger", + "log4r", + "logging" + ], + "VignetteBuilder": "knitr", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Gergely Daróczi [aut, cre] (ORCID: ), Hadley Wickham [aut] (ORCID: ), Jonathan Carroll [ctb] (ORCID: ), Spare Cores [fnd], System1 [fnd]", + "Maintainer": "Gergely Daróczi ", + "Repository": "CRAN" + }, "magrittr": { "Package": "magrittr", "Version": "2.0.4", @@ -3070,7 +3128,7 @@ "NeedsCompilation": "yes", "Author": "Stefan Milton Bache [aut, cph] (Original author and creator of magrittr), Hadley Wickham [aut], Lionel Henry [cre], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Lionel Henry ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "mathjaxr": { "Package": "mathjaxr", @@ -3407,7 +3465,7 @@ "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Oliver Keyes [ctb]", "Maintainer": "Jeroen Ooms ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "packrat": { "Package": "packrat", @@ -3443,7 +3501,7 @@ "NeedsCompilation": "no", "Author": "Aron Atkins [aut, cre], Toph Allen [aut], Kevin Ushey [aut], Jonathan McPherson [aut], Joe Cheng [aut], JJ Allaire [aut], Posit Software, PBC [cph, fnd]", "Maintainer": "Aron Atkins ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "pbapply": { "Package": "pbapply", @@ -3529,7 +3587,7 @@ "NeedsCompilation": "no", "Author": "Kirill Müller [aut, cre] (ORCID: ), Hadley Wickham [aut], RStudio [cph]", "Maintainer": "Kirill Müller ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "pkgbuild": { "Package": "pkgbuild", @@ -3710,7 +3768,7 @@ "NeedsCompilation": "no", "Author": "Hadley Wickham [aut], Winston Chang [aut], Jim Hester [aut], Lionel Henry [aut, cre], Posit Software, PBC [cph, fnd], R Core team [ctb] (Some namespace and vignette code extracted from base R)", "Maintainer": "Lionel Henry ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "plotly": { "Package": "plotly", @@ -3806,7 +3864,7 @@ ], "Collate": "'adjective.R' 'adverb.R' 'exclamation.R' 'verb.R' 'rpackage.R' 'package.R'", "NeedsCompilation": "no", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest", + "Repository": "CRAN", "Encoding": "UTF-8" }, "prettyunits": { @@ -3832,7 +3890,7 @@ "NeedsCompilation": "no", "Author": "Gabor Csardi [aut, cre], Bill Denney [ctb] (), Christophe Regouby [ctb]", "Maintainer": "Gabor Csardi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "processx": { "Package": "processx", @@ -3907,7 +3965,7 @@ "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre], Winston Chang [aut], Javier Luraschi [aut], Timothy Mastny [aut], Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/htmlwidgets/lib/jquery/AUTHORS.txt), Mike Bostock [ctb, cph] (D3 library), D3 contributors [ctb] (D3 library), Ivan Sagalaev [ctb, cph] (highlight.js library)", "Maintainer": "Hadley Wickham ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "progress": { "Package": "progress", @@ -4136,7 +4194,7 @@ "SystemRequirements": "freetype2, libpng, libtiff, libjpeg, libwebp, libwebpmux", "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit Software, PBC [cph, fnd] (ROR: )", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "rappdirs": { "Package": "rappdirs", @@ -4167,7 +4225,7 @@ "NeedsCompilation": "yes", "Author": "Hadley Wickham [trl, cre, cph], Sridhar Ratnakumar [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs), Eddy Petrisor [ctb], Trevor Davis [trl, aut] (ORCID: ), Gabor Csardi [ctb], Gregory Jefferis [ctb], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Hadley Wickham ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "rcmdcheck": { "Package": "rcmdcheck", @@ -4211,7 +4269,7 @@ "NeedsCompilation": "no", "Author": "Gábor Csárdi [cre, aut]", "Maintainer": "Gábor Csárdi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "readr": { "Package": "readr", @@ -4479,7 +4537,7 @@ "NeedsCompilation": "yes", "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], mikefc [cph] (Hash implementation based on Mike's xxhashlite), Yann Collet [cph] (Author of the embedded xxHash library), Posit, PBC [cph, fnd]", "Maintainer": "Lionel Henry ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "rmarkdown": { "Package": "rmarkdown", @@ -4535,7 +4593,7 @@ "NeedsCompilation": "no", "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] (ORCID: ), Christophe Dervieux [aut] (ORCID: ), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (ORCID: ), Andrew Dunning [ctb] (ORCID: ), Atsushi Yasumoto [ctb, cph] (ORCID: , cph: Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (ORCID: ), Devon Ryan [ctb] (ORCID: ), Frederik Aust [ctb] (ORCID: ), Jeff Allen [ctb], JooYoung Seo [ctb] (ORCID: ), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], Posit Software, PBC [cph, fnd], jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)", "Maintainer": "Yihui Xie ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "rootSolve": { "Package": "rootSolve", @@ -4611,7 +4669,7 @@ "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre, cph] (ORCID: ), Peter Danenberg [aut, cph], Gábor Csárdi [aut], Manuel Eugster [aut, cph], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Hadley Wickham ", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "rprojroot": { "Package": "rprojroot", @@ -4645,7 +4703,7 @@ "NeedsCompilation": "no", "Author": "Kirill Müller [aut, cre] (ORCID: )", "Maintainer": "Kirill Müller ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "rsconnect": { "Package": "rsconnect", @@ -4872,7 +4930,7 @@ "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Gábor Csárdi [cre], Hadley Wickham [aut], Winston Chang [aut], Robert Flight [aut], Kirill Müller [aut], Jim Hester [aut], R Core team [ctb], Posit Software, PBC [cph, fnd]", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "shiny": { "Package": "shiny", @@ -5013,7 +5071,7 @@ "NeedsCompilation": "no", "Author": "Dean Attali [aut, cre] (Maintainer/developer of shinycssloaders since 2019, ), Andras Sali [aut] (Original creator of shinycssloaders package), Luke Hass [ctb, cph] (Author of included CSS loader code)", "Maintainer": "Dean Attali ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "shinydashboard": { "Package": "shinydashboard", @@ -5119,7 +5177,7 @@ "NeedsCompilation": "no", "Author": "Jeroen Ooms [cre, aut] (ORCID: ), Jim Hester [aut]", "Maintainer": "Jeroen Ooms ", - "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "stringi": { "Package": "stringi", @@ -5217,7 +5275,7 @@ "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] (), Gábor Csárdi [ctb]", "Maintainer": "Jeroen Ooms ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "systemfonts": { "Package": "systemfonts", @@ -5324,7 +5382,7 @@ "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd], R Core team [ctb] (Implementation of utils::recover())", "Maintainer": "Hadley Wickham ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "textshaping": { "Package": "textshaping", @@ -5550,7 +5608,7 @@ "NeedsCompilation": "no", "Author": "Yihui Xie [aut, cre, cph] (ORCID: ), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (ORCID: ), Devon Ryan [ctb] (ORCID: ), Ethan Heinzen [ctb], Fernando Cagua [ctb]", "Maintainer": "Yihui Xie ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "tzdb": { "Package": "tzdb", @@ -5609,7 +5667,7 @@ "NeedsCompilation": "no", "Author": "R Core team [aut] (The code in urltools.R adapted from the tools package), Jim Hester [aut] (), Gábor Csárdi [aut, cre], RStudio [cph, fnd]", "Maintainer": "Gábor Csárdi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "usethis": { "Package": "usethis", @@ -5670,7 +5728,7 @@ "NeedsCompilation": "no", "Author": "Hadley Wickham [aut] (ORCID: ), Jennifer Bryan [aut, cre] (ORCID: ), Malcolm Barrett [aut] (ORCID: ), Andy Teucher [aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Jennifer Bryan ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "utf8": { "Package": "utf8", @@ -5883,7 +5941,7 @@ "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "whisker": { "Package": "whisker", @@ -5902,7 +5960,7 @@ ], "RoxygenNote": "6.1.1", "NeedsCompilation": "no", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest", + "Repository": "CRAN", "Encoding": "UTF-8" }, "withr": { @@ -5989,7 +6047,7 @@ "NeedsCompilation": "yes", "Author": "Yihui Xie [aut, cre, cph] (ORCID: , URL: https://yihui.org), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (ORCID: ), Christophe Dervieux [ctb]", "Maintainer": "Yihui Xie ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "RSPM" }, "xml2": { "Package": "xml2", @@ -6059,7 +6117,7 @@ "NeedsCompilation": "no", "Author": "Gábor Csárdi [aut, cre], Fathi Boudra [aut], Rex Dieter [aut], Kevin Krammer [aut], Jeremy White [aut], Posit Software, PBC [cph, fnd]", "Maintainer": "Gábor Csárdi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "xtable": { "Package": "xtable", @@ -6115,7 +6173,7 @@ "NeedsCompilation": "yes", "Author": "Hadley Wickham [cre] (ORCID: ), Shawn Garbett [ctb] (ORCID: ), Jeremy Stephens [aut, ctb], Kirill Simonov [aut], Yihui Xie [ctb] (ORCID: ), Zhuoer Dong [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb] (ORCID: ), Brendan O'Connor [ctb], Michael Quinn [ctb], Charlie Gao [ctb], Gregory R. Warnes [ctb], Zhian N. Kamvar [ctb]", "Maintainer": "Hadley Wickham ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" }, "zip": { "Package": "zip", @@ -6143,7 +6201,7 @@ "NeedsCompilation": "yes", "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Gábor Csárdi ", - "Repository": "https://ppm-dev.titans.int.bayer.com/cran/__linux__/jammy/latest" + "Repository": "CRAN" } } } From 8e0de4784b584f95aef11329db687f17f53569de Mon Sep 17 00:00:00 2001 From: CarlosEpiStats Date: Wed, 10 Jun 2026 15:19:21 +0000 Subject: [PATCH 2/3] Add TRTSDT and TRTEDT as default start and end dates --- R/mod_upload.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/mod_upload.R b/R/mod_upload.R index 4b4a95a..a250e3c 100644 --- a/R/mod_upload.R +++ b/R/mod_upload.R @@ -776,7 +776,7 @@ mod_upload_server <- function(id, r) { update_variables_input( data_req = adsl_data_prepared(), var_names = adsl_variable_names(), - name_pattern = "RFSTDT|RANDDT", + name_pattern = "TRTSDT|RFSTDT|RANDDT", input_id = "exposure_start_variable", session = session ) @@ -786,7 +786,7 @@ mod_upload_server <- function(id, r) { update_variables_input( data_req = adsl_data_prepared(), var_names = adsl_variable_names(), - name_pattern = "RFENDT|EOSDT", + name_pattern = "TRTEDT|RFENDT|EOSDT", input_id = "exposure_end_variable", session = session ) From 0f8f2a6b441eaee441e54d7f41eb57297cc42af3 Mon Sep 17 00:00:00 2001 From: CarlosEpiStats Date: Wed, 10 Jun 2026 15:25:05 +0000 Subject: [PATCH 3/3] Increment version number to 3.0.1.9000 --- DESCRIPTION | 2 +- NEWS.md | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 03aa7bd..dd424e8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: DetectoR Title: Stay Safe; Don't Miss Any Adverse-Event Signal -Version: 3.0.1 +Version: 3.0.1.9000 Authors@R: c( person("Carlos", "Fernandez-Escobar", , "carlos.fernandez4.ext@bayer.com", role = c("aut", "cre")), person("Steffen", "Jeske", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 0406640..15883fa 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# DetectoR (development version) + +* Add logger messages if there is an error in incidence rate calculation, due to incorrect date variables. +* Update default ADSL variables in select inputs. + # DetectoR 3.0.1 * Add jarl linter * Apply jarl fixes