From a1fc01632a4dadaa91106eed19c68bb92ec44bb7 Mon Sep 17 00:00:00 2001 From: Timon Date: Mon, 16 Feb 2026 15:34:00 +0100 Subject: [PATCH] Add ignored directories to renv settings for better version control management --- .renvignore | 3 + r_app/80_calculate_kpis.R | 8 +- renv.lock | 2035 +++---------------------------------- renv/settings.json | 9 +- 4 files changed, 153 insertions(+), 1902 deletions(-) diff --git a/.renvignore b/.renvignore index d48919b..eaa6c15 100644 --- a/.renvignore +++ b/.renvignore @@ -5,9 +5,12 @@ laravel_app/ data_validation_tool/ python_app/harvest_detection_experiments/ python_app/experiments/ +r_app/old_scripts/ +r_app/experiments/ phase2_refinement/ webapps/ tools/ +old_sh/ output/ renv/ *.py diff --git a/r_app/80_calculate_kpis.R b/r_app/80_calculate_kpis.R index c0f5a2b..5ed21d3 100644 --- a/r_app/80_calculate_kpis.R +++ b/r_app/80_calculate_kpis.R @@ -141,12 +141,8 @@ suppressPackageStartupMessages({ library(writexl) # For writing Excel outputs (KPI summary tables) library(progress) # For progress bars during field processing - # ML/Analysis (optional - only for harvest model inference) - tryCatch({ - library(torch) # For PyTorch model inference (harvest readiness prediction) - }, error = function(e) { - message("Note: torch package not available - harvest model inference will be skipped") - }) + # Note: ML model inference is handled via Python/PyTorch (conda pytorch_gpu) + # No R torch package needed }) # ============================================================================ diff --git a/renv.lock b/renv.lock index d1cff92..9e78b85 100644 --- a/renv.lock +++ b/renv.lock @@ -9,71 +9,6 @@ ] }, "Packages": { - "CAST": { - "Package": "CAST", - "Version": "1.0.3", - "Source": "Repository", - "Type": "Package", - "Title": "'caret' Applications for Spatial-Temporal Models", - "Authors@R": "c(person(\"Hanna\", \"Meyer\", email = \"hanna.meyer@uni-muenster.de\", role = c(\"cre\", \"aut\")), person(\"Carles\", \"Milà\", role = c(\"aut\")), person(\"Marvin\", \"Ludwig\", role = c(\"aut\")), person(\"Jan\", \"Linnenbrink\", role = c(\"aut\")), person(\"Fabian\", \"Schumacher\", role = c(\"aut\")), person(\"Philipp\", \"Otto\", role = c(\"ctb\")), person(\"Chris\", \"Reudenbach\", role = c(\"ctb\")), person(\"Thomas\", \"Nauss\", role = c(\"ctb\")), person(\"Edzer\", \"Pebesma\", role = c(\"ctb\")), person(\"Jakub\", \"Nowosad\", role = c(\"ctb\")))", - "Author": "Hanna Meyer [cre, aut], Carles Milà [aut], Marvin Ludwig [aut], Jan Linnenbrink [aut], Fabian Schumacher [aut], Philipp Otto [ctb], Chris Reudenbach [ctb], Thomas Nauss [ctb], Edzer Pebesma [ctb], Jakub Nowosad [ctb]", - "Maintainer": "Hanna Meyer ", - "Description": "Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) ; Meyer et al. (2019) ; Meyer and Pebesma (2021) ; Milà et al. (2022) ; Meyer and Pebesma (2022) ; Linnenbrink et al. (2023) ; Schumacher et al. (2024) . The package is described in detail in Meyer et al. (2024) .", - "License": "GPL (>= 2)", - "URL": "https://github.com/HannaMeyer/CAST, https://hannameyer.github.io/CAST/", - "Encoding": "UTF-8", - "LazyData": "false", - "Depends": [ - "R (>= 4.1.0)" - ], - "BugReports": "https://github.com/HannaMeyer/CAST/issues/", - "Imports": [ - "caret", - "stats", - "utils", - "ggplot2", - "graphics", - "FNN", - "plyr", - "zoo", - "methods", - "grDevices", - "data.table", - "sf", - "forcats", - "twosamples", - "terra", - "sp" - ], - "Suggests": [ - "doParallel", - "lubridate", - "randomForest", - "knitr", - "geodata", - "mapview", - "rmarkdown", - "scales", - "parallel", - "gridExtra", - "viridis", - "stars", - "scam", - "rnaturalearth", - "MASS", - "RColorBrewer", - "tmap", - "PCAmixdata", - "gower", - "clustMixType", - "testthat (>= 3.0.0)" - ], - "RoxygenNote": "7.3.2", - "VignetteBuilder": "knitr", - "Config/testthat/edition": "3", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, "DBI": { "Package": "DBI", "Version": "1.2.3", @@ -123,28 +58,6 @@ "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, - "FNN": { - "Package": "FNN", - "Version": "1.1.4.1", - "Source": "Repository", - "Date": "2023-12-31", - "Title": "Fast Nearest Neighbor Search Algorithms and Applications", - "Authors@R": "c(person(\"Alina\", \"Beygelzimer\", role = \"aut\", comment = \"cover tree library\"), person(\"Sham\", \"Kakadet\", role = \"aut\", comment = \"cover tree library\"), person(\"John\", \"Langford\", role = \"aut\", comment = \"cover tree library\"), person(\"Sunil\", \"Arya\", role = \"aut\", comment = \"ANN library 1.1.2 for the kd-tree approach\"), person(\"David\", \"Mount\", role = \"aut\", comment = \"ANN library 1.1.2 for the kd-tree approach\"), person(\"Shengqiao\", \"Li\", role = c(\"aut\", \"cre\"), email = \"lishengqiao@yahoo.com\"))", - "Copyright": "ANN Copyright (c) 1997-2010 University of Maryland and Sunil Arya and David Mount. All Rights Reserved.", - "Depends": [ - "R (>= 4.0.0)" - ], - "Suggests": [ - "chemometrics", - "mvtnorm" - ], - "Description": "Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.", - "License": "GPL (>= 2)", - "NeedsCompilation": "yes", - "Repository": "CRAN", - "Author": "Alina Beygelzimer [aut] (cover tree library), Sham Kakadet [aut] (cover tree library), John Langford [aut] (cover tree library), Sunil Arya [aut] (ANN library 1.1.2 for the kd-tree approach), David Mount [aut] (ANN library 1.1.2 for the kd-tree approach), Shengqiao Li [aut, cre]", - "Maintainer": "Shengqiao Li " - }, "KernSmooth": { "Package": "KernSmooth", "Version": "2.23-24", @@ -251,36 +164,6 @@ "Maintainer": "Martin Maechler ", "Repository": "CRAN" }, - "ModelMetrics": { - "Package": "ModelMetrics", - "Version": "1.2.2.2", - "Source": "Repository", - "Title": "Rapid Calculation of Model Metrics", - "Date": "2018-11-03", - "Authors@R": "person(\"Tyler\", \"Hunt\", email = \"thunt@snapfinance.com\", role = c(\"aut\", \"cre\"))", - "Description": "Collection of metrics for evaluating models written in C++ using 'Rcpp'. Popular metrics include area under the curve, log loss, root mean square error, etc.", - "Depends": [ - "R (>= 3.2.2)" - ], - "License": "GPL (>= 2)", - "Encoding": "UTF-8", - "LazyData": "true", - "LinkingTo": [ - "Rcpp" - ], - "Imports": [ - "Rcpp", - "data.table" - ], - "RoxygenNote": "6.0.1", - "Suggests": [ - "testthat" - ], - "NeedsCompilation": "yes", - "Author": "Tyler Hunt [aut, cre]", - "Maintainer": "Tyler Hunt ", - "Repository": "CRAN" - }, "R6": { "Package": "R6", "Version": "2.6.1", @@ -353,161 +236,6 @@ "Maintainer": "Dirk Eddelbuettel ", "Repository": "CRAN" }, - "RcppArmadillo": { - "Package": "RcppArmadillo", - "Version": "15.2.2-1", - "Source": "Repository", - "Type": "Package", - "Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library", - "Date": "2025-11-21", - "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))", - "Description": "'Armadillo' is a templated C++ linear algebra library aiming towards a good balance between speed and ease of use. It provides high-level syntax and functionality deliberately similar to Matlab. It is useful for algorithm development directly in C++, or quick conversion of research code into production environments. It provides efficient classes for vectors, matrices and cubes where dense and sparse matrices are supported. Integer, floating point and complex numbers are supported. A sophisticated expression evaluator (based on template meta-programming) automatically combines several operations to increase speed and efficiency. Dynamic evaluation automatically chooses optimal code paths based on detected matrix structures. Matrix decompositions are provided through integration with LAPACK, or one of its high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can automatically use 'OpenMP' multi-threading (parallelisation) to speed up computationally expensive operations. . The 'RcppArmadillo' package includes the header files from the 'Armadillo' library; users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. Starting from release 15.0.0, the minimum compilation standard is C++14 so 'Armadillo' version 14.6.3 is included as a fallback when an R package forces the C++11 standard. Package authors should set a '#define' to select the 'current' version, or select the 'legacy' version (also chosen as default) if they must. See 'GitHub issue #475' for details. . Since release 7.800.0, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", - "License": "GPL (>= 2)", - "LazyLoad": "yes", - "Depends": [ - "R (>= 3.3.0)" - ], - "LinkingTo": [ - "Rcpp" - ], - "Imports": [ - "Rcpp (>= 1.0.12)", - "stats", - "utils", - "methods" - ], - "Suggests": [ - "tinytest", - "Matrix (>= 1.3.0)", - "pkgKitten", - "reticulate", - "slam" - ], - "URL": "https://github.com/RcppCore/RcppArmadillo, https://dirk.eddelbuettel.com/code/rcpp.armadillo.html", - "BugReports": "https://github.com/RcppCore/RcppArmadillo/issues", - "RoxygenNote": "6.0.1", - "NeedsCompilation": "yes", - "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), Binxiang Ni [aut], Conrad Sanderson [aut] (ORCID: )", - "Maintainer": "Dirk Eddelbuettel ", - "Repository": "CRAN" - }, - "RcppTOML": { - "Package": "RcppTOML", - "Version": "0.2.3", - "Source": "Repository", - "Type": "Package", - "Title": "'Rcpp' Bindings to Parser for \"Tom's Obvious Markup Language\"", - "Date": "2025-03-08", - "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Mark\", \"Gillard\", role = \"aut\", comment = \"Author of 'toml++' header library\"))", - "Description": "The configuration format defined by 'TOML' (which expands to \"Tom's Obvious Markup Language\") specifies an excellent format (described at ) suitable for both human editing as well as the common uses of a machine-readable format. This package uses 'Rcpp' to connect to the 'toml++' parser written by Mark Gillard to R.", - "SystemRequirements": "A C++17 compiler", - "BugReports": "https://github.com/eddelbuettel/rcpptoml/issues", - "URL": "http://dirk.eddelbuettel.com/code/rcpp.toml.html", - "Imports": [ - "Rcpp (>= 1.0.8)" - ], - "Depends": [ - "R (>= 3.3.0)" - ], - "LinkingTo": [ - "Rcpp" - ], - "Suggests": [ - "tinytest" - ], - "License": "GPL (>= 2)", - "NeedsCompilation": "yes", - "Author": "Dirk Eddelbuettel [aut, cre] (), Mark Gillard [aut] (Author of 'toml++' header library)", - "Maintainer": "Dirk Eddelbuettel ", - "Repository": "CRAN", - "Encoding": "UTF-8" - }, - "Rdpack": { - "Package": "Rdpack", - "Version": "2.6.4", - "Source": "Repository", - "Type": "Package", - "Title": "Update and Manipulate Rd Documentation Objects", - "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )", - "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.", - "URL": "https://geobosh.github.io/Rdpack/ (doc), https://github.com/GeoBosh/Rdpack (devel)", - "BugReports": "https://github.com/GeoBosh/Rdpack/issues", - "Depends": [ - "R (>= 2.15.0)", - "methods" - ], - "Imports": [ - "tools", - "utils", - "rbibutils (>= 1.3)" - ], - "Suggests": [ - "grDevices", - "testthat", - "rstudioapi", - "rprojroot", - "gbRd" - ], - "License": "GPL (>= 2)", - "LazyLoad": "yes", - "RoxygenNote": "7.1.1", - "NeedsCompilation": "no", - "Author": "Georgi N. Boshnakov [aut, cre] (), Duncan Murdoch [ctb]", - "Maintainer": "Georgi N. Boshnakov ", - "Repository": "CRAN", - "Encoding": "UTF-8" - }, - "SQUAREM": { - "Package": "SQUAREM", - "Version": "2021.1", - "Source": "Repository", - "Date": "2021-01-12", - "Title": "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms", - "Description": "Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette(\"SQUAREM\"). Refer to the J Stat Software article: .", - "Depends": [ - "R (>= 3.0)" - ], - "Suggests": [ - "setRNG" - ], - "LazyLoad": "yes", - "License": "GPL (>= 2)", - "Author": "Ravi Varadhan", - "Maintainer": "Ravi Varadhan ", - "URL": "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html", - "Repository": "CRAN", - "NeedsCompilation": "no" - }, - "TTR": { - "Package": "TTR", - "Version": "0.24.4", - "Source": "Repository", - "Type": "Package", - "Title": "Technical Trading Rules", - "Authors@R": "c( person(given=\"Joshua\", family=\"Ulrich\", role=c(\"cre\",\"aut\"), email=\"josh.m.ulrich@gmail.com\"), person(given=c(\"Ethan\",\"B.\"), family=\"Smith\", role=\"ctb\") )", - "Imports": [ - "xts (>= 0.10-0)", - "zoo", - "curl" - ], - "LinkingTo": [ - "xts" - ], - "Enhances": [ - "quantmod" - ], - "Suggests": [ - "RUnit" - ], - "Description": "A collection of over 50 technical indicators for creating technical trading rules. The package also provides fast implementations of common rolling-window functions, and several volatility calculations.", - "License": "GPL (>= 2)", - "URL": "https://github.com/joshuaulrich/TTR", - "BugReports": "https://github.com/joshuaulrich/TTR/issues", - "NeedsCompilation": "yes", - "Author": "Joshua Ulrich [cre, aut], Ethan B. Smith [ctb]", - "Maintainer": "Joshua Ulrich ", - "Repository": "CRAN" - }, "XML": { "Package": "XML", "Version": "3.99-0.18", @@ -620,47 +348,6 @@ "NeedsCompilation": "yes", "Repository": "CRAN" }, - "bfast": { - "Package": "bfast", - "Version": "1.7.1", - "Source": "Repository", - "Title": "Breaks for Additive Season and Trend", - "Authors@R": "c(person(given = \"Jan\", family = \"Verbesselt\", role = c(\"aut\"), email = \"Jan.Verbesselt@wur.nl\"), person(given = \"Dainius\", family = \"Masili\\u016Bnas\", role = c(\"aut\", \"cre\"), email = \"pastas4@gmail.com\", comment = c(ORCID = \"0000-0001-5654-1277\")), person(given = \"Achim\", family = \"Zeileis\", role = \"aut\", email = \"Achim.Zeileis@R-project.org\"), person(given = \"Rob\", family = \"Hyndman\", role = \"ctb\", email = \"Rob.Hyndman@buseco.monash.edu.au\"), person(given = \"Marius\", family = \"Appel\", role = \"aut\", email = \"marius.appel@uni-muenster.de\"), person(given = \"Martin\", family = \"Jung\", role = \"ctb\", email = \"m.jung@sussex.ac.uk\"), person(given = \"Andrei\", family = \"M\\u00EEr\\u021B\", role = \"ctb\", email = \"andrei.mirt@wur.nl\", comment = c(ORCID = \"0000-0003-3654-2090\")), person(given = c(\"Paulo\", \"Negri\"), family = \"Bernardino\", role = \"ctb\", email = \"paulo.negribernardino@wur.nl\"), person(given = \"Dongdong\", family = \"Kong\", role = \"ctb\", email = \"kongdd@mail2.sysu.edu.cn\", comment = c(ORCID = \"0000-0003-1836-8172\")) )", - "Description": "Decomposition of time series into trend, seasonal, and remainder components with methods for detecting and characterizing abrupt changes within the trend and seasonal components. 'BFAST' can be used to analyze different types of satellite image time series and can be applied to other disciplines dealing with seasonal or non-seasonal time series, such as hydrology, climatology, and econometrics. The algorithm can be extended to label detected changes with information on the parameters of the fitted piecewise linear models. 'BFAST' monitoring functionality is described in Verbesselt et al. (2010) . 'BFAST monitor' provides functionality to detect disturbance in near real-time based on 'BFAST'- type models, and is described in Verbesselt et al. (2012) . 'BFAST Lite' approach is a flexible approach that handles missing data without interpolation, and will be described in an upcoming paper. Furthermore, different models can now be used to fit the time series data and detect structural changes (breaks).", - "Depends": [ - "R (>= 3.0.0)", - "strucchangeRcpp (>= 1.5-4)" - ], - "Imports": [ - "graphics", - "stats", - "zoo", - "forecast", - "Rcpp (>= 0.12.7)", - "Rdpack (>= 0.7)" - ], - "Suggests": [ - "MASS", - "sfsmisc", - "stlplus", - "terra" - ], - "License": "GPL (>= 2)", - "URL": "https://bfast2.github.io/", - "BugReports": "https://github.com/bfast2/bfast/issues", - "LazyLoad": "yes", - "LazyData": "yes", - "LinkingTo": [ - "Rcpp" - ], - "RoxygenNote": "7.3.2", - "RdMacros": "Rdpack", - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Author": "Jan Verbesselt [aut], Dainius Masiliūnas [aut, cre] (ORCID: ), Achim Zeileis [aut], Rob Hyndman [ctb], Marius Appel [aut], Martin Jung [ctb], Andrei Mîrț [ctb] (ORCID: ), Paulo Negri Bernardino [ctb], Dongdong Kong [ctb] (ORCID: )", - "Maintainer": "Dainius Masiliūnas ", - "Repository": "CRAN" - }, "bit": { "Package": "bit", "Version": "4.6.0", @@ -1030,78 +717,6 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, - "caret": { - "Package": "caret", - "Version": "7.0-1", - "Source": "Repository", - "Title": "Classification and Regression Training", - "Authors@R": "c(person(given = \"Max\", family = \"Kuhn\", role = c(\"aut\", \"cre\"), email = \"mxkuhn@gmail.com\", comment = c(ORCID = \"0000-0003-2402-136X\")), person(given = \"Jed\", family = \"Wing\", role = \"ctb\"), person(given = \"Steve\", family = \"Weston\", role = \"ctb\"), person(given = \"Andre\", family = \"Williams\", role = \"ctb\"), person(given = \"Chris\", family = \"Keefer\", role = \"ctb\"), person(given = \"Allan\", family = \"Engelhardt\", role = \"ctb\"), person(given = \"Tony\", family = \"Cooper\", role = \"ctb\"), person(given = \"Zachary\", family = \"Mayer\", role = \"ctb\"), person(given = \"Brenton\", family = \"Kenkel\", role = \"ctb\"), person(given = \"R Core Team\", role = \"ctb\"), person(given = \"Michael\", family = \"Benesty\", role = \"ctb\"), person(given = \"Reynald\", family = \"Lescarbeau\", role = \"ctb\"), person(given = \"Andrew\", family = \"Ziem\", role = \"ctb\"), person(given = \"Luca\", family = \"Scrucca\", role = \"ctb\"), person(given = \"Yuan\", family = \"Tang\", role = \"ctb\"), person(given = \"Can\", family = \"Candan\", role = \"ctb\"), person(given = \"Tyler\", family = \"Hunt\", role = \"ctb\"))", - "Description": "Misc functions for training and plotting classification and regression models.", - "License": "GPL (>= 2)", - "URL": "https://github.com/topepo/caret/", - "BugReports": "https://github.com/topepo/caret/issues", - "Depends": [ - "ggplot2", - "lattice (>= 0.20)", - "R (>= 3.2.0)" - ], - "Imports": [ - "e1071", - "foreach", - "grDevices", - "methods", - "ModelMetrics (>= 1.2.2.2)", - "nlme", - "plyr", - "pROC", - "recipes (>= 0.1.10)", - "reshape2", - "stats", - "stats4", - "utils", - "withr (>= 2.0.0)" - ], - "Suggests": [ - "BradleyTerry2", - "covr", - "Cubist", - "dplyr", - "earth (>= 2.2-3)", - "ellipse", - "fastICA", - "gam (>= 1.15)", - "ipred", - "kernlab", - "klaR", - "knitr", - "MASS", - "Matrix", - "mda", - "mgcv", - "mlbench", - "MLmetrics", - "nnet", - "pamr", - "party (>= 0.9-99992)", - "pls", - "proxy", - "randomForest", - "RANN", - "rmarkdown", - "rpart", - "spls", - "superpc", - "testthat (>= 0.9.1)", - "themis (>= 0.1.3)" - ], - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Max Kuhn [aut, cre] (), Jed Wing [ctb], Steve Weston [ctb], Andre Williams [ctb], Chris Keefer [ctb], Allan Engelhardt [ctb], Tony Cooper [ctb], Zachary Mayer [ctb], Brenton Kenkel [ctb], R Core Team [ctb], Michael Benesty [ctb], Reynald Lescarbeau [ctb], Andrew Ziem [ctb], Luca Scrucca [ctb], Yuan Tang [ctb], Can Candan [ctb], Tyler Hunt [ctb]", - "Maintainer": "Max Kuhn ", - "Repository": "CRAN" - }, "cellranger": { "Package": "cellranger", "Version": "1.1.0", @@ -1273,52 +888,6 @@ "Maintainer": "Matthew Lincoln ", "Repository": "CRAN" }, - "clock": { - "Package": "clock", - "Version": "0.7.3", - "Source": "Repository", - "Title": "Date-Time Types and Tools", - "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Provides a comprehensive library for date-time manipulations using a new family of orthogonal date-time classes (durations, time points, zoned-times, and calendars) that partition responsibilities so that the complexities of time zones are only considered when they are really needed. Capabilities include: date-time parsing, formatting, arithmetic, extraction and updating of components, and rounding.", - "License": "MIT + file LICENSE", - "URL": "https://clock.r-lib.org, https://github.com/r-lib/clock", - "BugReports": "https://github.com/r-lib/clock/issues", - "Depends": [ - "R (>= 4.0.0)" - ], - "Imports": [ - "cli (>= 3.6.4)", - "lifecycle (>= 1.0.4)", - "rlang (>= 1.1.5)", - "tzdb (>= 0.5.0)", - "vctrs (>= 0.6.5)" - ], - "Suggests": [ - "covr", - "knitr", - "magrittr", - "pillar", - "rmarkdown", - "slider (>= 0.3.2)", - "testthat (>= 3.0.0)", - "withr" - ], - "LinkingTo": [ - "cpp11 (>= 0.5.2)", - "tzdb (>= 0.5.0)" - ], - "VignetteBuilder": "knitr", - "Config/build/compilation-database": "true", - "Config/Needs/website": "lubridate, tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "LazyData": "true", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Davis Vaughan [aut, cre], Posit Software, PBC [cph, fnd]", - "Maintainer": "Davis Vaughan ", - "Repository": "CRAN" - }, "codetools": { "Package": "codetools", "Version": "0.2-20", @@ -1759,27 +1328,6 @@ "NeedsCompilation": "yes", "Repository": "CRAN" }, - "diagram": { - "Package": "diagram", - "Version": "1.6.5", - "Source": "Repository", - "Title": "Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams", - "Author": "Karline Soetaert ", - "Maintainer": "Karline Soetaert ", - "Depends": [ - "R (>= 2.01)", - "shape" - ], - "Imports": [ - "stats", - "graphics" - ], - "Description": "Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book \"A practical guide to ecological modelling - using R as a simulation platform\" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb).", - "License": "GPL (>= 2)", - "LazyData": "yes", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, "dichromat": { "Package": "dichromat", "Version": "2.0-0.1", @@ -2003,46 +1551,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "exactextractr": { - "Package": "exactextractr", - "Version": "0.10.0", - "Source": "Repository", - "Title": "Fast Extraction from Raster Datasets using Polygons", - "Authors@R": "c( person(\"Daniel Baston\", email = \"dbaston@isciences.com\", role = c(\"aut\", \"cre\")), person(\"ISciences, LLC\", role=\"cph\"))", - "Description": "Quickly and accurately summarizes raster values over polygonal areas (\"zonal statistics\").", - "Depends": [ - "R (>= 3.4.0)" - ], - "License": "Apache License (== 2.0)", - "SystemRequirements": "GEOS (>= 3.5.0)", - "Imports": [ - "Rcpp (>= 0.12.12)", - "methods", - "raster", - "sf (>= 0.9.0)" - ], - "URL": "https://isciences.gitlab.io/exactextractr/, https://github.com/isciences/exactextractr", - "BugReports": "https://github.com/isciences/exactextractr/issues", - "LinkingTo": [ - "Rcpp" - ], - "Suggests": [ - "dplyr", - "foreign", - "knitr", - "ncdf4", - "rmarkdown", - "testthat", - "terra (>= 1.5.17)" - ], - "Encoding": "UTF-8", - "RoxygenNote": "7.1.2", - "VignetteBuilder": "knitr", - "NeedsCompilation": "yes", - "Author": "Daniel Baston [aut, cre], ISciences, LLC [cph]", - "Maintainer": "Daniel Baston ", - "Repository": "CRAN" - }, "fansi": { "Package": "fansi", "Version": "1.0.6", @@ -2324,124 +1832,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "foreach": { - "Package": "foreach", - "Version": "1.5.2", - "Source": "Repository", - "Type": "Package", - "Title": "Provides Foreach Looping Construct", - "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Hong\", \"Ooi\", role=\"ctb\"), person(\"Rich\", \"Calaway\", role=\"ctb\"), person(\"Microsoft\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", - "Description": "Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.", - "License": "Apache License (== 2.0)", - "URL": "https://github.com/RevolutionAnalytics/foreach", - "BugReports": "https://github.com/RevolutionAnalytics/foreach/issues", - "Depends": [ - "R (>= 2.5.0)" - ], - "Imports": [ - "codetools", - "utils", - "iterators" - ], - "Suggests": [ - "randomForest", - "doMC", - "doParallel", - "testthat", - "knitr", - "rmarkdown" - ], - "VignetteBuilder": "knitr", - "RoxygenNote": "7.1.1", - "Collate": "'callCombine.R' 'foreach.R' 'do.R' 'foreach-ext.R' 'foreach-pkg.R' 'getDoPar.R' 'getDoSeq.R' 'getsyms.R' 'iter.R' 'nextElem.R' 'onLoad.R' 'setDoPar.R' 'setDoSeq.R' 'times.R' 'utils.R'", - "NeedsCompilation": "no", - "Author": "Folashade Daniel [cre], Hong Ooi [ctb], Rich Calaway [ctb], Microsoft [aut, cph], Steve Weston [aut]", - "Maintainer": "Folashade Daniel ", - "Repository": "CRAN" - }, - "forecast": { - "Package": "forecast", - "Version": "8.24.0", - "Source": "Repository", - "Title": "Forecasting Functions for Time Series and Linear Models", - "Description": "Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.", - "Depends": [ - "R (>= 3.5.0)" - ], - "Imports": [ - "colorspace", - "fracdiff", - "generics (>= 0.1.2)", - "ggplot2 (>= 2.2.1)", - "graphics", - "lmtest", - "magrittr", - "nnet", - "parallel", - "Rcpp (>= 0.11.0)", - "stats", - "timeDate", - "tseries", - "urca", - "withr", - "zoo" - ], - "Suggests": [ - "forecTheta", - "knitr", - "methods", - "rmarkdown", - "rticles", - "scales", - "seasonal", - "testthat (>= 3.0.0)", - "uroot" - ], - "LinkingTo": [ - "Rcpp (>= 0.11.0)", - "RcppArmadillo (>= 0.2.35)" - ], - "LazyData": "yes", - "ByteCompile": "TRUE", - "Authors@R": "c( person(\"Rob\", \"Hyndman\", email = \"Rob.Hyndman@monash.edu\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0002-2140-5352\")), person(\"George\", \"Athanasopoulos\", role = \"aut\", comment = c(ORCID = \"0000-0002-5389-2802\")), person(\"Christoph\", \"Bergmeir\", role = \"aut\", comment = c(ORCID = \"0000-0002-3665-9021\")), person(\"Gabriel\", \"Caceres\", role = \"aut\", comment = c(ORCID = \"0000-0002-2947-2023\")), person(\"Leanne\", \"Chhay\", role = \"aut\"), person(\"Kirill\", \"Kuroptev\", role = \"aut\"), person(\"Mitchell\", \"O'Hara-Wild\", role = \"aut\", comment = c(ORCID = \"0000-0001-6729-7695\")), person(\"Fotios\", \"Petropoulos\", role = \"aut\", comment = c(ORCID = \"0000-0003-3039-4955\")), person(\"Slava\", \"Razbash\", role = \"aut\"), person(\"Earo\", \"Wang\", role = \"aut\", comment = c(ORCID = \"0000-0001-6448-5260\")), person(\"Farah\", \"Yasmeen\", role = \"aut\", comment = c(ORCID = \"0000-0002-1479-5401\")), person(\"Federico\", \"Garza\", role = \"ctb\"), person(\"Daniele\", \"Girolimetto\", role = \"ctb\"), person(\"Ross\", \"Ihaka\", role = c(\"ctb\", \"cph\")), person(\"R Core Team\", role = c(\"ctb\", \"cph\")), person(\"Daniel\", \"Reid\", role = \"ctb\"), person(\"David\", \"Shaub\", role = \"ctb\"), person(\"Yuan\", \"Tang\", role = \"ctb\", comment = c(ORCID = \"0000-0001-5243-233X\")), person(\"Xiaoqian\", \"Wang\", role = \"ctb\"), person(\"Zhenyu\", \"Zhou\", role = \"ctb\") )", - "BugReports": "https://github.com/robjhyndman/forecast/issues", - "License": "GPL-3", - "URL": "https://pkg.robjhyndman.com/forecast/, https://github.com/robjhyndman/forecast", - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Config/testthat/edition": "3", - "NeedsCompilation": "yes", - "Author": "Rob Hyndman [aut, cre, cph] (), George Athanasopoulos [aut] (), Christoph Bergmeir [aut] (), Gabriel Caceres [aut] (), Leanne Chhay [aut], Kirill Kuroptev [aut], Mitchell O'Hara-Wild [aut] (), Fotios Petropoulos [aut] (), Slava Razbash [aut], Earo Wang [aut] (), Farah Yasmeen [aut] (), Federico Garza [ctb], Daniele Girolimetto [ctb], Ross Ihaka [ctb, cph], R Core Team [ctb, cph], Daniel Reid [ctb], David Shaub [ctb], Yuan Tang [ctb] (), Xiaoqian Wang [ctb], Zhenyu Zhou [ctb]", - "Maintainer": "Rob Hyndman ", - "Repository": "CRAN" - }, - "fracdiff": { - "Package": "fracdiff", - "Version": "1.5-3", - "Source": "Repository", - "VersionNote": "Released 1.5-0 on 2019-12-09, 1.5-1 on 2020-01-20, 1.5-2 on 2022-10-31", - "Date": "2024-02-01", - "Title": "Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models", - "Authors@R": "c(person(\"Martin\",\"Maechler\", role=c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) , person(\"Chris\", \"Fraley\", role=c(\"ctb\",\"cph\"), comment = \"S original; Fortran code\") , person(\"Friedrich\", \"Leisch\", role = \"ctb\", comment = c(\"R port\", ORCID = \"0000-0001-7278-1983\")) , person(\"Valderio\", \"Reisen\", role=\"ctb\", comment = \"fdGPH() & fdSperio()\") , person(\"Artur\", \"Lemonte\", role=\"ctb\", comment = \"fdGPH() & fdSperio()\") , person(\"Rob\", \"Hyndman\", email=\"Rob.Hyndman@monash.edu\", role=\"ctb\", comment = c(\"residuals() & fitted()\", ORCID = \"0000-0002-2140-5352\")) )", - "Description": "Maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); including inference and basic methods. Some alternative algorithms to estimate \"H\".", - "Imports": [ - "stats" - ], - "Suggests": [ - "longmemo", - "forecast", - "urca" - ], - "License": "GPL (>= 2)", - "URL": "https://github.com/mmaechler/fracdiff", - "BugReports": "https://github.com/mmaechler/fracdiff/issues", - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Author": "Martin Maechler [aut, cre] (), Chris Fraley [ctb, cph] (S original; Fortran code), Friedrich Leisch [ctb] (R port, ), Valderio Reisen [ctb] (fdGPH() & fdSperio()), Artur Lemonte [ctb] (fdGPH() & fdSperio()), Rob Hyndman [ctb] (residuals() & fitted(), )", - "Maintainer": "Martin Maechler ", - "Repository": "CRAN" - }, "fs": { "Package": "fs", "Version": "1.6.5", @@ -2563,41 +1953,6 @@ "Maintainer": "Henrik Bengtsson ", "Repository": "CRAN" }, - "future.apply": { - "Package": "future.apply", - "Version": "1.11.3", - "Source": "Repository", - "Title": "Apply Function to Elements in Parallel using Futures", - "Depends": [ - "R (>= 3.2.0)", - "future (>= 1.28.0)" - ], - "Imports": [ - "globals (>= 0.16.1)", - "parallel", - "utils" - ], - "Suggests": [ - "datasets", - "stats", - "tools", - "listenv (>= 0.8.0)", - "R.rsp", - "markdown" - ], - "VignetteBuilder": "R.rsp", - "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"R Core Team\", role = c(\"cph\", \"ctb\")))", - "Description": "Implementations of apply(), by(), eapply(), lapply(), Map(), .mapply(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework .", - "License": "GPL (>= 2)", - "LazyLoad": "TRUE", - "URL": "https://future.apply.futureverse.org, https://github.com/futureverse/future.apply", - "BugReports": "https://github.com/futureverse/future.apply/issues", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Henrik Bengtsson [aut, cre, cph] (), R Core Team [cph, ctb]", - "Maintainer": "Henrik Bengtsson ", - "Repository": "CRAN" - }, "gargle": { "Package": "gargle", "Version": "1.5.2", @@ -2859,6 +2214,57 @@ "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" }, + "ggspatial": { + "Package": "ggspatial", + "Version": "1.1.10", + "Source": "Repository", + "Type": "Package", + "Title": "Spatial Data Framework for ggplot2", + "Authors@R": "c( person(\"Dewey\", \"Dunnington\", email = \"dewey@fishandwhistle.net\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9415-4582\") ), person(\"Brent\", \"Thorne\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1099-3857\")), person(\"Diego\", \"Hernangómez\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8457-4658\")) )", + "Maintainer": "Dewey Dunnington ", + "Description": "Spatial data plus the power of the ggplot2 framework means easier mapping when input data are already in the form of spatial objects.", + "License": "GPL-3", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ + "sf", + "ggplot2 (>= 3.0.0)", + "rosm (>= 0.2)", + "abind", + "methods", + "tibble", + "scales", + "tidyr", + "rlang", + "grid", + "glue" + ], + "Suggests": [ + "prettymapr", + "knitr", + "rmarkdown", + "sp", + "raster", + "terra", + "testthat (>= 3.0.0)", + "dplyr", + "withr", + "ggrepel", + "stars", + "covr", + "vdiffr", + "lwgeom" + ], + "URL": "https://paleolimbot.github.io/ggspatial/, https://github.com/paleolimbot/ggspatial", + "BugReports": "https://github.com/paleolimbot/ggspatial/issues", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Dewey Dunnington [aut, cre] (ORCID: ), Brent Thorne [ctb] (ORCID: ), Diego Hernangómez [ctb] (ORCID: )", + "Repository": "CRAN" + }, "globals": { "Package": "globals", "Version": "0.16.3", @@ -3024,57 +2430,6 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, - "gower": { - "Package": "gower", - "Version": "1.0.2", - "Source": "Repository", - "Maintainer": "Mark van der Loo ", - "License": "GPL-3", - "Title": "Gower's Distance", - "Type": "Package", - "LazyLoad": "yes", - "Authors@R": "c( person(\"Mark\", \"van der Loo\", role=c(\"aut\",\"cre\"),email=\"mark.vanderloo@gmail.com\") , person(\"David\", \"Turner\", role=\"ctb\"))", - "Description": "Compute Gower's distance (or similarity) coefficient between records. Compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.", - "URL": "https://github.com/markvanderloo/gower", - "BugReports": "https://github.com/markvanderloo/gower/issues", - "Suggests": [ - "tinytest (>= 0.9.3)" - ], - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Mark van der Loo [aut, cre], David Turner [ctb]", - "Repository": "CRAN" - }, - "gridExtra": { - "Package": "gridExtra", - "Version": "2.3", - "Source": "Repository", - "Authors@R": "c(person(\"Baptiste\", \"Auguie\", email = \"baptiste.auguie@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Anton\", \"Antonov\", email = \"tonytonov@gmail.com\", role = c(\"ctb\")))", - "License": "GPL (>= 2)", - "Title": "Miscellaneous Functions for \"Grid\" Graphics", - "Type": "Package", - "Description": "Provides a number of user-level functions to work with \"grid\" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.", - "VignetteBuilder": "knitr", - "Imports": [ - "gtable", - "grid", - "grDevices", - "graphics", - "utils" - ], - "Suggests": [ - "ggplot2", - "egg", - "lattice", - "knitr", - "testthat" - ], - "RoxygenNote": "6.0.1", - "NeedsCompilation": "no", - "Author": "Baptiste Auguie [aut, cre], Anton Antonov [ctb]", - "Maintainer": "Baptiste Auguie ", - "Repository": "CRAN" - }, "gtable": { "Package": "gtable", "Version": "0.3.6", @@ -3115,52 +2470,6 @@ "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" }, - "hardhat": { - "Package": "hardhat", - "Version": "1.4.1", - "Source": "Repository", - "Title": "Construct Modeling Packages", - "Authors@R": "c( person(\"Hannah\", \"Frick\", , \"hannah@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6049-5258\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Building modeling packages is hard. A large amount of effort generally goes into providing an implementation for a new method that is efficient, fast, and correct, but often less emphasis is put on the user interface. A good interface requires specialized knowledge about S3 methods and formulas, which the average package developer might not have. The goal of 'hardhat' is to reduce the burden around building new modeling packages by providing functionality for preprocessing, predicting, and validating input.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/tidymodels/hardhat, https://hardhat.tidymodels.org", - "BugReports": "https://github.com/tidymodels/hardhat/issues", - "Depends": [ - "R (>= 3.5.0)" - ], - "Imports": [ - "cli (>= 3.6.0)", - "glue (>= 1.6.2)", - "rlang (>= 1.1.0)", - "sparsevctrs (>= 0.2.0)", - "tibble (>= 3.2.1)", - "vctrs (>= 0.6.0)" - ], - "Suggests": [ - "covr", - "crayon", - "devtools", - "knitr", - "Matrix", - "modeldata (>= 0.0.2)", - "recipes (>= 1.0.5)", - "rmarkdown (>= 2.3)", - "roxygen2", - "testthat (>= 3.0.0)", - "usethis (>= 2.1.5)", - "withr (>= 3.0.0)" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "LazyData": "true", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Hannah Frick [aut, cre] (), Davis Vaughan [aut], Max Kuhn [aut], Posit Software, PBC [cph, fnd]", - "Maintainer": "Hannah Frick ", - "Repository": "CRAN" - }, "haven": { "Package": "haven", "Version": "2.5.4", @@ -3248,6 +2557,42 @@ "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, + "hexbin": { + "Package": "hexbin", + "Version": "1.28.5", + "Source": "Repository", + "Title": "Hexagonal Binning Routines", + "Authors@R": "c(person(given = \"Dan\", family = \"Carr\", role = \"aut\", email = \"dcarr@voxel.galaxy.gmu.edu\"), person(given = c(\"Nicholas\"), family = \"Lewin-Koh\", role = \"aut\"), person(given = \"Martin\", family = \"Maechler\", role = \"aut\", email = \"maechler@stat.math.ethz.ch\"), person(given = \"Deepayan\", family = \"Sarkar\", role = \"aut\", email = \"deepayan.sarkar@r-project.org\"), person(given = \"Edzer\", family = \"Pebesma\", role = \"cre\", comment = c(ORCID = \"0000-0001-8049-7069\"), email = \"edzer.pebesma@uni-muenster.de\"))", + "Depends": [ + "R (>= 2.0.1)", + "methods" + ], + "Imports": [ + "lattice", + "grid", + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "marray", + "affy", + "Biobase", + "limma", + "knitr" + ], + "Description": "Binning and plotting functions for hexagonal bins.", + "Collate": "lattice.R BTC.R BTY.R grid.hexagons.R grid.hexlegend.R hbox.R hdiffplot.R hexbinList.R hexbinplot.R hexbin.s4.R hexpanel.R hexplom.R hexPlotMA.R hexutil.R hexViewport.R HO.R LINGRAY.R LOCS.R MAG.R RB.R smoothHexbin.R", + "License": "GPL-2", + "VignetteBuilder": "knitr", + "NeedsCompilation": "yes", + "URL": "https://github.com/edzer/hexbin", + "Author": "Dan Carr [aut], Nicholas Lewin-Koh [aut], Martin Maechler [aut], Deepayan Sarkar [aut], Edzer Pebesma [cre] ()", + "Maintainer": "Edzer Pebesma ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, "highr": { "Package": "highr", "Version": "0.11", @@ -3496,38 +2841,6 @@ "Maintainer": "Rich FitzJohn ", "Repository": "CRAN" }, - "ipred": { - "Package": "ipred", - "Version": "0.9-15", - "Source": "Repository", - "Title": "Improved Predictors", - "Date": "2024-07-18", - "Authors@R": "c(person(\"Andrea\", \"Peters\", role = \"aut\"), person(\"Torsten\", \"Hothorn\", role = c(\"aut\", \"cre\"), email = \"Torsten.Hothorn@R-project.org\"), person(\"Brian D.\", \"Ripley\", role = \"ctb\"), person(\"Terry\", \"Therneau\", role = \"ctb\"), person(\"Beth\", \"Atkinson\", role = \"ctb\"))", - "Description": "Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.", - "Depends": [ - "R (>= 2.10)" - ], - "Imports": [ - "rpart (>= 3.1-8)", - "MASS", - "survival", - "nnet", - "class", - "prodlim" - ], - "Suggests": [ - "mvtnorm", - "mlbench", - "TH.data", - "randomForest", - "party" - ], - "License": "GPL (>= 2)", - "NeedsCompilation": "yes", - "Author": "Andrea Peters [aut], Torsten Hothorn [aut, cre], Brian D. Ripley [ctb], Terry Therneau [ctb], Beth Atkinson [ctb]", - "Maintainer": "Torsten Hothorn ", - "Repository": "CRAN" - }, "isoband": { "Package": "isoband", "Version": "0.2.7", @@ -3564,28 +2877,25 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "iterators": { - "Package": "iterators", - "Version": "1.0.14", + "jpeg": { + "Package": "jpeg", + "Version": "0.1-11", "Source": "Repository", - "Type": "Package", - "Title": "Provides Iterator Construct", - "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Revolution\", \"Analytics\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"))", - "Description": "Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.", - "URL": "https://github.com/RevolutionAnalytics/iterators", + "Title": "Read and write JPEG images", + "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.org, )", + "Authors@R": "person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.org\", ORCID=\"0000-0003-2297-1732\"))", + "Maintainer": "Simon Urbanek ", "Depends": [ - "R (>= 2.5.0)", - "utils" + "R (>= 2.9.0)" ], - "Suggests": [ - "RUnit", - "foreach" - ], - "License": "Apache License (== 2.0)", - "NeedsCompilation": "no", - "Author": "Folashade Daniel [cre], Revolution Analytics [aut, cph], Steve Weston [aut]", - "Maintainer": "Folashade Daniel ", - "Repository": "CRAN" + "Description": "This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.", + "License": "GPL-2 | GPL-3", + "SystemRequirements": "libjpeg", + "URL": "https://www.rforge.net/jpeg/", + "BugReports": "https://github.com/s-u/jpeg/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Encoding": "UTF-8" }, "jquerylib": { "Package": "jquerylib", @@ -3829,68 +3139,6 @@ "Maintainer": "Deepayan Sarkar ", "Repository": "CRAN" }, - "lava": { - "Package": "lava", - "Version": "1.8.1", - "Source": "Repository", - "Type": "Package", - "Title": "Latent Variable Models", - "Authors@R": "c(person(\"Klaus K.\", \"Holst\", email=\"klaus@holst.it\", role=c(\"aut\", \"cre\")), person(\"Brice\", \"Ozenne\", role = \"ctb\"), person(\"Thomas\", \"Gerds\", role = \"ctb\"))", - "Author": "Klaus K. Holst [aut, cre], Brice Ozenne [ctb], Thomas Gerds [ctb]", - "Maintainer": "Klaus K. Holst ", - "Description": "A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) ). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) ). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.", - "URL": "https://kkholst.github.io/lava/", - "BugReports": "https://github.com/kkholst/lava/issues", - "License": "GPL-3", - "LazyLoad": "yes", - "Depends": [ - "R (>= 3.0)" - ], - "Imports": [ - "cli", - "future.apply", - "graphics", - "grDevices", - "methods", - "numDeriv", - "progressr", - "stats", - "survival", - "SQUAREM", - "utils" - ], - "Suggests": [ - "KernSmooth", - "Rgraphviz", - "data.table", - "ellipse", - "fields", - "geepack", - "graph", - "knitr", - "rmarkdown", - "igraph (>= 0.6)", - "lavaSearch2", - "lme4 (>= 1.1.35.1)", - "MASS", - "Matrix (>= 1.6.3)", - "mets (>= 1.1)", - "nlme", - "optimx", - "polycor", - "quantreg", - "rgl", - "targeted (>= 0.4)", - "testthat (>= 0.11)", - "visNetwork" - ], - "VignetteBuilder": "knitr,rmarkdown", - "ByteCompile": "yes", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, "lazyeval": { "Package": "lazyeval", "Version": "0.2.2", @@ -4200,38 +3448,6 @@ "Maintainer": "Henrik Bengtsson ", "Repository": "CRAN" }, - "lmtest": { - "Package": "lmtest", - "Version": "0.9-40", - "Source": "Repository", - "Title": "Testing Linear Regression Models", - "Date": "2022-03-21", - "Authors@R": "c(person(given = \"Torsten\", family = \"Hothorn\", role = \"aut\", email = \"Torsten.Hothorn@R-project.org\", comment = c(ORCID = \"0000-0001-8301-0471\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = c(\"Richard\", \"W.\"), family = \"Farebrother\", role = \"aut\", comment = \"pan.f\"), person(given = \"Clint\", family = \"Cummins\", role = \"aut\", comment = \"pan.f\"), person(given = \"Giovanni\", family = \"Millo\", role = \"ctb\"), person(given = \"David\", family = \"Mitchell\", role = \"ctb\"))", - "Description": "A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.", - "LazyData": "yes", - "Depends": [ - "R (>= 3.0.0)", - "stats", - "zoo" - ], - "Suggests": [ - "car", - "strucchange", - "sandwich", - "dynlm", - "stats4", - "survival", - "AER" - ], - "Imports": [ - "graphics" - ], - "License": "GPL-2 | GPL-3", - "NeedsCompilation": "yes", - "Author": "Torsten Hothorn [aut] (), Achim Zeileis [aut, cre] (), Richard W. Farebrother [aut] (pan.f), Clint Cummins [aut] (pan.f), Giovanni Millo [ctb], David Mitchell [ctb]", - "Maintainer": "Achim Zeileis ", - "Repository": "CRAN" - }, "logger": { "Package": "logger", "Version": "0.4.0", @@ -4584,50 +3800,6 @@ "Maintainer": "R Core Team ", "Repository": "CRAN" }, - "nnet": { - "Package": "nnet", - "Version": "7.3-19", - "Source": "Repository", - "Priority": "recommended", - "Date": "2023-05-02", - "Depends": [ - "R (>= 3.0.0)", - "stats", - "utils" - ], - "Suggests": [ - "MASS" - ], - "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"ripley@stats.ox.ac.uk\"), person(\"William\", \"Venables\", role = \"cph\"))", - "Description": "Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.", - "Title": "Feed-Forward Neural Networks and Multinomial Log-Linear Models", - "ByteCompile": "yes", - "License": "GPL-2 | GPL-3", - "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", - "NeedsCompilation": "yes", - "Author": "Brian Ripley [aut, cre, cph], William Venables [cph]", - "Maintainer": "Brian Ripley ", - "Repository": "CRAN" - }, - "numDeriv": { - "Package": "numDeriv", - "Version": "2016.8-1.1", - "Source": "Repository", - "Title": "Accurate Numerical Derivatives", - "Description": "Methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.", - "Depends": [ - "R (>= 2.11.1)" - ], - "LazyLoad": "yes", - "ByteCompile": "yes", - "License": "GPL-2", - "Copyright": "2006-2011, Bank of Canada. 2012-2016, Paul Gilbert", - "Author": "Paul Gilbert and Ravi Varadhan", - "Maintainer": "Paul Gilbert ", - "URL": "http://optimizer.r-forge.r-project.org/", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, "officer": { "Package": "officer", "Version": "0.7.0", @@ -4705,47 +3877,6 @@ "Maintainer": "Jeroen Ooms ", "Repository": "CRAN" }, - "pROC": { - "Package": "pROC", - "Version": "1.18.5", - "Source": "Repository", - "Type": "Package", - "Title": "Display and Analyze ROC Curves", - "Date": "2023-11-01", - "Encoding": "UTF-8", - "Depends": [ - "R (>= 2.14)" - ], - "Imports": [ - "methods", - "plyr", - "Rcpp (>= 0.11.1)" - ], - "Suggests": [ - "microbenchmark", - "tcltk", - "MASS", - "logcondens", - "doParallel", - "testthat", - "vdiffr", - "ggplot2", - "rlang" - ], - "LinkingTo": [ - "Rcpp" - ], - "Authors@R": "c(person(\"Xavier\", \"Robin\", role = c(\"cre\", \"aut\"), email = \"pROC-cran@xavier.robin.name\", comment = c(ORCID = \"0000-0002-6813-3200\")), person(\"Natacha\", \"Turck\", role = \"aut\"), person(\"Alexandre\", \"Hainard\", role = \"aut\"), person(\"Natalia\", \"Tiberti\", role = \"aut\"), person(\"Frédérique\", \"Lisacek\", role = \"aut\"), person(\"Jean-Charles\", \"Sanchez\", role = \"aut\"), person(\"Markus\", \"Müller\", role = \"aut\"), person(\"Stefan\", \"Siegert\", role = \"ctb\", comment = \"Fast DeLong code\", email = \"stefan_siegert@gmx.de\"), person(\"Matthias\", \"Doering\", role = \"ctb\", comment = \"Hand & Till Multiclass\"), person(\"Zane\", \"Billings\", role = \"ctb\", comment = \"DeLong paired test CI\"))", - "Description": "Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.", - "License": "GPL (>= 3)", - "URL": "https://xrobin.github.io/pROC/", - "BugReports": "https://github.com/xrobin/pROC/issues", - "LazyData": "yes", - "NeedsCompilation": "yes", - "Author": "Xavier Robin [cre, aut] (), Natacha Turck [aut], Alexandre Hainard [aut], Natalia Tiberti [aut], Frédérique Lisacek [aut], Jean-Charles Sanchez [aut], Markus Müller [aut], Stefan Siegert [ctb] (Fast DeLong code), Matthias Doering [ctb] (Hand & Till Multiclass), Zane Billings [ctb] (DeLong paired test CI)", - "Maintainer": "Xavier Robin ", - "Repository": "CRAN" - }, "parallelly": { "Package": "parallelly", "Version": "1.43.0", @@ -4775,50 +3906,6 @@ "Maintainer": "Henrik Bengtsson ", "Repository": "CRAN" }, - "patchwork": { - "Package": "patchwork", - "Version": "1.3.2", - "Source": "Repository", - "Type": "Package", - "Title": "The Composer of Plots", - "Authors@R": "person(given = \"Thomas Lin\", family = \"Pedersen\", role = c(\"cre\", \"aut\"), email = \"thomasp85@gmail.com\", comment = c(ORCID = \"0000-0002-5147-4711\"))", - "Maintainer": "Thomas Lin Pedersen ", - "Description": "The 'ggplot2' package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. 'patchwork' is a package that expands the API to allow for arbitrarily complex composition of plots by, among others, providing mathematical operators for combining multiple plots. Other packages that try to address this need (but with a different approach) are 'gridExtra' and 'cowplot'.", - "License": "MIT + file LICENSE", - "Encoding": "UTF-8", - "Imports": [ - "ggplot2 (>= 3.0.0)", - "gtable (>= 0.3.6)", - "grid", - "stats", - "grDevices", - "utils", - "graphics", - "rlang (>= 1.0.0)", - "cli", - "farver" - ], - "RoxygenNote": "7.3.2", - "URL": "https://patchwork.data-imaginist.com, https://github.com/thomasp85/patchwork", - "BugReports": "https://github.com/thomasp85/patchwork/issues", - "Suggests": [ - "knitr", - "rmarkdown", - "gridGraphics", - "gridExtra", - "ragg", - "testthat (>= 2.1.0)", - "vdiffr", - "covr", - "png", - "gt (>= 0.11.0)" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "gifski", - "NeedsCompilation": "no", - "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: )", - "Repository": "CRAN" - }, "pillar": { "Package": "pillar", "Version": "1.10.2", @@ -4900,43 +3987,6 @@ "NeedsCompilation": "no", "Repository": "CRAN" }, - "plyr": { - "Package": "plyr", - "Version": "1.8.9", - "Source": "Repository", - "Title": "Tools for Splitting, Applying and Combining Data", - "Authors@R": "person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\"))", - "Description": "A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'.", - "License": "MIT + file LICENSE", - "URL": "http://had.co.nz/plyr, https://github.com/hadley/plyr", - "BugReports": "https://github.com/hadley/plyr/issues", - "Depends": [ - "R (>= 3.1.0)" - ], - "Imports": [ - "Rcpp (>= 0.11.0)" - ], - "Suggests": [ - "abind", - "covr", - "doParallel", - "foreach", - "iterators", - "itertools", - "tcltk", - "testthat" - ], - "LinkingTo": [ - "Rcpp" - ], - "Encoding": "UTF-8", - "LazyData": "true", - "RoxygenNote": "7.2.3", - "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut, cre]", - "Maintainer": "Hadley Wickham ", - "Repository": "CRAN" - }, "png": { "Package": "png", "Version": "0.1-8", @@ -5019,37 +4069,6 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, - "prodlim": { - "Package": "prodlim", - "Version": "2024.06.25", - "Source": "Repository", - "Title": "Product-Limit Estimation for Censored Event History Analysis", - "Author": "Thomas A. Gerds", - "Description": "Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.", - "Depends": [ - "R (>= 2.9.0)" - ], - "Imports": [ - "Rcpp (>= 0.11.5)", - "stats", - "data.table", - "grDevices", - "graphics", - "diagram", - "survival", - "KernSmooth", - "lava" - ], - "LinkingTo": [ - "Rcpp" - ], - "Maintainer": "Thomas A. Gerds ", - "BugReports": "https://github.com/tagteam/prodlim/issues", - "License": "GPL (>= 2)", - "RoxygenNote": "7.3.1", - "NeedsCompilation": "yes", - "Repository": "CRAN" - }, "progress": { "Package": "progress", "Version": "1.2.3", @@ -5083,53 +4102,6 @@ "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, - "progressr": { - "Package": "progressr", - "Version": "0.15.1", - "Source": "Repository", - "Title": "An Inclusive, Unifying API for Progress Updates", - "Description": "A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will also work with parallel processing via the 'future' framework, e.g. future.apply::future_lapply(), furrr::future_map(), and 'foreach' with 'doFuture'. The package is compatible with Shiny applications.", - "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")))", - "License": "GPL (>= 3)", - "Depends": [ - "R (>= 3.5.0)" - ], - "Imports": [ - "digest", - "utils" - ], - "Suggests": [ - "graphics", - "tcltk", - "beepr", - "cli", - "crayon", - "pbmcapply", - "progress", - "purrr", - "foreach", - "plyr", - "doFuture", - "future", - "future.apply", - "furrr", - "ntfy", - "RPushbullet", - "rstudioapi", - "shiny", - "commonmark", - "base64enc", - "tools" - ], - "VignetteBuilder": "progressr", - "URL": "https://progressr.futureverse.org, https://github.com/futureverse/progressr", - "BugReports": "https://github.com/futureverse/progressr/issues", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Henrik Bengtsson [aut, cre, cph] ()", - "Maintainer": "Henrik Bengtsson ", - "Repository": "CRAN" - }, "promises": { "Package": "promises", "Version": "1.3.2", @@ -5282,60 +4254,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "quadprog": { - "Package": "quadprog", - "Version": "1.5-8", - "Source": "Repository", - "Type": "Package", - "Title": "Functions to Solve Quadratic Programming Problems", - "Date": "2019-11-20", - "Author": "S original by Berwin A. Turlach R port by Andreas Weingessel Fortran contributions from Cleve Moler (dposl/LINPACK and (a modified version of) dpodi/LINPACK)", - "Maintainer": "Berwin A. Turlach ", - "Description": "This package contains routines and documentation for solving quadratic programming problems.", - "Depends": [ - "R (>= 3.1.0)" - ], - "License": "GPL (>= 2)", - "NeedsCompilation": "yes", - "Repository": "CRAN" - }, - "quantmod": { - "Package": "quantmod", - "Version": "0.4.28", - "Source": "Repository", - "Type": "Package", - "Title": "Quantitative Financial Modelling Framework", - "Authors@R": "c( person(given=c(\"Jeffrey\",\"A.\"), family=\"Ryan\", role=c(\"aut\",\"cph\")), person(given=c(\"Joshua\",\"M.\"), family=\"Ulrich\", role=c(\"cre\",\"aut\"), email=\"josh.m.ulrich@gmail.com\"), person(given=c(\"Ethan\",\"B.\"), family=\"Smith\", role=\"ctb\"), person(given=\"Wouter\", family=\"Thielen\", role=\"ctb\"), person(given=\"Paul\", family=\"Teetor\", role=\"ctb\"), person(given=\"Steve\", family=\"Bronder\", role=\"ctb\") )", - "Depends": [ - "R (>= 3.2.0)", - "xts(>= 0.9-0)", - "zoo", - "TTR(>= 0.2)", - "methods" - ], - "Imports": [ - "curl", - "jsonlite(>= 1.1)" - ], - "Suggests": [ - "DBI", - "RMySQL", - "RSQLite", - "timeSeries", - "xml2", - "downloader", - "tinytest" - ], - "Description": "Specify, build, trade, and analyse quantitative financial trading strategies.", - "LazyLoad": "yes", - "License": "GPL-3", - "URL": "https://www.quantmod.com/, https://github.com/joshuaulrich/quantmod", - "BugReports": "https://github.com/joshuaulrich/quantmod/issues", - "NeedsCompilation": "no", - "Author": "Jeffrey A. Ryan [aut, cph], Joshua M. Ulrich [cre, aut], Ethan B. Smith [ctb], Wouter Thielen [ctb], Paul Teetor [ctb], Steve Bronder [ctb]", - "Maintainer": "Joshua M. Ulrich ", - "Repository": "CRAN" - }, "ragg": { "Package": "ragg", "Version": "1.3.3", @@ -5371,29 +4289,6 @@ "Author": "Thomas Lin Pedersen [cre, aut] (), 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, PBC [cph, fnd]", "Repository": "CRAN" }, - "randomForest": { - "Package": "randomForest", - "Version": "4.7-1.2", - "Source": "Repository", - "Title": "Breiman and Cutlers Random Forests for Classification and Regression", - "Date": "2022-01-24", - "Depends": [ - "R (>= 4.1.0)", - "stats" - ], - "Suggests": [ - "RColorBrewer", - "MASS" - ], - "Authors@R": "c(person(\"Leo\", \"Breiman\", role = \"aut\", comment = \"Fortran original\"), person(\"Adele\", \"Cutler\", role = \"aut\", comment = \"Fortran original\"), person(\"Andy\", \"Liaw\", role = c(\"aut\", \"cre\"), email = \"andy_liaw@merck.com\", comment = \"R port\"), person(\"Matthew\", \"Wiener\", role = \"aut\", comment = \"R port\"))", - "Description": "Classification and regression based on a forest of trees using random inputs, based on Breiman (2001) .", - "License": "GPL (>= 2)", - "URL": "https://www.stat.berkeley.edu/~breiman/RandomForests/", - "NeedsCompilation": "yes", - "Repository": "CRAN", - "Author": "Leo Breiman [aut] (Fortran original), Adele Cutler [aut] (Fortran original), Andy Liaw [aut, cre] (R port), Matthew Wiener [aut] (R port)", - "Maintainer": "Andy Liaw " - }, "rapidjsonr": { "Package": "rapidjsonr", "Version": "1.2.0", @@ -5484,34 +4379,6 @@ "Maintainer": "Robert J. Hijmans ", "Repository": "CRAN" }, - "rbibutils": { - "Package": "rbibutils", - "Version": "2.4", - "Source": "Repository", - "Type": "Package", - "Title": "Read 'Bibtex' Files and Convert Between Bibliography Formats", - "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), \t email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(\"R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)\", comment = c(ORCID = \"0000-0003-2839-346X\")) ), person(given = \"Chris\", family = \"Putman\", role = \"aut\", comment = \"src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/\"), person(given = \"Richard\", family = \"Mathar\", role = \"ctb\", comment = \"src/addsout.c\"), person(given = \"Johannes\", family = \"Wilm\", role = \"ctb\", comment = \"src/biblatexin.c, src/bltypes.c\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's bibentry and bibstyle implementation\") )", - "Description": "Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam . Supports all bibliography formats and character encodings implemented in 'bibutils'.", - "License": "GPL-2", - "URL": "https://geobosh.github.io/rbibutils/ (doc), https://github.com/GeoBosh/rbibutils (devel)", - "BugReports": "https://github.com/GeoBosh/rbibutils/issues", - "Depends": [ - "R (>= 2.10)" - ], - "Imports": [ - "utils", - "tools" - ], - "Suggests": [ - "testthat" - ], - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Config/Needs/memcheck": "devtools, rcmdcheck", - "Author": "Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code), comment.ORCID: 0000-0003-2839-346X), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c), R Core Team [ctb] (base R's bibentry and bibstyle implementation)", - "Maintainer": "Georgi N. Boshnakov ", - "Repository": "CRAN" - }, "readr": { "Package": "readr", "Version": "2.1.5", @@ -5608,77 +4475,6 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, - "recipes": { - "Package": "recipes", - "Version": "1.2.1", - "Source": "Repository", - "Title": "Preprocessing and Feature Engineering Steps for Modeling", - "Authors@R": "c( person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = \"aut\"), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "A recipe prepares your data for modeling. We provide an extensible framework for pipeable sequences of feature engineering steps provides preprocessing tools to be applied to data. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting processed output can then be used as inputs for statistical or machine learning models.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/tidymodels/recipes, https://recipes.tidymodels.org/", - "BugReports": "https://github.com/tidymodels/recipes/issues", - "Depends": [ - "dplyr (>= 1.1.0)", - "R (>= 3.6)" - ], - "Imports": [ - "cli", - "clock (>= 0.6.1)", - "generics (>= 0.1.2)", - "glue", - "gower", - "hardhat (>= 1.4.1)", - "ipred (>= 0.9-12)", - "lifecycle (>= 1.0.3)", - "lubridate (>= 1.8.0)", - "magrittr", - "Matrix", - "purrr (>= 1.0.0)", - "rlang (>= 1.1.0)", - "sparsevctrs (>= 0.3.0)", - "stats", - "tibble", - "tidyr (>= 1.0.0)", - "tidyselect (>= 1.2.0)", - "timeDate", - "utils", - "vctrs (>= 0.5.0)", - "withr" - ], - "Suggests": [ - "covr", - "ddalpha", - "dials (>= 1.2.0)", - "ggplot2", - "igraph", - "kernlab", - "knitr", - "methods", - "modeldata (>= 0.1.1)", - "parsnip (>= 1.2.0)", - "RANN", - "RcppRoll", - "rmarkdown", - "rpart", - "rsample", - "RSpectra", - "splines2", - "testthat (>= 3.0.0)", - "workflows", - "xml2" - ], - "VignetteBuilder": "knitr", - "RdMacros": "lifecycle", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Max Kuhn [aut, cre], Hadley Wickham [aut], Emil Hvitfeldt [aut], Posit Software, PBC [cph, fnd]", - "Maintainer": "Max Kuhn ", - "Repository": "CRAN" - }, "rematch": { "Package": "rematch", "Version": "2.0.0", @@ -5829,89 +4625,6 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, - "reshape2": { - "Package": "reshape2", - "Version": "1.4.4", - "Source": "Repository", - "Title": "Flexibly Reshape Data: A Reboot of the Reshape Package", - "Author": "Hadley Wickham ", - "Maintainer": "Hadley Wickham ", - "Description": "Flexibly restructure and aggregate data using just two functions: melt and 'dcast' (or 'acast').", - "License": "MIT + file LICENSE", - "URL": "https://github.com/hadley/reshape", - "BugReports": "https://github.com/hadley/reshape/issues", - "Depends": [ - "R (>= 3.1)" - ], - "Imports": [ - "plyr (>= 1.8.1)", - "Rcpp", - "stringr" - ], - "Suggests": [ - "covr", - "lattice", - "testthat (>= 0.8.0)" - ], - "LinkingTo": [ - "Rcpp" - ], - "Encoding": "UTF-8", - "LazyData": "true", - "RoxygenNote": "7.1.0", - "NeedsCompilation": "yes", - "Repository": "CRAN" - }, - "reticulate": { - "Package": "reticulate", - "Version": "1.43.0", - "Source": "Repository", - "Type": "Package", - "Title": "Interface to 'Python'", - "Authors@R": "c( person(\"Tomasz\", \"Kalinowski\", role = c(\"ctb\", \"cre\"), email = \"tomasz@posit.co\"), person(\"Kevin\", \"Ushey\", role = c(\"aut\"), email = \"kevin@posit.co\"), person(\"JJ\", \"Allaire\", role = c(\"aut\"), email = \"jj@posit.co\"), person(\"RStudio\", role = c(\"cph\", \"fnd\")), person(\"Yuan\", \"Tang\", role = c(\"aut\", \"cph\"), email = \"terrytangyuan@gmail.com\", comment = c(ORCID = \"0000-0001-5243-233X\")), person(\"Dirk\", \"Eddelbuettel\", role = c(\"ctb\", \"cph\"), email = \"edd@debian.org\"), person(\"Bryan\", \"Lewis\", role = c(\"ctb\", \"cph\"), email = \"blewis@illposed.net\"), person(\"Sigrid\", \"Keydana\", role = c(\"ctb\"), email = \"sigrid@posit.co\"), person(\"Ryan\", \"Hafen\", role = c(\"ctb\", \"cph\"), email = \"rhafen@gmail.com\"), person(\"Marcus\", \"Geelnard\", role = c(\"ctb\", \"cph\"), comment = \"TinyThread library, http://tinythreadpp.bitsnbites.eu/\") )", - "Description": "Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.", - "License": "Apache License 2.0", - "URL": "https://rstudio.github.io/reticulate/, https://github.com/rstudio/reticulate", - "BugReports": "https://github.com/rstudio/reticulate/issues", - "SystemRequirements": "Python (>= 2.7.0)", - "Encoding": "UTF-8", - "Depends": [ - "R (>= 3.5)" - ], - "Imports": [ - "Matrix", - "Rcpp (>= 1.0.7)", - "RcppTOML", - "graphics", - "here", - "jsonlite", - "methods", - "png", - "rappdirs", - "utils", - "rlang", - "withr" - ], - "Suggests": [ - "callr", - "knitr", - "glue", - "cli", - "rmarkdown", - "pillar", - "testthat" - ], - "LinkingTo": [ - "Rcpp" - ], - "RoxygenNote": "7.3.2", - "VignetteBuilder": "knitr", - "Config/build/compilation-database": "true", - "NeedsCompilation": "yes", - "Author": "Tomasz Kalinowski [ctb, cre], Kevin Ushey [aut], JJ Allaire [aut], RStudio [cph, fnd], Yuan Tang [aut, cph] (ORCID: ), Dirk Eddelbuettel [ctb, cph], Bryan Lewis [ctb, cph], Sigrid Keydana [ctb], Ryan Hafen [ctb, cph], Marcus Geelnard [ctb, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/)", - "Maintainer": "Tomasz Kalinowski ", - "Repository": "CRAN" - }, "rlang": { "Package": "rlang", "Version": "1.1.5", @@ -6016,33 +4729,47 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, - "rpart": { - "Package": "rpart", - "Version": "4.1.23", + "rosm": { + "Package": "rosm", + "Version": "0.3.1", "Source": "Repository", - "Priority": "recommended", - "Date": "2023-12-04", - "Authors@R": "c(person(\"Terry\", \"Therneau\", role = \"aut\", email = \"therneau@mayo.edu\"), person(\"Beth\", \"Atkinson\", role = c(\"aut\", \"cre\"), email = \"atkinson@mayo.edu\"), person(\"Brian\", \"Ripley\", role = \"trl\", email = \"ripley@stats.ox.ac.uk\", comment = \"producer of the initial R port, maintainer 1999-2017\"))", - "Description": "Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.", - "Title": "Recursive Partitioning and Regression Trees", - "Depends": [ - "R (>= 2.15.0)", - "graphics", - "stats", - "grDevices" + "Type": "Package", + "Title": "Plot Raster Map Tiles from Open Street Map and Other Sources", + "Encoding": "UTF-8", + "Authors@R": "c(person(\"Dewey\", \"Dunnington\", role = c(\"aut\", \"cre\"), email = \"dewey@fishandwhistle.net\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Timothée\", \"Giraud\", role = \"ctb\"))", + "Maintainer": "Dewey Dunnington ", + "Description": "Download and plot Open Street Map , Bing Maps and other tiled map sources. Use to create basemaps quickly and add hillshade to vector-based maps.", + "License": "GPL-2", + "Imports": [ + "curl", + "jpeg", + "png", + "wk", + "glue", + "progress", + "rlang" ], "Suggests": [ - "survival" + "sp", + "plyr", + "raster", + "testthat (>= 3.0.0)", + "withr", + "sf", + "terra", + "abind", + "methods", + "jsonlite", + "tiff", + "vdiffr" ], - "License": "GPL-2 | GPL-3", - "LazyData": "yes", - "ByteCompile": "yes", - "NeedsCompilation": "yes", - "Author": "Terry Therneau [aut], Beth Atkinson [aut, cre], Brian Ripley [trl] (producer of the initial R port, maintainer 1999-2017)", - "Maintainer": "Beth Atkinson ", - "Repository": "CRAN", - "URL": "https://github.com/bethatkinson/rpart, https://cran.r-project.org/package=rpart", - "BugReports": "https://github.com/bethatkinson/rpart/issues" + "URL": "https://github.com/paleolimbot/rosm", + "BugReports": "https://github.com/paleolimbot/rosm/issues", + "RoxygenNote": "7.3.3", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Dewey Dunnington [aut, cre] (ORCID: ), Timothée Giraud [ctb]", + "Repository": "CRAN" }, "rprojroot": { "Package": "rprojroot", @@ -6076,61 +4803,6 @@ "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, - "rsample": { - "Package": "rsample", - "Version": "1.3.0", - "Source": "Repository", - "Title": "General Resampling Infrastructure", - "Authors@R": "c( person(\"Hannah\", \"Frick\", , \"hannah@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6049-5258\")), person(\"Fanny\", \"Chow\", , \"fannybchow@gmail.com\", role = \"aut\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"aut\"), person(\"Michael\", \"Mahoney\", , \"mike.mahoney.218@gmail.com\", role = c(\"aut\"), comment = c(ORCID = \"0000-0003-2402-304X\")), person(\"Julia\", \"Silge\", , \"julia.silge@posit.co\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-3671-836X\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).", - "License": "MIT + file LICENSE", - "URL": "https://rsample.tidymodels.org, https://github.com/tidymodels/rsample", - "BugReports": "https://github.com/tidymodels/rsample/issues", - "Depends": [ - "R (>= 3.6)" - ], - "Imports": [ - "cli", - "dplyr (>= 1.1.1)", - "furrr", - "generics", - "glue", - "lifecycle", - "methods", - "pillar", - "purrr (>= 1.0.0)", - "rlang (>= 1.1.0)", - "slider (>= 0.1.5)", - "tibble", - "tidyr", - "tidyselect", - "vctrs (>= 0.5.0)" - ], - "Suggests": [ - "broom", - "covr", - "ggplot2", - "knitr", - "modeldata", - "recipes (>= 0.1.4)", - "rmarkdown", - "stats", - "testthat (>= 3.0.0)", - "utils", - "whisker", - "withr", - "xml2" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "GGally, nlstools, tidymodels, tidyverse/tidytemplate", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Config/testthat/edition": "3", - "NeedsCompilation": "no", - "Author": "Hannah Frick [aut, cre] (), Fanny Chow [aut], Max Kuhn [aut], Michael Mahoney [aut] (), Julia Silge [aut] (), Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", - "Maintainer": "Hannah Frick ", - "Repository": "CRAN" - }, "rstudioapi": { "Package": "rstudioapi", "Version": "0.17.1", @@ -6241,48 +4913,6 @@ "Maintainer": "Edzer Pebesma ", "Repository": "CRAN" }, - "sandwich": { - "Package": "sandwich", - "Version": "3.1-1", - "Source": "Repository", - "Date": "2024-09-16", - "Title": "Robust Covariance Matrix Estimators", - "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Thomas\", family = \"Lumley\", role = \"aut\", email = \"t.lumley@auckland.ac.nz\", comment = c(ORCID = \"0000-0003-4255-5437\")), person(given = \"Nathaniel\", family = \"Graham\", role = \"ctb\", email = \"npgraham1@gmail.com\", comment = c(ORCID = \"0009-0002-1215-5256\")), person(given = \"Susanne\", family = \"Koell\", role = \"ctb\"))", - "Description": "Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. Details can be found in Zeileis et al. (2020) , Zeileis (2004) and Zeileis (2006) .", - "Depends": [ - "R (>= 3.0.0)" - ], - "Imports": [ - "stats", - "utils", - "zoo" - ], - "Suggests": [ - "AER", - "car", - "geepack", - "lattice", - "lme4", - "lmtest", - "MASS", - "multiwayvcov", - "parallel", - "pcse", - "plm", - "pscl", - "scatterplot3d", - "stats4", - "strucchange", - "survival" - ], - "License": "GPL-2 | GPL-3", - "URL": "https://sandwich.R-Forge.R-project.org/", - "BugReports": "https://sandwich.R-Forge.R-project.org/contact.html", - "NeedsCompilation": "no", - "Author": "Achim Zeileis [aut, cre] (), Thomas Lumley [aut] (), Nathaniel Graham [ctb] (), Susanne Koell [ctb]", - "Maintainer": "Achim Zeileis ", - "Repository": "CRAN" - }, "sass": { "Package": "sass", "Version": "0.4.9", @@ -6541,26 +5171,6 @@ "Maintainer": "David Cooley ", "Repository": "CRAN" }, - "shape": { - "Package": "shape", - "Version": "1.4.6.1", - "Source": "Repository", - "Title": "Functions for Plotting Graphical Shapes, Colors", - "Author": "Karline Soetaert ", - "Maintainer": "Karline Soetaert ", - "Depends": [ - "R (>= 2.01)" - ], - "Imports": [ - "stats", - "graphics", - "grDevices" - ], - "Description": "Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...", - "License": "GPL (>= 3)", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, "shiny": { "Package": "shiny", "Version": "1.10.0", @@ -6630,49 +5240,6 @@ "Maintainer": "Winston Chang ", "Repository": "CRAN" }, - "slider": { - "Package": "slider", - "Version": "0.3.2", - "Source": "Repository", - "Title": "Sliding Window Functions", - "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Provides type-stable rolling window functions over any R data type. Cumulative and expanding windows are also supported. For more advanced usage, an index can be used as a secondary vector that defines how sliding windows are to be created.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/r-lib/slider, https://slider.r-lib.org", - "BugReports": "https://github.com/r-lib/slider/issues", - "Depends": [ - "R (>= 4.0.0)" - ], - "Imports": [ - "cli (>= 3.6.1)", - "rlang (>= 1.1.1)", - "vctrs (>= 0.6.3)", - "warp" - ], - "Suggests": [ - "covr", - "dplyr (>= 1.0.0)", - "knitr", - "lubridate", - "rmarkdown", - "testthat (>= 3.0.0)" - ], - "LinkingTo": [ - "vctrs (>= 0.6.3)" - ], - "VignetteBuilder": "knitr", - "Config/build/compilation-database": "true", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2024-10-25", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Collate": "'arithmetic.R' 'block.R' 'conditions.R' 'hop-common.R' 'hop-index-common.R' 'hop-index.R' 'hop-index2.R' 'hop.R' 'hop2.R' 'phop-index.R' 'phop.R' 'slide-index2.R' 'pslide-index.R' 'slide-period2.R' 'pslide-period.R' 'slide2.R' 'pslide.R' 'segment-tree.R' 'slide-common.R' 'slide-index-common.R' 'slide-index.R' 'slide-period-common.R' 'slide-period.R' 'slide.R' 'slider-package.R' 'summary-index.R' 'summary-slide.R' 'utils.R' 'zzz.R'", - "NeedsCompilation": "yes", - "Author": "Davis Vaughan [aut, cre], Posit Software, PBC [cph, fnd]", - "Maintainer": "Davis Vaughan ", - "Repository": "CRAN" - }, "sourcetools": { "Package": "sourcetools", "Version": "0.1.7-1", @@ -6802,43 +5369,6 @@ "NeedsCompilation": "no", "Author": "Glenn Davis [aut, cre]" }, - "sparsevctrs": { - "Package": "sparsevctrs", - "Version": "0.3.2", - "Source": "Repository", - "Title": "Sparse Vectors for Use in Data Frames", - "Authors@R": "c( person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0679-1945\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Provides sparse vectors powered by ALTREP (Alternative Representations for R Objects) that behave like regular vectors, and can thus be used in data frames. Also provides tools to convert between sparse matrices and data frames with sparse columns and functions to interact with sparse vectors.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/r-lib/sparsevctrs, https://r-lib.github.io/sparsevctrs/", - "BugReports": "https://github.com/r-lib/sparsevctrs/issues", - "Depends": [ - "R (>= 4.0.0)" - ], - "Imports": [ - "cli (>= 3.4.0)", - "rlang (>= 1.1.0)", - "vctrs" - ], - "Suggests": [ - "knitr", - "Matrix", - "methods", - "rmarkdown", - "testthat (>= 3.0.0)", - "tibble", - "withr" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate, rmarkdown, lobstr, ggplot2, bench, tidyr, ggbeeswarm", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Emil Hvitfeldt [aut, cre] (), Davis Vaughan [ctb], Posit Software, PBC [cph, fnd]", - "Maintainer": "Emil Hvitfeldt ", - "Repository": "CRAN" - }, "spdep": { "Package": "spdep", "Version": "1.4-1", @@ -7078,80 +5608,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "strucchangeRcpp": { - "Package": "strucchangeRcpp", - "Version": "1.5-4-1.0.1", - "Source": "Repository", - "Title": "Testing, Monitoring, and Dating Structural Changes: C++ Version", - "Authors@R": "c(person(given = \"Dainius\", family = \"Masiliunas\", role = c(\"aut\", \"cre\"), email = \"pastas4@gmail.com\", comment = c(ORCID = \"0000-0001-5654-1277\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Marius\", family = \"Appel\", role = \"aut\", email = \"marius.appel@uni-muenster.de\"), person(given = \"Friedrich\", family = \"Leisch\", role = \"aut\", email = \"Friedrich.Leisch@R-project.org\"), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\"), person(given = \"Christian\", family = \"Kleiber\", role = \"aut\", email = \"Christian.Kleiber@unibas.ch\"), person(given = \"Andrei\", family = \"Mirt\", role = \"ctb\", email = \"andrei.mirt@wur.nl\", comment = c(ORCID = \"0000-0003-3654-2090\")), person(given = \"Bruce\", family = \"Hansen\", role = \"ctb\"), person(given = c(\"Edgar\", \"C.\"), family = \"Merkle\", role = \"ctb\"), person(given = \"Nikolaus\", family = \"Umlauf\", role = \"ctb\"))", - "Description": "A fast implementation with additional experimental features for testing, monitoring and dating structural changes in (linear) regression models. 'strucchangeRcpp' features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g. cumulative/moving sum, recursive/moving estimates) and F statistics, respectively. These methods are described in Zeileis et al. (2002) . Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals, and their magnitude as well as the model fit can be evaluated using a variety of statistical measures.", - "LazyData": "yes", - "LinkingTo": [ - "Rcpp", - "RcppArmadillo" - ], - "Depends": [ - "R (>= 2.10.0)", - "zoo", - "sandwich" - ], - "Suggests": [ - "stats4", - "car", - "dynlm", - "e1071", - "foreach", - "lmtest", - "mvtnorm", - "tseries", - "bfast" - ], - "Imports": [ - "graphics", - "stats", - "Rcpp (>= 0.12.7)", - "utils" - ], - "License": "GPL-2 | GPL-3", - "URL": "https://github.com/bfast2/strucchangeRcpp/", - "BugReports": "https://github.com/bfast2/strucchangeRcpp/issues", - "RoxygenNote": "7.1.1", - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Author": "Dainius Masiliunas [aut, cre] (ORCID: ), Achim Zeileis [aut] (ORCID: ), Marius Appel [aut], Friedrich Leisch [aut], Kurt Hornik [aut], Christian Kleiber [aut], Andrei Mirt [ctb] (ORCID: ), Bruce Hansen [ctb], Edgar C. Merkle [ctb], Nikolaus Umlauf [ctb]", - "Maintainer": "Dainius Masiliunas ", - "Repository": "CRAN" - }, - "survival": { - "Package": "survival", - "Version": "3.7-0", - "Source": "Repository", - "Title": "Survival Analysis", - "Priority": "recommended", - "Date": "2024-06-01", - "Depends": [ - "R (>= 3.5.0)" - ], - "Imports": [ - "graphics", - "Matrix", - "methods", - "splines", - "stats", - "utils" - ], - "LazyData": "Yes", - "LazyDataCompression": "xz", - "ByteCompile": "Yes", - "Authors@R": "c(person(c(\"Terry\", \"M\"), \"Therneau\", email=\"therneau.terry@mayo.edu\", role=c(\"aut\", \"cre\")), person(\"Thomas\", \"Lumley\", role=c(\"ctb\", \"trl\"), comment=\"original S->R port and R maintainer until 2009\"), person(\"Atkinson\", \"Elizabeth\", role=\"ctb\"), person(\"Crowson\", \"Cynthia\", role=\"ctb\"))", - "Description": "Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.", - "License": "LGPL (>= 2)", - "URL": "https://github.com/therneau/survival", - "NeedsCompilation": "yes", - "Author": "Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009), Atkinson Elizabeth [ctb], Crowson Cynthia [ctb]", - "Maintainer": "Terry M Therneau ", - "Repository": "CRAN" - }, "sys": { "Package": "sys", "Version": "3.4.3", @@ -7533,34 +5989,6 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, - "timeDate": { - "Package": "timeDate", - "Version": "4041.110", - "Source": "Repository", - "Title": "Rmetrics - Chronological and Calendar Objects", - "Authors@R": "c(person(\"Diethelm\", \"Wuertz\", role=\"aut\", comment = \"original code\") , person(\"Tobias\", \"Setz\", role = c(\"aut\"), email = \"tobias.setz@live.com\") , person(\"Yohan\", \"Chalabi\", role = \"aut\") , person(\"Martin\",\"Maechler\", role = \"ctb\", email = \"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) , person(given = c(\"Joe\", \"W.\"), family = \"Byers\", role = \"ctb\") , person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"cre\", \"aut\"), email = \"georgi.boshnakov@manchester.ac.uk\") )", - "Description": "The 'timeDate' class fulfils the conventions of the ISO 8601 standard as well as of the ANSI C and POSIX standards. Beyond these standards it provides the \"Financial Center\" concept which allows to handle data records collected in different time zones and mix them up to have always the proper time stamps with respect to your personal financial center, or alternatively to the GMT reference time. It can thus also handle time stamps from historical data records from the same time zone, even if the financial centers changed day light saving times at different calendar dates.", - "Depends": [ - "R (>= 3.6.0)", - "methods" - ], - "Imports": [ - "graphics", - "utils", - "stats" - ], - "Suggests": [ - "RUnit" - ], - "License": "GPL (>= 2)", - "Encoding": "UTF-8", - "URL": "https://geobosh.github.io/timeDateDoc/ (doc), https://r-forge.r-project.org/scm/viewvc.php/pkg/timeDate/?root=rmetrics (devel), https://www.rmetrics.org", - "BugReports": "https://r-forge.r-project.org/projects/rmetrics", - "NeedsCompilation": "no", - "Author": "Diethelm Wuertz [aut] (original code), Tobias Setz [aut], Yohan Chalabi [aut], Martin Maechler [ctb] (), Joe W. Byers [ctb], Georgi N. Boshnakov [cre, aut]", - "Maintainer": "Georgi N. Boshnakov ", - "Repository": "CRAN" - }, "timechange": { "Package": "timechange", "Version": "0.3.0", @@ -7724,56 +6152,6 @@ "Maintainer": "Martijn Tennekes ", "Repository": "CRAN" }, - "tseries": { - "Package": "tseries", - "Version": "0.10-58", - "Source": "Repository", - "Title": "Time Series Analysis and Computational Finance", - "Authors@R": "c(person(\"Adrian\", \"Trapletti\", role = \"aut\", email = \"adrian@trapletti.org\"), person(\"Kurt\", \"Hornik\", role = c(\"aut\", \"cre\"), email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Blake\", \"LeBaron\", role = \"ctb\", comment = \"BDS test code\"))", - "Description": "Time series analysis and computational finance.", - "Depends": [ - "R (>= 3.4.0)" - ], - "Imports": [ - "graphics", - "stats", - "utils", - "quadprog", - "zoo", - "quantmod (>= 0.4-9)", - "jsonlite" - ], - "License": "GPL-2 | GPL-3", - "NeedsCompilation": "yes", - "Author": "Adrian Trapletti [aut], Kurt Hornik [aut, cre] (), Blake LeBaron [ctb] (BDS test code)", - "Maintainer": "Kurt Hornik ", - "Repository": "CRAN" - }, - "twosamples": { - "Package": "twosamples", - "Version": "2.0.1", - "Source": "Repository", - "Type": "Package", - "Title": "Fast Permutation Based Two Sample Tests", - "Authors@R": "person(\"Connor\", \"Dowd\", , \"cd@codowd.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9782-0931\"))", - "Description": "Fast randomization based two sample tests. Testing the hypothesis that two samples come from the same distribution using randomization to create p-values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, Anderson-Darling, Wasserstein, and DTS. The default test (two_sample) is based on the DTS test statistic, as it is the most powerful, and thus most useful to most users. The DTS test statistic builds on the Wasserstein distance by using a weighting scheme like that of Anderson-Darling. See the companion paper at or for details of that test statistic, and non-standard uses of the package (parallel for big N, weighted observations, one sample tests, etc). We also include the permutation scheme to make test building simple for others.", - "License": "GPL (>= 2)", - "Encoding": "UTF-8", - "LinkingTo": [ - "cpp11" - ], - "RoxygenNote": "7.2.3", - "URL": "https://twosampletest.com, https://github.com/cdowd/twosamples", - "BugReports": "https://github.com/cdowd/twosamples/issues", - "Suggests": [ - "testthat (>= 3.0.0)" - ], - "Config/testthat/edition": "3", - "NeedsCompilation": "yes", - "Author": "Connor Dowd [aut, cre] ()", - "Maintainer": "Connor Dowd ", - "Repository": "CRAN" - }, "tzdb": { "Package": "tzdb", "Version": "0.5.0", @@ -7847,30 +6225,6 @@ "Maintainer": "Edzer Pebesma ", "Repository": "CRAN" }, - "urca": { - "Package": "urca", - "Version": "1.3-4", - "Source": "Repository", - "Date": "2024-05-25", - "Title": "Unit Root and Cointegration Tests for Time Series Data", - "Authors@R": "c(person(\"Bernhard\", \"Pfaff\", email = \"bernhard@pfaffikus.de\", role = c(\"aut\", \"cre\")), person(\"Eric\", \"Zivot\",email = \"ezivot@u.washington.edu\", role = \"ctb\"), person(\"Matthieu\", \"Stigler\", role = \"ctb\"))", - "Depends": [ - "R (>= 2.0.0)", - "methods" - ], - "Imports": [ - "nlme", - "graphics", - "stats" - ], - "LazyLoad": "yes", - "Description": "Unit root and cointegration tests encountered in applied econometric analysis are implemented.", - "License": "GPL (>= 2)", - "NeedsCompilation": "yes", - "Author": "Bernhard Pfaff [aut, cre], Eric Zivot [ctb], Matthieu Stigler [ctb]", - "Maintainer": "Bernhard Pfaff ", - "Repository": "CRAN" - }, "utf8": { "Package": "utf8", "Version": "1.2.4", @@ -7967,52 +6321,6 @@ "Maintainer": "Davis Vaughan ", "Repository": "CRAN" }, - "viridis": { - "Package": "viridis", - "Version": "0.6.5", - "Source": "Repository", - "Type": "Package", - "Title": "Colorblind-Friendly Color Maps for R", - "Date": "2024-01-28", - "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", - "Maintainer": "Simon Garnier ", - "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This package also contains 'ggplot2' bindings for discrete and continuous color and fill scales. A lean version of the package called 'viridisLite' that does not include the 'ggplot2' bindings can be found at .", - "License": "MIT + file LICENSE", - "Encoding": "UTF-8", - "Depends": [ - "R (>= 2.10)", - "viridisLite (>= 0.4.0)" - ], - "Imports": [ - "ggplot2 (>= 1.0.1)", - "gridExtra" - ], - "Suggests": [ - "hexbin (>= 1.27.0)", - "scales", - "MASS", - "knitr", - "dichromat", - "colorspace", - "httr", - "mapproj", - "vdiffr", - "svglite (>= 1.2.0)", - "testthat", - "covr", - "rmarkdown", - "maps", - "terra" - ], - "LazyData": "true", - "VignetteBuilder": "knitr", - "URL": "https://sjmgarnier.github.io/viridis/, https://github.com/sjmgarnier/viridis/", - "BugReports": "https://github.com/sjmgarnier/viridis/issues", - "RoxygenNote": "7.3.1", - "NeedsCompilation": "no", - "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", - "Repository": "CRAN" - }, "viridisLite": { "Package": "viridisLite", "Version": "0.4.2", @@ -8111,34 +6419,6 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, - "warp": { - "Package": "warp", - "Version": "0.2.1", - "Source": "Repository", - "Title": "Group Dates", - "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Tooling to group dates by a variety of periods including: yearly, monthly, by second, by week of the month, and more. The groups are defined in such a way that they also represent the distance between dates in terms of the period. This extracts valuable information that can be used in further calculations that rely on a specific temporal spacing between observations.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/DavisVaughan/warp, https://davisvaughan.github.io/warp/", - "BugReports": "https://github.com/DavisVaughan/warp/issues", - "Depends": [ - "R (>= 3.2)" - ], - "Suggests": [ - "covr", - "knitr", - "rmarkdown", - "testthat (>= 3.0.0)" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "NeedsCompilation": "yes", - "Author": "Davis Vaughan [aut, cre], Posit Software, PBC [cph, fnd]", - "Maintainer": "Davis Vaughan ", - "Repository": "CRAN" - }, "withr": { "Package": "withr", "Version": "3.0.2", @@ -8349,41 +6629,6 @@ "NeedsCompilation": "no", "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" }, - "xts": { - "Package": "xts", - "Version": "0.14.1", - "Source": "Repository", - "Type": "Package", - "Title": "eXtensible Time Series", - "Authors@R": "c( person(given=c(\"Jeffrey\",\"A.\"), family=\"Ryan\", role=c(\"aut\",\"cph\")), person(given=c(\"Joshua\",\"M.\"), family=\"Ulrich\", role=c(\"cre\",\"aut\"), email=\"josh.m.ulrich@gmail.com\"), person(given=\"Ross\", family=\"Bennett\", role=\"ctb\"), person(given=\"Corwin\", family=\"Joy\", role=\"ctb\") )", - "Depends": [ - "R (>= 3.6.0)", - "zoo (>= 1.7-12)" - ], - "Imports": [ - "methods" - ], - "LinkingTo": [ - "zoo" - ], - "Suggests": [ - "timeSeries", - "timeDate", - "tseries", - "chron", - "tinytest" - ], - "LazyLoad": "yes", - "Description": "Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.", - "License": "GPL (>= 2)", - "URL": "https://joshuaulrich.github.io/xts/, https://github.com/joshuaulrich/xts", - "BugReports": "https://github.com/joshuaulrich/xts/issues", - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Author": "Jeffrey A. Ryan [aut, cph], Joshua M. Ulrich [cre, aut], Ross Bennett [ctb], Corwin Joy [ctb]", - "Maintainer": "Joshua M. Ulrich ", - "Repository": "CRAN" - }, "yaml": { "Package": "yaml", "Version": "2.3.10", diff --git a/renv/settings.json b/renv/settings.json index ffdbb32..c35954b 100644 --- a/renv/settings.json +++ b/renv/settings.json @@ -15,5 +15,12 @@ "vcs.ignore.cellar": true, "vcs.ignore.library": true, "vcs.ignore.local": true, - "vcs.manage.ignores": true + "vcs.manage.ignores": true, + "ignored.directories": [ + "old_sh", + "r_app/old_scripts", + "r_app/experiments", + "python_app/experiments", + "webapps" + ] }