{ "_id": "6a494e3ef6c47c441949a0a1", "Package": "spatialFDA", "Title": "A Tool for Spatial Multi-sample Comparisons", "Version": "1.5.0", "Authors@R": "c(\nperson(\"Martin\", \"Emons\", , \"martin.emons@uzh.ch\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0000-5219-5311\")),\nperson(\"Samuel\", \"Gunz\", ,role=\"aut\",\ncomment = c(ORCID = \"0000-0002-8909-0932\")),\nperson(\"Fabian\", \"Scheipl\", , role=\"aut\",\ncomment = c(ORCID = \"0000-0001-8172-3603\")),\nperson(\"Elizabeth\", \"Purdom\", , role=\"aut\",\ncomment = c(ORCID = \"0000-0001-9455-7990\")),\nperson(\"Mark D.\", \"Robinson\", , \"mark.robinson@mls.uzh.ch\", role = c(\"aut\", \"fnd\"),\ncomment = c(ORCID = \"0000-0002-3048-5518\")))", "URL": "https://github.com/mjemons/spatialFDA", "BugReports": "https://github.com/mjemons/spatialFDA/issues", "Description": "spatialFDA is a package to calculate spatial statistics\nmetrics. The package takes a SpatialExperiment object and\ncalculates spatial statistics metrics using the package\nspatstat. Then it compares the resulting functions across\nsamples/conditions using functional additive models as\nimplemented in the package refund. Furthermore, it provides\nexploratory visualisations using functional principal component\nanalysis, as well implemented in refund.", "License": "GPL (>= 3) + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "biocViews": "Software, Spatial, Transcriptomics", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts libicu-dev\nlibpng-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:04:16 UTC", "RemoteUrl": "https://github.com/bioc/spatialFDA", "RemoteRef": "HEAD", "RemoteSha": "a662089b4f14980d2effbb98935d037cd846be87", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 23:02:55 UTC", "User": "root" }, "Author": "Martin Emons [aut, cre] (ORCID:\n),\nSamuel Gunz [aut] (ORCID: ),\nFabian Scheipl [aut] (ORCID: ),\nElizabeth Purdom [aut] (ORCID: ),\nMark D. Robinson [aut, fnd] (ORCID:\n)", "Maintainer": "Martin Emons ", "_user": "bioc", "_type": "src", "_file": "spatialFDA_1.5.0.tar.gz", "_fileid": "https://r2.ropensci.org/062dc397ae2a44a275b8a01f33a6601e0f8fad0abf2dc7176db05825f3331933", "_filesize": 6137227, "_sha256": "062dc397ae2a44a275b8a01f33a6601e0f8fad0abf2dc7176db05825f3331933", "_expires": "2026-10-12T18:17:32.000Z", "_created": "2026-07-03T23:02:55.000Z", "_published": "2026-07-04T18:17:34.166Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477", "_status": "success", "_upstream": "https://github.com/bioc/spatialFDA", "_commit": { "id": "a662089b4f14980d2effbb98935d037cd846be87", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381456 }, "_maintainer": { "name": "Martin Emons", "email": "martin.emons@uzh.ch", "login": "mjemons", "description": "PhD Student in Statistical Bioinformatics @uzh ", "uuid": 55688661 }, "_distro": "resolute", "_jobs": [ { "job": 85155566978, "time": 214, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8075949484" }, { "job": 85155566940, "time": 631, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8076006168" }, { "job": 85155566916, "time": 628, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8076005292" }, { "job": 85155567065, "time": 489, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8075986918" }, { "job": 85155566939, "time": 491, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8075987315" }, { "job": 85155566821, "time": 433, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8075918945" }, { "job": 85155566912, "time": 185, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8075944959" }, { "job": 85155566966, "time": 558, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8075996486" }, { "job": 85155567076, "time": 652, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8076008595" }, { "job": 85155566943, "time": 558, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8075996600" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "refund", "role": "Imports" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "spatstat.explore", "role": "Imports" }, { "package": "spatstat.geom", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "fda", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "ExperimentHub", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "mgcv", "role": "Imports" }, { "package": "stringr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 4 }, { "week": "2025-33", "n": 9 }, { "week": "2025-34", "n": 2 }, { "week": "2025-35", "n": 3 }, { "week": "2025-36", "n": 5 }, { "week": "2025-39", "n": 1 }, { "week": "2025-40", "n": 4 }, { "week": "2025-41", "n": 5 }, { "week": "2025-42", "n": 4 }, { "week": "2025-43", "n": 9 }, { "week": "2025-44", "n": 2 }, { "week": "2025-45", "n": 2 }, { "week": "2026-12", "n": 1 }, { "week": "2026-13", "n": 1 }, { "week": "2026-16", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23" } ], "_topics": [ "software", "spatial", "transcriptomics" ], "_stars": 8, "_contributors": [ { "user": "mjemons", "count": 187, "uuid": 55688661 }, { "user": "sgunz", "count": 13, "uuid": 24435148 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/mjemons/spatialfda", "_searchresults": 31, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/spatialFDA.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/mjemons/spatialfda", "_realowner": "bioc", "_cranurl": false, "_exports": [ ".dfToppp", ".extractMetric", ".loadExample", ".speToDf", "calcCrossMetricPerFov", "calcMetricPerFov", "crossSpatialInference", "extractCrossInferenceData", "functionalGam", "functionalPCA", "plotCrossFOV", "plotCrossHeatmap", "plotCrossMetricPerFov", "plotFbPlot", "plotFpca", "plotMdl", "plotMetricPerFov", "prepData", "rMaxHeuristic", "spatialInference" ], "_help": [ { "page": "dot-dfToppp", "title": "Convert SpatialExperiment object to ppp object", "topics": [ ".dfToppp" ] }, { "page": "dot-extractMetric", "title": "Compute a spatial metric on a SpatialExperiment object", "topics": [ ".extractMetric" ] }, { "page": "dot-loadExample", "title": "load Example dataset from Damond et al. (2019)", "topics": [ ".loadExample" ] }, { "page": "dot-speToDf", "title": "Transform a SpatialExperiment into a dataframe", "topics": [ ".speToDf" ] }, { "page": "calcCrossMetricPerFov", "title": "Calculate cross spatial metrics for all combinations per FOV", "topics": [ "calcCrossMetricPerFov" ] }, { "page": "calcMetricPerFov", "title": "Calculate a spatial metric on a 'SpatialExperiment' object per field of view", "topics": [ "calcMetricPerFov" ] }, { "page": "coef.functionalGam", "title": "Coef for functionalGam object", "topics": [ "coef.functionalGam" ] }, { "page": "crossSpatialInference", "title": "Function for Cross Spatial Inference", "topics": [ "crossSpatialInference" ] }, { "page": "extractCrossInferenceData", "title": "Reshaping the Result of a Cross Spatial Inference to a Dataframe", "topics": [ "extractCrossInferenceData" ] }, { "page": "functionalGam", "title": "General additive model with functional response", "topics": [ "functionalGam" ] }, { "page": "functionalPCA", "title": "Functional Principal Component Analysis", "topics": [ "functionalPCA" ] }, { "page": "plotCrossFOV", "title": "Creates a nXn plot of the cross metrics per sample", "topics": [ "plotCrossFOV" ] }, { "page": "plotCrossHeatmap", "title": "Plotting the Result of a Cross Spatial Inference", "topics": [ "plotCrossHeatmap" ] }, { "page": "plotCrossMetricPerFov", "title": "Plot a cross type spatial metric per field of view", "topics": [ "plotCrossMetricPerFov" ] }, { "page": "plotFbPlot", "title": "Functional boxplot of spatstat curves", "topics": [ "plotFbPlot" ] }, { "page": "plotFpca", "title": "Plot a biplot from an fPCA analysis", "topics": [ "plotFpca" ] }, { "page": "plotMdl", "title": "Plot a pffr model object", "topics": [ "plotMdl" ] }, { "page": "plotMetricPerFov", "title": "Plot a spatial metric per field of view", "topics": [ "plotMetricPerFov" ] }, { "page": "prepData", "title": "Prepare data from calcMetricRes to be in the right format for FDA", "topics": [ "prepData" ] }, { "page": "print.fpca", "title": "print the fPCA results", "topics": [ "print.fpca" ] }, { "page": "rMaxHeuristic", "title": "Heuristic for the choice of rMax", "topics": [ "rMaxHeuristic" ] }, { "page": "spatialInference", "title": "Statistical Inference on Spatial Statistics Functions", "topics": [ "spatialInference" ] }, { "page": "summary.functionalGam", "title": "Summary for functionalGam object", "topics": [ "summary.functionalGam" ] } ], "_readme": "https://github.com/bioc/spatialFDA/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationHub", "ash", "askpass", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "Biostrings", "bit", "bit64", "bitops", "blob", "boot", "cachem", "cli", "cluster", "colorspace", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "deldir", "deSolve", "dplyr", "ExperimentHub", "farver", "fastmap", "fda", "fds", "filelock", "FNN", "gamm4", "generics", "GenomicRanges", "ggplot2", "glue", "goftest", "grpreg", "gtable", "hdrcde", "httr", "httr2", "IRanges", "isoband", "jsonlite", "KEGGREST", "kernlab", "KernSmooth", "ks", "labeling", "lattice", "lifecycle", "lme4", "locfit", "magic", "magick", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mgcv", "mime", "minqa", "multicool", "mvtnorm", "nlme", "nloptr", "openssl", "patchwork", "pbs", "pcaPP", "pillar", "pkgconfig", "png", "polyclip", "pracma", "purrr", "R6", "rainbow", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "Rdpack", "reformulas", "refund", "rjson", "rlang", "RLRsim", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "SummarizedExperiment", "sys", "tensor", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector", "yaml" ], "_vignettes": [ { "source": "DiabetesIsletExample.Rmd", "filename": "DiabetesIsletExample.html", "title": "Functional Data Analysis of Spatial Metrics", "author": "Martin Emons, Fabian Scheipl, Mark D. Robinson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Getting started", "Loading the data", "Visualising the raw data", "Calculating Spatial Statistics Metrics", "Correlation", "Spacing", "Functional boxplot", "Functional principal component analysis", "Functional additive mixed models", "Model evaluation" ], "created": "2024-09-19 16:16:04", "modified": "2026-03-22 10:43:47", "commits": 36 }, { "source": "DiabetesIsletExampleBrief.Rmd", "filename": "DiabetesIsletExampleBrief.html", "title": "Overview Functional Data Analysis of Spatial Metrics", "author": "Martin Emons, Fabian Scheipl, Mark D. Robinson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Getting started", "Loading the data", "Visualising the raw data", "Spatial Inference", "Spatial Statistics Curves", "Functional Boxplot", "Functional GAMM", "Model evaluation" ], "created": "2025-08-12 15:14:04", "modified": "2026-03-25 06:30:02", "commits": 12 } ], "_score": 6.899601659146122, "_indexed": true, "_nocasepkg": "spatialfda", "_universes": [ "bioc", "mjemons" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.0", "date": "2026-07-03T23:07:05.000Z", "distro": "resolute", "commit": "a662089b4f14980d2effbb98935d037cd846be87", "fileid": "https://r2.ropensci.org/b8b4d1c8d248cf03b6885c0ec6c61187d8b7d8619d3b8f185cd3fd83fb66e696", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477" }, { "r": "4.6.1", "os": "linux", "version": "1.5.0", "date": "2026-07-03T23:06:37.000Z", "distro": "resolute", "commit": "a662089b4f14980d2effbb98935d037cd846be87", "fileid": "https://r2.ropensci.org/da282d1a7e65ad364f96319dce82d82e14b757a10efd28e884d5571a4107fe54", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477" }, { "r": "4.5.3", "os": "mac", "version": "1.5.0", "date": "2026-07-03T23:04:51.000Z", "commit": "a662089b4f14980d2effbb98935d037cd846be87", "fileid": "https://r2.ropensci.org/b8eccdea7147b545d97eb7761f6db18c357491e2799335a55948edab265b1da5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477" }, { "r": "4.6.1", "os": "mac", "version": "1.5.0", "date": "2026-07-03T23:05:17.000Z", "commit": "a662089b4f14980d2effbb98935d037cd846be87", "fileid": "https://r2.ropensci.org/feaab6f1c4781d8ab60e380cbd4e8bdbc881fa85f9923fcbb53c969813b6b5fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.0", "date": "2026-07-03T23:06:36.000Z", "commit": "a662089b4f14980d2effbb98935d037cd846be87", "fileid": "https://r2.ropensci.org/ed56fb865de3237a58d3d20cdee2cc8b51d5fd67930b49fedba21161fe135d12", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477" }, { "r": "4.7.0", "os": "win", "version": "1.5.0", "date": "2026-07-03T23:04:38.000Z", "commit": "a662089b4f14980d2effbb98935d037cd846be87", "fileid": "https://r2.ropensci.org/bc3f60eceb43915e1e085c037fe3c3a2de5626200a52486af39ccdf123001f2e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477" }, { "r": "4.5.3", "os": "win", "version": "1.5.0", "date": "2026-07-03T23:04:51.000Z", "commit": "a662089b4f14980d2effbb98935d037cd846be87", "fileid": "https://r2.ropensci.org/4c1a1c418ca2a1f1ee40d58deaa28e2d4bce48c40f6f71c8ef2b3df6114d44b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477" }, { "r": "4.6.1", "os": "win", "version": "1.5.0", "date": "2026-07-03T23:04:38.000Z", "commit": "a662089b4f14980d2effbb98935d037cd846be87", "fileid": "https://r2.ropensci.org/0795dd90aaedaed9474c7b90edc2919dd2be373a6613f8b6aaf4cf4f8c3c7edc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686841477" } ] }