diff --git a/longitudinal/renv.lock b/longitudinal/renv.lock index 09bba445..919eb69f 100644 --- a/longitudinal/renv.lock +++ b/longitudinal/renv.lock @@ -464,7 +464,7 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.12.3", + "Version": "2.13.0", "Source": "Repository", "Depends": [ "R (>= 2.14.0)", @@ -490,8 +490,7 @@ "URL": "https://henrikbengtsson.github.io/R.utils/, https://github.com/HenrikBengtsson/R.utils", "BugReports": "https://github.com/HenrikBengtsson/R.utils/issues", "NeedsCompilation": "no", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "BioC.CRAN" }, "R6": { "Package": "R6", @@ -2647,10 +2646,10 @@ }, "formatters": { "Package": "formatters", - "Version": "0.5.10.9001", + "Version": "0.5.10.9002", "Source": "GitHub", "Title": "ASCII Formatting for Values and Tables", - "Date": "2025-02-05", + "Date": "2025-02-24", "Authors@R": "c( person(\"Gabriel\", \"Becker\", , \"gabembecker@gmail.com\", role = \"aut\", comment = \"original creator of the package\"), person(\"Adrian\", \"Waddell\", , \"adrian.waddell@gene.com\", role = \"aut\"), person(\"Davide\", \"Garolini\", , \"davide.garolini@roche.com\", role = \"aut\"), person(\"Emily\", \"de la Rua\", , \"emily.de_la_rua@contractors.roche.com\", role = \"aut\"), person(\"Abinaya\", \"Yogasekaram\", , \"abinaya.yogasekaram@contractors.roche.com\", role = \"ctb\"), person(\"Joe\", \"Zhu\", , \"joe.zhu@roche.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7566-2787\")), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", "Description": "We provide a framework for rendering complex tables to ASCII, and a set of formatters for transforming values or sets of values into ASCII-ready display strings.", "License": "Apache License 2.0", @@ -2693,7 +2692,7 @@ "RemoteUsername": "insightsengineering", "RemoteRepo": "formatters", "RemoteRef": "main", - "RemoteSha": "ee566c9b53f010edae9d0d9a64af82b41cee7b66" + "RemoteSha": "fcc4fb86c1ff7753fa52ded1a79df1aa39987a58" }, "fs": { "Package": "fs", @@ -3041,7 +3040,7 @@ }, "ggnewscale": { "Package": "ggnewscale", - "Version": "0.5.0", + "Version": "0.5.1", "Source": "Repository", "Language": "en-GB", "Title": "Multiple Fill and Colour Scales in 'ggplot2'", @@ -3063,7 +3062,7 @@ "NeedsCompilation": "no", "Author": "Elio Campitelli [cre, aut] ()", "Maintainer": "Elio Campitelli ", - "Repository": "RSPM" + "Repository": "BioC.CRAN" }, "ggplot2": { "Package": "ggplot2", @@ -3471,11 +3470,11 @@ }, "goshawk": { "Package": "goshawk", - "Version": "0.1.18.9010", + "Version": "0.1.19.9000", "Source": "GitHub", "Type": "Package", "Title": "Longitudinal Visualization Functions", - "Date": "2025-01-31", + "Date": "2025-02-24", "Authors@R": "c( person(\"Nick\", \"Paszty\", , \"nick.paszty@gene.com\", role = c(\"aut\", \"cre\")), person(\"Dawid\", \"Kaledkowski\", , \"dawid.kaledkowski@roche.com\", role = \"aut\"), person(\"Ondrej\", \"Slama\", , \"ondrej.slama@roche.com\", role = \"aut\"), person(\"Adrian\", \"Waddell\", , \"adrian.waddell@gene.com\", role = \"aut\"), person(\"Wenyi\", \"Liu\", , \"liu.wenyi@roche.com\", role = \"aut\"), person(\"Jeffrey\", \"Tomlinson\", , \"tomlinson.jeffrey@roche.com\", role = \"aut\"), person(\"Bali\", \"Toth\", , \"toth.balazs@gene.com\", role = \"aut\"), person(\"Junlue\", \"Zhao\", role = \"aut\"), person(\"Maciej\", \"Nasinski\", role = \"aut\"), person(\"Konrad\", \"Pagacz\", role = \"aut\"), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", "Description": "Functions that plot and summarize biomarkers/labs of interest. Visualizations include: box plot, correlation plot, density distribution, line plot and spaghetti plot. Data are expected in ADaM structure. Requires analysis subject level (ADSL) and analysis laboratory (ADLB) data sets. Beyond core variables, Limit of Quantification flag variable (LOQFL) is expected with levels 'Y', 'N' or NA.", "License": "Apache License 2.0 | file LICENSE", @@ -3520,7 +3519,7 @@ "RemoteUsername": "insightsengineering", "RemoteRepo": "goshawk", "RemoteRef": "main", - "RemoteSha": "9b26438da392b5ff838651840f80493097195905" + "RemoteSha": "68947caed3940e8823e1187b0740e6a35ffc96c0" }, "gridExtra": { "Package": "gridExtra", @@ -6510,10 +6509,10 @@ }, "rtables": { "Package": "rtables", - "Version": "0.6.11.9006", + "Version": "0.6.11.9007", "Source": "GitHub", "Title": "Reporting Tables", - "Date": "2025-02-21", + "Date": "2025-02-24", "Authors@R": "c( person(\"Gabriel\", \"Becker\", , \"gabembecker@gmail.com\", role = \"aut\", comment = \"Original creator of the package\"), person(\"Adrian\", \"Waddell\", , \"adrian.waddell@gene.com\", role = \"aut\"), person(\"Daniel\", \"Sabanés Bové\", , \"daniel.sabanes_bove@roche.com\", role = \"ctb\"), person(\"Maximilian\", \"Mordig\", , \"maximilian_oliver.mordig@roche.com\", role = \"ctb\"), person(\"Davide\", \"Garolini\", , \"davide.garolini@roche.com\", role = \"aut\"), person(\"Emily\", \"de la Rua\", , \"emily.de_la_rua@contractors.roche.com\", role = \"aut\"), person(\"Abinaya\", \"Yogasekaram\", , \"abinaya.yogasekaram@contractors.roche.com\", role = \"ctb\"), person(\"Joe\", \"Zhu\", , \"joe.zhu@roche.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7566-2787\")), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", "Description": "Reporting tables often have structure that goes beyond simple rectangular data. The 'rtables' package provides a framework for declaring complex multi-level tabulations and then applying them to data. This framework models both tabulation and the resulting tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting or grouping of data in row and column dimensions, cells containing multiple values, and the concept of contextual summary computations. A convenient pipe-able interface is provided for declaring table layouts and the corresponding computations, and then applying them to data.", "License": "Apache License 2.0 | file LICENSE", @@ -6537,6 +6536,7 @@ "car (>= 3.0-13)", "dplyr (>= 1.0.5)", "knitr (>= 1.42)", + "lme4 (>= 1.1-35.5)", "r2rtf (>= 0.3.2)", "rmarkdown (>= 2.23)", "survival (>= 3.3-1)", @@ -6561,7 +6561,7 @@ "RemoteUsername": "insightsengineering", "RemoteRepo": "rtables", "RemoteRef": "main", - "RemoteSha": "4b7f2fc266fa4bee8c01cc2374e8a975aca3eb55" + "RemoteSha": "aece54c627d09209970f829291e21c2c6dbf5f53" }, "rtables.officer": { "Package": "rtables.officer", @@ -7327,11 +7327,11 @@ }, "teal": { "Package": "teal", - "Version": "0.15.2.9131", + "Version": "0.16.0.9000", "Source": "GitHub", "Type": "Package", "Title": "Exploratory Web Apps for Analyzing Clinical Trials Data", - "Date": "2025-02-12", + "Date": "2025-02-24", "Authors@R": "c( person(\"Dawid\", \"Kaledkowski\", , \"dawid.kaledkowski@roche.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-9533-457X\")), person(\"Pawel\", \"Rucki\", , \"pawel.rucki@roche.com\", role = \"aut\"), person(\"Aleksander\", \"Chlebowski\", , \"aleksander.chlebowski@contractors.roche.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-5018-6294\")), person(\"Andre\", \"Verissimo\", , \"andre.verissimo@roche.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-2212-339X\")), person(\"Kartikeya\", \"Kirar\", , \"kartikeya.kirar@businesspartner.roche.com\", role = \"aut\"), person(\"Vedha\", \"Viyash\", , \"vedha.viyash@roche.com\", role = \"aut\"), person(\"Marcin\", \"Kosinski\", , \"marcin.kosinski.mk1@roche.com\", role = \"aut\"), person(\"Adrian\", \"Waddell\", , \"adrian.waddell@gene.com\", role = \"aut\"), person(\"Chendi\", \"Liao\", , \"chendi.liao@roche.com\", role = \"rev\"), person(\"Dony\", \"Unardi\", , \"unardid@gene.com\", role = \"rev\"), person(\"Nikolas\", \"Burkoff\", role = \"aut\"), person(\"Mahmoud\", \"Hallal\", role = \"aut\"), person(\"Maciej\", \"Nasinski\", role = \"aut\"), person(\"Konrad\", \"Pagacz\", role = \"aut\"), person(\"Junlue\", \"Zhao\", role = \"aut\"), person(\"Tadeusz\", \"Lewandowski\", role = \"aut\"), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")), person(\"Maximilian\", \"Mordig\", role = \"ctb\") )", "Description": "A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.", "License": "Apache License 2.0", @@ -7354,8 +7354,8 @@ "rlang (>= 1.0.0)", "shinyjs", "stats", - "teal.code (>= 0.6.0)", - "teal.logger (>= 0.3.1)", + "teal.code (>= 0.6.1)", + "teal.logger (>= 0.3.2)", "teal.reporter (>= 0.4.0)", "teal.widgets (>= 0.4.3)", "tools", @@ -7395,7 +7395,7 @@ "RemoteUsername": "insightsengineering", "RemoteRepo": "teal", "RemoteRef": "main", - "RemoteSha": "c75f39ed4f4eb989059e7a22aace4a8cfb020bc6" + "RemoteSha": "e8373eef279e459049b0fd2f3eac390c9bbb51c8" }, "teal.code": { "Package": "teal.code", @@ -7612,10 +7612,10 @@ }, "teal.modules.clinical": { "Package": "teal.modules.clinical", - "Version": "0.9.1.9067", + "Version": "0.9.1.9068", "Source": "GitHub", "Title": "'teal' Modules for Standard Clinical Outputs", - "Date": "2025-02-21", + "Date": "2025-02-24", "Authors@R": "c( person(\"Joe\", \"Zhu\", , \"joe.zhu@roche.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-7566-2787\")), person(\"Jana\", \"Stoilova\", , \"jana.stoilova@roche.com\", role = \"aut\"), person(\"Davide\", \"Garolini\", , \"davide.garolini@roche.com\", role = \"aut\"), person(\"Emily\", \"de la Rua\", , \"emily.de_la_rua@contractors.roche.com\", role = \"aut\"), person(\"Abinaya\", \"Yogasekaram\", , \"abinaya.yogasekaram@contractors.roche.com\", role = \"aut\"), person(\"Mahmoud\", \"Hallal\", , \"mahmoud.hallal@roche.com\", role = \"aut\"), person(\"Dawid\", \"Kaledkowski\", , \"dawid.kaledkowski@roche.com\", role = c(\"aut\", \"cre\")), person(\"Rosemary\", \"Li\", , \"li.yaqiong@gene.com\", role = \"aut\"), person(\"Heng\", \"Wang\", , \"wang.heng@gene.com\", role = \"aut\"), person(\"Pawel\", \"Rucki\", , \"pawel.rucki@roche.com\", role = \"aut\"), person(\"Nikolas\", \"Burkoff\", role = \"aut\"), person(\"Konrad\", \"Pagacz\", role = \"aut\"), person(\"Vaakesan\", \"Sundrelingam\", role = \"ctb\"), person(\"Francois\", \"Collin\", role = \"ctb\"), person(\"Imanol\", \"Zubizarreta\", role = \"ctb\"), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", "Description": "Provides user-friendly tools for creating and customizing clinical trial reports. By leveraging the 'teal' framework, this package provides 'teal' modules to easily create an interactive panel that allows for seamless adjustments to data presentation, thereby streamlining the creation of detailed and accurate reports.", "License": "Apache License 2.0", @@ -7623,7 +7623,7 @@ "BugReports": "https://github.com/insightsengineering/teal.modules.clinical/issues", "Depends": [ "R (>= 4.0)", - "teal (>= 0.15.2.9103)", + "teal (>= 0.16.0)", "teal.transform (>= 0.6.0)", "tern (>= 0.9.7)" ], @@ -7687,16 +7687,15 @@ "RemoteUsername": "insightsengineering", "RemoteRepo": "teal.modules.clinical", "RemoteRef": "main", - "RemoteSha": "fa5566d08f2176ff2c9b361680d1764cf1190a1c", - "Remotes": "insightsengineering/teal" + "RemoteSha": "8bd5c56ef2b54124d2963359daf8bf8fe053b180" }, "teal.modules.general": { "Package": "teal.modules.general", - "Version": "0.3.0.9089", + "Version": "0.3.0.9090", "Source": "GitHub", "Type": "Package", "Title": "General Modules for 'teal' Applications", - "Date": "2025-02-21", + "Date": "2025-02-24", "Authors@R": "c( person(\"Dawid\", \"Kaledkowski\", , \"dawid.kaledkowski@roche.com\", role = c(\"aut\", \"cre\")), person(\"Pawel\", \"Rucki\", , \"pawel.rucki@roche.com\", role = \"aut\"), person(\"Mahmoud\", \"Hallal\", , \"mahmoud.hallal@roche.com\", role = \"aut\"), person(\"Ondrej\", \"Slama\", , \"ondrej.slama@roche.com\", role = \"ctb\"), person(\"Maciej\", \"Nasinski\", role = \"aut\"), person(\"Konrad\", \"Pagacz\", role = \"aut\"), person(\"Nikolas\", \"Burkoff\", role = \"aut\"), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", "Description": "Prebuilt 'shiny' modules containing tools for viewing data, visualizing data, understanding missing and outlier values within your data and performing simple data analysis. This extends 'teal' framework that supports reproducible research and analysis.", "License": "Apache License 2.0", @@ -7707,7 +7706,7 @@ "ggplot2 (>= 3.4.0)", "R (>= 4.1)", "shiny (>= 1.6.0)", - "teal (>= 0.15.2.9103)", + "teal (>= 0.16.0)", "teal.transform (>= 0.6.0)" ], "Imports": [ @@ -7777,8 +7776,7 @@ "RemoteUsername": "insightsengineering", "RemoteRepo": "teal.modules.general", "RemoteRef": "main", - "RemoteSha": "5b00f0b63c26b5f074cbfbb52ab0c30c676ce7ff", - "Remotes": "insightsengineering/teal" + "RemoteSha": "690b32bebf06c641f2d0d5a757d48f06ac5cf3f0" }, "teal.reporter": { "Package": "teal.reporter", @@ -8020,10 +8018,10 @@ }, "tern": { "Package": "tern", - "Version": "0.9.7.9005", + "Version": "0.9.7.9008", "Source": "GitHub", "Title": "Create Common TLGs Used in Clinical Trials", - "Date": "2025-02-21", + "Date": "2025-02-24", "Authors@R": "c( person(\"Joe\", \"Zhu\", , \"joe.zhu@roche.com\", role = c(\"aut\", \"cre\")), person(\"Daniel\", \"Sabanés Bové\", , \"daniel.sabanes_bove@roche.com\", role = \"aut\"), person(\"Jana\", \"Stoilova\", , \"jana.stoilova@roche.com\", role = \"aut\"), person(\"Davide\", \"Garolini\", , \"davide.garolini@roche.com\", role = \"aut\"), person(\"Emily\", \"de la Rua\", , \"emily.de_la_rua@contractors.roche.com\", role = \"aut\"), person(\"Abinaya\", \"Yogasekaram\", , \"abinaya.yogasekaram@contractors.roche.com\", role = \"aut\"), person(\"Heng\", \"Wang\", , \"wang.heng@gene.com\", role = \"aut\"), person(\"Francois\", \"Collin\", role = \"aut\"), person(\"Adrian\", \"Waddell\", , \"adrian.waddell@gene.com\", role = \"aut\"), person(\"Pawel\", \"Rucki\", , \"pawel.rucki@roche.com\", role = \"aut\"), person(\"Chendi\", \"Liao\", , \"chendi.liao@roche.com\", role = \"aut\"), person(\"Jennifer\", \"Li\", , \"li.jing@gene.com\", role = \"aut\"), person(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")) )", "Description": "Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.", "License": "Apache License 2.0", @@ -8089,7 +8087,7 @@ "RemoteUsername": "insightsengineering", "RemoteRepo": "tern", "RemoteRef": "main", - "RemoteSha": "a88ae148cfa8af4fb1debf17db2972f980305562" + "RemoteSha": "22e51e2c3270521f3729d32177a0d8a6be8b2cb7" }, "tern.gee": { "Package": "tern.gee",