From 792e23c27f35266a8ed3d39739b4f397a234a4d0 Mon Sep 17 00:00:00 2001 From: jvli4n Date: Tue, 12 Nov 2024 17:38:39 +0100 Subject: [PATCH 1/2] Adding set seed to confidence interval Adding a set seed option to the confidence interval analysis in the Learn Stats module. Additionally, adding a dependency for the tree plot table, so it disappears when the check box is no longer selected. --- .Rbuildignore | 2 + .Rprofile | 1 + R/LSTconfidenceIntervals.R | 225 ++--- inst/qml/LSTconfidenceIntervals.qml | 13 +- renv/.gitignore | 7 + renv/activate.R | 1305 +++++++++++++++++++++++++++ 6 files changed, 1435 insertions(+), 118 deletions(-) create mode 100644 .Rprofile create mode 100644 renv/.gitignore create mode 100644 renv/activate.R diff --git a/.Rbuildignore b/.Rbuildignore index 112ad26..7d392e5 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,5 @@ +^renv$ +^renv\.lock$ ^.*\.Rproj$ ^\.Rproj\.user$ ^\.travis\.yml$ diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000..81b960f --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/R/LSTconfidenceIntervals.R b/R/LSTconfidenceIntervals.R index c181528..3eec5c8 100644 --- a/R/LSTconfidenceIntervals.R +++ b/R/LSTconfidenceIntervals.R @@ -16,51 +16,52 @@ # LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { - + confidenceContainer <- .getConfidenceContainer(jaspResults) - + .simulateDatasets(confidenceContainer, options) - + .computeConfidenceIntervals(confidenceContainer, options) - + .makeSummaryTable(confidenceContainer, options) - + .plotTreePlot(confidenceContainer, options) - + .makeTreeTable(confidenceContainer, options) - + .plotDatasets(confidenceContainer, options) - + .plotConvergencePlot(confidenceContainer, options) - + return() } .getConfidenceContainer <- function(jaspResults) { - confidenceContainer <- jaspResults[["confidenceContainer"]] %setOrRetrieve% createJaspContainer(dependencies = c("mu", "sigma", "n", "confidenceIntervalInterval", "nReps", "treePlot")) + confidenceContainer <- jaspResults[["confidenceContainer"]] %setOrRetrieve% createJaspContainer(dependencies = c("mu", "sigma", "n", "confidenceIntervalInterval", "nReps", "treePlot", "seed")) return(confidenceContainer) } .simulateDatasets <- function(jaspContainer, options) { if (!is.null(jaspContainer[["simulatedDatasets"]])) return() - + + jaspBase::.setSeedJASP(options) listWithData <- lapply(seq_len(options[["nReps"]]), function(x) rnorm(options$n, options$mu, options$sigma)) - + jaspContainer[["simulatedDatasets"]] <- createJaspState(object = listWithData) - + return() } .computeConfidenceIntervals <- function(jaspContainer, options) { if (!is.null(jaspContainer[["computedConfidenceIntervals"]])) return() - + listWithData <- jaspContainer[["simulatedDatasets"]][["object"]] - - meanCI <- t(sapply(listWithData, function(x) c(mean(x), + + meanCI <- t(sapply(listWithData, function(x) c(mean(x), t.test(x, conf.level = options$confidenceIntervalInterval)$conf.int[1:2]))) meanCI <- as.data.frame(meanCI) colnames(meanCI) <- c("mean", "lower", "upper") @@ -69,27 +70,27 @@ LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { meanCI[["colorCI"]] <- ifelse(meanCI[["successfulCI"]], "A", "B") meanCI[["sd"]] <- sapply(listWithData, sd) meanCI[["n"]] <- sapply(listWithData, length) - - + + jaspContainer[["computedConfidenceIntervals"]] <- createJaspState(object = meanCI) - + return() } .makeSummaryTable <- function(jaspContainer, options) { if (!is.null(jaspContainer[["resultTable"]])) return() - + resultTable <- createJaspTable(title = "Results Table") jaspContainer[["resultTable"]] <- resultTable - + resultTable$addColumnInfo(name = "Repetitions", type = "integer") resultTable$addColumnInfo(name = "mu", type = "number", title="μ") resultTable$addColumnInfo(name = "sigma", title="σ", type = "number") resultTable$addColumnInfo(name = "n", type = "integer") resultTable$addColumnInfo(name = "coverage", type = "integer",title=gettext("Coverage")) resultTable$addColumnInfo(name = "coveragePercentage", type = "number", format = "pc", title=gettextf("Coverage %%")) - + meanCI <- jaspContainer[["computedConfidenceIntervals"]][["object"]] tableDat <- data.frame(mu = options$mu, sigma = options$sigma, @@ -97,92 +98,92 @@ LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { n = options$n, coverage = sum(meanCI[["successfulCI"]]), coveragePercentage = mean(meanCI[["successfulCI"]])) - + resultTable$setData(tableDat) - + return() } .makeTreeTable <- function(jaspContainer, options) { if (!is.null(jaspContainer[["treeTable"]]) || !options$tableTreePlot) return() - - treeTable <- createJaspTable(title = "Confidence Interval Table") + + treeTable <- createJaspTable(title = "Confidence Interval Table", dependencies = "tableTreePlot") jaspContainer[["containerTreePlot"]][["treeTable"]] <- treeTable - + treeTable$addColumnInfo(name = "Repetition", type = "integer") treeTable$addColumnInfo(name = "mean", type = "number", title=gettext("Mean")) treeTable$addColumnInfo(name = "n", title=gettext("Estimate"), type = "integer") treeTable$addColumnInfo(name = "sd", type = "number") - + thisOverTitle <- gettextf("%s%% CI for Mean Difference", options$confidenceIntervalInterval * 100) treeTable$addColumnInfo(name="lower", type = "number", title = gettext("Lower"), overtitle = thisOverTitle) treeTable$addColumnInfo(name="upper", type = "number", title = gettext("Upper"), overtitle = thisOverTitle) treeTable$addColumnInfo(name = "successfulCI", type = "string", title=gettextf("CI contains %s?", "μ")) - + meanCI <- jaspContainer[["computedConfidenceIntervals"]][["object"]] meanCI[["successfulCI"]] <- ifelse(meanCI[["successfulCI"]], "Yes", "No") meanCI <- meanCI[1:options$dataPlotShowN,] # Show data only for CIs that are also plotted - + treeTable$showSpecifiedColumnsOnly <- TRUE treeTable$setData(meanCI) - + return() } .plotTreePlot <- function(jaspContainer, options) { if (!is.null(jaspContainer[["containerTreePlot"]]) || !options$treePlot) return() - + treePlotContainer <- createJaspContainer(title = gettext("Tree Plot")) jaspContainer[["containerTreePlot"]] <- treePlotContainer treePlotContainer$dependOn(c("treePlot", "treePlotAdditionalInfo", "fixAxisTreePlot", "fixAxisLower", "fixAxisUpper", "dataPlotShowN")) - treePlotContainer[["treePlot"]] <- createJaspPlot(title = "", width = 480, + treePlotContainer[["treePlot"]] <- createJaspPlot(title = "", width = 480, height = 320 * min((options$nReps %/% 50 + 1), 5)) - - + + if (options$fixAxisLower >= options$fixAxisUpper) { treePlotContainer$setError(gettext("Make sure to specify a lower bound that is lower than the upper bound for the x-axis.")) return() } - + meanCI <- jaspContainer[["computedConfidenceIntervals"]][["object"]] meanCI$Repetition <- rev(meanCI$Repetition) meanCItrimmed <- meanCI[seq_len(options$dataPlotShowN), ] - + myTicks <- jaspGraphs::getPrettyAxisBreaks(1:options$nReps) myTicks[1] <- 1 - p <- ggplot2::ggplot(meanCItrimmed, + p <- ggplot2::ggplot(meanCItrimmed, ggplot2::aes(x = mean, y = Repetition)) + ggplot2::geom_point(ggplot2::aes(color = colorCI), size = 6, shape = 18) + ggplot2::geom_errorbarh(ggplot2::aes(xmin = lower, - xmax = upper, + xmax = upper, color = colorCI)) + ggplot2::scale_color_manual(values = c("A" = "black", "B" = "red")) + ggplot2::geom_vline(data = data.frame(options$mu), ggplot2::aes(xintercept = options$mu), linetype = "dashed") + - ggplot2::scale_y_continuous(limits = c(0, options$nReps+1), + ggplot2::scale_y_continuous(limits = c(0, options$nReps+1), breaks = jaspGraphs::getPrettyAxisBreaks(1:options$nReps), labels = rev(myTicks)) + - ggplot2::xlab(gettextf("Observed mean and %s%% CI", options$confidenceIntervalInterval * 100)) + ggplot2::xlab(gettextf("Observed mean and %s%% CI", options$confidenceIntervalInterval * 100)) if (options$fixAxisTreePlot) { p <- p + ggplot2::scale_x_continuous(limits = c(options$fixAxisLower, options$fixAxisUpper)) } - + p <- p + jaspGraphs::geom_rangeframe() + # add lines on the x-axis and y-axis jaspGraphs::themeJaspRaw() # add the JASP theme - + if(isTryError(p)) treePlotContainer[["treePlot"]]$setError(.extractErrorMessage(p)) else treePlotContainer[["treePlot"]]$plotObject <- p - + return() } @@ -190,12 +191,12 @@ LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { .plotDatasets <- function(jaspContainer, options) { if (!is.null(jaspContainer[["containerRainCloudPlots"]]) || !options$dataPlot) return() - - jaspContainer[["containerRainCloudPlots"]] <- createJaspContainer(gettext("Data plots"), + + jaspContainer[["containerRainCloudPlots"]] <- createJaspContainer(gettext("Data plots"), dependencies = c("dataPlotShowN", "dataPlot", "ciSampleShowType", "ciFirstOrLastSamples", "ciFromSample", "ciToSample")) - + rainData <- jaspContainer[["simulatedDatasets"]][["object"]] maxSamples <- length(rainData) fromTo <- .getFromToSampleShow(options[["ciSampleShowType"]], maxSamples, singleValue = options[["ciFirstOrLastSamples"]], @@ -205,12 +206,12 @@ LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { visibleRainData <- rainData[from:to] rows <- .getPlotMatDetails(length(visibleRainData))$rows plotHeight <- rows * 250 - matrixPlot <- createJaspPlot(title = gettext("Samples"), width = 1200, + matrixPlot <- createJaspPlot(title = gettext("Samples"), width = 1200, height = plotHeight) - + plotList <- list() for (i in seq_along(visibleRainData)){ - thisRainData <- data.frame(y = visibleRainData[[i]], + thisRainData <- data.frame(y = visibleRainData[[i]], group = rep(1, options$n)) repetitionNumber <- from + i - 1 plotList[[i]] <- try(jaspTTests::.descriptivesPlotsRainCloudFill(thisRainData, "y", "group", @@ -231,27 +232,27 @@ LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { .plotConvergencePlot <- function(jaspContainer, options) { if (!is.null(jaspContainer[["containerConvergencePlot"]]) || !options$convergencePlot) return() - + containerConvergencePlot <- createJaspContainer(title = gettext("Convergence Plot")) jaspContainer[["containerConvergencePlot"]] <- containerConvergencePlot containerConvergencePlot$dependOn(c("convergencePlot", "convergenceZoomIn", "convergenceZoomMargin")) - containerConvergencePlot[["convergencePlot"]] <- createJaspPlot(title = "", width = 480, height = 320) - + containerConvergencePlot[["convergencePlot"]] <- createJaspPlot(title = "", width = 480, height = 320) + meanCI <- jaspContainer[["computedConfidenceIntervals"]][["object"]] - + myTicks <- jaspGraphs::getPrettyAxisBreaks(1:options$nReps) myTicks[1] <- 1 if (options$convergenceZoomIn) { myYlim <- c(max(0, options$confidenceIntervalInterval - options$convergenceZoomMargin), - min(1, options$confidenceIntervalInterval + options$convergenceZoomMargin)) + min(1, options$confidenceIntervalInterval + options$convergenceZoomMargin)) } else { myYlim <- c(0, 1) } - + cumSuccessProportion <- cumsum(meanCI$successfulCI)/1:options$nReps simulMatrix <- matrix(0, nrow = 1000, ncol = options$nReps) - + for (i in 1:options$nReps){ simulMatrix[ , i] <- rbeta(1e3, cumSuccessProportion[i]*i+1, i-cumSuccessProportion[i]*i+1) } @@ -262,111 +263,111 @@ LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { p <- ggplot2::ggplot(data= NULL) + ggplot2::xlab(gettext("Number of Replications")) + ggplot2::ylab(gettext("p(Coverage)")) + - ggplot2::coord_cartesian(xlim = c(0, options$nReps), ylim = myYlim) + + ggplot2::coord_cartesian(xlim = c(0, options$nReps), ylim = myYlim) + ggplot2::geom_polygon(ggplot2::aes(x = c(1:options$nReps,options$nReps:1), y = c(yUpper, rev(yLower))), fill = "lightsteelblue") + # CI - ggplot2::geom_line(color = "darkred", ggplot2::aes(x = 1:options$nReps, + ggplot2::geom_line(color = "darkred", ggplot2::aes(x = 1:options$nReps, y = rep(options$confidenceIntervalInterval, options$nReps))) + # confidence level - ggplot2::geom_line(data= NULL, ggplot2::aes(x = 1:options$nReps, + ggplot2::geom_line(data= NULL, ggplot2::aes(x = 1:options$nReps, y = cumsum(meanCI$successfulCI)/1:options$nReps)) + # observed coverage - ggplot2::scale_x_continuous(breaks = jaspGraphs::getPrettyAxisBreaks(1:options$nReps), labels = myTicks) + ggplot2::scale_x_continuous(breaks = jaspGraphs::getPrettyAxisBreaks(1:options$nReps), labels = myTicks) p <- p + jaspGraphs::geom_rangeframe() + # add lines on the x-axis and y-axis jaspGraphs::themeJaspRaw() # add the JASP theme - + if(isTryError(p)) containerConvergencePlot[["convergencePlot"]]$setError(.extractErrorMessage(p)) else containerConvergencePlot[["convergencePlot"]]$plotObject <- p - + return() } .plotTreePlotOLD <- function(jaspContainer, options) { if (!is.null(jaspContainer[["containerTreePlot"]]) || !options$treePlot) return() - + treePlotContainer <- createJaspContainer(title = gettext("Tree Plot")) jaspContainer[["containerTreePlot"]] <- treePlotContainer treePlotContainer$dependOn(c("treePlot", "treePlotAdditionalInfo", "fixAxisTreePlot", "fixAxisLower", "fixAxisUpper")) - treePlotContainer[["treePlot"]] <- createJaspPlot(title = "", width = 480, height = 320) - + treePlotContainer[["treePlot"]] <- createJaspPlot(title = "", width = 480, height = 320) + if (options$fixAxisLower >= options$fixAxisUpper) { treePlotContainer$setError(gettext("Make sure to specify a lower bound that is lower than the upper bound for the x-axis.")) return() } - - + + meanCI <- jaspContainer[["computedConfidenceIntervals"]][["object"]] - - p <- ggplot2::ggplot(meanCI, + + p <- ggplot2::ggplot(meanCI, ggplot2::aes(x = mean, y = Repetition)) + ggplot2::geom_point(ggplot2::aes(color = colorCI), size = 6, shape = 18) + ggplot2::geom_errorbarh(ggplot2::aes(xmin = lower, - xmax = upper, + xmax = upper, color = colorCI)) + ggplot2::scale_color_manual(values = c("A" = "black", "B" = "red")) + ggplot2::geom_vline(data = data.frame(options$mu), ggplot2::aes(xintercept = options$mu), linetype = "dashed") + ggplot2::scale_y_continuous(breaks= jaspGraphs::getPrettyAxisBreaks(1:options$nReps)) + - ggplot2::xlab(gettextf("Observed mean and %s%% CI", options$confidenceIntervalInterval * 100)) - + ggplot2::xlab(gettextf("Observed mean and %s%% CI", options$confidenceIntervalInterval * 100)) + if (options$fixAxisTreePlot) { p <- p + ggplot2::scale_x_continuous(limits = c(options$fixAxisLower, options$fixAxisUpper)) } - + p <- p + jaspGraphs::geom_rangeframe() + # add lines on the x-axis and y-axis jaspGraphs::themeJaspRaw() # add the JASP theme - + if(isTryError(p)) treePlotContainer[["treePlot"]]$setError(.extractErrorMessage(p)) else treePlotContainer[["treePlot"]]$plotObject <- p - + return() } .plotDatasetsOLD <- function(jaspContainer, options) { if (!is.null(jaspContainer[["containerRainCloudPlots"]]) || !options$dataPlot) return() - + rainCloudPlotsContainer <- createJaspContainer(title = gettext("Data plots")) # rainCloudPlotsContainer$position <- 3 jaspContainer[["containerRainCloudPlots"]] <- rainCloudPlotsContainer rainCloudPlotsContainer$dependOn(c("dataPlotShowN", "dataPlot")) - - rainData <- data.frame(y = unlist(jaspContainer[["simulatedDatasets"]][["object"]]), + + rainData <- data.frame(y = unlist(jaspContainer[["simulatedDatasets"]][["object"]]), group = rep(1:options$nReps, each = options$n)) - + singlePlot <- createJaspPlot(title = "", width = 480, height = 320) rainCloudPlotsContainer[["rainCloudPlotAll"]] <- singlePlot - p <- try(jaspTTests::.descriptivesPlotsRainCloudFill(rainData, "y", "group", - yLabel = gettext("Dependent"), - xLabel = gettext("Rep"), + p <- try(jaspTTests::.descriptivesPlotsRainCloudFill(rainData, "y", "group", + yLabel = gettext("Dependent"), + xLabel = gettext("Rep"), testValue = options$mu, addLines = FALSE, horiz = FALSE)) if(isTryError(p)) singlePlot$setError(.extractErrorMessage(p)) else singlePlot$plotObject <- p - + for (i in seq_len(options$dataPlotShowN)) { - + thisRainData <- data.frame( - y = unlist(jaspContainer[["simulatedDatasets"]][["object"]][[I]]), + y = unlist(jaspContainer[["simulatedDatasets"]][["object"]][[I]]), group = rep(1, options$n) ) - + singlePlot <- createJaspPlot(title = "", width = 480, height = 320) rainCloudPlotsContainer[[paste0("rainCloudPlotSingle", i)]] <- singlePlot - p <- try(jaspTTests::.descriptivesPlotsRainCloudFill(thisRainData, "y", "group", - yLabel = "Dependent", + p <- try(jaspTTests::.descriptivesPlotsRainCloudFill(thisRainData, "y", "group", + yLabel = "Dependent", xLabel = "Rep", testValue = options$mu, addLines = FALSE, horiz = FALSE)) @@ -374,66 +375,66 @@ LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { singlePlot$setError(.extractErrorMessage(p)) else singlePlot$plotObject <- p - + } - + return() } .plotDatasetsOLD2 <- function(jaspContainer, options) { if (!is.null(jaspContainer[["containerRainCloudPlots"]]) || !options$dataPlot) return() - - jaspContainer[["containerRainCloudPlots"]] <- createJaspContainer(gettext("Data plots"), + + jaspContainer[["containerRainCloudPlots"]] <- createJaspContainer(gettext("Data plots"), dependencies = c("dataPlotShowN", "dataPlot")) - + rainData <- jaspContainer[["simulatedDatasets"]][["object"]] - + nRows <- min((options$dataPlotShowN %/% 3) + 1, 3) nCols <- ifelse(nRows == 1, options$dataPlotShowN, 3) addDots <- ifelse(options$dataPlotShowN > 9, TRUE, FALSE) - - matrixPlot <- createJaspPlot(title = gettext("Samples"), width = 960/(3/nCols), + + matrixPlot <- createJaspPlot(title = gettext("Samples"), width = 960/(3/nCols), height = 800/(3/nRows)) - + plotList <- list() - + if (addDots) { loopingVector <- c(1, 2, (options$dataPlotShowN-6):options$dataPlotShowN) } else { loopingVector <- 1:options$dataPlotShowN } - + listCounter <- 1 for (i in loopingVector) { - + if (addDots && listCounter == 2) { plotList[[listCounter]] <- ggplot2::ggplot(data = data.frame(x = c(-1,1), y = c(-1,1))) + ggplot2::theme_void() + - ggplot2::annotate("text", x = -3, y = -2.5, - label = "...", + ggplot2::annotate("text", x = -3, y = -2.5, + label = "...", size = 60) } else { - - thisRainData <- data.frame(y = rainData[[i]], - group = rep(1, options$n)) - + + thisRainData <- data.frame(y = rainData[[i]], + group = rep(1, options$n)) + plotList[[listCounter]] <- try(jaspTTests::.descriptivesPlotsRainCloudFill(thisRainData, "y", "group", yLabel = gettext("Dependent"), xLabel = gettextf("Repetition %d", i), testValue = options$mu, addLines = FALSE, horiz = FALSE)) - - + + if(isTryError(plotList[[listCounter]])) matrixPlot$setError(.extractErrorMessage(plotList[[listCounter]])) - + } listCounter <- listCounter + 1 } - + p <- jaspGraphs::ggMatrixPlot(matrix(plotList, nrow = nRows, ncol = nCols, byrow = TRUE)) matrixPlot$plotObject <- p jaspContainer[["containerRainCloudPlots"]][["plotObject"]] <- matrixPlot - + return() } diff --git a/inst/qml/LSTconfidenceIntervals.qml b/inst/qml/LSTconfidenceIntervals.qml index 3fb1641..b1c09e5 100644 --- a/inst/qml/LSTconfidenceIntervals.qml +++ b/inst/qml/LSTconfidenceIntervals.qml @@ -63,6 +63,7 @@ Form defaultValue: 100 id:nReps } + SetSeed{} } Group { @@ -161,9 +162,9 @@ Form Group { - + columns: 3 - + DropDown { name: "ciSampleShowType" @@ -189,8 +190,8 @@ Form max: ciSampleAmount.value min: 1 } - - + + IntegerField { name: "ciFromSample" @@ -202,7 +203,7 @@ Form min: 1 max: ciToSample.value } - + IntegerField { name: "ciToSample" @@ -216,7 +217,7 @@ Form } } } - + CheckBox { name: "convergencePlot" diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..0eb5108 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1305 @@ + +local({ + + # the requested version of renv + version <- "1.0.11" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide: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`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + 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) + + } + + # 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()) + + } + + 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] + } + + # 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) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) From 3328e2e2e0ee135c56c41690b4982b221b053f0d Mon Sep 17 00:00:00 2001 From: jvli4n Date: Sat, 16 Nov 2024 18:46:46 +0100 Subject: [PATCH 2/2] Adding dependency & changing position of set seed 1) Adding dependency on checkbox 2) Changing position of Repeatability to be at the end after divider --- R/LSTconfidenceIntervals.R | 2 +- inst/qml/LSTconfidenceIntervals.qml | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/R/LSTconfidenceIntervals.R b/R/LSTconfidenceIntervals.R index 3eec5c8..464f1be 100644 --- a/R/LSTconfidenceIntervals.R +++ b/R/LSTconfidenceIntervals.R @@ -37,7 +37,7 @@ LSTconfidenceIntervals <- function(jaspResults, dataset = NULL, options) { } .getConfidenceContainer <- function(jaspResults) { - confidenceContainer <- jaspResults[["confidenceContainer"]] %setOrRetrieve% createJaspContainer(dependencies = c("mu", "sigma", "n", "confidenceIntervalInterval", "nReps", "treePlot", "seed")) + confidenceContainer <- jaspResults[["confidenceContainer"]] %setOrRetrieve% createJaspContainer(dependencies = c("mu", "sigma", "n", "confidenceIntervalInterval", "nReps", "treePlot", "setSeed", "seed")) return(confidenceContainer) } diff --git a/inst/qml/LSTconfidenceIntervals.qml b/inst/qml/LSTconfidenceIntervals.qml index b1c09e5..ed37db5 100644 --- a/inst/qml/LSTconfidenceIntervals.qml +++ b/inst/qml/LSTconfidenceIntervals.qml @@ -63,7 +63,6 @@ Form defaultValue: 100 id:nReps } - SetSeed{} } Group { @@ -240,5 +239,7 @@ Form } } + Divider{} + SetSeed{} }