{ "_id": "6a1efe03b401979e73419cfb", "Package": "mxfda", "Title": "A Functional Data Analysis Package for Spatial Single Cell Data", "Version": "0.2.3", "Date": "2025-02-19", "Authors@R": "c(\nperson(\"Julia\", \"Wrobel\", role = c(\"aut\"),\nemail = \"julia.wrobel@emory.edu\",\ncomment = c(ORCID = \"0000-0001-6783-1421\")),\nperson(\"Alex\", \"Soupir\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-1251-9179\"),\nemail = \"alex.soupir@moffitt.org\")\n)", "Description": "Methods and tools for deriving spatial summary functions\nfrom single-cell imaging data and performing functional data\nanalyses. Functions can be applied to other single-cell\ntechnologies such as spatial transcriptomics. Functional\nregression and functional principal component analysis methods\nare in the 'refund' package\n while calculation\nof the spatial summary functions are from the 'spatstat'\npackage .", "License": "MIT + file LICENSE", "URL": "https://github.com/julia-wrobel/mxfda/,\nhttp://juliawrobel.com/mxfda/", "BugReports": "https://github.com/julia-wrobel/mxfda/issues/", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "LazyData": "true", "LazyDataCompression": "bzip2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libx11-dev", "Repository": "https://julia-wrobel.r-universe.dev", "Date/Publication": "2026-02-16 16:15:04 UTC", "RemoteUrl": "https://github.com/julia-wrobel/mxfda", "RemoteRef": "HEAD", "RemoteSha": "0d0d924229d05df16450c2600bb78fc832621c60", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-18 09:48:07 UTC", "User": "root" }, "Author": "Julia Wrobel [aut] (ORCID: ),\nAlex Soupir [aut, cre] (ORCID: )", "Maintainer": "Alex Soupir ", "MD5sum": "1adf768c2e2d61a56a447971c9c1954b", "_user": "julia-wrobel", "_type": "src", "_file": "mxfda_0.2.3.tar.gz", "_fileid": "ed6942a4a70edf866dcd6e439bf4d7ee60d160636f1dbd118f17a611f8ff028f", "_filesize": 5293871, "_sha256": "ed6942a4a70edf866dcd6e439bf4d7ee60d160636f1dbd118f17a611f8ff028f", "_created": "2026-05-18T09:48:07.000Z", "_published": "2026-06-02T16:00:03.416Z", "_distro": "noble", "_jobs": [ { "job": 79114491736, "time": 288, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7054668717" }, { "job": 79114492013, "time": 279, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7054665858" }, { "job": 79114491531, "time": 345, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7054673929" }, { "job": 79114491661, "time": 243, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7054641749" }, { "job": 79114491923, "time": 383, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7054570087" }, { "job": 79114490798, "time": 208, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7363066578" }, { "job": 79114491513, "time": 260, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7054659745" }, { "job": 79114491529, "time": 213, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7054645606" }, { "job": 79114491874, "time": 203, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7054641642" } ], "_buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/julia-wrobel/mxfda", "_commit": { "id": "0d0d924229d05df16450c2600bb78fc832621c60", "author": "ACSoupir ", "committer": "ACSoupir ", "message": "fix long formula parsing, increment patch number\n", "time": 1771258504 }, "_maintainer": { "name": "Alex Soupir", "email": "alex.soupir@moffitt.org", "orcid": "0000-0003-1251-9179" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "magrittr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "refund", "version": ">= 0.1-35", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "mgcv", "role": "Imports" }, { "package": "spatstat.geom", "role": "Imports" }, { "package": "spatstat.explore", "role": "Imports" }, { "package": "SpatEntropy", "role": "Imports" }, { "package": "SimDesign", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "survival", "role": "Suggests" }, { "package": "ggpubr", "role": "Suggests" }, { "package": "spatialTIME", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "broom", "role": "Suggests" }, { "package": "refund.shiny", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "SeuratObject", "role": "Suggests" } ], "_owner": "julia-wrobel", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-35", "n": 1 }, { "week": "2026-08", "n": 1 } ], "_tags": [], "_stars": 1, "_contributors": [ { "user": "acsoupir", "count": 190, "uuid": 34483643 }, { "user": "julia-wrobel", "count": 81, "uuid": 11615315 } ], "_userbio": { "uuid": 11615315, "type": "user", "name": "Julia Wrobel" }, "_downloads": { "count": 212, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mxfda" }, "_devurl": "https://github.com/julia-wrobel/mxfda", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mxfda.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/julia-wrobel/mxfda", "_realowner": "julia-wrobel", "_cranurl": true, "_releases": [ { "version": "0.2.1", "date": "2024-05-08" }, { "version": "0.2.2", "date": "2024-10-07" }, { "version": "0.2.2-1", "date": "2025-02-19" } ], "_exports": [ "%>%", "add_summary_function", "bivariate", "can_permute", "entropy", "extract_c", "extract_entropy", "extract_fpca_object", "extract_fpca_scores", "extract_model", "extract_spatial_summary", "extract_summary_functions", "extract_surface", "filter_data", "filter_spatial", "Gcross", "Gest", "get_data", "is.empty", "Kcross", "Kest", "Lcross", "Lest", "make_mxfda", "metric.exists", "one_zero", "plot_fpc", "plot_mfpc", "run_fcm", "run_fpca", "run_mfcm", "run_mfpca", "run_sofr", "spatialTIME_summary_functions", "univariate" ], "_datasets": [ { "name": "lung_df", "title": "Multiplex imaging data from a non-small cell lung cancer study.", "object": "lung_df", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "image_id", "patient_id", "cell_id", "patientImage_id", "x", "y", "gender", "age", "immune", "survival_days", "survival_status", "phenotype_ck", "phenotype_cd8", "phenotype_cd14", "phenotype_other", "phenotype_cd19", "phenotype_cd4", "stage" ], "rows": 285412, "table": true, "tojson": true }, { "name": "lung_FDA", "title": "Multiplex imaging data from a non-small cell lung cancer study", "object": "lung_FDA", "class": [ "mxFDA" ], "fields": [], "table": false, "tojson": false }, { "name": "ovarian_FDA", "title": "Multiplex imaging data from an ovarian cancer tumor microarray", "object": "ovarian_FDA", "class": [ "mxFDA" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "add_summary_function", "title": "Add Summary Function", "topics": [ "add_summary_function" ] }, { "page": "bivariate", "title": "bivariate", "topics": [ "bivariate" ] }, { "page": "entropy", "title": "Entropy", "topics": [ "entropy" ] }, { "page": "extract_entropy", "title": "extract_entropy", "topics": [ "extract_entropy" ] }, { "page": "extract_fpca_object", "title": "Extract FPCA object", "topics": [ "extract_fpca_object" ] }, { "page": "extract_fpca_scores", "title": "Extract FPCA scores", "topics": [ "extract_fpca_scores" ] }, { "page": "extract_model", "title": "Extract Model", "topics": [ "extract_model" ] }, { "page": "extract_spatial_summary", "title": "Summarise spatial data in mxFDA object", "topics": [ "extract_spatial_summary" ] }, { "page": "extract_summary_functions", "title": "Extract Summary Functions", "topics": [ "extract_summary_functions" ] }, { "page": "extract_surface", "title": "Extract Surface", "topics": [ "extract_surface" ] }, { "page": "filter_spatial", "title": "Filter Spatial data", "topics": [ "filter_spatial" ] }, { "page": "lung_df", "title": "Multiplex imaging data from a non-small cell lung cancer study.", "topics": [ "lung_df" ] }, { "page": "lung_FDA", "title": "Multiplex imaging data from a non-small cell lung cancer study", "topics": [ "lung_FDA" ] }, { "page": "make_mxfda", "title": "Make mxFDA class object", "topics": [ "make_mxfda" ] }, { "page": "ovarian_FDA", "title": "Multiplex imaging data from an ovarian cancer tumor microarray", "topics": [ "ovarian_FDA" ] }, { "page": "plot_fpc", "title": "Create plot of mean +/- scaled eigenfunctions from FPCA", "topics": [ "plot_fpc" ] }, { "page": "plot_mfpc", "title": "Create plot of mean +/- scaled eigenfunctions from FPCA", "topics": [ "plot_mfpc" ] }, { "page": "plot.afcmSurface", "title": "Plot afcm object", "topics": [ "plot.afcmSurface" ] }, { "page": "plot.lfcmSurface", "title": "Plot lfcm surface", "topics": [ "plot.lfcmSurface" ] }, { "page": "plot.mxFDA", "title": "Plot mxFDA object", "topics": [ "plot.mxFDA" ] }, { "page": "plot.sofr", "title": "Plot sofr object", "topics": [ "plot.sofr" ] }, { "page": "run_fcm", "title": "Run Function Cox Models", "topics": [ "run_fcm" ] }, { "page": "run_fpca", "title": "run_fpca", "topics": [ "run_fpca" ] }, { "page": "run_mfcm", "title": "Run function Cox models for data with multiple samples per subject", "topics": [ "run_mfcm" ] }, { "page": "run_mfpca", "title": "run_fpca", "topics": [ "run_mfpca" ] }, { "page": "run_sofr", "title": "Run Scalar on Function Regression", "topics": [ "run_sofr" ] }, { "page": "summary.mxFDA", "title": "Summary method for object of class 'mxFDA'", "topics": [ "summary.mxFDA" ] }, { "page": "univariate", "title": "univariate", "topics": [ "univariate" ] } ], "_pkglogo": "https://github.com/julia-wrobel/mxfda/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/julia-wrobel/mxfda/raw/HEAD/README.md", "_rundeps": [ "abind", "ash", "audio", "beepr", "bitops", "boot", "brio", "callr", "class", "cli", "clipr", "cluster", "codetools", "colorspace", "cpp11", "crayon", "deldir", "desc", "deSolve", "diffobj", "digest", "dplyr", "e1071", "evaluate", "farver", "fda", "fds", "FNN", "fs", "future", "future.apply", "gamm4", "generics", "ggplot2", "globals", "glue", "goftest", "grpreg", "gtable", "hdrcde", "isoband", "jsonlite", "kernlab", "KernSmooth", "ks", "labeling", "lattice", "lifecycle", "listenv", "lme4", "locfit", "magic", "magrittr", "MASS", "Matrix", "mclust", "mgcv", "minqa", "mirai", "multicool", "mvtnorm", "nanonext", "nlme", "nloptr", "parallelly", "pbapply", "pbs", "pcaPP", "pillar", "pkgbuild", "pkgconfig", "pkgload", "plyr", "polyclip", "pracma", "praise", "processx", "progressr", "proxy", "ps", "purrr", "qs2", "R.methodsS3", "R.oo", "R.utils", "R6", "rainbow", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "RCurl", "Rdpack", "reformulas", "refund", "reshape2", "rlang", "RLRsim", "rpart", "rprojroot", "S7", "scales", "sessioninfo", "SimDesign", "SpatEntropy", "spatstat", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.linnet", "spatstat.model", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringfish", "stringi", "stringr", "tensor", "testthat", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "waldo", "withr" ], "_vignettes": [ { "source": "mx_fda.Rmd", "filename": "mx_fda.html", "title": "Defining an mxFDA object", "engine": "knitr::rmarkdown", "headings": [ "VectraPolarisData", "Setting up the mxFDA object", "Make mxFDAobject", "Spatial summary functions based on point processes", "Univariate summary functions", "Plotting the mxFDA object", "Bivariate summary functions", "Plotting bivariate G", "Entropy", "Exploring the S4 object", "SpatialTIME", "References" ], "created": "2023-05-16 12:57:33", "modified": "2024-10-04 14:33:55", "commits": 28 }, { "source": "mx_fpca.Rmd", "filename": "mx_fpca.html", "title": "Functional principal component analysis for spatial summary functions", "engine": "knitr::rmarkdown", "headings": [ "Functional data notation", "Functional principal components analysis (FPCA)", "Background on FPCA", "Implementing FPCA", "Load and visualize data", "Run and visualize FPCA", "Multilevel functional principal components analysis (MFPCA)", "MFPCA Background", "Implementing MFPCA", "Run and visualize MFPCA", "References" ], "created": "2023-11-16 17:41:01", "modified": "2024-10-04 14:33:55", "commits": 11 }, { "source": "mx_funreg.Rmd", "filename": "mx_funreg.html", "title": "Functional regression with spatial summary functions as covariates", "engine": "knitr::rmarkdown", "headings": [ "Ovarian cancer multiplex imaging data", "Functional regression models for survival outcomes", "Cox regression using functional principal components as covariates", "Linear and additive functional Cox regression models", "Linear functional Cox model (LFCM)", "Additive functional Cox model (AFCM)", "Model summaries and C-index", "Functional regression models for binary and continuous outcomes", "Continuous outcome", "Binary outcome" ], "created": "2023-05-16 12:57:33", "modified": "2024-10-04 14:33:55", "commits": 31 } ], "_score": 4.518513939877888, "_indexed": true, "_nocasepkg": "mxfda", "_universes": [ "julia-wrobel" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.3", "date": "2026-05-18T09:52:13.000Z", "distro": "noble", "commit": "0d0d924229d05df16450c2600bb78fc832621c60", "fileid": "15f1141451802477a6c656f39fdbfc57fe9fd3b48d5209ff6179de0b454a56b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754" }, { "r": "4.6.0", "os": "linux", "version": "0.2.3", "date": "2026-05-18T09:51:56.000Z", "distro": "noble", "commit": "0d0d924229d05df16450c2600bb78fc832621c60", "fileid": "73715fcdd1b89c2fb316f4fb0dafcfe40a4c130eef6a120d6eb76391eb876cf4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754" }, { "r": "4.5.3", "os": "mac", "version": "0.2.3", "date": "2026-05-18T09:52:03.000Z", "commit": "0d0d924229d05df16450c2600bb78fc832621c60", "fileid": "40086db7262b3c7d23e3acd37e3282cf503d8bcdb1b1228bdd84364f33f9e53e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754" }, { "r": "4.6.0", "os": "mac", "version": "0.2.3", "date": "2026-05-18T09:50:45.000Z", "commit": "0d0d924229d05df16450c2600bb78fc832621c60", "fileid": "13109f94bdf88291bf72ba465630d3fbcd536e2371ecc2c7ce97190e14173ff7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754" }, { "r": "4.7.0", "os": "win", "version": "0.2.3", "date": "2026-05-18T09:51:19.000Z", "commit": "0d0d924229d05df16450c2600bb78fc832621c60", "fileid": "b84b2b6c23204ffd815bf06229ef5280817c18df020048d15c7438dcd1abb667", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754" }, { "r": "4.5.3", "os": "win", "version": "0.2.3", "date": "2026-05-18T09:50:42.000Z", "commit": "0d0d924229d05df16450c2600bb78fc832621c60", "fileid": "01cb3ea965941f9ef160fcd835f6a7b9553c5f4a7eae049c3139193bba63975e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754" }, { "r": "4.6.0", "os": "win", "version": "0.2.3", "date": "2026-05-18T09:50:25.000Z", "commit": "0d0d924229d05df16450c2600bb78fc832621c60", "fileid": "cae731fad2b9b4af4c1079eaa203cfbd2813a3935bb3742c60bd7f3757ad81a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.3", "date": "2026-06-02T15:59:24.000Z", "commit": "0d0d924229d05df16450c2600bb78fc832621c60", "fileid": "87bad41a57b7fe45587b559de9708b3c0d01847dac6dad22bb0aa24410433e60", "status": "success", "buildurl": "https://github.com/r-universe/julia-wrobel/actions/runs/26025736754" } ] }