diff --git a/spatial/.Rprofile b/spatial/.Rprofile new file mode 100644 index 00000000..81b960f5 --- /dev/null +++ b/spatial/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/spatial/.gitignore b/spatial/.gitignore new file mode 100644 index 00000000..05d6433b --- /dev/null +++ b/spatial/.gitignore @@ -0,0 +1,2 @@ +data/ +*.html # temporary! diff --git a/spatial/.renvignore b/spatial/.renvignore new file mode 100644 index 00000000..8fce6030 --- /dev/null +++ b/spatial/.renvignore @@ -0,0 +1 @@ +data/ diff --git a/spatial/01-processing_visium.Rmd b/spatial/01-processing_visium.Rmd new file mode 100644 index 00000000..6c269684 --- /dev/null +++ b/spatial/01-processing_visium.Rmd @@ -0,0 +1,640 @@ +--- +title: "Reading, processing, and exploring Visium data" +author: Data Lab for ALSF +date: 2026 +output: + html_notebook: + toc: true + toc_float: true +--- + +## Objectives + +- Quality control and post-processing of a Visium dataset +- Learn visualization approaching for spatial data +- Apply descriptive statistics for lattice-based spatial data + + +--- + + +This notebook will analyze an anaplastic Wilms Tumor sample from a 3 year old male biopsied at initial diagnosis. +The dataset comes from the Single-cell Pediatric Cancer Atlas Portal, [project `SCPCP000006`](https://scpca.alexslemonade.org/projects/SCPCP000006). + +## Set up + +Load libraries and set random seed: + + +```{r} +suppressPackageStartupMessages({ + library(SpatialExperiment) # core object + library(VisiumIO) # I/O, but we'll still use :: in the code + library(ggspavis) # plotting + library(ggplot2) # plotting + library(patchwork) # plotting + library(Voyager) # SFE object & spatial descriptive stats +}) +set.seed(2026) +``` + +Paths: + +```{r} +data_path <- here::here( + "data", + "SCPCS000190", + "SCPCL000429_spatial" +) +``` + +What's in Space Ranger output? +Must note that this was processed with an older version of Space Ranger `1.3.1`. + +```{r} +dir(data_path) +dir(file.path(data_path, "spatial")) +``` + +## Import Visium data + +We'll use the `VisiumIO` package: + +```{r} +# define handle, essentially +tenx_object_raw_matrix <- VisiumIO::TENxVisium( + resources = file.path(data_path, "raw_feature_bc_matrix"), + spatialResource = file.path(data_path, "spatial"), + # this argument is needed: the default argument includes "cytassist" + # but ScPCA samples don't have that one; only have these + images = c("lowres", "hires", "detected", "aligned") +) + +# actually import it +spe <- VisiumIO::import(tenx_object_raw_matrix) +``` + + +Let's have a look: + +```{r} +spe +``` + +It's essentially an `SCE`, but with a few more bells and whistles. + +Note that we have 4992 spots - this is not a random value! +It's the number of spots on Visium's 6.5 x 6.5 slide. + +Unlike `SCE`s, we have spatial information in a dedicated `spatialCoords` slot: + +```{r} +# handy function from our code package SpatialExperiment +# literally is giving x/y coordinates +head(spatialCoords(spe)) +``` + +We also have a slot that just holds the images, `imgData`, although looking at it directly isn't very interesting. +But, this stored information will help us make figures! + +```{r} +imgData(spe) +``` + +We should also point out what's in `colData`. +Unlike an `SCE`, this isn't cell metadata. +In an `SPE`, it's _spot_ metadata; recall that each spot may contain multiple cells, which can even include partial cells! + +```{r} +head(colData(spe)) +``` + +Hmmm, check out that `in_tissue` column! +It contains 0/1 because we read in the `raw` Space Ranger output, which includes all spots including those which don't actually overlap tissue. +Ultimately, we won't want to analyze the spots that are not on top of tissue, so we'll have to deal with that. + +Having all this image information in the `SPE` object means we can plot directly. +The package `ggspavis` provides several useful functions for plotting, let's see the highlights: + +```{r, fig.width = 5} +# Spots overlaying the H&E, and we can see the slide boundaries as well +ggspavis::plotVisium(spe) +``` + +By default this shows the spots, but we can hide them and zoom into the tissue on the slide. +This is a helpful way to pop up the H&E for side-by-side comparisons with other plots you might make. + +```{r, fig.width = 5} +ggspavis::plotVisium(spe, spots = FALSE, zoom = TRUE) +``` + +Let's take a moment to chat about Wilm's Tumor - these tumors in the developing kidney are often composed of a couple histologic compartments, blastemal, stromal (with mesenchymal biology), and sometimes epithelial components. +In this section, we can see two major components: the bluer indicating densely cellular, ECM-poor regions consistent with blastema, and paler pink regions consistent with stromal tissue. + +Let's actually go ahead and save this plot to a variable; it will be a convenient way for us to quickly pop up the H&E for side-by-side comparison with other plots we'll make later. + +```{r} +p_he <- ggspavis::plotVisium(spe, spots = FALSE, zoom = TRUE) +``` + + +There's another function called `plotCoords` which hides the H&E to just show the spots; this plot is not currently very compelling, but once we start coloring by things it will be much more fun! + +```{r, fig.width = 5} +# no H&E +ggspavis::plotCoords(spe, point_size = 1) +``` + + +## Quality control + +### Removing uninformative bins + +We only care about spots on top of tissue, so let's begin by removing the `in_tissue = 0` spots. +(Note that reading in the `filtered_feature_bc_matrix` version of Space Ranger output would already be filtered to only `1` in this column, so we're only taking this step because we read in the `raw` output). + +We can visualize which spots those are, and we'll do it over the H&E to clearly see the relationship. +We'll use the `annotate` argument, but `plotVisium` sees that this column is an integer and forces it to use a continuous color scale; we'll go ahead and make it a factor for plotting. + +```{r, fig.width = 5} +# make a factor version of this column to plot with +spe$in_tissue_factor <- as.factor(spe$in_tissue) + +ggspavis::plotVisium( + spe, + annotate = "in_tissue_factor", + # custom palette so we can see clearly + pal = c("red", "lightblue") +) +``` + +- The tissue overhang on the left isn't colored at all - indeed, there aren't spots at those coordinates outside the slide +- Red points are those to filter out - they are uninformative. +Worth noting that some of these appear "inside" the tissue. + +```{r} +# keep only spots that are in the tissue +spe <- spe[, spe$in_tissue == 1] +spe +``` + +Now, we're down to 3701 spots and we can see this reflected in a plot. +We now only see spots with tissue underneath. +Onwards! + +```{r, fig.width = 5} +ggspavis::plotVisium(spe) +``` + +### Filtering for bin quality + + +We _could_ do the same kind of QC that we do for single-cell data, which (usually) involves defining global thresholds for e.g. number of detected UMIs or percent mito. +However, spatial data doesn't lend itself as well to this type of filtering since global thresholds may not be suitable for the different tissues. +Compared to spatial data, single-cell data more closely (but of course not exactly!) resembles a homogeneous pool of cells. + + +Let's go ahead and calculate some QC stats and visualize them: + +```{r} +is_mito <- grepl("(^MT-)|(^mt-)", rowData(spe)$Symbol) +mito_ensembl <- rownames(spe)[is_mito] +spe <- scater::addPerCellQC(spe, subsets=list(mito=mito_ensembl)) +``` + +`ggspavis` comes with a helpful QC plotter (makes histograms by default but has a couple more options!) + +```{r, fig.width = 8, fig.height = 4} +p1 <- ggspavis::plotObsQC(spe, x_metric = "sum") + ggtitle("sum") +p2 <- ggspavis::plotObsQC(spe, x_metric = "detected") + ggtitle("detected") +p3 <- ggspavis::plotObsQC(spe, x_metric = "subsets_mito_percent") + ggtitle("mito %") + +p1 + p2 + p3 +``` + +Distributions don't look like there are any _major_ issues with quality here. +One reason for this is - these are all spots (aggregates of cells), not cells! +Data is sparse, but not quite as sparse. + +Let's plot the same stats on the slide: + +```{r, fig.width = 10} +p1 <- plotCoords(spe, annotate="sum", point_size = 1) + ggtitle("sum") +p2 <- plotCoords(spe, annotate="detected", point_size = 1) + ggtitle("detected") +p3 <- plotCoords(spe, annotate="subsets_mito_percent", point_size = 1) + ggtitle("mito %") +p1 + p2 + p3 + p_he +``` + +We _do_ see a relationship here with tissue type and QC stats that suggests we don't have globally homogeneous patterns - + +- the likely stromal regions look like they have relatively higher mito (although it's low all around!) +- the likely blastema regions tend to have more detected genes + +This tells us that there is local structure in the data, and using global thresholds could be too aggressive/not aggressive enough depending on the local context. + +### Local filtering with Spot Sweeper + +A more spatially-suited approach comes from `SpotSweeper` which models QC stats to identify _local_ outliers. + +We'll detect local outliers based on these three QC stats. +This function will add some `colData` columns we we can use to find all the local outliers. + +```{r} +spe <- SpotSweeper::localOutliers(spe, metric="sum", direction="lower", log=TRUE) # lower-value outliers should be detected +spe <- SpotSweeper::localOutliers(spe, metric="detected", direction="lower", log=TRUE) # lower-value outliers should be detected +spe <- SpotSweeper::localOutliers(spe, metric="subsets_mito_percent", direction="higher", log=FALSE) # higher-value outliers should be detected +``` + +How many of each kind of outlier? + +```{r} +c("sum_outliers", "detected_outliers", "subsets_mito_percent_outliers") |> + purrr::set_names() |> + purrr::map(\(x) table(spe[[x]])) +``` + +We'll use a built-in plotting function from `SpotSweeper` to plot these results (the `ggspavis` plotting isn't quite as nice in this case). +Each plot highlights the spots to remove, and spots are colored based on a different stat. +Again we'll include the H&E as a panel for ease of comparison. + +```{r, fig.width = 10} +p1 <- SpotSweeper::plotQCmetrics(spe, metric = "sum_log", outliers = "sum_outliers") + ggtitle("log sum") +p2 <- SpotSweeper::plotQCmetrics(spe, metric = "detected_log", outliers = "detected_outliers") + ggtitle("log detected") +p3 <- SpotSweeper::plotQCmetrics(spe, metric = "subsets_mito_percent", outliers = "subsets_mito_percent_outliers") + ggtitle("mito %") + +p1 + p2 + p3 + p_he +``` +Some of these spots are being flagged by multiple stats, in particular both `sum` and `detected`. +Let's go ahead and filter all these cells out: + +```{r} +# combine all outliers into "local_outliers" column to filter on +spe$local_outliers <- as.logical(spe$sum_outliers) | + as.logical(spe$detected_outliers) | + as.logical(spe$subsets_mito_percent_outliers) + +spe <- spe[, spe$local_outliers == FALSE] +``` + + + + +## Normalization + +With single-cell, a popular normalization approach we adopt involves deconvolution - we do a quick clustering so we can get groups of cells that will share a size factor, for faster processing. +But this isn't suitable for spot-based spatial data since our units aren't cells, but potentially heterogeneous groups of cells (whole or partial). + +We'll therefore use going to use library-size normalization here to correct for sequencing depth but preserve the other heterogeneous biological signal. +Bear in mind the caveat that in some cases library size itself is [also confounded with spatial structure]((https://link.springer.com/article/10.1186/s13059-024-03241-7); so, keep your eyes peeled for normalization developments, since this space is evolving rapidly! + +```{r} +spe <- scuttle::computeLibraryFactors(spe) +spe <- scuttle::logNormCounts(spe) +spe # now we have a logcounts assay +``` + +## Dimension reduction + +For this step, we're going to get a reduced dimension representation using _just_ the lens of gene expression, "ignoring" spatial information. +(Later, we'll see complementary approaches to some of this which leverages spatial information). + +This all tells us we have to be careful when interpreting analyses on spatial data: "to what extent was spatial information taken into account" is something you'll want to understand. + +Let's do HVG selection (again, this does not consider spatial patterns! we'll learn about _spatially_ variable genes later), PCA, UMAP, and clustering (once again, this won't be spatial regions! just _spot_ similarity based on expression - that's not the same as cells, either!) +So, we'll use a `SCE`-style approach: + + +```{r} +num_genes <- 2000 +gene_variance <- scran::modelGeneVar(spe) +hv_genes <- scran::getTopHVGs(gene_variance, n = num_genes) + +spe <- scater::runPCA(spe, subset_row = hv_genes) +spe <- scater::runUMAP(spe, dimred = "PCA") + +nn_clusters <- scran::clusterCells( + spe, # object to perform clustering on + use.dimred = "PCA", # perform clustering on the PCA matrix + BLUSPARAM = bluster::NNGraphParam( + k = 20, + type = "jaccard", + cluster.fun = "louvain" + ) +) +spe$nn_cluster <- nn_clusters +``` + + +We'll plot the UMAP colored by clusters, because we love UMAPs: + +```{r} +scater::plotUMAP(spe, color_by = "nn_cluster") + + # use distinct palette so we can match up with a spatial view next + ggokabeito::scale_color_okabe_ito() +``` + +How do these clusters come out when using the spatial layout? +We have coordinates, after all - let's use them! + +```{r, fig.width = 8} +p1 <- ggspavis::plotCoords(spe, annotate = "nn_cluster", point_size = 1) + + # matching palette to UMAP + ggokabeito::scale_color_okabe_ito() + +p1 + p_he +``` + +A lot of the clusters are intermingled in space, showing that this analysis is really not spatially-aware! +But, we do see some interesting patterns - check out clusters 1, 5, & 7 in particular - they look stroma-y; also, cluster 8 ooks like a defined region in the H&E, but I'm not a pathologist so let's not overinterpret here. +When expression and tissue structure are correlated, expression-only clusters can pick up on certain spatial regions, but this is _not_ the same as finding "true" spatial domains. + + +## Exploring spot-based spatial data + +Let's explore this data a little more, using some marker genes. +We don't have specific cells as units here, but we can use marker gene expression to build some descriptive intuition for the data. + +We've defined some marker genes here for visualization that correspond to expected Wilm's Tumor biology: + +```{r} +marker_genes <- c( + "WT1 (kidney development, maglinant in WT)" = "ENSG00000184937", + "SIX1 (blastema, malignant)" = "ENSG00000126778", + "MYCN (malignant)" = "ENSG00000134323", + "COL1A1 (fibroblast/mesenchymal)" = "ENSG00000108821", + "TAGLN (myofibroblast/mesenchymal)" = "ENSG00000149591" +) +``` + +Let's plot the expression of these genes, using both UMAP and the spatial layouts to compare: + +```{r, fig.width = 14} +cluster_umap <- scater::plotUMAP(spe, color_by = "nn_cluster", point_size = 0.5, point_alpha = 0.5) + + ggtitle("expression-based clusters") + + coord_equal() + + ggokabeito::scale_color_okabe_ito() + +marker_umaps <- marker_genes |> + purrr::imap( + \(ensembl, gene_name) { + scater::plotUMAP(spe, color_by = ensembl, point_size = 0.5, point_alpha = 0.5) + ggtitle(gene_name) + coord_equal() + } + ) |> + # cluster umap and then the marker gene umaps + append(values = cluster_umap, after = 0) + +patchwork::wrap_plots(marker_umaps, nrow = 2) +``` + + +```{r, fig.width = 12} +cluster_coords <- ggspavis::plotCoords(spe, annotate = "nn_cluster", point_size = 0.75) + + ggtitle("expression-based clusters") + + ggokabeito::scale_color_okabe_ito() + +marker_coords <- marker_genes |> + purrr::imap( + \(ensembl, gene_name) { + # default assay is counts, override! + ggspavis::plotCoords(spe, annotate = ensembl, point_size = 0.75, assay = "logcounts") + + scale_color_distiller(palette = "Blues", direction = 1) + + ggtitle(gene_name) + } + ) |> + # cluster cooords and then the marker gene coords + append(values = cluster_coords, after = 0) + +p_he + patchwork::wrap_plots(marker_coords, nrow = 2) + plot_layout(widths = c(1,2)) +``` + + +Based on these observations, it seems like there could be some spatial patterns/variability here; _interpret_. +We'll talk more rigorously about quantifying spatially-variable genes later in the workshop, but for now, we can take this opportunity to to ask some descriptive questions about these genes' expression across space. + + + +### Spatial descriptive statistics + +Although spatial analysis is an emerging field in transcriptomics, it's not new to science! +Folks in geography, epidemiology, ecology, and more have been thinking about spatial data for a long time, so we can draw from existing quantitative approaches. + +Spot-based spatial data is analogous to "lattice-structure" spatial data, in contrast to high-res spatial technologies that are "point-pattern" data; see [the pasta paper](https://academic.oup.com/nar/article/53/17/gkaf870/8250477). + +The R package `spdep` already exists to work with lattice-structure spatial data, and helpfully folks have already started to put this (and other spatial platforms) to work for transcriptomics data. +The `Voyager`/`SpatialFeatureExperiment`: framework is complementary to `SpatialExperiment` and can help us use these tools. +The `SFE` object is an expanded `SPE` object with more slots to facilitate spatial analysis with existing tools (we won't get into these weeds much though, suffice to say it's a super rich environment). + +When working with spot data, we can turn it into a graph and ask descriptive (not modeling!) questions about spatial structure directly. +Let's go! + +First, we'll need to get it into the `SFE` framework and convert the `SPE` to an `SFE` object. + +```{r} +# TODO: I have to remove the image before converting, errors otherwise. Can this be avoided? +# Error: [ext] invalid extent +spe_noimg <- spe +imgData(spe_noimg) <- imgData(spe_noimg)[0, , drop=FALSE] +sfe <- toSpatialFeatureExperiment(spe_noimg) +#sfe <- mirror(sfe, direction = "vertical") # use mirror so plots between ggspavis and this one match. +# OR, let it be a mirror to serve as a teachable moment about space! +``` + +One way to make a graph is using k-nearest neighbors, but there's other ways (all of these choices matter to some degree, and we should discuss that!): +Now we'll make a graph using: + +- spot centroids as nodes (don't skip that this is a _choice_!) +- knn approach with k = 10, as a starting point +- no weighting + +```{r} +colGraph(sfe, "knn10") <- SpatialFeatureExperiment::findSpatialNeighbors( + sfe, + type = "centroids", + method = "knearneigh", + k = 10 +) +``` + +This will get stored in `colGraph` slot in the `SFE` object. + +We can visualize it - check out those edges and nodes, it's a graph! + +```{r} +Voyager::plotColGraph( + sfe, + colGraphName = "knn10", + colGeometryName = "centroids", + segment_size = 0.1, + geometry_size = 0.3 +) + + theme_void() # we just want the graph +``` + +Hey notice anything interesting about this image? +It's a mirror of how `ggspavis` plotted it! +Is that a problem? +Well, no - in space we can mirror and rotate and such, but the spatial relationships are preserved. +This is a big hint that specific coordinates may not always be the same, but the distances should be. + + +It seems potentially cute to zoom in to prove to you that `k = 10`: + +```{r} +Voyager::plotColGraph( + sfe, + colGraphName = "knn10", + colGeometryName = "centroids", + segment_size = 0.1, + geometry_size = 5 +) + + scale_y_continuous(limits = c(11500, 12000)) + + scale_x_continuous(limits = c(4000,4300)) + + theme_void() +``` + + +Alright, now that we have a graph, let's see an example of using it for exploratory analysis. +A common descriptive statistic used for lattice spatial data is "Moran's I" which quantifies spatial autocorrelation. +It asks, is the spatial distribution of a variable of interest dispersed, random, or clustered? +We'll use it to look at gene expression of some of our marker genes of interest. +In this case, Moran's I tells us: do neighboring spots (hint: this will depend on your definition of a _neighborhood_!_) have very similar, very dissimilar, or totally unrelated gene expression, where: + +- close to 1 values: Nearby spots tend to have similar expression +- ~0: looks random in space +- close to -1 values: Nearby spots tend to have different expression (less commonly of interest in this sort of biology) + +We'll calculate this with `Voyager` on our `SFE` object using the graph we just built. + +```{r} +sfe <- Voyager::runUnivariate( + sfe, + type = "moran", + features = marker_genes, + colGraphName = "knn10" +) +``` + +This stores results in `rowData`: + +```{r} +rowData(sfe)[marker_genes, ] +``` + +This makes some sense given what we when plotting gene expression: + +- `SIX1` and `MYCN` were just splotched all around randomly in much of the slide +- `COL1A1` and `TAGLN` were more concentrated in certain areas +- `WT1` was somewhere in the middle - generally expressed by less variation from spot-to-spot in the plots earlier, per vibes + +This global statistic gave us an overall picture, but we can calculate a variant of this statistic also called Local Moran's I which is, you guessed it, a local version. +Rather than giving a single value for the dataset, we'll get a _per-spot_ value (or rather, per node in the graph) that tells us "how much does this spot agree with its immediate neighborhood"? + +- high: spot is similar to neighbors and all are high _OR_ all are low +- ~0: spatially neutral, no real relationship to neighbors +- low: spot is different from neighbors where high surrounded by low or vice versa + +Let's go: + +```{r} +sfe <- Voyager::runUnivariate( + sfe, + type = "localmoran", + features = marker_genes, + colGraphName = "knn10", + name = "localmoran_knn10" # save it as this name +) + +# stores it here, not so pretty... +localResults(sfe)$localmoran_knn10 +``` + + +```{r, fig.width = 10} +# we can plot with voyager, since it's in a special slot +# or we'd have to pull it out to store back in our SPE +Voyager::plotLocalResult( + sfe, + name = "localmoran_knn10", + features = marker_genes, + colGeometryName = "centroids", + divergent = TRUE, # palette + diverge_center = 0 # palette + ) +``` + +For easier comparison, we can also use the standardized (z-score) values by specifying the specific attribute (the default was `"Ii"`, the actual stat). + +```{r, fig.width = 10} +Voyager::plotLocalResult( + sfe, + name = "localmoran_knn10", + features = marker_genes, + attribute = "Z.Ii", # plot the normalized moran's i + colGeometryName = "centroids", + divergent = TRUE, + diverge_center = 0 + ) +``` + +### Scale matters! + +We did a graph with 10 nearest neighbors. +The number of neighbors is going to matter here! + +Pick one gene (provide the ensembl id) and see how interpretation differs at different `k`'s. +Try out a really high (`k>=50`) and really low number (`k<=3`) below to calculate and plot Local Moran's I again - the real value, not scaled. +What do you see? + +```{r} +gene <- marker_genes[1] # WT1, for example +colGraph(sfe, "knn100") <- findSpatialNeighbors(sfe, type="centroids", method = "knearneigh", k=100) +colGraph(sfe, "knn2") <- findSpatialNeighbors(sfe, type="centroids", method = "knearneigh", k=2) + +sfe <- Voyager::runUnivariate( + sfe, + type="localmoran", + features = gene, + colGraphName="knn100", + name = "localmoran_knn100" +) +sfe <- Voyager::runUnivariate( + sfe, + type="localmoran", + features = gene, + colGraphName="knn2", + name = "localmoran_knn2" +) + +p1 <- Voyager::plotLocalResult( + sfe, + name = "localmoran_knn100", + features = gene, + colGeometryName = "centroids", + divergent = TRUE, + diverge_center = 0 +) + + +p2 <- Voyager::plotLocalResult( + sfe, + name = "localmoran_knn2", + features = gene, + colGeometryName = "centroids", + divergent = TRUE, + diverge_center = 0 +) + +p1 + p2 +``` + +When `k` is very high, there's a lot of neighbors being consider. +Expression will have to be similar cross them all to get a high value for this stat. +But, when `k` is very low, there's very few neighbors! +Much finer-grained picture of similarity between spots. + + +## Session Info + +```{r} +sessionInfo() +``` diff --git a/spatial/README.md b/spatial/README.md new file mode 100644 index 00000000..f8dc5736 --- /dev/null +++ b/spatial/README.md @@ -0,0 +1,5 @@ +# Spatial Transcriptomics Training Module + +_This module is in active development._ + +Note that the `renv` environment can be temporarily used for development until the Docker image is bumped to R 4.5. diff --git a/spatial/renv.lock b/spatial/renv.lock new file mode 100644 index 00000000..7b9bd5df --- /dev/null +++ b/spatial/renv.lock @@ -0,0 +1,8566 @@ +{ + "R": { + "Version": "4.5.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + }, + { + "Name": "BioCsoft", + "URL": "https://bioconductor.org/packages/3.22/bioc" + }, + { + "Name": "BioCann", + "URL": "https://bioconductor.org/packages/3.22/data/annotation" + }, + { + "Name": "BioCexp", + "URL": "https://bioconductor.org/packages/3.22/data/experiment" + }, + { + "Name": "BioCworkflows", + "URL": "https://bioconductor.org/packages/3.22/workflows" + }, + { + "Name": "BioCbooks", + "URL": "https://bioconductor.org/packages/3.22/books" + } + ] + }, + "Bioconductor": { + "Version": "3.22" + }, + "Packages": { + "BH": { + "Package": "BH", + "Version": "1.90.0-1", + "Source": "Repository", + "Type": "Package", + "Title": "Boost C++ Header Files", + "Date": "2025-12-13", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"John W.\", \"Emerson\", role = \"aut\"), person(\"Michael J.\", \"Kane\", role = \"aut\", comment = c(ORCID = \"0000-0003-1899-6662\")))", + "Description": "Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. 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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(\"Angel\", \"Feliz\", role=\"ctb\"), person(\"Michael\",\"Young\", role=\"ctb\"), person(\"Mark\", \"Seeto\", role=\"ctb\"), person(\"Philippe\", \"Grosjean\", role=\"ctb\"), person(\"Vincent\", \"Runge\", role=\"ctb\"), person(\"Christian\", \"Wia\", role=\"ctb\"), person(\"Elise\", \"Maigné\", role=\"ctb\"), person(\"Vincent\", \"Rocher\", role=\"ctb\"), person(\"Vijay\", \"Lulla\", role=\"ctb\"), person(\"Aljaž\", \"Sluga\", role=\"ctb\"), person(\"Bill\", \"Evans\", role=\"ctb\"), person(\"Reino\", \"Bruner\", role=\"ctb\"), person(given=\"@badasahog\", role=\"ctb\", comment=\"GitHub user\"), person(\"Vinit\", \"Thakur\", role=\"ctb\"), person(\"Mukul\", \"Kumar\", role=\"ctb\"), person(\"Ildikó\", \"Czeller\", role=\"ctb\") )", + "NeedsCompilation": "yes", + "Author": "Tyson Barrett [aut, cre] (ORCID: ), Matt Dowle [aut], Arun Srinivasan [aut], Jan Gorecki [aut], Michael Chirico [aut] (ORCID: ), Toby Hocking [aut] (ORCID: ), Benjamin Schwendinger [aut] (ORCID: ), Ivan Krylov [aut] (ORCID: ), 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] (GitHub user), Marc Halperin [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], Angel Feliz [ctb], Michael Young [ctb], Mark Seeto [ctb], Philippe Grosjean [ctb], Vincent Runge [ctb], Christian Wia [ctb], Elise Maigné [ctb], Vincent Rocher [ctb], Vijay Lulla [ctb], Aljaž Sluga [ctb], Bill Evans [ctb], Reino Bruner [ctb], @badasahog [ctb] (GitHub user), Vinit Thakur [ctb], Mukul Kumar [ctb], Ildikó Czeller [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "CRAN" + }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.1", + "Source": "Repository", + "Type": "Package", + "Title": "A 'dplyr' Back End for Databases", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Edgar\", \"Ruiz\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.", + "License": "MIT + file LICENSE", + "URL": "https://dbplyr.tidyverse.org/, https://github.com/tidyverse/dbplyr", + "BugReports": "https://github.com/tidyverse/dbplyr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "blob (>= 1.2.0)", + "cli (>= 3.6.1)", + "DBI (>= 1.1.3)", + "dplyr (>= 1.1.2)", + "glue (>= 1.6.2)", + "lifecycle (>= 1.0.3)", + "magrittr", + "methods", + "pillar (>= 1.9.0)", + "purrr (>= 1.0.1)", + "R6 (>= 2.2.2)", + "rlang (>= 1.1.1)", + "tibble (>= 3.2.1)", + "tidyr (>= 1.3.0)", + "tidyselect (>= 1.2.1)", + "utils", + "vctrs (>= 0.6.3)", + "withr (>= 2.5.0)" + ], + "Suggests": [ + "bit64", + "covr", + "knitr", + "Lahman", + "nycflights13", + "odbc (>= 1.4.2)", + "RMariaDB (>= 1.2.2)", + "rmarkdown", + "RPostgres (>= 1.4.5)", + "RPostgreSQL", + "RSQLite (>= 2.3.8)", + "testthat (>= 3.1.10)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Encoding": "UTF-8", + "Language": "en-gb", + "RoxygenNote": "7.3.3", + "Collate": "'db-sql.R' 'utils-check.R' 'import-standalone-types-check.R' 'import-standalone-obj-type.R' 'utils.R' 'sql.R' 'escape.R' 'translate-sql-cut.R' 'translate-sql-quantile.R' 'translate-sql-string.R' 'translate-sql-paste.R' 'translate-sql-helpers.R' 'translate-sql-window.R' 'translate-sql-conditional.R' 'backend-.R' 'backend-access.R' 'backend-hana.R' 'backend-hive.R' 'backend-impala.R' 'verb-copy-to.R' 'backend-mssql.R' 'backend-mysql.R' 'backend-odbc.R' 'backend-oracle.R' 'backend-postgres.R' 'backend-postgres-old.R' 'backend-redshift.R' 'backend-snowflake.R' 'backend-spark-sql.R' 'backend-sqlite.R' 'backend-teradata.R' 'build-sql.R' 'data-cache.R' 'data-lahman.R' 'data-nycflights13.R' 'db-escape.R' 'db-io.R' 'db.R' 'dbplyr.R' 'explain.R' 'ident.R' 'import-standalone-s3-register.R' 'join-by-compat.R' 'join-cols-compat.R' 'lazy-join-query.R' 'lazy-ops.R' 'lazy-query.R' 'lazy-select-query.R' 'lazy-set-op-query.R' 'memdb.R' 'optimise-utils.R' 'pillar.R' 'progress.R' 'sql-build.R' 'query-join.R' 'query-select.R' 'query-semi-join.R' 'query-set-op.R' 'query.R' 'reexport.R' 'remote.R' 'rows.R' 'schema.R' 'simulate.R' 'sql-clause.R' 'sql-expr.R' 'src-sql.R' 'src_dbi.R' 'table-name.R' 'tbl-lazy.R' 'tbl-sql.R' 'test-frame.R' 'testthat.R' 'tidyeval-across.R' 'tidyeval.R' 'translate-sql.R' 'utils-format.R' 'verb-arrange.R' 'verb-compute.R' 'verb-count.R' 'verb-distinct.R' 'verb-do-query.R' 'verb-do.R' 'verb-expand.R' 'verb-fill.R' 'verb-filter.R' 'verb-group_by.R' 'verb-head.R' 'verb-joins.R' 'verb-mutate.R' 'verb-pivot-longer.R' 'verb-pivot-wider.R' 'verb-pull.R' 'verb-select.R' 'verb-set-ops.R' 'verb-slice.R' 'verb-summarise.R' 'verb-uncount.R' 'verb-window.R' 'zzz.R'", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Maximilian Girlich [aut], Edgar Ruiz [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "deldir": { + "Package": "deldir", + "Version": "2.0-4", + "Source": "Repository", + "Date": "2024-02-27", + "Title": "Delaunay Triangulation and Dirichlet (Voronoi) Tessellation", + "Author": "Rolf Turner", + "Maintainer": "Rolf Turner ", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "polyclip" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Description": "Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.\tCalculates the centroidal Voronoi (Dirichlet) tessellation using Lloyd's algorithm.", + "LazyData": "true", + "ByteCompile": "true", + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Repository": "https://packagemanager.posit.co/cran/latest", + "Encoding": "UTF-8" + }, + "digest": { + "Package": "digest", + "Version": "0.6.39", + "Source": "Repository", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\", comment = c(ORCID = \"0000-0002-8059-9767\")), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8552-0029\")), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0492-6647\")), person(\"Ion\", \"Suruceanu\", role=\"ctb\", comment = c(ORCID = \"0009-0005-6446-4909\")), person(\"Bill\", \"Denney\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\", comment = c(ORCID = \"0009-0008-8480-1329\")), person(\"Sergey\", \"Fedorov\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5970-7233\")), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\", comment = c(ORCID = \"0009-0000-5948-4503\")), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Carl\", \"Pearson\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0701-7860\")))", + "Date": "2025-11-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as 'hmac()' to create hash-based message authentication code. 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://eddelbuettel.github.io/digest/, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown", + "rbenchmark" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Antoine Lucas [ctb] (ORCID: ), Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (ORCID: ), Simon Urbanek [ctb] (ORCID: ), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb] (ORCID: ), Duncan Murdoch [ctb], Jim Hester [ctb] (ORCID: ), Wush Wu [ctb] (ORCID: ), Qiang Kou [ctb] (ORCID: ), Thierry Onkelinx [ctb] (ORCID: ), Michel Lang [ctb] (ORCID: ), Viliam Simko [ctb], Kurt Hornik [ctb] (ORCID: ), Radford Neal [ctb] (ORCID: ), Kendon Bell [ctb] (ORCID: ), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb] (ORCID: ), Ion Suruceanu [ctb] (ORCID: ), Bill Denney [ctb] (ORCID: ), Dirk Schumacher [ctb], András Svraka [ctb] (ORCID: ), Sergey Fedorov [ctb] (ORCID: ), Will Landau [ctb] (ORCID: ), Floris Vanderhaeghe [ctb] (ORCID: ), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (ORCID: ), Mark van der Loo [ctb] (ORCID: ), Chris Muir [ctb] (ORCID: ), Moritz Beller [ctb] (ORCID: ), Sebastian Campbell [ctb] (ORCID: ), Winston Chang [ctb] (ORCID: ), Dean Attali [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Kevin Ushey [ctb] (ORCID: ), Carl Pearson [ctb] (ORCID: )", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository", + "Type": "Package", + "Title": "A Grammar of Data Manipulation", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Kirill\", \"Müller\", role = \"aut\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A fast, consistent tool for working with data frame like objects, both in memory and out of memory.", + "License": "MIT + file LICENSE", + "URL": "https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr", + "BugReports": "https://github.com/tidyverse/dplyr/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "generics", + "glue (>= 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"Repository": "https://packagemanager.posit.co/cran/latest" + }, + "dqrng": { + "Package": "dqrng", + "Version": "0.4.1", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Pseudo Random Number Generators", + "Authors@R": "c( person(\"Ralf\", \"Stubner\", email = \"ralf.stubner@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0009-1908-106X\")), person(\"daqana GmbH\", role = \"cph\"), person(\"David Blackman\", role = \"cph\", comment = \"Xoroshiro / Xoshiro family\"), person(\"Melissa O'Neill\", email = \"oneill@pcg-random.org\", role = \"cph\", comment = \"PCG family\"), person(\"Sebastiano Vigna\", email = \"vigna@acm.org\", role = \"cph\", comment = \"Xoroshiro / Xoshiro family\"), person(\"Aaron\", \"Lun\", role=\"ctb\"), person(\"Kyle\", \"Butts\", role = \"ctb\", email = \"kyle.butts@colorado.edu\"), person(\"Henrik\", \"Sloot\", role = \"ctb\"), person(\"Philippe\", \"Grosjean\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-2694-9471\")) )", + "Description": "Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 ) as well as the Xoroshiro / Xoshiro family by Blackman and Vigna (2021 ). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, ). The fast sampling methods support unweighted sampling both with and without replacement. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+/++/** and Xoshiro256+/++/** as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011, ) as provided by the package 'sitmo'.", + "License": "AGPL-3", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "Rcpp (>= 0.12.16)" + ], + "LinkingTo": [ + "Rcpp", + "BH (>= 1.64.0-1)", + "sitmo (>= 2.0.0)" + ], + "RoxygenNote": "7.3.1", + "Suggests": [ + "BH", + "testthat", + "knitr", + "rmarkdown", + "mvtnorm (>= 1.2-3)", + "bench", + "sitmo" + ], + "VignetteBuilder": "knitr", + "URL": "https://daqana.github.io/dqrng/, https://github.com/daqana/dqrng", + "BugReports": "https://github.com/daqana/dqrng/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Ralf Stubner [aut, cre] (), daqana GmbH [cph], David Blackman [cph] (Xoroshiro / Xoshiro family), Melissa O'Neill [cph] (PCG family), Sebastiano Vigna [cph] (Xoroshiro / Xoshiro family), Aaron Lun [ctb], Kyle Butts [ctb], Henrik Sloot [ctb], Philippe Grosjean [ctb] ()", + "Maintainer": "Ralf Stubner ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "e1071": { + "Package": "e1071", + "Version": "1.7-17", + "Source": "Repository", + "Title": "Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien", + "Imports": [ + "graphics", + "grDevices", + "class", + "stats", + "methods", + "utils", + "proxy" + ], + "Suggests": [ + "cluster", + "mlbench", + "nnet", + "randomForest", + "rpart", + "SparseM", + "xtable", + "Matrix", + "MASS", + "slam" + ], + "Authors@R": "c(person(given = \"David\", family = \"Meyer\", role = c(\"aut\", \"cre\"), email = \"David.Meyer@R-project.org\", comment = c(ORCID = \"0000-0002-5196-3048\")), person(given = \"Evgenia\", family = \"Dimitriadou\", role = c(\"aut\",\"cph\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = \"Andreas\", family = \"Weingessel\", role = \"aut\"), person(given = \"Friedrich\", family = \"Leisch\", role = \"aut\"), person(given = \"Chih-Chung\", family = \"Chang\", role = c(\"ctb\",\"cph\"), comment = \"libsvm C++-code\"), person(given = \"Chih-Chen\", family = \"Lin\", role = c(\"ctb\",\"cph\"), comment = \"libsvm C++-code\"))", + "Description": "Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour ...", + "License": "GPL-2 | GPL-3", + "LazyLoad": "yes", + "NeedsCompilation": "yes", + "Author": "David Meyer [aut, cre] (ORCID: ), Evgenia Dimitriadou [aut, cph], Kurt Hornik [aut] (ORCID: ), Andreas Weingessel [aut], Friedrich Leisch [aut], Chih-Chung Chang [ctb, cph] (libsvm C++-code), Chih-Chen Lin [ctb, cph] (libsvm C++-code)", + "Maintainer": "David Meyer ", + "Repository": "CRAN" + }, + "edgeR": { + "Package": "edgeR", + "Version": "4.8.2", + "Source": "Bioconductor", + "Date": "2025-12-23", + "Title": "Empirical Analysis of Digital Gene Expression Data in R", + "Description": "Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.", + "Author": "Yunshun Chen, Lizhong Chen, Aaron TL Lun, Davis J McCarthy, Pedro Baldoni, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth", + "Maintainer": "Yunshun Chen , Gordon Smyth , Aaron Lun , Mark Robinson ", + "License": "GPL (>=2)", + "Depends": [ + "R (>= 3.6.0)", + "limma (>= 3.63.6)" + ], + "Imports": [ + "methods", + "graphics", + "stats", + "utils", + "locfit" + ], + "Suggests": [ + "arrow", + "jsonlite", + "knitr", + "Matrix", + "readr", + "rhdf5", + "SeuratObject", + "splines", + "AnnotationDbi", + "Biobase", + "BiocStyle", + "org.Hs.eg.db", + "SummarizedExperiment" + ], + "VignetteBuilder": "knitr", + "URL": "https://bioinf.wehi.edu.au/edgeR/, https://bioconductor.org/packages/edgeR", + "biocViews": "AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, ChIPSeq, Clustering, Coverage, DifferentialExpression, DifferentialMethylation, DifferentialSplicing, DNAMethylation, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pathways, Proteomics, QualityControl, Regression, RNASeq, SAGE, Sequencing, SingleCell, SystemsBiology, TimeCourse, Transcription, Transcriptomics", + "NeedsCompilation": "yes", + "Repository": "https://bioc-release.r-universe.dev", + "RemoteUrl": "https://github.com/bioc/edgeR", + "RemoteRef": "RELEASE_3_22", + "RemoteSha": "af0343acbb3998d2d2bb3e3d259bbee17a2c8a7e" + }, + "escheR": { + "Package": "escheR", + "Version": "1.10.0", + "Source": "Bioconductor", + "Title": "Unified multi-dimensional visualizations with Gestalt principles", + "Authors@R": "c( person(\"Boyi\", \"Guo\", email = \"boyi.guo.work@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-2950-2349\")), person(c(\"Stephanie\", \"C.\"), \"Hicks\", role = c(\"aut\"), email = \"shicks19@jhu.edu\", comment = c(ORCID = \"0000-0002-7858-0231\")), person(c(\"Erik\", \"D.\"), \"Nelson\", email = \"erik.nelson116@gmail.com\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0001-8477-0982\")) )", + "Description": "The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.2.3", + "biocViews": "Spatial, SingleCell, Transcriptomics, Visualization, Software", + "Depends": [ + "ggplot2", + "R (>= 4.3)" + ], + "Imports": [ + "SpatialExperiment (>= 1.6.1)", + "SingleCellExperiment", + "rlang", + "SummarizedExperiment" + ], + "BugReports": "https://github.com/boyiguo1/escheR/issues", + "URL": "https://github.com/boyiguo1/escheR", + "Suggests": [ + "STexampleData", + "BumpyMatrix", + "knitr", + "rmarkdown", + "BiocStyle", + "ggpubr", + "scran", + "scater", + "scuttle", + "Seurat", + "hexbin" + ], + "VignetteBuilder": "knitr", + "git_url": "https://git.bioconductor.org/packages/escheR", + "git_branch": "RELEASE_3_22", + "git_last_commit": "3f79e54", + "git_last_commit_date": "2025-10-29", + "Repository": "Bioconductor 3.22", + "NeedsCompilation": "no", + "Author": "Boyi Guo [aut, cre] (ORCID: ), Stephanie C. Hicks [aut] (ORCID: ), Erik D. Nelson [ctb] (ORCID: )", + "Maintainer": "Boyi Guo " + }, + "evaluate": { + "Package": "evaluate", + "Version": "1.0.5", + "Source": "Repository", + "Type": "Package", + "Title": "Parsing and Evaluation Tools that Provide More Details than the Default", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"aut\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Michael\", \"Lawrence\", role = \"ctb\"), person(\"Thomas\", \"Kluyver\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Adam\", \"Ryczkowski\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Michel\", \"Lang\", role = \"ctb\"), person(\"Karolis\", \"Koncevičius\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.", + "License": "MIT + file LICENSE", + "URL": "https://evaluate.r-lib.org/, https://github.com/r-lib/evaluate", + "BugReports": "https://github.com/r-lib/evaluate/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Suggests": [ + "callr", + "covr", + "ggplot2 (>= 3.3.6)", + "lattice", + "methods", + "pkgload", + "ragg (>= 1.4.0)", + "rlang (>= 1.1.5)", + "knitr", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Yihui Xie [aut] (ORCID: ), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb], Karolis Koncevičius [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "farver": { + "Package": "farver", + "Version": "2.1.2", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance Colour Space Manipulation", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Berendea\", \"Nicolae\", role = \"aut\", comment = \"Author of the ColorSpace C++ library\"), person(\"Romain\", \"François\", , \"romain@purrple.cat\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The encoding of colour can be handled in many different ways, using different colour spaces. 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": "https://packagemanager.posit.co/cran/latest" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.2.0", + "Source": "Repository", + "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. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Suggests": [ + "testthat (>= 2.1.1)" + ], + "URL": "https://r-lib.github.io/fastmap/, https://github.com/r-lib/fastmap", + "BugReports": "https://github.com/r-lib/fastmap/issues", + "NeedsCompilation": "yes", + "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd], Tessil [cph] (hopscotch_map library)", + "Maintainer": "Winston Chang ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "fftwtools": { + "Package": "fftwtools", + "Version": "0.9-11", + "Source": "Repository", + "Title": "Wrapper for 'FFTW3' Includes: One-Dimensional, Two-Dimensional, Three-Dimensional, and Multivariate Transforms", + "Author": "Karim Rahim ", + "Maintainer": "Karim Rahim ", + "Depends": [ + "R (>= 3.0)" + ], + "SystemRequirements": "fftw3 (libfftw3-dev (deb), or fftw-devel (rpm))", + "Suggests": [ + "fftw" + ], + "Description": "Provides a wrapper for several 'FFTW' functions. This package provides access to the two-dimensional 'FFT', the multivariate 'FFT', and the one-dimensional real to complex 'FFT' using the 'FFTW3' library. The package includes the functions fftw() and mvfftw() which are designed to mimic the functionality of the R functions fft() and mvfft(). The 'FFT' functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.", + "License": "GPL (>= 2)", + "ByteCompile": "true", + "URL": "https://github.com/krahim/fftwtools", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "filelock": { + "Package": "filelock", + "Version": "1.0.3", + "Source": "Repository", + "Title": "Portable File Locking", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Place an exclusive or shared lock on a file. It uses 'LockFile' on Windows and 'fcntl' locks on Unix-like systems.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/filelock/, https://github.com/r-lib/filelock", + "BugReports": "https://github.com/r-lib/filelock/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Suggests": [ + "callr (>= 2.0.0)", + "covr", + "testthat (>= 3.0.0)" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.3", + "Source": "Repository", + "Type": "Package", + "Title": "Easily Work with 'Font Awesome' Icons", + "Description": "Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents and 'Shiny' apps. These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. There is also a utility function for exporting 'Font Awesome' icons as 'PNG' images for those situations where raster graphics are needed.", + "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"rich@posit.co\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"ctb\"), person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome font\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/fontawesome, https://rstudio.github.io/fontawesome/", + "BugReports": "https://github.com/rstudio/fontawesome/issues", + "Encoding": "UTF-8", + "ByteCompile": "true", + "RoxygenNote": "7.3.2", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "rlang (>= 1.0.6)", + "htmltools (>= 0.5.1.1)" + ], + "Suggests": [ + "covr", + "dplyr (>= 1.0.8)", + "gt (>= 0.9.0)", + "knitr (>= 1.31)", + "testthat (>= 3.0.0)", + "rsvg" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Richard Iannone [aut, cre] (), Christophe Dervieux [ctb] (), Winston Chang [ctb], Dave Gandy [ctb, cph] (Font-Awesome font), Posit Software, PBC [cph, fnd]", + "Maintainer": "Richard Iannone ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "formatR": { + "Package": "formatR", + "Version": "1.14", + "Source": "Repository", + "Type": "Package", + "Title": "Format R Code Automatically", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Ed\", \"Lee\", role = \"ctb\"), person(\"Eugene\", \"Ha\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Pavel\", \"Krivitsky\", role = \"ctb\"), person() )", + "Description": "Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. 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It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)", + "License": "GPL (>= 2) | file LICENSE", + "URL": "https://github.com/rstudio/httpuv", + "BugReports": "https://github.com/rstudio/httpuv/issues", + "Depends": [ + "R (>= 2.15.1)" + ], + "Imports": [ + "later (>= 0.8.0)", + "promises", + "R6", + "Rcpp (>= 1.0.7)", + "utils" + ], + "Suggests": [ + "callr", + "curl", + "jsonlite", + "testthat", + "websocket" + ], + "LinkingTo": [ + "later", + "Rcpp" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "GNU make, zlib", + "Collate": "'RcppExports.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Winston Chang [aut, cre], Posit, PBC fnd [cph], Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph] (optional.hpp), libuv project contributors [cph] (libuv library, see src/libuv/AUTHORS file), Joyent, Inc. and other Node contributors [cph] (libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file), Niels Provos [cph] (libuv subcomponent: tree.h), Internet Systems Consortium, Inc. [cph] (libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c), Alexander Chemeris [cph] (libuv subcomponent: stdint-msvc2008.h (from msinttypes)), Google, Inc. [cph] (libuv subcomponent: pthread-fixes.c), Sony Mobile Communcations AB [cph] (libuv subcomponent: pthread-fixes.c), Berkeley Software Design Inc. [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Kenneth MacKay [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016) [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Steve Reid [aut] (SHA-1 implementation), James Brown [aut] (SHA-1 implementation), Bob Trower [aut] (base64 implementation), Alexander Peslyak [aut] (MD5 implementation), Trantor Standard Systems [cph] (base64 implementation), Igor Sysoev [cph] (http-parser)", + "Maintainer": "Winston Chang ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "httr2": { + "Package": "httr2", + "Version": "1.2.2", + "Source": "Repository", + "Title": "Perform HTTP Requests and Process the Responses", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Maximilian\", \"Girlich\", role = \"ctb\") )", + "Description": "Tools for creating and modifying HTTP requests, then performing them and processing the results. 'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.", + "License": "MIT + file LICENSE", + "URL": "https://httr2.r-lib.org, https://github.com/r-lib/httr2", + "BugReports": "https://github.com/r-lib/httr2/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "cli (>= 3.0.0)", + "curl (>= 6.4.0)", + "glue", + "lifecycle", + "magrittr", + "openssl", + "R6", + "rappdirs", + "rlang (>= 1.1.0)", + "vctrs (>= 0.6.3)", + "withr" + ], + "Suggests": [ + "askpass", + "bench", + "clipr", + "covr", + "docopt", + "httpuv", + "jose", + "jsonlite", + "knitr", + "later (>= 1.4.0)", + "nanonext", + "otel (>= 0.2.0)", + "otelsdk (>= 0.2.0)", + "paws.common (>= 0.8.0)", + "promises", + "rmarkdown", + "testthat (>= 3.1.8)", + "tibble", + "webfakes (>= 1.4.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "resp-stream, req-perform", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd], Maximilian Girlich [ctb]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "igraph": { + "Package": "igraph", + "Version": "2.2.1", + "Source": "Repository", + "Title": "Network Analysis and Visualization", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-7098-9676\")), person(\"Tamás\", \"Nepusz\", , \"ntamas@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-1451-338X\")), person(\"Vincent\", \"Traag\", role = \"aut\", comment = c(ORCID = \"0000-0003-3170-3879\")), person(\"Szabolcs\", \"Horvát\", , \"szhorvat@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-3100-523X\")), person(\"Fabio\", \"Zanini\", , \"fabio.zanini@unsw.edu.au\", role = \"aut\", comment = c(ORCID = \"0000-0001-7097-8539\")), person(\"Daniel\", \"Noom\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Michael\", \"Antonov\", role = \"ctb\"), person(\"Chan Zuckerberg Initiative\", role = \"fnd\", comment = c(ROR = \"02qenvm24\")), person(\"David\", \"Schoch\", , \"david.schoch@cynkra.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-2952-4812\")), person(\"Maëlle\", \"Salmon\", , \"maelle@cynkra.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-2815-0399\")) )", + "Description": "Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.", + "License": "GPL (>= 2)", + "URL": "https://r.igraph.org/, https://igraph.org/, https://igraph.discourse.group/", + "BugReports": "https://github.com/igraph/rigraph/issues", + "Depends": [ + "methods", + "R (>= 3.5.0)" + ], + "Imports": [ + "cli", + "graphics", + "grDevices", + "lifecycle", + "magrittr", + "Matrix", + "pkgconfig (>= 2.0.0)", + "rlang (>= 1.1.0)", + "stats", + "utils", + "vctrs" + ], + "Suggests": [ + "ape (>= 5.7-0.1)", + "callr", + "decor", + "digest", + "igraphdata", + "knitr", + "rgl (>= 1.3.14)", + "rmarkdown", + "scales", + "stats4", + "tcltk", + "testthat", + "vdiffr", + "withr" + ], + "Enhances": [ + "graph" + ], + "LinkingTo": [ + "cpp11 (>= 0.5.0)" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "false", + "Config/build/never-clean": "true", + "Config/comment/compilation-database": "Generate manually with pkgload:::generate_db() for faster pkgload::load_all()", + "Config/Needs/build": "r-lib/roxygen2, devtools, irlba, pkgconfig, igraph/igraph.r2cdocs, moodymudskipper/devtag", + "Config/Needs/coverage": "covr", + "Config/Needs/website": "here, readr, tibble, xmlparsedata, xml2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "aaa-auto, vs-es, scan, vs-operators, weakref, watts.strogatz.game", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3.9000", + "SystemRequirements": "libxml2 (optional), glpk (>= 4.57, optional)", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut] (ORCID: ), Tamás Nepusz [aut] (ORCID: ), Vincent Traag [aut] (ORCID: ), Szabolcs Horvát [aut] (ORCID: ), Fabio Zanini [aut] (ORCID: ), Daniel Noom [aut], Kirill Müller [aut, cre] (ORCID: ), Michael Antonov [ctb], Chan Zuckerberg Initiative [fnd] (ROR: ), David Schoch [aut] (ORCID: ), Maëlle Salmon [aut] (ORCID: )", + "Maintainer": "Kirill Müller ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "irlba": { + "Package": "irlba", + "Version": "2.3.5.1", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices", + "Date": "2021-12-05", + "Authors@R": "c( person(\"Jim\", \"Baglama\", role=c(\"aut\", \"cph\"), email=\"jbaglama@uri.edu\"), person(\"Lothar\", \"Reichel\", role=c(\"aut\", \"cph\"), email=\"reichel@math.kent.edu\"), person(\"B. W.\", \"Lewis\", role=c(\"aut\",\"cre\",\"cph\"), email=\"blewis@illposed.net\"))", + "Description": "Fast and memory efficient methods for truncated singular value decomposition and principal components analysis of large sparse and dense matrices.", + "Depends": [ + "R (>= 3.6.2)", + "Matrix" + ], + "LinkingTo": [ + "Matrix" + ], + "Imports": [ + "stats", + "methods" + ], + "License": "GPL-3", + "BugReports": "https://github.com/bwlewis/irlba/issues", + "RoxygenNote": "5.0.1", + "NeedsCompilation": "yes", + "Author": "Jim Baglama [aut, cph], Lothar Reichel [aut, cph], B. W. Lewis [aut, cre, cph]", + "Maintainer": "B. W. 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Wilke [aut] (Original author, ORCID: ), Thomas Lin Pedersen [aut, cre] (ORCID: ), Posit, PBC [cph, fnd] (ROR: )", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "jpeg": { + "Package": "jpeg", + "Version": "0.1-11", + "Source": "Repository", + "Title": "Read and write JPEG images", + "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.org, )", + "Authors@R": "person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.org\", ORCID=\"0000-0003-2297-1732\"))", + "Maintainer": "Simon Urbanek ", + "Depends": [ + "R (>= 2.9.0)" + ], + "Description": "This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.", + "License": "GPL-2 | GPL-3", + "SystemRequirements": "libjpeg", + "URL": "https://www.rforge.net/jpeg/", + "BugReports": "https://github.com/s-u/jpeg/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository", + "Title": "Obtain 'jQuery' as an HTML Dependency Object", + "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )", + "Description": "Obtain any major version of 'jQuery' () and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "RoxygenNote": "7.0.2", + "Imports": [ + "htmltools" + ], + "Suggests": [ + "testthat" + ], + "NeedsCompilation": "no", + "Author": "Carson Sievert [aut, cre] (), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)", + "Maintainer": "Carson Sievert ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "2.0.0", + "Source": "Repository", + "Title": "A Simple and Robust JSON Parser and Generator for R", + "License": "MIT + file LICENSE", + "Depends": [ + "methods" + ], + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))", + "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805", + "BugReports": "https://github.com/jeroen/jsonlite/issues", + "Maintainer": "Jeroen Ooms ", + "VignetteBuilder": "knitr, R.rsp", + "Description": "A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. 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Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. 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The rsvd package provides several randomized matrix algorithms such as the randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). 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High-performance constructors and exporters provide high compatibility with existing spatial packages, transformers construct new geometries from existing geometries, predicates provide a means to select geometries based on spatial relationships, and accessors extract information about geometries.", + "License": "Apache License (== 2.0)", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "SystemRequirements": "cmake, OpenSSL >= 1.0.1, Abseil >= 20230802.0", + "LinkingTo": [ + "Rcpp", + "wk" + ], + "Imports": [ + "Rcpp", + "wk (>= 0.6.0)" + ], + "Suggests": [ + "bit64", + "testthat (>= 3.0.0)", + "vctrs" + ], + "URL": "https://r-spatial.github.io/s2/, https://github.com/r-spatial/s2, http://s2geometry.io/", + "BugReports": "https://github.com/r-spatial/s2/issues", + "Depends": [ + "R (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Dewey Dunnington [aut] (ORCID: ), Edzer Pebesma [aut, cre] (ORCID: ), Ege Rubak [aut], Jeroen Ooms [ctb] (configure script), Google, Inc. 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Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. Details can be found in Zeileis et al. 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Automatic \"reactive\" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.", + "License": "GPL-3 | file LICENSE", + "URL": "https://shiny.posit.co/, https://github.com/rstudio/shiny", + "BugReports": "https://github.com/rstudio/shiny/issues", + "Depends": [ + "methods", + "R (>= 3.0.2)" + ], + "Imports": [ + "bslib (>= 0.6.0)", + "cachem (>= 1.1.0)", + "cli", + "commonmark (>= 2.0.0)", + "fastmap (>= 1.1.1)", + "fontawesome (>= 0.4.0)", + "glue (>= 1.3.2)", + "grDevices", + "htmltools (>= 0.5.4)", + "httpuv (>= 1.5.2)", + "jsonlite (>= 0.9.16)", + "later (>= 1.0.0)", + "lifecycle (>= 0.2.0)", + "mime (>= 0.3)", + "otel", + "promises (>= 1.5.0)", + "R6 (>= 2.0)", + "rlang (>= 0.4.10)", + "sourcetools", + "tools", + "utils", + "withr", + "xtable" + ], + "Suggests": [ + "Cairo (>= 1.5-5)", + "coro (>= 1.1.0)", + "datasets", + "DT", + "dygraphs", + "future", + "ggplot2", + "knitr (>= 1.6)", + "magrittr", + "markdown", + "mirai", + "otelsdk (>= 0.2.0)", + "ragg", + "reactlog (>= 1.0.0)", + "rmarkdown", + "sass", + "showtext", + "testthat (>= 3.2.1)", + "watcher", + "yaml" + ], + "Config/Needs/check": "shinytest2", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "Collate": "'globals.R' 'app-state.R' 'app_template.R' 'bind-cache.R' 'bind-event.R' 'bookmark-state-local.R' 'bookmark-state.R' 'bootstrap-deprecated.R' 'bootstrap-layout.R' 'conditions.R' 'map.R' 'utils.R' 'bootstrap.R' 'busy-indicators-spinners.R' 'busy-indicators.R' 'cache-utils.R' 'deprecated.R' 'devmode.R' 'diagnose.R' 'extended-task.R' 'fileupload.R' 'graph.R' 'reactives.R' 'reactive-domains.R' 'history.R' 'hooks.R' 'html-deps.R' 'image-interact-opts.R' 'image-interact.R' 'imageutils.R' 'input-action.R' 'input-checkbox.R' 'input-checkboxgroup.R' 'input-date.R' 'input-daterange.R' 'input-file.R' 'input-numeric.R' 'input-password.R' 'input-radiobuttons.R' 'input-select.R' 'input-slider.R' 'input-submit.R' 'input-text.R' 'input-textarea.R' 'input-utils.R' 'insert-tab.R' 'insert-ui.R' 'jqueryui.R' 'knitr.R' 'middleware-shiny.R' 'middleware.R' 'timer.R' 'shiny.R' 'mock-session.R' 'modal.R' 'modules.R' 'notifications.R' 'otel-attr-srcref.R' 'otel-collect.R' 'otel-enable.R' 'otel-error.R' 'otel-label.R' 'otel-reactive-update.R' 'otel-session.R' 'otel-shiny.R' 'otel-with.R' 'priorityqueue.R' 'progress.R' 'react.R' 'reexports.R' 'render-cached-plot.R' 'render-plot.R' 'render-table.R' 'run-url.R' 'runapp.R' 'serializers.R' 'server-input-handlers.R' 'server-resource-paths.R' 'server.R' 'shiny-options.R' 'shiny-package.R' 'shinyapp.R' 'shinyui.R' 'shinywrappers.R' 'showcase.R' 'snapshot.R' 'staticimports.R' 'tar.R' 'test-export.R' 'test-server.R' 'test.R' 'update-input.R' 'utils-lang.R' 'utils-tags.R' 'version_bs_date_picker.R' 'version_ion_range_slider.R' 'version_jquery.R' 'version_jqueryui.R' 'version_selectize.R' 'version_strftime.R' 'viewer.R'", + "NeedsCompilation": "no", + "Author": "Winston Chang [aut] (ORCID: ), Joe Cheng [aut], JJ Allaire [aut], Carson Sievert [aut, cre] (ORCID: ), Barret Schloerke [aut] (ORCID: ), Garrick Aden-Buie [aut] (ORCID: ), Yihui Xie [aut], Jeff Allen [aut], Jonathan McPherson [aut], Alan Dipert [aut], Barbara Borges [aut], Posit Software, PBC [cph, fnd] (ROR: ), jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Prem Nawaz Khan [ctb] (Bootstrap accessibility plugin), Victor Tsaran [ctb] (Bootstrap accessibility plugin), Dennis Lembree [ctb] (Bootstrap accessibility plugin), Srinivasu Chakravarthula [ctb] (Bootstrap accessibility plugin), Cathy O'Connor [ctb] (Bootstrap accessibility plugin), PayPal, Inc [cph] (Bootstrap accessibility plugin), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Brian Reavis [ctb, cph] (selectize.js library), Salmen Bejaoui [ctb, cph] (selectize-plugin-a11y library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "sitmo": { + "Package": "sitmo", + "Version": "2.0.2", + "Source": "Repository", + "Title": "Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files", + "Authors@R": "c(person(\"James\", \"Balamuta\", email = \"balamut2@illinois.edu\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-2826-8458\")), person(\"Thijs\",\"van den Berg\", email = \"thijs@sitmo.com\", role = c(\"aut\", \"cph\")), person(\"Ralf\", \"Stubner\", email = \"ralf.stubner@daqana.com\", role = c(\"ctb\")))", + "Description": "Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence. The objective of this library to consolidate the distribution of the 'sitmo' (C++98 & C++11), 'threefry' and 'vandercorput' (C++11-only) engines on CRAN by enabling others to link to the header files inside of 'sitmo' instead of including a copy of each engine within their individual package. Lastly, the package contains example implementations using the 'sitmo' package and three accompanying vignette that provide additional information.", + "Depends": [ + "R (>= 3.2.0)" + ], + "URL": "https://github.com/coatless/sitmo, http://thecoatlessprofessor.com/projects/sitmo/, https://github.com/stdfin/random/", + "BugReports": "https://github.com/coatless/sitmo/issues", + "License": "MIT + file LICENSE", + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 0.12.13)" + ], + "RoxygenNote": "7.1.1", + "Suggests": [ + "knitr", + "rmarkdown", + "ggplot2" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "James Balamuta [aut, cre, cph] (), Thijs van den Berg [aut, cph], Ralf Stubner [ctb]", + "Maintainer": "James Balamuta ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "snow": { + "Package": "snow", + "Version": "0.4-4", + "Source": "Repository", + "Title": "Simple Network of Workstations", + "Author": "Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova", + "Description": "Support for simple parallel computing in R.", + "Maintainer": "Luke Tierney ", + "Suggests": [ + "rlecuyer" + ], + "Enhances": [ + "Rmpi" + ], + "License": "GPL", + "Depends": [ + "R (>= 2.13.1)", + "utils" + ], + "NeedsCompilation": "no", + "Repository": "https://packagemanager.posit.co/cran/latest", + "Encoding": "UTF-8" + }, + "sourcetools": { + "Package": "sourcetools", + "Version": "0.1.7-1", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for Reading, Tokenizing and Parsing R Code", + "Author": "Kevin Ushey", + "Maintainer": "Kevin Ushey ", + "Description": "Tools for the reading and tokenization of R code. The 'sourcetools' package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.", + "License": "MIT + file LICENSE", + "Depends": [ + "R (>= 3.0.2)" + ], + "Suggests": [ + "testthat" + ], + "RoxygenNote": "5.0.1", + "BugReports": "https://github.com/kevinushey/sourcetools/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "sp": { + "Package": "sp", + "Version": "2.2-0", + "Source": "Repository", + "Title": "Classes and Methods for Spatial Data", + "Authors@R": "c(person(\"Edzer\", \"Pebesma\", role = c(\"aut\", \"cre\"), email = \"edzer.pebesma@uni-muenster.de\"), person(\"Roger\", \"Bivand\", role = \"aut\", email = \"Roger.Bivand@nhh.no\"), person(\"Barry\", \"Rowlingson\", role = \"ctb\"), person(\"Virgilio\", \"Gomez-Rubio\", role = \"ctb\"), person(\"Robert\", \"Hijmans\", role = \"ctb\"), person(\"Michael\", \"Sumner\", role = \"ctb\"), person(\"Don\", \"MacQueen\", role = \"ctb\"), person(\"Jim\", \"Lemon\", role = \"ctb\"), person(\"Finn\", \"Lindgren\", role = \"ctb\"), person(\"Josh\", \"O'Brien\", role = \"ctb\"), person(\"Joseph\", \"O'Rourke\", role = \"ctb\"), person(\"Patrick\", \"Hausmann\", role = \"ctb\"))", + "Depends": [ + "R (>= 3.5.0)", + "methods" + ], + "Imports": [ + "utils", + "stats", + "graphics", + "grDevices", + "lattice", + "grid" + ], + "Suggests": [ + "RColorBrewer", + "gstat", + "deldir", + "knitr", + "maps", + "mapview", + "rmarkdown", + "sf", + "terra", + "raster" + ], + "Description": "Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see for details.", + "License": "GPL (>= 2)", + "URL": "https://github.com/edzer/sp/ https://edzer.github.io/sp/", + "BugReports": "https://github.com/edzer/sp/issues", + "Collate": "bpy.colors.R AAA.R Class-CRS.R CRS-methods.R Class-Spatial.R Spatial-methods.R projected.R Class-SpatialPoints.R SpatialPoints-methods.R Class-SpatialPointsDataFrame.R SpatialPointsDataFrame-methods.R Class-SpatialMultiPoints.R SpatialMultiPoints-methods.R Class-SpatialMultiPointsDataFrame.R SpatialMultiPointsDataFrame-methods.R Class-GridTopology.R Class-SpatialGrid.R Class-SpatialGridDataFrame.R Class-SpatialLines.R SpatialLines-methods.R Class-SpatialLinesDataFrame.R SpatialLinesDataFrame-methods.R Class-SpatialPolygons.R Class-SpatialPolygonsDataFrame.R SpatialPolygons-methods.R SpatialPolygonsDataFrame-methods.R GridTopology-methods.R SpatialGrid-methods.R SpatialGridDataFrame-methods.R SpatialPolygons-internals.R point.in.polygon.R SpatialPolygons-displayMethods.R zerodist.R image.R stack.R bubble.R mapasp.R select.spatial.R gridded.R asciigrid.R spplot.R over.R spsample.R recenter.R dms.R gridlines.R spdists.R rbind.R flipSGDF.R chfids.R loadmeuse.R compassRose.R surfaceArea.R spOptions.R subset.R disaggregate.R sp_spat1.R merge.R aggregate.R elide.R sp2Mondrian.R", + "VignetteBuilder": "knitr", + "NeedsCompilation": "yes", + "Author": "Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson [ctb], Virgilio Gomez-Rubio [ctb], Robert Hijmans [ctb], Michael Sumner [ctb], Don MacQueen [ctb], Jim Lemon [ctb], Finn Lindgren [ctb], Josh O'Brien [ctb], Joseph O'Rourke [ctb], Patrick Hausmann [ctb]", + "Maintainer": "Edzer Pebesma ", + "Repository": "https://packagemanager.posit.co/cran/latest", + "Encoding": "UTF-8" + }, + "spData": { + "Package": "spData", + "Version": "2.3.4", + "Source": "Repository", + "Title": "Datasets for Spatial Analysis", + "Authors@R": "c(person(\"Roger\", \"Bivand\", role = \"aut\", email=\"Roger.Bivand@nhh.no\", comment = c(ORCID = \"0000-0003-2392-6140\")), person(\"Jakub\", \"Nowosad\", role = c(\"aut\", \"cre\"), email=\"nowosad.jakub@gmail.com\", comment = c(ORCID = \"0000-0002-1057-3721\")), person(\"Robin\", \"Lovelace\", role = \"aut\", comment = c(ORCID = \"0000-0001-5679-6536\")), person(\"Angelos\", \"Mimis\", role = \"ctb\"), person(\"Mark\", \"Monmonier\", role = \"ctb\", comment = \"author of the state.vbm dataset\"), person(\"Greg\", \"Snow\", role = \"ctb\", comment = \"author of the state.vbm dataset\") )", + "Description": "Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep'). Unlike other spatial data packages such as 'rnaturalearth' and 'maps', it also contains data stored in a range of file formats including GeoJSON and GeoPackage, but from version 2.3.4, no longer ESRI Shapefile - use GeoPackage instead. Some of the datasets are designed to illustrate specific analysis techniques. cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "sp" + ], + "Suggests": [ + "foreign", + "sf (>= 0.9-1)", + "spDataLarge (>= 0.4.0)", + "spdep", + "spatialreg" + ], + "License": "CC0", + "RoxygenNote": "7.3.2", + "LazyData": "true", + "URL": "https://jakubnowosad.com/spData/", + "BugReports": "https://github.com/Nowosad/spData/issues", + "Additional_repositories": "https://jakubnowosad.com/drat", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Roger Bivand [aut] (), Jakub Nowosad [aut, cre] (), Robin Lovelace [aut] (), Angelos Mimis [ctb], Mark Monmonier [ctb] (author of the state.vbm dataset), Greg Snow [ctb] (author of the state.vbm dataset)", + "Maintainer": "Jakub Nowosad ", + "Repository": "CRAN" + }, + "sparseMatrixStats": { + "Package": "sparseMatrixStats", + "Version": "1.22.0", + "Source": "Bioconductor", + "Type": "Package", + "Title": "Summary Statistics for Rows and Columns of Sparse Matrices", + "Authors@R": "person(\"Constantin\", \"Ahlmann-Eltze\", email = \"artjom31415@googlemail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3762-068X\"))", + "Description": "High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp", + "Matrix", + "matrixStats (>= 0.60.0)", + "methods" + ], + "Depends": [ + "MatrixGenerics (>= 1.5.3)" + ], + "Suggests": [ + "testthat (>= 2.1.0)", + "knitr", + "bench", + "rmarkdown", + "BiocStyle" + ], + "SystemRequirements": "C++11", + "VignetteBuilder": "knitr", + "URL": "https://github.com/const-ae/sparseMatrixStats", + "BugReports": "https://github.com/const-ae/sparseMatrixStats/issues", + "biocViews": "Infrastructure, Software, DataRepresentation", + "git_url": "https://git.bioconductor.org/packages/sparseMatrixStats", + "git_branch": "RELEASE_3_22", + "git_last_commit": "3acf348", + "git_last_commit_date": "2025-10-29", + "Repository": "Bioconductor 3.22", + "NeedsCompilation": "yes", + "Author": "Constantin Ahlmann-Eltze [aut, cre] (ORCID: )", + "Maintainer": "Constantin Ahlmann-Eltze " + }, + "spatialEco": { + "Package": "spatialEco", + "Version": "2.0-3", + "Source": "Repository", + "Type": "Package", + "Title": "Spatial Analysis and Modelling Utilities", + "Date": "2025-09-29", + "Authors@R": "c( person(family=\"Evans\", given=\"Jeffrey S.\", email = \"jeffrey_evans@tnc.org\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5533-7044\")), person(family=\"Murphy\", given=\"Melanie A.\", role = \"ctb\"),\t\t\t person(family=\"Ram\", given=\"Karthik\", role = \"ctb\") )", + "Description": "Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.", + "Depends": [ + "R (>= 4.2)" + ], + "Imports": [ + "sf", + "terra" + ], + "Suggests": [ + "spatstat.geom (>= 3.0-3)", + "spatstat.explore", + "spdep", + "ks", + "cluster", + "readr", + "RCurl", + "RANN", + "rms", + "yaImpute", + "mgcv", + "zyp", + "SpatialPack (>= 0.3)", + "MASS", + "caret", + "dplyr", + "earth", + "Matrix", + "gstat", + "spatstat.data", + "methods", + "units", + "sp", + "stringr", + "lwgeom", + "geodata" + ], + "Maintainer": "Jeffrey S. Evans ", + "License": "GPL-3", + "URL": "https://github.com/jeffreyevans/spatialEco, https://jeffreyevans.github.io/spatialEco/", + "BugReports": "https://github.com/jeffreyevans/spatialEco/issues", + "NeedsCompilation": "no", + "Repository": "https://packagemanager.posit.co/cran/latest", + "LazyData": "true", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "Author": "Jeffrey S. Evans [aut, cre] (ORCID: ), Melanie A. 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These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) . The models are further described by 'Anselin' (1988) . Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) and (1999) are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determinant term in maximum likelihood and MCMC fitting are compared by 'Bivand et al.' (2013) , and model fitting methods by 'Bivand' and 'Piras' (2015) ; both of these articles include extensive lists of references. A recent review is provided by 'Bivand', 'Millo' and 'Piras' (2021) . 'spatialreg' >= 1.1-* corresponded to 'spdep' >= 1.1-1, in which the model fitting functions were deprecated and passed through to 'spatialreg', but masked those in 'spatialreg'. From versions 1.2-*, the functions have been made defunct in 'spdep'. From version 1.3-6, add Anselin-Kelejian (1997) test to `stsls` for residual spatial autocorrelation .", + "License": "GPL-2", + "URL": "https://github.com/r-spatial/spatialreg/, https://r-spatial.github.io/spatialreg/", + "BugReports": "https://github.com/r-spatial/spatialreg/issues/", + "VignetteBuilder": "knitr", + "NeedsCompilation": "yes", + "RoxygenNote": "6.1.1", + "Author": "Roger Bivand [cre, aut] (ORCID: ), Gianfranco Piras [aut], Luc Anselin [ctb], Andrew Bernat [ctb], Eric Blankmeyer [ctb], Yongwan Chun [ctb], Virgilio Gómez-Rubio [ctb], Daniel Griffith [ctb], Martin Gubri [ctb], Rein Halbersma [ctb], James LeSage [ctb], Angela Li [ctb], Hongfei Li [ctb], Jielai Ma [ctb], Abhirup Mallik [ctb, trl], Giovanni Millo [ctb], Kelley Pace [ctb], Josiah Parry [ctb] (ORCID: ), Pedro Peres-Neto [ctb], Tobias Rüttenauer [ctb], Mauricio Sarrias [ctb], JuanTomas Sayago [ctb], Michael Tiefelsdorf [ctb]", + "Maintainer": "Roger Bivand ", + "Repository": "CRAN" + }, + "spdep": { + "Package": "spdep", + "Version": "1.4-1", + "Source": "Repository", + "Date": "2025-08-25", + "Title": "Spatial Dependence: Weighting Schemes, Statistics", + "Encoding": "UTF-8", + "Authors@R": "c(person(\"Roger\", \"Bivand\", role = c(\"cre\", \"aut\"), email = \"Roger.Bivand@nhh.no\", comment=c(ORCID=\"0000-0003-2392-6140\")), person(\"Micah\", \"Altman\", role = \"ctb\"), person(\"Luc\", \"Anselin\", role = \"ctb\"), person(\"Renato\", \"Assunção\", role = \"ctb\"), person(\"Anil\", \"Bera\", role = \"ctb\"), person(\"Olaf\", \"Berke\", role = \"ctb\"), person(\"F. 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The implementation of most of these measures is described in 'Bivand' and 'Wong' (2018) , with further extensions in 'Bivand' (2022) . 'Lagrange' multiplier tests for spatial dependence in linear models are provided ('Anselin et al'. 1996) , as are 'Rao' score tests for hypothesised spatial 'Durbin' models based on linear models ('Koley' and 'Bera' 2023) . Additions in 2024 include Local Indicators for Categorical Data based on 'Carrer et al.' (2021) and 'Bivand et al.' (2017) ; also Weighted Multivariate Spatial Autocorrelation Measures ('Bavaud' 2024) . . A local indicators for categorical data (LICD) implementation based on 'Carrer et al.' (2021) and 'Bivand et al.' (2017) was added in 1.3-7. Multivariate 'spatialdelta' ('Bavaud' 2024) was added in 1.3-13 ('Bivand' 2025 . From 'spdep' and 'spatialreg' versions >= 1.2-1, the model fitting functions previously present in this package are defunct in 'spdep' and may be found in 'spatialreg'.", + "License": "GPL (>= 2)", + "VignetteBuilder": "knitr", + "RoxygenNote": "RoxygenNote: 6.1.1", + "NeedsCompilation": "yes", + "Author": "Roger Bivand [cre, aut] (ORCID: ), Micah Altman [ctb], Luc Anselin [ctb], Renato Assunção [ctb], Anil Bera [ctb], Olaf Berke [ctb], F. 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Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear model functions including Tweedie and Digamma distributional families, secure convergence and exact distributional calculations for unit deviances.", + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "yes", + "Author": "Gordon Smyth [cre, aut], Lizhong Chen [aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]", + "Repository": "https://packagemanager.posit.co/cran/latest", + "Encoding": "UTF-8" + }, + "stringi": { + "Package": "stringi", + "Version": "1.8.7", + "Source": "Repository", + "Date": "2025-03-27", + "Title": "Fast and Portable Character String Processing Facilities", + "Description": "A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. Documentation about 'stringi' is provided via its website at and the paper by Gagolewski (2022, ).", + "URL": "https://stringi.gagolewski.com/, https://github.com/gagolews/stringi, https://icu.unicode.org/", + "BugReports": "https://github.com/gagolews/stringi/issues", + "SystemRequirements": "ICU4C (>= 61, optional)", + "Type": "Package", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "tools", + "utils", + "stats" + ], + "Biarch": "TRUE", + "License": "file LICENSE", + "Authors@R": "c(person(given = \"Marek\", family = \"Gagolewski\", role = c(\"aut\", \"cre\", \"cph\"), email = \"marek@gagolewski.com\", comment = c(ORCID = \"0000-0003-0637-6028\")), person(given = \"Bartek\", family = \"Tartanus\", role = \"ctb\"), person(\"Unicode, Inc. and others\", role=\"ctb\", comment = \"ICU4C source code, Unicode Character Database\") )", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Marek Gagolewski [aut, cre, cph] (), Bartek Tartanus [ctb], Unicode, Inc. and others [ctb] (ICU4C source code, Unicode Character Database)", + "Maintainer": "Marek Gagolewski ", + "License_is_FOSS": "yes", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "stringr": { + "Package": "stringr", + "Version": "1.6.0", + "Source": "Repository", + "Title": "Simple, Consistent Wrappers for Common String Operations", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with \"NA\"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.", + "License": "MIT + file LICENSE", + "URL": "https://stringr.tidyverse.org, https://github.com/tidyverse/stringr", + "BugReports": "https://github.com/tidyverse/stringr/issues", + "Depends": [ + "R (>= 4.1.0)" + ], + "Imports": [ + "cli", + "glue (>= 1.6.1)", + "lifecycle (>= 1.0.3)", + "magrittr", + "rlang (>= 1.0.0)", + "stringi (>= 1.5.3)", + "vctrs (>= 0.4.0)" + ], + "Suggests": [ + "covr", + "dplyr", + "gt", + "htmltools", + "htmlwidgets", + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/potools/style": "explicit", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre, cph], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "survival": { + "Package": "survival", + "Version": "3.8-3", + "Source": "Repository", + "Title": "Survival Analysis", + "Priority": "recommended", + "Date": "2024-12-17", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "Matrix", + "methods", + "splines", + "stats", + "utils" + ], + "LazyData": "Yes", + "LazyDataCompression": "xz", + "ByteCompile": "Yes", + "Authors@R": "c(person(c(\"Terry\", \"M\"), \"Therneau\", email=\"therneau.terry@mayo.edu\", role=c(\"aut\", \"cre\")), person(\"Thomas\", \"Lumley\", role=c(\"ctb\", \"trl\"), comment=\"original S->R port and R maintainer until 2009\"), person(\"Atkinson\", \"Elizabeth\", role=\"ctb\"), person(\"Crowson\", \"Cynthia\", role=\"ctb\"))", + "Description": "Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.", + "License": "LGPL (>= 2)", + "URL": "https://github.com/therneau/survival", + "NeedsCompilation": "yes", + "Author": "Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009), Atkinson Elizabeth [ctb], Crowson Cynthia [ctb]", + "Maintainer": "Terry M Therneau ", + "Repository": "CRAN" + }, + "sys": { + "Package": "sys", + "Version": "3.4.3", + "Source": "Repository", + "Type": "Package", + "Title": "Powerful and Reliable Tools for Running System Commands in R", + "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"ctb\"))", + "Description": "Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. 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The main use is intended to be from compiled code but 'systemfonts' also provides access from R.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/systemfonts, https://systemfonts.r-lib.org", + "BugReports": "https://github.com/r-lib/systemfonts/issues", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "base64enc", + "grid", + "jsonlite", + "lifecycle", + "tools", + "utils" + ], + "Suggests": [ + "covr", + "farver", + "ggplot2", + "graphics", + "knitr", + "ragg", + "rmarkdown", + "svglite", + "testthat (>= 2.1.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.1)" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/usethis/last-upkeep": "2025-04-23", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "fontconfig, freetype2", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [aut, cre] (ORCID: ), Jeroen Ooms [aut] (ORCID: ), Devon Govett [aut] (Author of font-manager), Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "terra": { + "Package": "terra", + "Version": "1.8-93", + "Source": "Repository", + "Type": "Package", + "Title": "Spatial Data Analysis", + "Date": "2026-01-11", + "Depends": [ + "R (>= 3.5.0)", + "methods" + ], + "Suggests": [ + "parallel", + "tinytest", + "ncdf4", + "sf (>= 0.9-8)", + "deldir", + "XML", + "leaflet (>= 2.2.1)", + "htmlwidgets" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 1.0-10)" + ], + "SystemRequirements": "C++17, GDAL (>= 2.2.3), GEOS (>= 3.4.0), PROJ (>= 4.9.3), TBB, sqlite3", + "Encoding": "UTF-8", + "Language": "en-US", + "Maintainer": "Robert J. Hijmans ", + "Description": "Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on to get started.", + "License": "GPL (>= 3)", + "URL": "https://rspatial.org/, https://rspatial.github.io/terra/", + "BugReports": "https://github.com/rspatial/terra/issues", + "LazyLoad": "yes", + "Authors@R": "c( person(\"Robert J.\", \"Hijmans\", role=c(\"cre\", \"aut\"), email=\"r.hijmans@gmail.com\", comment=c(ORCID=\"0000-0001-5872-2872\")),\t\t\t person(\"Márcia\", \"Barbosa\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8972-7713\")), person(\"Roger\", \"Bivand\", role=\"ctb\", comment=c(ORCID=\"0000-0003-2392-6140\")), person(\"Andrew\", \"Brown\", role=\"ctb\", comment=c(ORCID=\"0000-0002-4565-533X\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment=c(ORCID=\"0000-0003-0787-087X\")), person(\"Emanuele\", \"Cordano\", role=\"ctb\",comment=c(ORCID=\"0000-0002-3508-5898\")), person(\"Krzysztof\", \"Dyba\", role=\"ctb\", comment=c(ORCID=\"0000-0002-8614-3816\")), person(\"Edzer\", \"Pebesma\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8049-7069\")), person(\"Barry\", \"Rowlingson\", role=\"ctb\", comment=c(ORCID=\"0000-0002-8586-6625\")), person(\"Michael D.\", \"Sumner\", role=\"ctb\", comment=c(ORCID=\"0000-0002-2471-7511\")))", + "NeedsCompilation": "yes", + "Author": "Robert J. Hijmans [cre, aut] (ORCID: ), Márcia Barbosa [ctb] (ORCID: ), Roger Bivand [ctb] (ORCID: ), Andrew Brown [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Emanuele Cordano [ctb] (ORCID: ), Krzysztof Dyba [ctb] (ORCID: ), Edzer Pebesma [ctb] (ORCID: ), Barry Rowlingson [ctb] (ORCID: ), Michael D. Sumner [ctb] (ORCID: )", + "Repository": "CRAN" + }, + "textshaping": { + "Package": "textshaping", + "Version": "1.0.4", + "Source": "Repository", + "Title": "Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. '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", + "stats", + "stringi", + "systemfonts (>= 1.3.0)", + "utils" + ], + "Suggests": [ + "covr", + "grDevices", + "grid", + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.1)", + "systemfonts (>= 1.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-23", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "freetype2, harfbuzz, fribidi", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "tibble": { + "Package": "tibble", + "Version": "3.3.1", + "Source": "Repository", + "Title": "Simple Data Frames", + "Authors@R": "c( person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"aut\"), person(\"Romain\", \"Francois\", , \"romain@r-enthusiasts.com\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", , \"jenny@rstudio.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "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": [ + "cli", + "lifecycle (>= 1.0.0)", + "magrittr", + "methods", + "pillar (>= 1.8.1)", + "pkgconfig", + "rlang (>= 1.0.2)", + "utils", + "vctrs (>= 0.5.0)" + ], + "Suggests": [ + "bench", + "bit64", + "blob", + "brio", + "callr", + "DiagrammeR", + "dplyr", + "evaluate", + "formattable", + "ggplot2", + "here", + "hms", + "htmltools", + "knitr", + "lubridate", + "nycflights13", + "pkgload", + "purrr", + "rmarkdown", + "stringi", + "testthat (>= 3.0.2)", + "tidyr", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/autostyle/rmd": "false", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "vignette-formats, as_tibble, add, invariants", + "Config/usethis/last-upkeep": "2025-06-07", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3.9000", + "NeedsCompilation": "yes", + "Author": "Kirill Müller [aut, cre] (ORCID: ), Hadley Wickham [aut], Romain Francois [ctb], Jennifer Bryan [ctb], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "tidyr": { + "Package": "tidyr", + "Version": "1.3.2", + "Source": "Repository", + "Title": "Tidy Messy Data", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\"), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevin@posit.co\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).", + "License": "MIT + file LICENSE", + "URL": "https://tidyr.tidyverse.org, https://github.com/tidyverse/tidyr", + "BugReports": "https://github.com/tidyverse/tidyr/issues", + "Depends": [ + "R (>= 4.1.0)" + ], + "Imports": [ + "cli (>= 3.4.1)", + "dplyr (>= 1.1.0)", + "glue", + "lifecycle (>= 1.0.3)", + "magrittr", + "purrr (>= 1.0.1)", + "rlang (>= 1.1.1)", + "stringr (>= 1.5.0)", + "tibble (>= 2.1.1)", + "tidyselect (>= 1.2.1)", + "utils", + "vctrs (>= 0.5.2)" + ], + "Suggests": [ + "covr", + "data.table", + "knitr", + "readr", + "repurrrsive (>= 1.1.0)", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.0)" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Davis Vaughan [aut], Maximilian Girlich [aut], Kevin Ushey [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.2.1", + "Source": "Repository", + "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'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.", + "License": "MIT + file LICENSE", + "URL": "https://tidyselect.r-lib.org, https://github.com/r-lib/tidyselect", + "BugReports": "https://github.com/r-lib/tidyselect/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli (>= 3.3.0)", + "glue (>= 1.3.0)", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.0.4)", + "vctrs (>= 0.5.2)", + "withr" + ], + "Suggests": [ + "covr", + "crayon", + "dplyr", + "knitr", + "magrittr", + "rmarkdown", + "stringr", + "testthat (>= 3.1.1)", + "tibble (>= 2.1.3)" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "true", + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.0.9000", + "NeedsCompilation": "yes", + "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "tiff": { + "Package": "tiff", + "Version": "0.1-12", + "Source": "Repository", + "Title": "Read and Write TIFF Images", + "Author": "Simon Urbanek [aut, cre], Kent Johnson [ctb]", + "Maintainer": "Simon Urbanek ", + "Depends": [ + "R (>= 2.9.0)" + ], + "Description": "Functions to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors, including native image representation.", + "License": "GPL-2 | GPL-3", + "SystemRequirements": "tiff and jpeg libraries", + "URL": "https://www.rforge.net/tiff/", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.58", + "Source": "Repository", + "Type": "Package", + "Title": "Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Devon\", \"Ryan\", role = \"ctb\", email = \"dpryan79@gmail.com\", comment = c(ORCID = \"0000-0002-8549-0971\")), person(\"Ethan\", \"Heinzen\", role = \"ctb\"), person(\"Fernando\", \"Cagua\", role = \"ctb\"), person() )", + "Description": "Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. 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": "7.3.3", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (ORCID: ), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (ORCID: ), Devon Ryan [ctb] (ORCID: ), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.5.0", + "Source": "Repository", + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.5.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "units": { + "Package": "units", + "Version": "1.0-0", + "Source": "Repository", + "Title": "Measurement Units for R Vectors", + "Authors@R": "c(person(\"Edzer\", \"Pebesma\", role = c(\"aut\", \"cre\"), email = \"edzer.pebesma@uni-muenster.de\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(\"Thomas\", \"Mailund\", role = \"aut\", email = \"mailund@birc.au.dk\"), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"James\", \"Hiebert\", role = \"ctb\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", email = \"iucar@fedoraproject.org\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Thomas Lin\", \"Pedersen\", role = \"ctb\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "Rcpp" + ], + "LinkingTo": [ + "Rcpp (>= 0.12.10)" + ], + "Suggests": [ + "NISTunits", + "measurements", + "xml2", + "magrittr", + "pillar (>= 1.3.0)", + "dplyr (>= 1.0.0)", + "vctrs (>= 0.3.1)", + "ggplot2 (> 3.2.1)", + "testthat (>= 3.0.0)", + "vdiffr", + "knitr", + "rvest", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "Description": "Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion. Documentation about 'units' is provided in the paper by Pebesma, Mailund & Hiebert (2016, ), included in this package as a vignette; see 'citation(\"units\")' for details.", + "SystemRequirements": "udunits-2", + "License": "GPL-2", + "URL": "https://r-quantities.github.io/units/, https://github.com/r-quantities/units", + "BugReports": "https://github.com/r-quantities/units/issues", + "RoxygenNote": "7.3.3", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Edzer Pebesma [aut, cre] (ORCID: ), Thomas Mailund [aut], Tomasz Kalinowski [aut], James Hiebert [ctb], Iñaki Ucar [aut] (ORCID: ), Thomas Lin Pedersen [ctb]", + "Maintainer": "Edzer Pebesma ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.6", + "Source": "Repository", + "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\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://krlmlr.github.io/utf8/, https://github.com/krlmlr/utf8", + "BugReports": "https://github.com/krlmlr/utf8/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre] (ORCID: ), Unicode, Inc. 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An implementation of the related LargeVis method of Tang et al. (2016) is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. 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These formats are useful in R only if the information they contain can be accessed in R, for which high-performance functions are provided here.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Suggests": [ + "testthat (>= 3.0.0)", + "vctrs (>= 0.3.0)", + "sf", + "tibble", + "readr" + ], + "URL": "https://paleolimbot.github.io/wk/, https://github.com/paleolimbot/wk", + "BugReports": "https://github.com/paleolimbot/wk/issues", + "Config/testthat/edition": "3", + "Depends": [ + "R (>= 2.10)" + ], + "LazyData": "true", + "NeedsCompilation": "yes", + "Author": "Dewey Dunnington [aut, cre] (ORCID: ), Edzer Pebesma [aut] (ORCID: ), Anthony North [ctb]", + "Repository": "CRAN" + }, + "xfun": { + "Package": "xfun", + "Version": "0.56", + "Source": "Repository", + "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\", URL = \"https://yihui.org\")), 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" + ], + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown (>= 0.6)", + "commonmark", + "knitr (>= 1.50)", + "remotes", + "pak", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "data.table", + "qs2" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (ORCID: , URL: https://yihui.org), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (ORCID: ), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Date": "2019-04-08", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott ", + "Imports": [ + "stats", + "utils" + ], + "Suggests": [ + "knitr", + "plm", + "zoo", + "survival" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "https://packagemanager.posit.co/cran/latest", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]", + "Encoding": "UTF-8" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.12", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"cre\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Shawn\", \"Garbett\", , \"shawn.garbett@vumc.org\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4079-5621\")), person(\"Jeremy\", \"Stephens\", role = c(\"aut\", \"ctb\")), person(\"Kirill\", \"Simonov\", role = \"aut\"), person(\"Yihui\", \"Xie\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Zhuoer\", \"Dong\", role = \"ctb\"), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"reikoch\", role = \"ctb\"), person(\"Will\", \"Beasley\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5613-5006\")), person(\"Brendan\", \"O'Connor\", role = \"ctb\"), person(\"Michael\", \"Quinn\", role = \"ctb\"), person(\"Charlie\", \"Gao\", role = \"ctb\"), person(c(\"Gregory\", \"R.\"), \"Warnes\", role = \"ctb\"), person(c(\"Zhian\", \"N.\"), \"Kamvar\", role = \"ctb\") )", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://yaml.r-lib.org, https://github.com/r-lib/yaml/", + "BugReports": "https://github.com/r-lib/yaml/issues", + "Suggests": [ + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "VignetteBuilder": "knitr", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [cre] (ORCID: ), Shawn Garbett [ctb] (ORCID: ), Jeremy Stephens [aut, ctb], Kirill Simonov [aut], Yihui Xie [ctb] (ORCID: ), Zhuoer Dong [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb] (ORCID: ), Brendan O'Connor [ctb], Michael Quinn [ctb], Charlie Gao [ctb], Gregory R. Warnes [ctb], Zhian N. Kamvar [ctb]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "zeallot": { + "Package": "zeallot", + "Version": "0.2.0", + "Source": "Repository", + "Type": "Package", + "Title": "Multiple, Unpacking, and Destructuring Assignment", + "Authors@R": "c( person(\"Nathan\", \"Teetor\", email = \"nate@haufin.ch\", role = c(\"aut\", \"cre\")), person(\"Paul\", \"Teetor\", role = \"ctb\"))", + "Description": "Provides a %<-% operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.", + "URL": "https://github.com/r-lib/zeallot", + "BugReports": "https://github.com/r-lib/zeallot/issues", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.2)" + ], + "Suggests": [ + "codetools", + "testthat", + "knitr", + "rmarkdown", + "purrr" + ], + "NeedsCompilation": "no", + "Author": "Nathan Teetor [aut, cre], Paul Teetor [ctb]", + "Maintainer": "Nathan Teetor ", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-15", + "Source": "Repository", + "Date": "2025-12-15", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "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 = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.5.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (ORCID: ), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + } + } +} diff --git a/spatial/renv/.gitignore b/spatial/renv/.gitignore new file mode 100644 index 00000000..0ec0cbba --- /dev/null +++ b/spatial/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/spatial/renv/activate.R b/spatial/renv/activate.R new file mode 100644 index 00000000..4eba67cf --- /dev/null +++ b/spatial/renv/activate.R @@ -0,0 +1,1403 @@ + +local({ + + # the requested version of renv + version <- "1.1.6" + attr(version, "md5") <- "3036c4b273d882c56e8cdd660ebaf6f0" + 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 + # 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;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-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) + + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # try to install renv from cache + md5 <- attr(version, "md5", exact = TRUE) + if (length(md5)) { + pkgpath <- renv_bootstrap_find(version) + if (length(pkgpath) && file.exists(pkgpath)) { + file.copy(pkgpath, library, recursive = TRUE) + return(invisible()) + } + } + + # 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)) { + + # split on ';' if present + parts <- strsplit(repos, ";", fixed = TRUE)[[1L]] + + # split into named repositories if present + idx <- regexpr("=", parts, fixed = TRUE) + keys <- substring(parts, 1L, idx - 1L) + vals <- substring(parts, idx + 1L) + names(vals) <- keys + + # if we have a single unnamed repository, call it CRAN + if (length(vals) == 1L && identical(keys, "")) + names(vals) <- "CRAN" + + return(vals) + + } + + # 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$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_find <- function(version) { + + path <- renv_bootstrap_find_cache(version) + if (length(path) && file.exists(path)) { + catf("- Using renv %s from global package cache", version) + return(path) + } + + } + + renv_bootstrap_find_cache <- function(version) { + + md5 <- attr(version, "md5", exact = TRUE) + if (is.null(md5)) + return() + + # infer path to renv cache + cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "") + if (!nzchar(cache)) { + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) { + root <- tools$R_user_dir("renv", "cache") + cache <- file.path(root, "cache") + } + } + + # start completing path to cache + file.path( + cache, + renv_bootstrap_cache_version(), + renv_bootstrap_platform_prefix(), + "renv", + version, + md5, + "renv" + ) + + } + + 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 (is.null(token)) + 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_default <- function() { + + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) + + # 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) + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() + + # build list of path components + components <- c(version, 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"]] + 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) { + 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(project, libpath, version) + } + + renv_bootstrap_run <- function(project, libpath, version) { + + # 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 = project)) + } + + # 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_bootstrap_cache_version <- function() { + # NOTE: users should normally not override the cache version; + # this is provided just to make testing easier + Sys.getenv("RENV_CACHE_VERSION", unset = "v5") + } + + renv_bootstrap_cache_version_previous <- function() { + version <- renv_bootstrap_cache_version() + number <- as.integer(substring(version, 2L)) + paste("v", number - 1L, sep = "") + } + + 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_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + + # arrays + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + + # maps + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + 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 + + } + + # 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 + + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # 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 -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) + renv_json_read_remap(result, patterns) + + } + + + # 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() + +}) diff --git a/spatial/renv/settings.json b/spatial/renv/settings.json new file mode 100644 index 00000000..42fe642f --- /dev/null +++ b/spatial/renv/settings.json @@ -0,0 +1,20 @@ +{ + "bioconductor.version": "3.22", + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.dev": false, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/spatial/spatial.Rproj b/spatial/spatial.Rproj new file mode 100644 index 00000000..98df0873 --- /dev/null +++ b/spatial/spatial.Rproj @@ -0,0 +1,16 @@ +Version: 1.0 + +RestoreWorkspace: No +SaveWorkspace: No +AlwaysSaveHistory: No + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes