From 843ed72e0cbaf0322ece05e4863ac4191d820dfc Mon Sep 17 00:00:00 2001 From: Julius Pfadt <38500953+juliuspfadt@users.noreply.github.com> Date: Fri, 7 Mar 2025 15:30:25 +0100 Subject: [PATCH] Sem fix (#240) * change wording for traditional sem * reorder variables in dataset according to appearance * small changes for paper * small adjustment help files for unidim rel * enable preloadData for raterAgreement * small qml changes * renv updates * fix agreement issues --- DESCRIPTION | 2 +- R/raterAgreement.R | 162 +- R/standardErrorOfMeasurement.R | 38 +- R/unidimensionalReliabilityFrequentist.R | 3 - inst/Description.qml | 1 - inst/help/standardErrorOfMeasurement.md | 4 +- .../help/unidimensionalReliabilityBayesian.md | 4 +- .../unidimensionalReliabilityFrequentist.md | 4 +- inst/qml/RaterAgreement.qml | 64 +- inst/qml/StandardErrorOfMeasurement.qml | 23 +- renv.lock | 5308 ++++++++++++++--- renv/activate.R | 196 +- tests/testthat/test-raterAgreement.R | 289 +- 13 files changed, 4616 insertions(+), 1482 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cafe1387..93756029 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: jaspReliability Type: Package Title: Reliability Module for JASP Version: 0.19.3 -Date: 2024-09-24 +Date: 2025-02-23 Author: JASP Team Website: https://github.com/jasp-stats/Reliability Maintainer: Julius M. Pfadt diff --git a/R/raterAgreement.R b/R/raterAgreement.R index bd0008e8..9664c6e7 100644 --- a/R/raterAgreement.R +++ b/R/raterAgreement.R @@ -20,7 +20,7 @@ raterAgreement <- function(jaspResults, dataset, options) { ready <- length(options[["variables"]]) > 1 - dataset <- .readDataCohensFleissKappa(dataset, options) + dataset <- .raterAgreementHandleData(dataset, options) if (options[["cohensKappa"]]) jaspResults[["cohensKappa"]] <- .computeCohensKappaTable(dataset, options, ready) @@ -35,12 +35,14 @@ raterAgreement <- function(jaspResults, dataset, options) { return() } -# Read in the dataset (copied from .reliabilityReadData) -.readDataCohensFleissKappa <- function(dataset, options) { - variables <- unlist(options[["variables"]]) - if (is.null(dataset)) { - dataset <- .readDataSetToEnd(columns.as.factor = variables) +.raterAgreementHandleData <- function(dataset, options) { + + if (options[["dataStructure"]] == "ratersInColumns") { + dataset <- dataset + } else { # raters in rows + dataset <- as.data.frame(t(dataset)) } + return(dataset) } @@ -62,7 +64,8 @@ raterAgreement <- function(jaspResults, dataset, options) { "cohensKappaType", "ci", "ciLevel", - "weightType" + "weightType", + "dataStructure" ) ) @@ -75,6 +78,7 @@ raterAgreement <- function(jaspResults, dataset, options) { if (ready) { + #calculate Cohen's Kappas possiblePairs <- combn(ncol(dataset), 2) nPairs <- ncol(possiblePairs) @@ -110,7 +114,17 @@ raterAgreement <- function(jaspResults, dataset, options) { tableData <- list("ratings" = c("Average kappa", allPairStrings), "cKappa" = c(averageKappa, allKappas)) - footnote <- gettextf('%1$i subjects/items and %2$i raters/measurements.', nrow(dataset), ncol(dataset)) + + # because cohens kappa uses pairwise rater agreements the number of subjects overall is not listwise deleted + if (options[["dataStructure"]] == "ratersInColumns") { + dataCount <- dataset[rowSums(is.na(dataset)) < ncol(dataset), ] + } else { + dataCount <- dataset[, colSums(is.na(dataset)) < nrow(dataset)] + } + + footnote <- gettextf('%1$i subjects/items and %2$i raters/measurements.', nrow(dataCount), ncol(dataCount)) + if (anyNA(dataset)) + footnote <- gettextf('%1$s Based on pairwise complete cases.', footnote) if (options[["ci"]]) { jaspTable$addColumnInfo(name = "SE", title = gettext("SE"), type = "number") @@ -147,7 +161,8 @@ raterAgreement <- function(jaspResults, dataset, options) { "variables", "fleissKappa", "ci", - "ciLevel" + "ciLevel", + "dataStructure" ) ) @@ -159,11 +174,14 @@ raterAgreement <- function(jaspResults, dataset, options) { if (ready) { #calculate Fleiss' Kappa - allKappaData <- .fleissKappaMod(dataset, detail = TRUE) + allKappaData <- irr::kappam.fleiss(dataset, detail = TRUE) overallKappa <- allKappaData$value - categoryKappas <- allKappaData$detail[, 1] - overallSE <- allKappaData$se - categorySE <- allKappaData$se_cat + categoryKappas <- allKappaData$detail[, "Kappa"] + # we can calculate the SE since we know the z value taken from a standard normal + SEkappa <- overallKappa / allKappaData$statistic + SEkappa.cat <- categoryKappas / allKappaData$detail[, "z"] + overallSE <- SEkappa + categorySE <- SEkappa.cat alpha <- 1 - options[["ciLevel"]] # for nominal text data we want the rating text to be displayed: @@ -180,11 +198,15 @@ raterAgreement <- function(jaspResults, dataset, options) { tableData <- list("ratings" = ratings, "fKappa" = c(overallKappa, categoryKappas)) - footnote <- gettextf('%1$i subjects/items and %2$i raters/measurements.', nrow(dataset), ncol(dataset)) + + footnote <- gettextf('%1$i subjects/items and %2$i raters/measurements.', allKappaData$subjects, allKappaData$raters) + if (anyNA(dataset)) + footnote <- gettextf('%1$s Based on listwise complete cases.', footnote) + if (options[["ci"]]) { nCategories <- length(categories) - SE <- c(overallSE, rep(categorySE, nCategories)) + SE <- c(overallSE, categorySE) overallCI <- overallKappa + c(-1, 1) * qnorm(1 - alpha / 2) * overallSE categoryCIL <- categoryKappas - qnorm(1 - alpha / 2) * categorySE categoryCIU <- categoryKappas + qnorm(1 - alpha / 2) * categorySE @@ -217,7 +239,8 @@ raterAgreement <- function(jaspResults, dataset, options) { "krippendorffsAlpha", "ci", "ciLevel", - "krippenDorffsAlphaDataStructure" + "dataStructure", + "krippendorffsAlphaBootstrapSamplesForCI" ) ) @@ -229,17 +252,15 @@ raterAgreement <- function(jaspResults, dataset, options) { if (ready) { #calculate Krippendorff's alpha - if (options[["krippendorffsAlphaDataStructure"]] == "ratersInColumns") { - kAlphaData <- t(as.matrix(dataset)) - } else { # raters in rows - kAlphaData <- as.matrix(dataset) - } method <- options[["krippendorffsAlphaMethod"]] - kAlpha <- irr::kripp.alpha(kAlphaData, method) + kAlpha <- irr::kripp.alpha(t(as.matrix(dataset)), method) # the irr-package expects raters to be in rows. tableData <- list("method" = paste0(toupper(substr(method, 1, 1)), substr(method, 2, nchar(method))), "kAlpha" = kAlpha$value) + footnote <- gettextf('%1$i subjects/items and %2$i raters/measurements.', kAlpha$subjects, kAlpha$raters) + if (anyNA(dataset)) + footnote <- gettextf('%1$s Based on pairwise complete cases.', footnote) if (options[["ci"]]) { alphas <- jaspResults[["bootstrapSamples"]]$object @@ -267,20 +288,13 @@ raterAgreement <- function(jaspResults, dataset, options) { bootstrapSamples <- createJaspState() method <- options[["krippendorffsAlphaMethod"]] - - if (options[["krippendorffsAlphaDataStructure"]] == "ratersInColumns") { - kAlphaData <- as.matrix(dataset) - } else { # raters in rows - kAlphaData <- t(as.matrix(dataset)) - } - - n <- nrow(kAlphaData) alphas <- numeric(options[["krippendorffsAlphaBootstrapSamplesForCI"]]) + n <- nrow(dataset) jaspBase::.setSeedJASP(options) for (i in seq_len(options[["krippendorffsAlphaBootstrapSamplesForCI"]])) { - bootData <- as.matrix(kAlphaData[sample.int(n, size = n, replace = TRUE), ]) + bootData <- as.matrix(dataset[sample.int(n, size = n, replace = TRUE), ]) alphas[i] <- irr::kripp.alpha(t(bootData), method = method)$value } bootstrapSamples$object <- alphas @@ -290,93 +304,9 @@ raterAgreement <- function(jaspResults, dataset, options) { "krippendorffsAlpha", "ci", "krippendorffsAlphaBootstrapSamplesForCI", - "krippendorffsAlphaDataStructure", + "dataStructure", "setSeed", "seed")) return() } - -##################################################### -#copied from IRR package, modified to output Std. Err. -###################################################### - -.fleissKappaMod <- function(ratings, exact = FALSE, detail = FALSE) -{ - ratings <- as.matrix(na.omit(ratings)) - ns <- nrow(ratings) - nr <- ncol(ratings) - lev <- levels(as.factor(ratings)) - for (i in 1:ns) { - frow <- factor(ratings[i, ], levels = lev) - if (i == 1) - ttab <- as.numeric(table(frow)) - else ttab <- rbind(ttab, as.numeric(table(frow))) - } - ttab <- matrix(ttab, nrow = ns) - agreeP <- sum((apply(ttab^2, 1, sum) - nr)/(nr * (nr - 1))/ns) - if (!exact) { - method <- "Fleiss' Kappa for m Raters" - chanceP <- sum(apply(ttab, 2, sum)^2)/(ns * nr)^2 - } - else { - method <- "Fleiss' Kappa for m Raters (exact value)" - for (i in 1:nr) { - rcol <- factor(ratings[, i], levels = lev) - if (i == 1) - rtab <- as.numeric(table(rcol)) - else rtab <- rbind(rtab, as.numeric(table(rcol))) - } - rtab <- rtab/ns - chanceP <- sum(apply(ttab, 2, sum)^2)/(ns * nr)^2 - - sum(apply(rtab, 2, var) * (nr - 1)/nr)/(nr - 1) - } - value <- (agreeP - chanceP)/(1 - chanceP) - if (!exact) { - pj <- apply(ttab, 2, sum)/(ns * nr) - qj <- 1 - pj - varkappa <- (2/(sum(pj * qj)^2 * (ns * nr * (nr - 1)))) * - (sum(pj * qj)^2 - sum(pj * qj * (qj - pj))) - SEkappa <- sqrt(varkappa) - u <- value/SEkappa - p.value <- 2 * (1 - pnorm(abs(u))) - if (detail) { - pj <- apply(ttab, 2, sum)/(ns * nr) - pjk <- (apply(ttab^2, 2, sum) - ns * nr * pj)/(ns * - nr * (nr - 1) * pj) - kappaK <- (pjk - pj)/(1 - pj) - varkappaK <- 2/(ns * nr * (nr - 1)) - SEkappaK <- sqrt(varkappaK) - uK <- kappaK/SEkappaK - p.valueK <- 2 * (1 - pnorm(abs(uK))) - tableK <- as.table(round(cbind(kappaK, uK, p.valueK), - digits = 3)) - rownames(tableK) <- lev - colnames(tableK) <- c("Kappa", "z", "p.value") - } - } - if (!exact) { - if (!detail) { - rval <- list(method = method, subjects = ns, raters = nr, - irr.name = "Kappa", value = value) - } - else { - ############### - #BEGIN CHANGES - ############### - rval <- list(method = method, subjects = ns, raters = nr, - irr.name = "Kappa", value = value, detail = tableK, se = SEkappa, se_cat = SEkappaK) - ############ - #END CHANGES - ############# - } - rval <- c(rval, stat.name = "z", statistic = u, p.value = p.value) - } - else { - rval <- list(method = method, subjects = ns, raters = nr, - irr.name = "Kappa", value = value) - } - class(rval) <- "irrlist" - return(rval) -} - diff --git a/R/standardErrorOfMeasurement.R b/R/standardErrorOfMeasurement.R index 55c69767..d3daae2a 100644 --- a/R/standardErrorOfMeasurement.R +++ b/R/standardErrorOfMeasurement.R @@ -18,11 +18,13 @@ #' @export standardErrorOfMeasurement <- function(jaspResults, dataset, options) { + # sink(file = "~/Downloads/log.txt") + # on.exit(sink(NULL)) + ready <- ncol(dataset) > 1 dataset <- .semHandleData(dataset, options) - .semErrorCheck(dataset, options, ready) .semCreateMainContainer(jaspResults, options) @@ -58,6 +60,10 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { # functions work only with numeric data dataset <- as.data.frame(lapply(dataset, function(x) as.numeric(as.character(x)))) + # dataset columns are by default ordered alphabetically (why???), so we change the order + if (length(options$variables) > 0) + dataset <- dataset[, options[["variables"]]] + return(dataset) } @@ -184,7 +190,7 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { if (!is.null(jaspResults[["semMainContainer"]][["coefficientTable"]])) return() - coefficientTable <- createJaspTable(gettext("Standard error of measurement"), + coefficientTable <- createJaspTable(gettext("Standard Error of Measurement"), dependencies = c("thorndike", "feldt", "mollenkopfFeldt", "anova", "irt", "lord", "keats", "lord2", "hideTable", "feldtNumberOfSplits", "mollenkopfFeldtNumberOfSplits", @@ -193,8 +199,8 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { coefficientTable$position <- 1 jaspResults[["semMainContainer"]][["coefficientTable"]] <- coefficientTable - coefficientTable$addColumnInfo(name = "score", title = gettext("Sum score"), type = "string") - coefficientTable$addColumnInfo(name = "average", title = gettext("Traditional"), type = "number") + coefficientTable$addColumnInfo(name = "score", title = gettext("Sum Score"), type = "string") + coefficientTable$addColumnInfo(name = "average", title = gettext("Score-Unrelated SEM"), type = "number") footnote <- "" @@ -209,14 +215,14 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { selected <- options[["selected"]] if (length(selected) > 0) { # at least one method is selected - coefficientTable <- createJaspTable(gettext("Standard error of measurement")) + coefficientTable <- createJaspTable(gettext("Standard Error of Measurement")) coefficientTable$dependOn(optionsFromObject = jaspResults[["semMainContainer"]][["coefficientTable"]]) coefficientTable$position <- 1 jaspResults[["semMainContainer"]][["coefficientTable"]] <- coefficientTable - coefficientTable$addColumnInfo(name = "score", title = gettext("Sum score"), type = "string") + coefficientTable$addColumnInfo(name = "score", title = gettext("Sum Score"), type = "string") coefficientTable$addColumnInfo(name = "counts", title = gettext("Counts"), type = "string") - footnote <- gettextf("%1$s The traditional sem value equals %2$1.3f.", footnote, average$est) + footnote <- gettextf("%1$s The score-unrelated SEM value equals %2$1.3f.", footnote, average$est) scrs <- jaspResults[["semMainContainer"]][["countsState"]]$object counts <- scrs$counts dtFill <- data.frame(score = scrs$scores) @@ -254,13 +260,13 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { if (!options[["sumScoreCiTable"]] || is.null(jaspResults[["semMainContainer"]][["ciDataState"]])) return() - ciTable <- createJaspTable(gettext("Sum score CI table")) + ciTable <- createJaspTable(gettext("Sum Score CI Table")) ciTable$dependOn(optionsFromObject = jaspResults[["semMainContainer"]][["coefficientTable"]], options = c("ciLevelTable", "sumScoreCiTable")) ciTable$position <- 2 jaspResults[["semMainContainer"]][["ciTable"]] <- ciTable - ciTable$addColumnInfo(name = "score", title = gettext("Sum score"), type = "string") + ciTable$addColumnInfo(name = "score", title = gettext("Sum Score"), type = "string") ci <- format(100 * options[["ciLevelTable"]], digits = 3, drop0trailing = TRUE) ciData <- jaspResults[["semMainContainer"]][["ciDataState"]]$object$table @@ -298,10 +304,10 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { p <- ggplot2::ggplot(ss) + ggplot2::geom_histogram(ggplot2::aes(scores), bins = nrow(unique(ss)), binwidth = .5) + ggplot2::ylab(gettext("Counts")) + - ggplot2::xlab(gettext("Sum scores")) + ggplot2::xlab(gettext("Sum Score")) p <- p + jaspGraphs::themeJaspRaw() + jaspGraphs::geom_rangeframe() - histPlot <- createJaspPlot(plot = p, title = gettext("Histogram of counts per sum score group"), width = 500, + histPlot <- createJaspPlot(plot = p, title = gettext("Histogram of Counts per Sum Score Group"), width = 500, dependencies = "histogramCounts") jaspResults[["semMainContainer"]][["histPlot"]] <- histPlot @@ -309,7 +315,7 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { } -.semPointPlots <- function(jaspResults, dataset, options, ready) { + .semPointPlots <- function(jaspResults, dataset, options, ready) { if (!is.null(jaspResults[["semMainContainer"]][["pointPlots"]]) || !options[["pointPlots"]] || !ready || jaspResults[["semMainContainer"]]$getError()) {return()} @@ -346,13 +352,13 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { colnames(dat)[1:2] <- c("score", "sem") pl <- ggplot2::ggplot(dat) + ggplot2::geom_point(ggplot2::aes(x = score, y = sem), size = 2.5) + - ggplot2::labs(x = gettext("Sum Score"), y = gettext("sem")) + ggplot2::labs(x = gettext("Sum Score"), y = gettext("SEM")) } else { dat <- as.data.frame(resultsObject$object$unbinned) colnames(dat)[1:2] <- c("score", "sem") pl <- ggplot2::ggplot(dat) + ggplot2::geom_line(ggplot2::aes(x = score, y = sem), size = 2.5) + - ggplot2::labs(x = gettext("Sum Score"), y = gettext("sem")) + ggplot2::labs(x = gettext("Sum Score"), y = gettext("SEM")) } pl <- pl + jaspGraphs::themeJaspRaw() + jaspGraphs::geom_rangeframe() @@ -399,7 +405,7 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { pl <- ggplot2::ggplot() + ggplot2::geom_point(data = dt, ggplot2::aes(x = score, y = sem, shape = Type), size = 2.5) + - ggplot2::labs(x = "Sum Score", y = "sem") + + ggplot2::labs(x = gettext("Sum Score"), y = gettext("SEM")) + ggplot2::theme(plot.margin = ggplot2::margin(t=1,r=5,b=1.5,l=1, "cm")) + jaspGraphs::themeJaspRaw(legend.position = "right") + jaspGraphs::geom_rangeframe() @@ -411,7 +417,7 @@ standardErrorOfMeasurement <- function(jaspResults, dataset, options) { shape = ggplot2::guide_legend(order = 1)) } - plot <- createJaspPlot(pl, title = gettext("Combined plot"), + plot <- createJaspPlot(pl, title = gettext("Combined Plot"), width = 600) plot$dependOn(optionsFromObject = jaspResults[["semMainContainer"]][["coefficientTable"]], options = "combinedPointPlot") diff --git a/R/unidimensionalReliabilityFrequentist.R b/R/unidimensionalReliabilityFrequentist.R index 46ac2c9d..208210bc 100644 --- a/R/unidimensionalReliabilityFrequentist.R +++ b/R/unidimensionalReliabilityFrequentist.R @@ -4,7 +4,6 @@ #' @export unidimensionalReliabilityFrequentist <- function(jaspResults, dataset, options) { - # check for listwise deletion datasetOld <- dataset dataset <- .handleData(datasetOld, options) @@ -1489,8 +1488,6 @@ unidimensionalReliabilityFrequentist <- function(jaspResults, dataset, options) if (options[["naAction"]] == "listwise") dataset <- dataset[complete.cases(dataset), ] - - # dataset columns are by default ordered alphabetically, so we change the order which we need to the splithalf-rel if (length(options$variables) > 0) dataset <- dataset[, options[["variables"]]] diff --git a/inst/Description.qml b/inst/Description.qml index af46a2fc..6dd000e5 100644 --- a/inst/Description.qml +++ b/inst/Description.qml @@ -40,7 +40,6 @@ Description title: qsTr("Rater Agreement") qml: "RaterAgreement.qml" func: "raterAgreement" - preloadData: false } Analysis { diff --git a/inst/help/standardErrorOfMeasurement.md b/inst/help/standardErrorOfMeasurement.md index 8f42c071..6267f8c3 100644 --- a/inst/help/standardErrorOfMeasurement.md +++ b/inst/help/standardErrorOfMeasurement.md @@ -29,7 +29,7 @@ The Standard Error of Measurement (sem) quantifies the precision of a measuremen ### Options - Sum score table: Displays a table with the sum scores and confidence intervals around them that differ per sem method. The CIs are normal-theory CIs that apply the sem in their calculation. - CI -- User defined reliability: Users can specify a custom reliability value to be used in the calculation of the traditional sem and the calculation of the Keats method +- User defined reliability: Users can specify a custom reliability value to be used in the calculation of the score-unrelated sem and the calculation of the Keats method - Minimum number of observations per score group: The sem methods except the Mollenkopf-Feldt and the IRT method require a minimum number of observations for a sum score to properly estimate the sem, if that number is not reached the sum score is merged with the subsequent sum score(s) until there are enough observations in the merged score group. - Hide sem table @@ -64,4 +64,4 @@ The Standard Error of Measurement (sem) quantifies the precision of a measuremen - Lord, F. M. (1955). Estimating test reliability. *Educational and Psychological Measurement, 15*(4), 325–336. https://doi.org/10.1177/001316445501500401 - Lord, F. M. (1965). A strong true-score theory, with applications. *Psychometrika, 30*(3), 239–270. https://doi.org/10.1007/BF02289490 - Samejima, F. (1968). Estimation of latent ability using a response pattern of graded scores. *Psychometrika, 34*(Suppl 1), 1–97. https://doi.org/10.1007/bf03372160 -- Thorndike, R. L. (1951). Reliability. In E. F. Lindquist (Ed.), *Educational measurement* (pp. 560–620). American Council on Education. \ No newline at end of file +- Thorndike, R. L. (1951). Reliability. In E. F. Lindquist (Ed.), *Educational measurement* (pp. 560–620). American Council on Education. diff --git a/inst/help/unidimensionalReliabilityBayesian.md b/inst/help/unidimensionalReliabilityBayesian.md index 347bd539..76cccc33 100644 --- a/inst/help/unidimensionalReliabilityBayesian.md +++ b/inst/help/unidimensionalReliabilityBayesian.md @@ -13,8 +13,8 @@ The Bayesian unidimensional reliability analysis allows the user to test the sca ### Scale Statistics - The CTT-coefficients alpha, lambda 2, and the split-half coefficient are computed from the data covariance matrix. Coefficient omega is computed from the centered data matrix. - Credible interval: default is 95% -- Coefficient omega (for unidimensional data, based on the single-factor model). Note the total test variance in the denominator of the reliability equation is the model implied total variance, that is, the summed model implied covariance matrix. -- Coefficient alpha (for binary items the coefficient equals KR20) +- Coefficient omega: The same as McDonald's omega (for unidimensional data, based on the single-factor model). Note the total test variance in the denominator of the reliability equation is the model implied total variance, that is, the summed model implied covariance matrix. +- Coefficient alpha: The same as Cronbach's alpha (for binary items the coefficient equals KR20) - Guttman's lambda 2 - Split-half coefficient: Correlates the sum scores of two test-halves. By default the variables are split into odd and even numbered items in order or appearance in the variables window. If another split is desired the variables just need to be reordered. - Average interitem correlation diff --git a/inst/help/unidimensionalReliabilityFrequentist.md b/inst/help/unidimensionalReliabilityFrequentist.md index 9638bd6a..94d44a02 100644 --- a/inst/help/unidimensionalReliabilityFrequentist.md +++ b/inst/help/unidimensionalReliabilityFrequentist.md @@ -12,8 +12,8 @@ The frequentist unidimensional reliability analysis allows the user to test the ### Scale Statistics - Confidence interval: default is 95% -- Coefficient omega (for unidimensional data, based on the single-factor model). Note the total test variance in the denominator of the reliability equation is the model implied total variance, that is, the summed model implied covariance matrix. -- Coefficient alpha (for binary items the coefficient equals KR20) +- Coefficient omega: The same as McDonald's omega (for unidimensional data, based on the single-factor model). Note the total test variance in the denominator of the reliability equation is the model implied total variance, that is, the summed model implied covariance matrix. +- Coefficient alpha: The same as Cronbach's alpha (for binary items the coefficient equals KR20) - Guttman's lambda 2 - Split-half coefficient: Correlates the sum scores of two test-halves. By default the variables are split into odd and even numbered items in order or appearance in the variables window. If another split is desired the variables just need to be reordered. - Average interitem correlation diff --git a/inst/qml/RaterAgreement.qml b/inst/qml/RaterAgreement.qml index d80c84dd..64a2059a 100644 --- a/inst/qml/RaterAgreement.qml +++ b/inst/qml/RaterAgreement.qml @@ -33,12 +33,30 @@ Form title: qsTr("Variables") allowedColumns: ["nominal"] } + + RadioButtonGroup + { + name: "dataStructure" + title: qsTr("Data Structure") + columns: 2 + RadioButton + { + name: "ratersInColumns" + label: qsTr("Raters are in columns") + checked: true + } + + RadioButton + { + name: "ratersInRows" + label: qsTr("Raters are in rows") + } + } } + Group { - - CheckBox { name: "cohensKappa" @@ -68,40 +86,20 @@ Form } } } - - } - + CheckBox { name: "fleissKappa" label: qsTr("Fleiss' kappa") checked: true } - + CheckBox { name: "krippendorffsAlpha" label: qsTr("Krippendorff's alpha") checked: true - - RadioButtonGroup - { - name: "krippendorffsAlphaDataStructure" - title: qsTr("Data Structure") - RadioButton - { - name: "ratersInColumns" - label: qsTr("Raters are in columns") - checked: true - } - - RadioButton - { - name: "ratersInRows" - label: qsTr("Raters are in rows") - } - } DropDown { @@ -124,23 +122,7 @@ Form min: 100 max: 1e7 } - - CheckBox - { - name: "setSeed" - label: qsTr("Set seed") - childrenOnSameRow: true - - IntegerField - { - name: "seed" - label: "" - defaultValue: 1234 - fieldWidth: 80 - min: 1 - max: 1e9 - } - } + SetSeed{} } } diff --git a/inst/qml/StandardErrorOfMeasurement.qml b/inst/qml/StandardErrorOfMeasurement.qml index 372890f1..e72d788f 100644 --- a/inst/qml/StandardErrorOfMeasurement.qml +++ b/inst/qml/StandardErrorOfMeasurement.qml @@ -61,24 +61,26 @@ Form lord2NumberOfSplits.values = newValuesLord } + } } Group { Layout.rowSpan: 2 - title: qsTr("Split-test methods") + title: qsTr("Split-Test Methods") CheckBox { name: "thorndike" label: qsTr("Thorndike") - + id: thorndike } CheckBox { name: "feldt" label: qsTr("Feldt") + id: feldt DropDown { name: "feldtNumberOfSplits" @@ -91,6 +93,7 @@ Form { name: "mollenkopfFeldt" label: qsTr("Mollenkopf-Feldt") + id: mollenkopfFeldt DropDown { name: "mollenkopfFeldtNumberOfSplits" @@ -103,8 +106,8 @@ Form name: "mollenkopfFeldtPolyDegree" label: qsTr("Degree of polynomial") min: 2 - max: 10 - defaultValue: 3 + max: 8 + defaultValue: 2 } } @@ -127,22 +130,26 @@ Form Group { - title: qsTr("Binomial methods") + title: qsTr("Binomial Methods") CheckBox { + enabled: !variables.columnsTypes.includes("ordinal") name: "lord" label: qsTr("Lord") } CheckBox { + enabled: !variables.columnsTypes.includes("ordinal") name: "keats" label: qsTr("Keats") } CheckBox { + enabled: !variables.columnsTypes.includes("ordinal") name: "lord2" label: qsTr("Lord's compound") + id: lord2 DropDown { name: "lord2NumberOfSplits" @@ -190,13 +197,13 @@ Form name: "minimumGroupSize" label: qsTr("Minimum number of observations per score group") min: 1 - defaultValue: 10 + defaultValue: 20 } CheckBox { name: "hideTable" - label: qsTr("Hide sem table") + label: qsTr("Hide SEM table") } } @@ -220,7 +227,7 @@ Form CheckBox { name: "combinedPointPlot" - label: qsTr("Plot all sems") + label: qsTr("Plot all SEMs") } Group { diff --git a/renv.lock b/renv.lock index ca7418a2..07947078 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.4.2", + "Version": "4.4.3", "Repositories": [ { "Name": "CRAN", @@ -13,1066 +13,2658 @@ "Package": "Bayesrel", "Version": "0.7.7", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Bayesian Reliability Estimation", + "Date": "2023-08-08", + "Authors@R": "c(person(\"Julius M.\", \"Pfadt\", email = \"julius.pfadt@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0758-5502\")), person(\"Don\", \"van den Bergh\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-9838-7308\")), person(\"Joris\", \"Goosen\", role = c(\"aut\")) )", + "Description": "Functionality for reliability estimates. For 'unidimensional' tests: Coefficient alpha, 'Guttman's' lambda-2/-4/-6, the Greatest lower bound and coefficient omega_u ('unidimensional') in a Bayesian and a frequentist version. For multidimensional tests: omega_t (total) and omega_h (hierarchical). The results include confidence and credible intervals, the probability of a coefficient being larger than a cutoff, and a check for the factor models, necessary for the omega coefficients. The method for the Bayesian 'unidimensional' estimates, except for omega_u, is sampling from the posterior inverse 'Wishart' for the covariance matrix based measures (see 'Murphy', 2007, . The Bayesian omegas (u, t, and h) are obtained by 'Gibbs' sampling from the conditional posterior distributions of (1) the single factor model, (2) the second-order factor model, (3) the bi-factor model, (4) the correlated factor model ('Lee', 2007, ).", + "URL": "https://github.com/juliuspfadt/Bayesrel", + "BugReports": "https://github.com/juliuspfadt/Bayesrel/issues", + "License": "GPL-3", + "Encoding": "UTF-8", + "LazyData": "true", + "Imports": [ "LaplacesDemon", "MASS", - "R", - "Rcpp", - "RcppArmadillo", - "Rdpack", - "coda", - "graphics", "lavaan", + "coda", "methods", - "stats" + "stats", + "graphics", + "Rdpack", + "Rcpp (>= 1.0.4.6)" + ], + "LinkingTo": [ + "Rcpp", + "RcppArmadillo" + ], + "RdMacros": "Rdpack", + "RoxygenNote": "7.2.3", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "tinytest" ], - "Hash": "2d3273dff153ee87f837f4d77d49b225" + "NeedsCompilation": "yes", + "Author": "Julius M. Pfadt [aut, cre] (), Don van den Bergh [aut] (), Joris Goosen [aut]", + "Maintainer": "Julius M. Pfadt ", + "Repository": "CRAN" }, "Deriv": { "Package": "Deriv", "Version": "4.1.6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Symbolic Differentiation", + "Date": "2024-09-12", + "Authors@R": "c(person(given=\"Andrew\", family=\"Clausen\", role=\"aut\"), person(given=\"Serguei\", family=\"Sokol\", role=c(\"aut\", \"cre\"), email=\"sokol@insa-toulouse.fr\", comment = c(ORCID = \"0000-0002-5674-3327\")), person(given=\"Andreas\", family=\"Rappold\", role=\"ctb\", email=\"arappold@gmx.at\"))", + "Description": "R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.", + "License": "GPL (>= 3)", + "Suggests": [ + "testthat (>= 0.11.0)" + ], + "BugReports": "https://github.com/sgsokol/Deriv/issues", + "RoxygenNote": "7.3.1", + "Imports": [ "methods" ], - "Hash": "cd52c065c9e687c60c56b51f10f7bcd3" + "NeedsCompilation": "no", + "Author": "Andrew Clausen [aut], Serguei Sokol [aut, cre] (), Andreas Rappold [ctb]", + "Maintainer": "Serguei Sokol ", + "Repository": "CRAN" }, "Formula": { "Package": "Formula", "Version": "1.2-5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Date": "2023-02-23", + "Title": "Extended Model Formulas", + "Description": "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side (see ).", + "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 = \"Yves\", family = \"Croissant\", role = \"aut\", email = \"Yves.Croissant@univ-reunion.fr\"))", + "Depends": [ + "R (>= 2.0.0)", "stats" ], - "Hash": "7a29697b75e027767a53fde6c903eca7" + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "no", + "Author": "Achim Zeileis [aut, cre] (), Yves Croissant [aut]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" }, "GPArotation": { "Package": "GPArotation", "Version": "2024.3-1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Gradient Projection Factor Rotation", + "Authors@R": "c( person(\"Coen\", \"Bernaards\", email = \"cab.gparotation@gmail.com\", role = c(\"aut\",\"cre\")), person(\"Paul\", \"Gilbert\", email = \"pgilbert.ttv9z@ncf.ca\", role = \"aut\"), person(\"Robert\", \"Jennrich\", role = \"aut\") )", + "Depends": [ + "R (>= 2.0.0)" + ], + "Description": "Gradient Projection Algorithms for Factor Rotation. For details see ?GPArotation. 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Gronau [ctb], Henrik Singmann [cre]", + "Maintainer": "Henrik Singmann ", + "Repository": "CRAN" }, "MASS": { "Package": "MASS", "Version": "7.3-61", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-06-10", + "Revision": "$Rev: 3657 $", + "Depends": [ + "R (>= 4.4.0)", "grDevices", "graphics", - "methods", "stats", "utils" ], - "Hash": "0cafd6f0500e5deba33be22c46bf6055" + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"ripley@stats.ox.ac.uk\"), person(\"Bill\", \"Venables\", role = c(\"aut\", \"cph\")), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\", comment = \"support functions for polr\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb] (support functions for polr)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "Matrix": { "Package": "Matrix", "Version": "1.7-1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2024-10-17", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", + "License": "GPL (>= 2) | file LICENCE", + "URL": "https://Matrix.R-forge.R-project.org", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's matrix implementation\"))", + "Depends": [ + "R (>= 4.4.0)", + "methods" + ], + "Imports": [ "grDevices", "graphics", "grid", "lattice", - "methods", "stats", "utils" ], - "Hash": "5122bb14d8736372411f955e1b16bc8a" + "Suggests": [ + "MASS", + "datasets", + "sfsmisc", + "tools" + ], + "Enhances": [ + "SparseM", + "graph" + ], + "LazyData": "no", + "LazyDataNote": "not possible, since we use data/*.R and our S4 classes", + "BuildResaveData": "no", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] (), Mikael Jagan [aut] (), Timothy A. Davis [ctb] (, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (base R's matrix implementation)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" }, "R.methodsS3": { "Package": "R.methodsS3", "Version": "1.8.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Depends": [ + "R (>= 2.13.0)" + ], + "Imports": [ "utils" ], - "Hash": "278c286fd6e9e75d0c2e8f731ea445c8" + "Suggests": [ + "codetools" + ], + "Title": "S3 Methods Simplified", + "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\"))", + "Author": "Henrik Bengtsson [aut, cre, cph]", + "Maintainer": "Henrik Bengtsson ", + "Description": "Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.", + "License": "LGPL (>= 2.1)", + "LazyLoad": "TRUE", + "URL": "https://github.com/HenrikBengtsson/R.methodsS3", + "BugReports": "https://github.com/HenrikBengtsson/R.methodsS3/issues", + "NeedsCompilation": "no", + "Repository": "CRAN" }, "R.oo": { "Package": "R.oo", "Version": "1.27.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R.methodsS3", + "Depends": [ + "R (>= 2.13.0)", + "R.methodsS3 (>= 1.8.2)" + ], + "Imports": [ "methods", "utils" ], - "Hash": "6ac79ff194202248cf946fe3a5d6d498" + "Suggests": [ + "tools" + ], + "Title": "R Object-Oriented Programming with or without References", + "Authors@R": "c(person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\"))", + "Author": "Henrik Bengtsson [aut, cre, cph]", + "Maintainer": "Henrik Bengtsson ", + "Description": "Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. 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Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. 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Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. 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'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.6.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 0.11.0)", "stats", "utils" ], - "Hash": "4ac8e423216b8b70cb9653d1b3f71eb9" + "Suggests": [ + "Matrix", + "inline", + "tinytest", + "pkgKitten", + "microbenchmark" + ], + "URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html", + "BugReports": "https://github.com/RcppCore/RcppEigen/issues", + "NeedsCompilation": "yes", + "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" }, "Rdpack": { "Package": "Rdpack", "Version": "2.6.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods", - "rbibutils", + "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\"), 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" + "utils", + "rbibutils (>= 1.3)" + ], + "Suggests": [ + "grDevices", + "testthat", + "rstudioapi", + "rprojroot", + "gbRd" ], - "Hash": "a9e2118c664c2cd694f03de074e8d4b3" + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "RoxygenNote": "7.1.1", + "NeedsCompilation": "no", + "Author": "Georgi N. 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The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. 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Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" }, "coda": { "Package": "coda", "Version": "0.19-4.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Date": "2020-09-30", + "Title": "Output Analysis and Diagnostics for MCMC", + "Authors@R": "c(person(\"Martyn\", \"Plummer\", role=c(\"aut\",\"cre\",\"trl\"), email=\"martyn.plummer@gmail.com\"), person(\"Nicky\", \"Best\", role=\"aut\"), person(\"Kate\", \"Cowles\", role=\"aut\"), person(\"Karen\", \"Vines\", role=\"aut\"), person(\"Deepayan\", \"Sarkar\", role=\"aut\"), person(\"Douglas\", \"Bates\", role=\"aut\"), person(\"Russell\", \"Almond\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"))", + "Depends": [ + "R (>= 2.14.0)" + ], + "Imports": [ "lattice" ], - "Hash": "af436915c590afc6fffc3ce3a5be1569" + "Description": "Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.", + "License": "GPL (>= 2)", + "NeedsCompilation": "no", + "Author": "Martyn Plummer [aut, cre, trl], Nicky Best [aut], Kate Cowles [aut], Karen Vines [aut], Deepayan Sarkar [aut], Douglas Bates [aut], Russell Almond [aut], Arni Magnusson [aut]", + "Maintainer": "Martyn Plummer ", + "Repository": "CRAN" }, "codetools": { "Package": "codetools", "Version": "0.2-20", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" ], - "Hash": "61e097f35917d342622f21cdc79c256e" + "Maintainer": "Luke Tierney ", + "URL": "https://gitlab.com/luke-tierney/codetools", + "License": "GPL", + "NeedsCompilation": "no", + "Repository": "CRAN" }, "colorspace": { "Package": "colorspace", "Version": "2.1-1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", + "Date": "2024-07-26", + "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", + "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", + "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ "graphics", - "methods", + "grDevices", "stats" ], - "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" }, "corpcor": { "Package": "corpcor", "Version": "1.6.10", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Date": "2021-09-16", + "Title": "Efficient Estimation of Covariance and (Partial) Correlation", + "Author": "Juliane Schafer, Rainer Opgen-Rhein, Verena Zuber, Miika Ahdesmaki, A. Pedro Duarte Silva, and Korbinian Strimmer.", + "Maintainer": "Korbinian Strimmer ", + "Depends": [ + "R (>= 3.0.2)" + ], + "Imports": [ "stats" ], - "Hash": "17ebe3b6d75d09c5bab3891880b34237" + "Suggests": [], + "Description": "Implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. The details of the method are explained in Schafer and Strimmer (2005) and Opgen-Rhein and Strimmer (2007) . The approach is both computationally as well as statistically very efficient, it is applicable to \"small n, large p\" data, and always returns a positive definite and well-conditioned covariance matrix. In addition to inferring the covariance matrix the package also provides shrinkage estimators for partial correlations and partial variances. The inverse of the covariance and correlation matrix can be efficiently computed, as well as any arbitrary power of the shrinkage correlation matrix. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.", + "License": "GPL (>= 3)", + "URL": "https://strimmerlab.github.io/software/corpcor/", + "NeedsCompilation": "no", + "Repository": "CRAN" }, "cpp11": { "Package": "cpp11", "Version": "0.5.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "9df43854f1c84685d095ed6270b52387" - }, - "crayon": { - "Package": "crayon", - "Version": "1.5.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "methods", - "utils" - ], - "Hash": "859d96e65ef198fd43e82b9628d593ef" - }, - "curl": { + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "curl": { "Package": "curl", "Version": "6.2.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Posit Software, PBC\", role = \"cph\"))", + "Description": "Bindings to 'libcurl' for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" ], - "Hash": "b580cbb010099fd990df6bfe44459e1a" + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "data.table": { "Package": "data.table", "Version": "1.16.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "methods" ], - "Hash": "38bbf05fc2503143db4c734a7e5cab66" + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), person(\"Pasha\",\"Stetsenko\", role=\"ctb\"), person(\"Tom\",\"Short\", role=\"ctb\"), person(\"Steve\",\"Lianoglou\", role=\"ctb\"), person(\"Eduard\",\"Antonyan\", role=\"ctb\"), person(\"Markus\",\"Bonsch\", role=\"ctb\"), person(\"Hugh\",\"Parsonage\", role=\"ctb\"), person(\"Scott\",\"Ritchie\", role=\"ctb\"), person(\"Kun\",\"Ren\", role=\"ctb\"), person(\"Xianying\",\"Tan\", role=\"ctb\"), person(\"Rick\",\"Saporta\", role=\"ctb\"), person(\"Otto\",\"Seiskari\", role=\"ctb\"), person(\"Xianghui\",\"Dong\", role=\"ctb\"), person(\"Michel\",\"Lang\", role=\"ctb\"), person(\"Watal\",\"Iwasaki\", role=\"ctb\"), person(\"Seth\",\"Wenchel\", role=\"ctb\"), person(\"Karl\",\"Broman\", role=\"ctb\"), person(\"Tobias\",\"Schmidt\", role=\"ctb\"), person(\"David\",\"Arenburg\", role=\"ctb\"), person(\"Ethan\",\"Smith\", role=\"ctb\"), person(\"Francois\",\"Cocquemas\", role=\"ctb\"), person(\"Matthieu\",\"Gomez\", role=\"ctb\"), person(\"Philippe\",\"Chataignon\", role=\"ctb\"), person(\"Nello\",\"Blaser\", role=\"ctb\"), person(\"Dmitry\",\"Selivanov\", role=\"ctb\"), person(\"Andrey\",\"Riabushenko\", role=\"ctb\"), person(\"Cheng\",\"Lee\", role=\"ctb\"), person(\"Declan\",\"Groves\", role=\"ctb\"), person(\"Daniel\",\"Possenriede\", role=\"ctb\"), person(\"Felipe\",\"Parages\", role=\"ctb\"), person(\"Denes\",\"Toth\", role=\"ctb\"), person(\"Mus\",\"Yaramaz-David\", role=\"ctb\"), person(\"Ayappan\",\"Perumal\", role=\"ctb\"), person(\"James\",\"Sams\", role=\"ctb\"), person(\"Martin\",\"Morgan\", role=\"ctb\"), person(\"Michael\",\"Quinn\", role=\"ctb\"), person(\"@javrucebo\",\"\", role=\"ctb\"), person(\"@marc-outins\",\"\", role=\"ctb\"), person(\"Roy\",\"Storey\", role=\"ctb\"), person(\"Manish\",\"Saraswat\", role=\"ctb\"), person(\"Morgan\",\"Jacob\", role=\"ctb\"), person(\"Michael\",\"Schubmehl\", role=\"ctb\"), person(\"Davis\",\"Vaughan\", role=\"ctb\"), person(\"Leonardo\",\"Silvestri\", role=\"ctb\"), person(\"Jim\",\"Hester\", role=\"ctb\"), person(\"Anthony\",\"Damico\", role=\"ctb\"), person(\"Sebastian\",\"Freundt\", role=\"ctb\"), person(\"David\",\"Simons\", role=\"ctb\"), person(\"Elliott\",\"Sales de Andrade\", role=\"ctb\"), person(\"Cole\",\"Miller\", role=\"ctb\"), person(\"Jens Peder\",\"Meldgaard\", role=\"ctb\"), person(\"Vaclav\",\"Tlapak\", role=\"ctb\"), person(\"Kevin\",\"Ushey\", role=\"ctb\"), person(\"Dirk\",\"Eddelbuettel\", role=\"ctb\"), person(\"Tony\",\"Fischetti\", role=\"ctb\"), person(\"Ofek\",\"Shilon\", role=\"ctb\"), person(\"Vadim\",\"Khotilovich\", role=\"ctb\"), person(\"Hadley\",\"Wickham\", role=\"ctb\"), person(\"Bennet\",\"Becker\", role=\"ctb\"), person(\"Kyle\",\"Haynes\", role=\"ctb\"), person(\"Boniface Christian\",\"Kamgang\", role=\"ctb\"), person(\"Olivier\",\"Delmarcell\", role=\"ctb\"), person(\"Josh\",\"O'Brien\", role=\"ctb\"), person(\"Dereck\",\"de Mezquita\", role=\"ctb\"), person(\"Michael\",\"Czekanski\", role=\"ctb\"), person(\"Dmitry\", \"Shemetov\", role=\"ctb\"), person(\"Nitish\", \"Jha\", role=\"ctb\"), person(\"Joshua\", \"Wu\", role=\"ctb\"), person(\"Iago\", \"Giné-Vázquez\", role=\"ctb\"), person(\"Anirban\", \"Chetia\", role=\"ctb\"), person(\"Doris\", \"Amoakohene\", role=\"ctb\"), person(\"Ivan\", \"Krylov\", role=\"ctb\") )", + "NeedsCompilation": "yes", + "Author": "Tyson Barrett [aut, cre] (), Matt Dowle [aut], Arun Srinivasan [aut], Jan Gorecki [aut], Michael Chirico [aut] (), Toby Hocking [aut] (), Benjamin Schwendinger [aut] (), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Ivan Krylov [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "CRAN" }, "dcurver": { "Package": "dcurver", "Version": "0.9.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Date": "2020-11-03", + "Title": "Utility Functions for Davidian Curves", + "Author": "Oğuzhan Öğreden", + "Maintainer": "Oğuzhan Öğreden ", + "Description": "A Davidian curve defines a seminonparametric density, whose shape and flexibility can be tuned by easy to estimate parameters. Since a special case of a Davidian curve is the standard normal density, Davidian curves can be used for relaxing normality assumption in statistical applications (Zhang & Davidian, 2001) . 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Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "utils" ], - "Hash": "33698c4b3127fc9f506654607fb73676" + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" }, "dplyr": { "Package": "dplyr", "Version": "1.1.4", "Source": "Repository", - 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As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", + "BugReports": "https://github.com/thomasp85/farver/issues", + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" }, "fastmap": { "Package": "fastmap", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" + "Title": "Fast Data Structures", + "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )", + "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. Environments are commonly used as key-value stores in R, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. 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The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold.", + "License": "GPL (>= 3)", + "URL": "https://strimmerlab.github.io/software/fdrtool/", + "NeedsCompilation": "yes", + "Author": "Bernd Klaus [aut], Korbinian Strimmer [aut, cre]", + "Maintainer": "Korbinian Strimmer ", + "Repository": "CRAN" }, "fontBitstreamVera": { "Package": "fontBitstreamVera", "Version": "0.1.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "f6068021eff4aba735a9b2353516636c" + "Title": "Fonts with 'Bitstream Vera Fonts' License", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel.hry@gmail.com\", c(\"cre\", \"aut\")), person(\"Bitstream\", role = \"cph\"))", + "Description": "Provides fonts licensed under the 'Bitstream Vera Fonts' license for the 'fontquiver' package.", + "Depends": [ + "R (>= 3.0.0)" + ], + "License": "file LICENCE", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "5.0.1", + "NeedsCompilation": "no", + "Author": "Lionel Henry [cre, aut], Bitstream [cph]", + "Maintainer": "Lionel Henry ", + "License_is_FOSS": "yes", + "Repository": "CRAN" }, "fontLiberation": { "Package": "fontLiberation", "Version": "0.1.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Liberation Fonts", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@rstudio.com\", \"cre\"), person(\"Pravin Satpute\", role = \"aut\"), person(\"Steve Matteson\", role = \"aut\"), person(\"Red Hat, Inc\", role = \"cph\"), person(\"Google Corporation\", role = \"cph\"))", + "Description": "A placeholder for the Liberation fontset intended for the `fontquiver` package. 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These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. 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Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael Nelson [ctb], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]", + "Maintainer": "R Core Team ", + "Repository": "CRAN" }, "fs": { "Package": "fs", "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Cross-Platform File System Operations Based on 'libuv'", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A cross-platform interface to file system operations, built on top of the 'libuv' C library.", + "License": "MIT + file LICENSE", + "URL": "https://fs.r-lib.org, https://github.com/r-lib/fs", + "BugReports": "https://github.com/r-lib/fs/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ "methods" ], - "Hash": "7f48af39fa27711ea5fbd183b399920d" + "Suggests": [ + "covr", + "crayon", + "knitr", + "pillar (>= 1.0.0)", + "rmarkdown", + "spelling", + "testthat (>= 3.0.0)", + "tibble (>= 1.1.0)", + "vctrs (>= 0.3.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Copyright": "file COPYRIGHTS", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "SystemRequirements": "GNU make", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut, cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "future": { "Package": "future", "Version": "1.34.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Unified Parallel and Distributed Processing in R for Everyone", + "Imports": [ "digest", - "globals", - "listenv", + "globals (>= 0.16.1)", + "listenv (>= 0.8.0)", "parallel", - "parallelly", + "parallelly (>= 1.38.0)", "utils" ], - "Hash": "475771e3edb711591476be387c9a8c2e" + "Suggests": [ + "methods", + "RhpcBLASctl", + "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\")))", + "Description": "The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. The simplest way to evaluate an expression in parallel is to use `x %<-% { expression }` with `plan(multisession)`. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers, etc. Because of its unified API, there is no need to modify any code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.", + "License": "LGPL (>= 2.1)", + "LazyLoad": "TRUE", + "ByteCompile": "TRUE", + "URL": "https://future.futureverse.org, https://github.com/HenrikBengtsson/future", + "BugReports": "https://github.com/HenrikBengtsson/future/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Henrik Bengtsson [aut, cre, cph] ()", + "Maintainer": "Henrik Bengtsson ", + "Repository": "CRAN" }, "future.apply": { "Package": "future.apply", "Version": "1.11.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "future", - "globals", + "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" ], - "Hash": "0efead26b03bb60716ed29971b1953dc" + "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" }, "gdtools": { "Package": "gdtools", "Version": "0.4.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "fontquiver", + "Title": "Utilities for Graphical Rendering and Fonts Management", + "Authors@R": "c( person(\"David\", \"Gohel\", , \"david.gohel@ardata.fr\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@rstudio.com\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", , \"jeroen@berkeley.edu\", role = \"aut\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Yixuan\", \"Qiu\", role = \"ctb\"), person(\"R Core Team\", role = \"cph\", comment = \"Cairo code from X11 device\"), person(\"ArData\", role = \"cph\"), person(\"RStudio\", role = \"cph\") )", + "Description": "Tools are provided to compute metrics of formatted strings and to check the availability of a font. Another set of functions is provided to support the collection of fonts from 'Google Fonts' in a cache. 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The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. 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Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "labeling": { "Package": "labeling", "Version": "0.4.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "graphics", - "stats" + "Type": "Package", + "Title": "Axis Labeling", + "Date": "2023-08-29", + "Author": "Justin Talbot,", + "Maintainer": "Nuno Sempere ", + "Description": "Functions which provide a range of axis labeling algorithms.", + "License": "MIT + file LICENSE | Unlimited", + "Collate": "'labeling.R'", + "NeedsCompilation": "no", + "Imports": [ + "stats", + "graphics" ], - "Hash": "b64ec208ac5bc1852b285f665d6368b3" + "Repository": "CRAN" }, "lattice": { "Package": "lattice", "Version": "0.22-6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Date": "2024-03-20", + "Priority": "recommended", + "Title": "Trellis Graphics for R", + "Authors@R": "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"), email = \"deepayan.sarkar@r-project.org\", comment = c(ORCID = \"0000-0003-4107-1553\")), person(\"Felix\", \"Andrews\", role = \"ctb\"), person(\"Kevin\", \"Wright\", role = \"ctb\", comment = \"documentation\"), person(\"Neil\", \"Klepeis\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous improvements\"), person(\"Zhijian (Jason)\", \"Wen\", role = \"cph\", comment = \"filled contour code\"), person(\"Paul\", \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"), person(\"Stefan\", \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"), person(\"Achim\", \"Zeileis\", role = \"ctb\", comment = \"modern colors\"), person(\"Alexandre\", \"Courtiol\", role = \"ctb\", comment = \"generics for larrows, lpolygon, lrect and lsegments\") )", + "Description": "A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. 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The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' \"glue\".", + "Depends": [ + "R (>= 3.6.0)", "Matrix", - "R", - "Rcpp", - "RcppEigen", - "boot", + "methods", + "stats" + ], + "LinkingTo": [ + "Rcpp (>= 0.10.5)", + "RcppEigen (>= 0.3.3.9.4)", + "Matrix (>= 1.2-3)" + ], + "Imports": [ "graphics", "grid", - "lattice", - "methods", - "minqa", - "nlme", - "nloptr", - "parallel", "splines", - "stats", - "utils" + "utils", + "parallel", + "MASS", + "lattice", + "boot", + "nlme (>= 3.1-123)", + "minqa (>= 1.1.15)", + "nloptr (>= 1.0.4)" ], - "Hash": "16a08fc75007da0d08e0c0388c7c33e6" + "Suggests": [ + "knitr", + "rmarkdown", + "MEMSS", + "testthat (>= 0.8.1)", + "ggplot2", + "mlmRev", + "optimx (>= 2013.8.6)", + "gamm4", + "pbkrtest", + "HSAUR3", + "numDeriv", + "car", + "dfoptim", + "mgcv", + "statmod", + "rr2", + "semEff", + "tibble", + "merDeriv" + ], + "VignetteBuilder": "knitr", + "LazyData": "yes", + "License": "GPL (>= 2)", + "URL": "https://github.com/lme4/lme4/", + "BugReports": "https://github.com/lme4/lme4/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut] (), Ben Bolker [aut, cre] (), Steven Walker [aut] (), Rune Haubo Bojesen Christensen [ctb] (), Henrik Singmann [ctb] (), Bin Dai [ctb], Fabian Scheipl [ctb] (), Gabor Grothendieck [ctb], Peter Green [ctb] (), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (, shared copyright on simulate.formula), Emi Tanaka [ctb] (), Mikael Jagan [ctb] ()", + "Maintainer": "Ben Bolker ", + "Repository": "CRAN" }, "lpSolve": { "Package": "lpSolve", "Version": "5.6.21", + "Version": "5.6.21", "Source": "Repository", - "Repository": "CRAN", - "Hash": "730a90bdc519fb0caff03df11218ddd8" + "Title": "Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"cre\"), person(\"Michel\", \"Berkelaar\", role = \"aut\") )", + "Description": "Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a \"wrapper\" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.", + "License": "LGPL-2", + "URL": "https://github.com/gaborcsardi/lpSolve", + "BugReports": "https://github.com/gaborcsardi/lpSolve/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [cre], Michel Berkelaar [aut]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "magrittr": { "Package": "magrittr", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Type": "Package", + "Title": "A Forward-Pipe Operator for R", + "Authors@R": "c( person(\"Stefan Milton\", \"Bache\", , \"stefan@stefanbache.dk\", role = c(\"aut\", \"cph\"), comment = \"Original author and creator of magrittr\"), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@rstudio.com\", role = \"cre\"), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"", + "License": "MIT + file LICENSE", + "URL": "https://magrittr.tidyverse.org, https://github.com/tidyverse/magrittr", + "BugReports": "https://github.com/tidyverse/magrittr/issues", + "Depends": [ + "R (>= 3.4.0)" + ], + "Suggests": [ + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat" ], - "Hash": "7ce2733a9826b3aeb1775d56fd305472" + "VignetteBuilder": "knitr", + "ByteCompile": "Yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.1.2", + "NeedsCompilation": "yes", + "Author": "Stefan Milton Bache [aut, cph] (Original author and creator of magrittr), Hadley Wickham [aut], Lionel Henry [cre], RStudio [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" }, "memoise": { "Package": "memoise", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "cachem", - "rlang" + "Title": "'Memoisation' of Functions", + "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = \"aut\", email = \"hadley@rstudio.com\"), person(given = \"Jim\", family = \"Hester\", role = \"aut\"), person(given = \"Winston\", family = \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@rstudio.com\"), person(given = \"Kirill\", family = \"Müller\", role = \"aut\", email = \"krlmlr+r@mailbox.org\"), person(given = \"Daniel\", family = \"Cook\", role = \"aut\", email = \"danielecook@gmail.com\"), person(given = \"Mark\", family = \"Edmondson\", role = \"ctb\", email = \"r@sunholo.com\"))", + "Description": "Cache the results of a function so that when you call it again with the same arguments it returns the previously computed value.", + "License": "MIT + file LICENSE", + "URL": "https://memoise.r-lib.org, https://github.com/r-lib/memoise", + "BugReports": "https://github.com/r-lib/memoise/issues", + "Imports": [ + "rlang (>= 0.4.10)", + "cachem" + ], + "Suggests": [ + "digest", + "aws.s3", + "covr", + "googleAuthR", + "googleCloudStorageR", + "httr", + "testthat" ], - "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" + "Encoding": "UTF-8", + "RoxygenNote": "7.1.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Winston Chang [aut, cre], Kirill Müller [aut], Daniel Cook [aut], Mark Edmondson [ctb]", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" }, "mgcv": { "Package": "mgcv", "Version": "1.9-1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Matrix", - "R", - "graphics", + "Author": "Simon Wood ", + "Maintainer": "Simon Wood ", + "Title": "Mixed GAM Computation Vehicle with Automatic Smoothness Estimation", + "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.", + "Priority": "recommended", + "Depends": [ + "R (>= 3.6.0)", + "nlme (>= 3.1-64)" + ], + "Imports": [ "methods", - "nlme", - "splines", "stats", + "graphics", + "Matrix", + "splines", "utils" ], - "Hash": "110ee9d83b496279960e162ac97764ce" + "Suggests": [ + "parallel", + "survival", + "MASS" + ], + "LazyLoad": "yes", + "ByteCompile": "yes", + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Repository": "CRAN" }, "mime": { "Package": "mime", "Version": "0.12", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Map Filenames to MIME Types", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"Beilei\", \"Bian\", role = \"ctb\") )", + "Description": "Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.", + "Imports": [ "tools" ], - "Hash": "18e9c28c1d3ca1560ce30658b22ce104" + "License": "GPL", + "URL": "https://github.com/yihui/mime", + "BugReports": "https://github.com/yihui/mime/issues", + "RoxygenNote": "7.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre] (), Jeffrey Horner [ctb], Beilei Bian [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "minqa": { "Package": "minqa", "Version": "1.2.8", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Derivative-Free Optimization Algorithms by Quadratic Approximation", + "Authors@R": "c(person(given = \"Douglas\", family = \"Bates\", role = \"aut\"), person(given = c(\"Katharine\", \"M.\"), family = \"Mullen\", role = c(\"aut\", \"cre\"), email = \"katharine.mullen@stat.ucla.edu\"), person(given = c(\"John\", \"C.\"), family = \"Nash\", role = \"aut\"), person(given = \"Ravi\", family = \"Varadhan\", role = \"aut\"))", + "Maintainer": "Katharine M. Mullen ", + "Description": "Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.", + "License": "GPL-2", + "URL": "http://optimizer.r-forge.r-project.org", + "Imports": [ + "Rcpp (>= 0.9.10)" + ], + "LinkingTo": [ "Rcpp" ], - "Hash": "785ef8e22389d4a7634c6c944f2dc07d" + "SystemRequirements": "GNU make", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Author": "Douglas Bates [aut], Katharine M. Mullen [aut, cre], John C. Nash [aut], Ravi Varadhan [aut]" }, "mirt": { "Package": "mirt", "Version": "1.43", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Deriv", + "Type": "Package", + "Title": "Multidimensional Item Response Theory", + "Authors@R": "c( person(\"Phil\", family=\"Chalmers\", email = \"rphilip.chalmers@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID=\"0000-0001-5332-2810\")), person(\"Joshua\", family=\"Pritikin\", role=c('ctb')), person(\"Alexander\", family=\"Robitzsch\", role=c('ctb')), person(\"Mateusz\", family=\"Zoltak\", role=c('ctb')), person(\"KwonHyun\", family=\"Kim\", role=c('ctb')), person(\"Carl F.\", family=\"Falk\", role=c('ctb')), person(\"Adam\", family=\"Meade\", role=c('ctb')), person(\"Lennart\", family=\"Schneider\", role=c('ctb')), person(\"David\", family=\"King\", role=c('ctb')), person(\"Chen-Wei\", family=\"Liu\", role=c('ctb')), person(\"Ogreden\", family=\"Oguzhan\", role=c('ctb')))", + "Description": "Analysis of discrete response data using unidimensional and multidimensional item analysis models under the Item Response Theory paradigm (Chalmers (2012) ). Exploratory and confirmatory item factor analysis models are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory bi-factor and two-tier models are available for modeling item testlets using dimension reduction EM algorithms, while multiple group analyses and mixed effects designs are included for detecting differential item, bundle, and test functioning, and for modeling item and person covariates. Finally, latent class models such as the DINA, DINO, multidimensional latent class, mixture IRT models, and zero-inflated response models are supported.", + "VignetteBuilder": "knitr", + "Depends": [ + "stats", + "R (>= 3.6.0)", + "stats4", + "lattice", + "methods" + ], + "Imports": [ "GPArotation", - "Matrix", - "R", - "Rcpp", - "RcppArmadillo", - "SimDesign", - "dcurver", "gridExtra", - "lattice", - "methods", + "Matrix (>= 1.5-0)", + "Rcpp", "mgcv", - "pbapply", + "vegan", + "Deriv", "splines", - "stats", - "stats4", - "vegan" + "pbapply (>= 1.3-0)", + "dcurver", + "SimDesign" + ], + "Suggests": [ + "boot", + "latticeExtra", + "directlabels", + "shiny", + "knitr", + "markdown", + "Rsolnp", + "nloptr", + "sirt", + "plink", + "mirtCAT", + "testthat (>= 3.0.0)" + ], + "ByteCompile": "yes", + "LazyLoad": "yes", + "LazyData": "yes", + "LinkingTo": [ + "Rcpp", + "RcppArmadillo" ], - "Hash": "7e9ce96897b75a9b275655a29a90bca7" + "License": "GPL (>= 3)", + "Encoding": "UTF-8", + "Repository": "CRAN", + "Maintainer": "Phil Chalmers ", + "URL": "https://philchalmers.github.io/mirt/, https://github.com/philchalmers/mirt/wiki, https://groups.google.com/forum/#!forum/mirt-package", + "BugReports": "https://github.com/philchalmers/mirt/issues?state=open", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Phil Chalmers [aut, cre] (), Joshua Pritikin [ctb], Alexander Robitzsch [ctb], Mateusz Zoltak [ctb], KwonHyun Kim [ctb], Carl F. Falk [ctb], Adam Meade [ctb], Lennart Schneider [ctb], David King [ctb], Chen-Wei Liu [ctb], Ogreden Oguzhan [ctb]" }, "mnormt": { "Package": "mnormt", "Version": "2.1.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Date": "2022-09-26", + "Title": "The Multivariate Normal and t Distributions, and Their Truncated Versions", + "Author": "Adelchi Azzalini [aut, cre], Alan Genz [aut] (most Fortran code), Alan Miller [ctb] (Fortran routine PHI), Michael J. Wichura [ctb] (Fortran routine PHINV), G. W. Hill [ctb] (Fortran routine STDINV), Yihong Ge [ctb] (Fortran routines BNVU and MVBVU).", + "Maintainer": "Adelchi Azzalini ", + "Depends": [ + "R (>= 2.2.0)" ], - "Hash": "c83992ef63553d1e4b97162a4a753470" + "Description": "Functions are provided for computing the density and the distribution function of d-dimensional normal and \"t\" random variables, possibly truncated (on one side or two sides), and for generating random vectors sampled from these distributions, except sampling from the truncated \"t\". Moments of arbitrary order of a multivariate truncated normal are computed, and converted to cumulants up to order 4. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d=3, d>3, if d denotes the dimensionality.", + "License": "GPL-2 | GPL-3", + "URL": "http://azzalini.stat.unipd.it/SW/Pkg-mnormt/", + "NeedsCompilation": "yes", + "Encoding": "UTF-8", + "Repository": "CRAN" }, "modules": { "Package": "modules", "Version": "0.13.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Self Contained Units of Source Code", + "Authors@R": "person(\"Sebastian\", \"Warnholz\", email = \"wahani@gmail.com\", role = c(\"aut\", \"cre\"))", + "Description": "Provides modules as an organizational unit for source code. Modules enforce to be more rigorous when defining dependencies and have a local search path. 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Provides a mapping between Munsell's original notation (e.g. \"5R 5/10\") and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.", + "Suggests": [ + "ggplot2", + "testthat" + ], + "Imports": [ "colorspace", "methods" ], - "Hash": "4fd8900853b746af55b81fda99da7695" + "License": "MIT + file LICENSE", + "URL": "https://cran.r-project.org/package=munsell, https://github.com/cwickham/munsell/", + "RoxygenNote": "7.3.1", + "Encoding": "UTF-8", + "BugReports": "https://github.com/cwickham/munsell/issues", + "NeedsCompilation": "no", + "Repository": "CRAN" }, "nlme": { "Package": "nlme", "Version": "3.1-166", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Date": "2024-08-13", + "Priority": "recommended", + "Title": "Linear and Nonlinear Mixed Effects Models", + "Authors@R": "c(person(\"José\", \"Pinheiro\", role = \"aut\", comment = \"S version\"), person(\"Douglas\", \"Bates\", role = \"aut\", comment = \"up to 2007\"), person(\"Saikat\", \"DebRoy\", role = \"ctb\", comment = \"up to 2002\"), person(\"Deepayan\", \"Sarkar\", role = \"ctb\", comment = \"up to 2005\"), person(\"EISPACK authors\", role = \"ctb\", comment = \"src/rs.f\"), person(\"Siem\", \"Heisterkamp\", role = \"ctb\", comment = \"Author fixed sigma\"), person(\"Bert\", \"Van Willigen\",role = \"ctb\", comment = \"Programmer fixed sigma\"), person(\"Johannes\", \"Ranke\", role = \"ctb\", comment = \"varConstProp()\"), person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cre\")))", + "Contact": "see 'MailingList'", + "Description": "Fit and compare Gaussian linear and nonlinear mixed-effects models.", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ "graphics", - "lattice", "stats", - "utils" + "utils", + "lattice" ], - "Hash": "ccbb8846be320b627e6aa2b4616a2ded" + "Suggests": [ + "MASS", + "SASmixed" + ], + "LazyData": "yes", + "Encoding": "UTF-8", + "License": "GPL (>= 2)", + "BugReports": "https://bugs.r-project.org", + "MailingList": "R-help@r-project.org", + "URL": "https://svn.r-project.org/R-packages/trunk/nlme/", + "NeedsCompilation": "yes", + "Author": "José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre]", + "Maintainer": "R Core Team ", + "Repository": "CRAN" }, "nloptr": { "Package": "nloptr", "Version": "2.1.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "27550641889a3abf3aec4d91186311ec" + "Type": "Package", + "Title": "R Interface to NLopt", + "Authors@R": "c(person(\"Jelmer\", \"Ypma\", role = \"aut\", email = \"uctpjyy@ucl.ac.uk\"), person(c(\"Steven\", \"G.\"), \"Johnson\", role = \"aut\", comment = \"author of the NLopt C library\"), person(\"Aymeric\", \"Stamm\", role = c(\"ctb\", \"cre\"), email = \"aymeric.stamm@cnrs.fr\", comment = c(ORCID = \"0000-0002-8725-3654\")), person(c(\"Hans\", \"W.\"), \"Borchers\", role = \"ctb\", email = \"hwborchers@googlemail.com\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", email = \"edd@debian.org\"), person(\"Brian\", \"Ripley\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Kurt\", \"Hornik\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Julien\", \"Chiquet\", role = \"ctb\"), person(\"Avraham\", \"Adler\", role = \"ctb\", email = \"Avraham.Adler@gmail.com\", comment = c(ORCID = \"0000-0002-3039-0703\")), person(\"Xiongtao\", \"Dai\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\", email = \"jeroen@berkeley.edu\"))", + "Description": "Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.", + "License": "LGPL (>= 3)", + "SystemRequirements": "cmake (>= 3.2.0) which is used only on Linux or macOS systems when no system build of nlopt (>= 2.7.0) can be found.", + "Biarch": "true", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Suggests": [ + "knitr", + "rmarkdown", + "covr", + "tinytest" + ], + "VignetteBuilder": "knitr", + "URL": "https://github.com/astamm/nloptr, https://astamm.github.io/nloptr/", + "BugReports": "https://github.com/astamm/nloptr/issues", + "NeedsCompilation": "yes", + "Author": "Jelmer Ypma [aut], Steven G. Johnson [aut] (author of the NLopt C library), Aymeric Stamm [ctb, cre] (), Hans W. Borchers [ctb], Dirk Eddelbuettel [ctb], Brian Ripley [ctb] (build process on multiple OS), Kurt Hornik [ctb] (build process on multiple OS), Julien Chiquet [ctb], Avraham Adler [ctb] (), Xiongtao Dai [ctb], Jeroen Ooms [ctb]", + "Maintainer": "Aymeric Stamm ", + "Repository": "CRAN" }, "nnet": { "Package": "nnet", "Version": "7.3-20", + "Version": "7.3-20", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2025-01-01", + "Depends": [ + "R (>= 3.0.0)", "stats", "utils" ], - "Hash": "c955edf99ff24a32e96bd0a22645af60" + "Suggests": [ + "MASS" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Brian.Ripley@R-project.org\"), 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", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "df58958f293b166e4ab885ebcad90e02" + "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": "0.6.7", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", + "Type": "Package", + "Title": "Manipulation of Microsoft Word and PowerPoint Documents", + "Authors@R": "c( person(\"David\", \"Gohel\", , \"david.gohel@ardata.fr\", role = c(\"aut\", \"cre\")), person(\"Stefan\", \"Moog\", , \"moogs@gmx.de\", role = \"aut\"), person(\"Mark\", \"Heckmann\", , \"heckmann.mark@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-0736-7417\")), person(\"ArData\", role = \"cph\"), person(\"Frank\", \"Hangler\", , \"frank@plotandscatter.com\", role = \"ctb\", comment = \"function body_replace_all_text\"), person(\"Liz\", \"Sander\", , \"lsander@civisanalytics.com\", role = \"ctb\", comment = \"several documentation fixes\"), person(\"Anton\", \"Victorson\", , \"anton@victorson.se\", role = \"ctb\", comment = \"fixes xml structures\"), person(\"Jon\", \"Calder\", , \"jonmcalder@gmail.com\", role = \"ctb\", comment = \"update vignettes\"), person(\"John\", \"Harrold\", , \"john.m.harrold@gmail.com\", role = \"ctb\", comment = \"function annotate_base\"), person(\"John\", \"Muschelli\", , \"muschellij2@gmail.com\", role = \"ctb\", comment = \"google doc compatibility\"), person(\"Bill\", \"Denney\", , \"wdenney@humanpredictions.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\", \"function as.matrix.rpptx\")), person(\"Nikolai\", \"Beck\", , \"beck.nikolai@gmail.com\", role = \"ctb\", comment = \"set speaker notes for .pptx documents\"), person(\"Greg\", \"Leleu\", , \"gregoire.leleu@gmail.com\", role = \"ctb\", comment = \"fields functionality in ppt\"), person(\"Majid\", \"Eismann\", role = \"ctb\"), person(\"Hongyuan\", \"Jia\", , \"hongyuanjia@cqust.edu.cn\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0075-8183\")) )", + "Description": "Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft PowerPoint' documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. The package does not require any installation of Microsoft products to be able to write Microsoft files.", + "License": "MIT + file LICENSE", + "URL": "https://ardata-fr.github.io/officeverse/, https://davidgohel.github.io/officer/", + "BugReports": "https://github.com/davidgohel/officer/issues", + "Imports": [ "cli", - "grDevices", "graphics", + "grDevices", "openssl", + "R6", "ragg", "stats", "utils", "uuid", - "xml2", - "zip" + "xml2 (>= 1.1.0)", + "zip (>= 2.1.0)" + ], + "Suggests": [ + "devEMF", + "doconv (>= 0.3.0)", + "ggplot2", + "knitr", + "magick", + "rmarkdown", + "rsvg", + "testthat" ], - "Hash": "d6c0a4e796301a5d252de42c92a9a8b9" + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "David Gohel [aut, cre], Stefan Moog [aut], Mark Heckmann [aut] (), ArData [cph], Frank Hangler [ctb] (function body_replace_all_text), Liz Sander [ctb] (several documentation fixes), Anton Victorson [ctb] (fixes xml structures), Jon Calder [ctb] (update vignettes), John Harrold [ctb] (function annotate_base), John Muschelli [ctb] (google doc compatibility), Bill Denney [ctb] (, function as.matrix.rpptx), Nikolai Beck [ctb] (set speaker notes for .pptx documents), Greg Leleu [ctb] (fields functionality in ppt), Majid Eismann [ctb], Hongyuan Jia [ctb] ()", + "Maintainer": "David Gohel ", + "Repository": "CRAN" }, "openssl": { "Package": "openssl", "Version": "2.3.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", + "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Oliver\", \"Keyes\", role = \"ctb\"))", + "Description": "Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/openssl", + "BugReports": "https://github.com/jeroen/openssl/issues", + "SystemRequirements": "OpenSSL >= 1.0.2", + "VignetteBuilder": "knitr", + "Imports": [ "askpass" ], - "Hash": "bc54d87ebf858b28de18df4bca6528d3" + "Suggests": [ + "curl", + "testthat (>= 2.1.0)", + "digest", + "knitr", + "rmarkdown", + "jsonlite", + "jose", + "sodium" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Oliver Keyes [ctb]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "parallelly": { "Package": "parallelly", "Version": "1.38.0", + "Version": "1.38.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Enhancing the 'parallel' Package", + "Imports": [ "parallel", "tools", "utils" ], - "Hash": "6e8b139c1904f5e9e14c69db64453bbe" + "Authors@R": "c( person(\"Henrik\", \"Bengtsson\", role = c(\"aut\", \"cre\", \"cph\"), email = \"henrikb@braju.com\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Mike\", \"Cheng\", role = c(\"ctb\"), email = \"mikefc@coolbutuseless.com\") )", + "Description": "Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.", + "License": "LGPL (>= 2.1)", + "LazyLoad": "TRUE", + "ByteCompile": "TRUE", + "URL": "https://parallelly.futureverse.org, https://github.com/HenrikBengtsson/parallelly", + "BugReports": "https://github.com/HenrikBengtsson/parallelly/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Henrik Bengtsson [aut, cre, cph] (), Mike Cheng [ctb]", + "Maintainer": "Henrik Bengtsson ", + "Repository": "CRAN" }, "pbapply": { "Package": "pbapply", "Version": "1.7-2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Type": "Package", + "Title": "Adding Progress Bar to '*apply' Functions", + "Date": "2023-06-27", + "Authors@R": "c(person(given = \"Peter\", family = \"Solymos\", comment = c(ORCID = \"0000-0001-7337-1740\"), role = c(\"aut\", \"cre\"), email = \"psolymos@gmail.com\"), person(given = \"Zygmunt\", family = \"Zawadzki\", role = \"aut\", email = \"zygmunt@zstat.pl\"), person(given = \"Henrik\", family = \"Bengtsson\", role = \"ctb\", email = \"henrikb@braju.com\"), person(\"R Core Team\", role = c(\"cph\", \"ctb\")))", + "Maintainer": "Peter Solymos ", + "Description": "A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where showing the progress is useful (e.g. bootstrap). The type and style of the progress bar (with percentages or remaining time) can be set through options. Supports several parallel processing backends including future.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ "parallel" ], - "Hash": "68a2d681e10cf72f0afa1d84d45380e5" + "Suggests": [ + "shiny", + "future", + "future.apply" + ], + "License": "GPL (>= 2)", + "URL": "https://github.com/psolymos/pbapply", + "BugReports": "https://github.com/psolymos/pbapply/issues", + "NeedsCompilation": "no", + "Author": "Peter Solymos [aut, cre] (), Zygmunt Zawadzki [aut], Henrik Bengtsson [ctb], R Core Team [cph, ctb]", + "Repository": "CRAN" }, "pbivnorm": { "Package": "pbivnorm", "Version": "0.6.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "643e16a7da6aac3e18cadc3e14abb94b" + "Title": "Vectorized Bivariate Normal CDF", + "Date": "2015-01-23", + "Author": "Fortran code by Alan Genz. R code by Brenton Kenkel, based on Adelchi Azzalini's 'mnormt' package.", + "Maintainer": "Brenton Kenkel ", + "Description": "Provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF.", + "License": "GPL (>= 2)", + "URL": "https://github.com/brentonk/pbivnorm", + "NeedsCompilation": "yes", + "Repository": "CRAN" }, "permute": { "Package": "permute", "Version": "0.9-7", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Functions for Generating Restricted Permutations of Data", + "Date": "2022-01-27", + "Authors@R": "c(person(given = \"Gavin L.\", family = \"Simpson\", email = \"ucfagls@gmail.com\", role = c(\"aut\", \"cph\", \"cre\"), comment = c(ORCID = \"0000-0002-9084-8413\")), person(given = \"R Core Team\", role = \"cph\"), person(given = \"Douglas M.\", family = \"Bates\", role = \"ctb\"), person(given = \"Jari\", family = \"Oksanen\", role = \"ctb\"))", + "Depends": [ + "R (>= 2.14.0)" + ], + "Imports": [ "stats" ], - "Hash": "abf0ca85c1c752e0d04f46334e635046" + "Suggests": [ + "vegan (>= 2.0-0)", + "testthat (>= 0.5)", + "parallel", + "knitr", + "rmarkdown", + "bookdown", + "sessioninfo" + ], + "Description": "A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 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'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/textshaping", + "BugReports": "https://github.com/r-lib/textshaping/issues", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ "lifecycle", - "systemfonts" + "systemfonts (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.1)", + "systemfonts (>= 1.0.0)" ], - "Hash": "5142f8bc78ed3d819d26461b641627ce" + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "SystemRequirements": "freetype2, harfbuzz, fribidi", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" }, "tibble": { "Package": "tibble", "Version": "3.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "fansi", - "lifecycle", + "Title": "Simple Data Frames", + "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Hadley\", family = \"Wickham\", role = \"aut\", email = \"hadley@rstudio.com\"), person(given = \"Romain\", family = \"Francois\", role = \"ctb\", email = \"romain@r-enthusiasts.com\"), person(given = \"Jennifer\", family = \"Bryan\", role = \"ctb\", email = \"jenny@rstudio.com\"), person(given = \"RStudio\", role = c(\"cph\", \"fnd\")))", + "Description": "Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional data frame.", + "License": "MIT + file LICENSE", + "URL": "https://tibble.tidyverse.org/, https://github.com/tidyverse/tibble", + "BugReports": "https://github.com/tidyverse/tibble/issues", + "Depends": [ + "R (>= 3.4.0)" + ], + "Imports": [ + "fansi (>= 0.4.0)", + "lifecycle (>= 1.0.0)", "magrittr", "methods", - "pillar", + "pillar (>= 1.8.1)", "pkgconfig", - "rlang", + "rlang (>= 1.0.2)", "utils", - "vctrs" + "vctrs (>= 0.4.2)" ], - "Hash": "a84e2cc86d07289b3b6f5069df7a004c" + "Suggests": [ + "bench", + "bit64", + "blob", + "brio", + "callr", + "cli", + "covr", + "crayon (>= 1.3.4)", + "DiagrammeR", + "dplyr", + "evaluate", + "formattable", + "ggplot2", + "here", + "hms", + "htmltools", + "knitr", + "lubridate", + "mockr", + "nycflights13", + "pkgbuild", + "pkgload", + "purrr", + "rmarkdown", + "stringi", + "testthat (>= 3.0.2)", + "tidyr", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "vignette-formats, as_tibble, add, invariants", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "true", + "Config/autostyle/rmd": "false", + "Config/Needs/website": "tidyverse/tidytemplate", + "NeedsCompilation": "yes", + "Author": "Kirill Müller [aut, cre] (), Hadley Wickham [aut], Romain Francois [ctb], Jennifer Bryan [ctb], RStudio [cph, fnd]", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" }, "tidyselect": { "Package": "tidyselect", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "rlang", - "vctrs", + "Title": "Select from a Set of Strings", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A backend for the selecting functions of the 'tidyverse'. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "utf8": { "Package": "utf8", "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). 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Simpson [aut], F. Guillaume Blanchet [aut], Roeland Kindt [aut], Pierre Legendre [aut], Peter R. Minchin [aut], R.B. O'Hara [aut], Peter Solymos [aut], M. Henry H. Stevens [aut], Eduard Szoecs [aut], Helene Wagner [aut], Matt Barbour [aut], Michael Bedward [aut], Ben Bolker [aut], Daniel Borcard [aut], Gustavo Carvalho [aut], Michael Chirico [aut], Miquel De Caceres [aut], Sebastien Durand [aut], Heloisa Beatriz Antoniazi Evangelista [aut], Rich FitzJohn [aut], Michael Friendly [aut], Brendan Furneaux [aut], Geoffrey Hannigan [aut], Mark O. Hill [aut], Leo Lahti [aut], Dan McGlinn [aut], Marie-Helene Ouellette [aut], Eduardo Ribeiro Cunha [aut], Tyler Smith [aut], Adrian Stier [aut], Cajo J.F. Ter Braak [aut], James Weedon [aut]", + "Maintainer": "Jari Oksanen ", + "Repository": "CRAN" }, "viridis": { "Package": "viridis", "Version": "0.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggplot2", - "gridExtra", - "viridisLite" - ], - "Hash": "acd96d9fa70adeea4a5a1150609b9745" + "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", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "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 is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" ], - "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "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" }, "waldo": { "Package": "waldo", "Version": "0.6.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Find Differences Between R Objects", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Compare complex R objects and reveal the key differences. Designed particularly for use in testing packages where being able to quickly isolate key differences makes understanding test failures much easier.", + "License": "MIT + file LICENSE", + "URL": "https://waldo.r-lib.org, https://github.com/r-lib/waldo", + "BugReports": "https://github.com/r-lib/waldo/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Imports": [ "cli", - "diffobj", + "diffobj (>= 0.3.4)", "glue", "methods", - "rlang" + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "bit64", + "R6", + "S7", + "testthat (>= 3.0.0)", + "withr", + "xml2" ], - "Hash": "52f574062a7b66e56926988c3fbdb3b7" + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "withr": { "Package": "withr", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics" + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" ], - "Hash": "cc2d62c76458d425210d1eb1478b30b4" + "Imports": [ + "graphics", + "grDevices" + ], + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" }, "xfun": { "Package": "xfun", "Version": "0.49", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ "grDevices", "stats", "tools" ], - "Hash": "8687398773806cfff9401a2feca96298" + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown", + "commonmark", + "knitr (>= 1.47)", + "remotes", + "pak", + "rhub", + "renv", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs", + "rmarkdown" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "xml2": { "Package": "xml2", "Version": "1.3.6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Parse XML", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Foundation\", role = \"ctb\", comment = \"Copy of R-project homepage cached as example\") )", + "Description": "Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org/, https://github.com/r-lib/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ "cli", "methods", - "rlang" + "rlang (>= 1.1.0)" ], - "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Jim Hester [aut], Jeroen Ooms [aut], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "yaml": { "Package": "yaml", "Version": "2.3.10", "Source": "Repository", - "Repository": "CRAN", - "Hash": "51dab85c6c98e50a18d7551e9d49f76c" + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" }, "zip": { "Package": "zip", "Version": "2.3.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" + "Title": "Cross-Platform 'zip' Compression", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", + "BugReports": "https://github.com/r-lib/zip/issues", + "Suggests": [ + "covr", + "processx", + "R6", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" } } } diff --git a/renv/activate.R b/renv/activate.R index 0eb51088..c9f59425 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.11" + version <- "1.1.2" attr(version, "sha") <- NULL # the project directory @@ -42,7 +42,7 @@ local({ return(FALSE) # next, check environment variables - # TODO: prefer using the configuration one in the future + # prefer using the configuration one in the future envvars <- c( "RENV_CONFIG_AUTOLOADER_ENABLED", "RENV_AUTOLOADER_ENABLED", @@ -135,12 +135,12 @@ local({ # R help links pattern <- "`\\?(renv::(?:[^`])+)`" - replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`" + replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`" text <- gsub(pattern, replacement, text, perl = TRUE) # runnable code pattern <- "`(renv::(?:[^`])+)`" - replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`" + replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`" text <- gsub(pattern, replacement, text, perl = TRUE) # return ansified text @@ -209,10 +209,6 @@ local({ } - startswith <- function(string, prefix) { - substring(string, 1, nchar(prefix)) == prefix - } - bootstrap <- function(version, library) { friendly <- renv_bootstrap_version_friendly(version) @@ -563,6 +559,9 @@ local({ # prepare download options token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + if (nzchar(Sys.which("curl")) && nzchar(token)) { fmt <- "--location --fail --header \"Authorization: token %s\"" extra <- sprintf(fmt, token) @@ -951,8 +950,14 @@ local({ } renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] - is.character(expected) && startswith(expected, version) + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + } renv_bootstrap_validate_version_release <- function(version, description) { @@ -1132,10 +1137,10 @@ local({ renv_bootstrap_exec <- function(project, libpath, version) { if (!renv_bootstrap_load(project, libpath, version)) - renv_bootstrap_run(version, libpath) + renv_bootstrap_run(project, libpath, version) } - renv_bootstrap_run <- function(version, libpath) { + renv_bootstrap_run <- function(project, libpath, version) { # perform bootstrap bootstrap(version, libpath) @@ -1146,7 +1151,7 @@ local({ # try again to load if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - return(renv::load(project = getwd())) + return(renv::load(project = project)) } # failed to download or load renv; warn the user @@ -1192,98 +1197,101 @@ local({ jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } - renv_json_read_default <- function(file = NULL, text = NULL) { - - # find strings in the JSON - text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' - locs <- gregexpr(pattern, text, perl = TRUE)[[1]] - - # if any are found, replace them with placeholders - replaced <- text - strings <- character() - replacements <- character() - - if (!identical(c(locs), -1L)) { - - # get the string values - starts <- locs - ends <- locs + attr(locs, "match.length") - 1L - strings <- substring(text, starts, ends) - - # only keep those requiring escaping - strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) - - # compute replacements - replacements <- sprintf('"\032%i\032"', seq_along(strings)) - - # replace the strings - mapply(function(string, replacement) { - replaced <<- sub(string, replacement, replaced, fixed = TRUE) - }, strings, replacements) + renv_json_read_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t"), + list("}", "\t\n\t)\t\n\t"), + + # arrays + list("[", "\t\n\tarray(\t\n\t"), + list("]", "\n\t\n)\n\t\n"), + + # maps + list(":", "\t\n\t=\t\n\t") + + ) + + } + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result } - - # transform the JSON into something the R parser understands - transformed <- replaced - transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) - transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) - transformed <- gsub("[]}]", ")", transformed, perl = TRUE) - transformed <- gsub(":", "=", transformed, fixed = TRUE) - text <- paste(transformed, collapse = "\n") - - # parse it - json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] - - # construct map between source strings, replaced strings - map <- as.character(parse(text = strings)) - names(map) <- as.character(parse(text = replacements)) - - # convert to list - map <- as.list(map) - - # remap strings in object - remapped <- renv_json_read_remap(json, map) - - # evaluate - eval(remapped, envir = baseenv()) - + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + } - renv_json_read_remap <- function(json, map) { - - # fix names - if (!is.null(names(json))) { - lhs <- match(names(json), names(map), nomatch = 0L) - rhs <- match(names(map), names(json), nomatch = 0L) - names(json)[rhs] <- map[lhs] + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + } - - # fix values - if (is.character(json)) - return(map[[json]] %||% json) - - # handle true, false, null - if (is.name(json)) { - text <- as.character(json) - if (text == "true") - return(TRUE) - else if (text == "false") - return(FALSE) - else if (text == "null") - return(NULL) + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } - # recurse - if (is.recursive(json)) { - for (i in seq_along(json)) { - json[i] <- list(renv_json_read_remap(json[[i]], map)) - } - } + renv_json_read_default <- function(file = NULL, text = NULL) { - json + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary + renv_json_read_remap(result, patterns) + } + # load the renv profile, if any renv_bootstrap_profile_load(project) diff --git a/tests/testthat/test-raterAgreement.R b/tests/testthat/test-raterAgreement.R index ee4c29bc..b1ebcb50 100644 --- a/tests/testthat/test-raterAgreement.R +++ b/tests/testthat/test-raterAgreement.R @@ -4,260 +4,50 @@ # Set options options <- analysisOptions("raterAgreement") -options$variables <- c("V1", "facFifty", "contNormal") -options$krippendorffsAlphaDataStructure <- "ratersInColumns" +options$variables <- paste0("V", 1:5) +options$dataStructure <- "ratersInColumns" +options$setSeed <- TRUE +options$krippendorffsAlphaBootstrapSamplesForCI <- 200 set.seed(1) -results <- runAnalysis("raterAgreement", "test.csv", options) +results <- runAnalysis("raterAgreement", testthat::test_path("binaryTestDt.csv"), options, makeTests = F) -test_that("Cohen's Unweighted kappa table results match", { +test_that("Cohen's kappa table results match", { table <- results[["results"]][["cohensKappa"]][["data"]] jaspTools::expect_equal_tables(table, - list("", "", "", 0.164983164983165, "Average kappa", 0.396961294518455, - 0.592937695380535, 0.049994898479747, 0.494949494949495, "V1 - facFifty", - 0, 0, 0, 0, "V1 - contNormal", 0, 0, 0, 0, "facFifty - contNormal" - )) + list("", "", "", 0.114984433765595, "Average kappa", 0.0924679737811612, + 0.357606541867125, 0.0676386326935962, 0.225037257824143, "V1 - V2", + -0.00101486089827027, 0.203411665159256, 0.052150582273454, + 0.101198402130493, "V1 - V3", -0.0200019787491091, 0.151023173354119, + 0.0436296670378263, 0.0655105973025049, "V2 - V3", 0.0576342926736923, + 0.309887992795108, 0.0643516161804914, 0.1837611427344, "V1 - V4", + -0.0882775571852617, 0.1399093155876, 0.0582120065911339, 0.025815879201169, + "V2 - V4", -0.032509269670062, 0.257559504097391, 0.0739984959048937, + 0.112525117213664, "V3 - V4", -0.0240223485028135, 0.221356704625165, + 0.0625978474766621, 0.0986671780611757, "V1 - V5", 0.0762065929175585, + 0.337621571800286, 0.0666887200338209, 0.206914082358922, "V2 - V5", + -0.0317077880237179, 0.0969460355453044, 0.0328204560348627, + 0.0326191237607932, "V3 - V5", 0.00907597751537415, 0.186515136621999, + 0.0452659233807975, 0.0977955570686868, "V4 - V5")) }) test_that("Fleiss' kappa table results match", { table <- results[["results"]][["fleissKappa"]][["data"]] jaspTools::expect_equal_tables(table, - list(0.151819081246537, 0.170328569760174, 0.00472189506022491, 0.161073825503356, - "Overall", -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, -3.023963827, -0.116158573407617, 0.110158573407617, - 0.0577350269189626, -0.003, -2.336742886, -0.116158573407617, - 0.110158573407617, 0.0577350269189626, -0.003, -2.15616121, - -0.116158573407617, 0.110158573407617, 0.0577350269189626, -0.003, - -1.953344972, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, -1.649937891, -0.116158573407617, 0.110158573407617, - 0.0577350269189626, -0.003, -1.627592736, -0.116158573407617, - 0.110158573407617, 0.0577350269189626, -0.003, -1.625143884, - 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-0.003, 79, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 80, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 81, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 82, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 83, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 84, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 85, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 86, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 87, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 88, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 89, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 90, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 91, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 92, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 93, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 94, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 95, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 96, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 97, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 98, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 99, -0.116158573407617, 0.110158573407617, 0.0577350269189626, - -0.003, 100)) + list(0.0321990251552643, 0.119851279212922, 0.0223606797749979, 0.0760251521840934, + "Overall", 0.0321890403455753, 0.119810959654425, 0.0223529411764706, + 0.076, 0, 0.0321890403455753, 0.119810959654425, 0.0223529411764706, + 0.076, 1)) }) - test_that("Krippendorff's alpha table results match", { table <- results[["results"]][["krippendorffsAlpha"]][["data"]] jaspTools::expect_equal_tables(table, - list(0.128688123975843, 0.192400836732261, 0.0164047879778507, 0.162472035794184, + list(0.0271069334114449, 0.124379082494376, 0.0257751838160253, 0.0762561458960466, "Nominal")) }) + ####Cohen's weighted kappa and Fleiss' kappa and Krippendorf's alpha with different CI range(99%)#### # Set options @@ -266,10 +56,10 @@ options$variables <- c("facGender", "facExperim", "debBinMiss20") options$ciLevel <- 0.99 options$cohensKappaType <- "weighted" options$krippendorffsAlphaBootstrapSamplesForCI <- 200 -options$krippendorffsAlphaDataStructure <- "ratersInColumns" +options$dataStructure <- "ratersInColumns" options$setSeed <- TRUE set.seed(1) -results <- runAnalysis("raterAgreement", "test.csv", options) +results <- runAnalysis("raterAgreement", "test.csv", options, makeTests = F) test_that("Cohen's Weighted kappa table results match", { @@ -287,19 +77,19 @@ test_that("Fleiss' kappa table results match", { table <- results[["results"]][["fleissKappa"]][["data"]] jaspTools::expect_equal_tables(table, list(-0.276327852798572, -0.127177258822542, 0.0289519561273983, -0.201752555810557, - "Overall", -0.360269066588632, -0.0277309334113677, 0.0645497224367903, - -0.194, "f", -0.372269066588632, -0.0397309334113677, 0.0645497224367903, - -0.206, "m", -0.384269066588632, -0.0517309334113677, 0.0645497224367903, - -0.218, "control", -0.348269066588632, -0.0157309334113677, - 0.0645497224367903, -0.182, "experimental", -0.337269066588632, - -0.00473093341136771, 0.0645497224367903, -0.171, 0, -0.397269066588632, - -0.0647309334113677, 0.0645497224367903, -0.231, 1)) + "Overall", -0.360528094860817, -0.0274719051391827, 0.0646502835538752, + -0.194, "f", -0.37243820115239, -0.0395617988476095, 0.0646153846153846, + -0.206, "m", -0.384084231935422, -0.0519157680645785, 0.0644779650990831, + -0.218, "control", -0.348005996191891, -0.0159940038081091, + 0.0644475920679887, -0.182, "experimental", -0.33723781932418, + -0.00476218067581949, 0.0645375914836993, -0.171, 0, -0.397234597910737, + -0.0647654020892627, 0.0645363408521303, -0.231, 1)) }) test_that("Krippendorff's alpha table results match", { table <- results[["results"]][["krippendorffsAlpha"]][["data"]] jaspTools::expect_equal_tables(table, - list(-0.212534930259255, -0.197193484221555, 0.00279613421372955, -0.199079048349962, + list(-0.209716461340596, -0.197507041090973, 0.00269939839460176, -0.199079048349962, "Nominal")) }) @@ -308,10 +98,12 @@ test_that("Krippendorff's alpha table results match", { test_that("Fleiss' kappa table results match", { options <- analysisOptions("raterAgreement") options$variables <- c("V1", "V2", "V3", "V4", "V5", "V6") + options$dataStructure <- "ratersInColumns" options$cohensKappa <- FALSE + options$krippendorffsAlpha <- FALSE options$ci <- FALSE set.seed(1) - results <- runAnalysis("raterAgreement", "Fleiss1971.csv", options) + results <- runAnalysis("raterAgreement", testthat::test_path("Fleiss1971.csv"), options) table <- results[["results"]][["fleissKappa"]][["data"]] jaspTools::expect_equal_tables(table, list(0.430244520060141, "Overall", 0.245, 1, 0.245, 2, 0.52, 3, 0.471, @@ -326,9 +118,10 @@ test_that("Cohen's kappa table results match with linear weighting", { options$krippendorffsAlpha <- FALSE options$ci <- FALSE options$cohensKappaType <- "weighted" + options$dataStructure <- "ratersInColumns" options$weightType <- "linear" set.seed(1) - results <- runAnalysis("raterAgreement", "Fleiss1971.csv", options) + results <- runAnalysis("raterAgreement", testthat::test_path("Fleiss1971.csv"), options) table <- results[["results"]][["cohensKappa"]][["data"]] jaspTools::expect_equal_tables(table, list(0.633093525179856, "Average kappa", 0.633093525179856, "V1 - V2"