{ "_id": "6a102a86acfb0bcc41c92115", "Package": "DGP4LCF", "Type": "Package", "Title": "Dependent Gaussian Processes for Longitudinal Correlated Factors", "Version": "1.0.0", "Maintainer": "Jiachen Cai ", "Authors@R": "person(\"Jiachen\", \"Cai\", email = \"jiachen.cai@mrc-bsu.cam.ac.uk\", role = c(\"aut\", \"cre\"))", "Description": "Model high-dimensional gene expression trajectories using\ndynamic factor analysis with dependent Gaussian processes", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make", "Repository": "https://jcai-1122.r-universe.dev", "Date/Publication": "2024-05-24 08:41:08 UTC", "RemoteUrl": "https://github.com/jcai-1122/dgp4lcf", "RemoteRef": "HEAD", "RemoteSha": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-22 09:57:35 UTC", "User": "root" }, "Author": "Jiachen Cai [aut, cre]", "MD5sum": "2bbdad41731558680bdf97b37711c925", "_user": "jcai-1122", "_type": "src", "_file": "DGP4LCF_1.0.0.tar.gz", "_fileid": "f4a7efc2befb92df8ae26e15c746b239549233ab3884ddec1706ac3313aa6450", "_filesize": 1128883, "_sha256": "f4a7efc2befb92df8ae26e15c746b239549233ab3884ddec1706ac3313aa6450", "_created": "2026-05-22T09:57:35.000Z", "_published": "2026-05-22T10:05:58.282Z", "_distro": "noble", "_jobs": [ { "job": 77357580544, "time": 192, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7157869162" }, { "job": 77357580532, "time": 194, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7157869894" }, { "job": 77357580521, "time": 183, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7157866001" }, { "job": 77357580622, "time": 172, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7157862375" }, { "job": 77357580652, "time": 202, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7157872207" }, { "job": 77357580572, "time": 427, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7157945161" }, { "job": 77357580553, "time": 176, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7157864603" }, { "job": 77357580620, "time": 252, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7157891755" }, { "job": 77356921888, "time": 259, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7157810062" }, { "job": 77357580515, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 77357580542, "time": 214, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7157875670" }, { "job": 77357580487, "time": 160, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7157858870" }, { "job": 77357580505, "time": 221, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7157878027" } ], "_buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jcai-1122/dgp4lcf", "_commit": { "id": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "author": "jcai-1122 <128384961+jcai-1122@users.noreply.github.com>", "committer": "GitHub ", "message": "Update DESCRIPTION\n\ncapitalize 'gaussian' to meet the requirement of CRAN submission", "time": 1716540068 }, "_maintainer": { "name": "Jiachen Cai", "email": "jiachen.cai@mrc-bsu.cam.ac.uk", "login": "jcai-1122", "description": "", "uuid": 128384961 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "GPFDA", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "factor.switching", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "combinat", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "corrplot", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "jcai-1122", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "jcai-1122", "count": 19, "uuid": 128384961 } ], "_userbio": { "uuid": 128384961, "type": "user", "name": "jcai-1122" }, "_downloads": { "count": 623, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DGP4LCF" }, "_devurl": "https://github.com/jcai-1122/dgp4lcf", "_searchresults": 3, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DGP4LCF.html", "manual.pdf" ], "_homeurl": "https://github.com/jcai-1122/dgp4lcf", "_realowner": "jcai-1122", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2024-05-28" }, { "version": "1.0.0.1", "date": "2025-03-08" } ], "_exports": [ "factor_loading_heatmap", "factor_score_trajectory", "gibbs_after_mcem_algorithm", "gibbs_after_mcem_combine_chains", "gibbs_after_mcem_diff_initials", "gibbs_after_mcem_load_chains", "mcem_algorithm", "mcem_cov_plot", "mcem_parameter_setup", "numerics_summary_do_not_need_alignment", "numerics_summary_need_alignment", "subject_specific_objects", "table_generator" ], "_datasets": [ { "name": "sim_fcs_init", "title": "Initials values.", "object": "sim_fcs_init", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "sim_fcs_results_irregular_6_8", "title": "Results when people have irregularly observed time points (some 6 while others 8).", "object": "sim_fcs_results_irregular_6_8", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "sim_fcs_results_regular_8", "title": "Results when people are observed at common 8 time points.", "object": "sim_fcs_results_regular_8", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "sim_fcs_truth", "title": "Truth of simulated data.", "object": "sim_fcs_truth", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "factor_loading_heatmap", "title": "Displaying significant factor loadings in the heatmap.", "topics": [ "factor_loading_heatmap" ] }, { "page": "factor_score_trajectory", "title": "Plotting figures for factor score trajectory.", "topics": [ "factor_score_trajectory" ] }, { "page": "gibbs_after_mcem_algorithm", "title": "Generating posterior samples for parameters (other than DGP parameters) in the model and predicted gene expression for one chain.", "topics": [ "gibbs_after_mcem_algorithm" ] }, { "page": "gibbs_after_mcem_combine_chains", "title": "Combining from all chains the posterior samples for parameters in the model and predicted gene expressions.", "topics": [ "gibbs_after_mcem_combine_chains" ] }, { "page": "gibbs_after_mcem_diff_initials", "title": "Generating different initials for multiple chains.", "topics": [ "gibbs_after_mcem_diff_initials" ] }, { "page": "gibbs_after_mcem_load_chains", "title": "Loading the saved posterior samples for parameters in the model and predicted gene expressions.", "topics": [ "gibbs_after_mcem_load_chains" ] }, { "page": "mcem_algorithm", "title": "Monte Carlo Expectation Maximization (MCEM) algorithm to return the Maximum Likelihood Estimate (MLE) of DGP Parameters.", "topics": [ "mcem_algorithm" ] }, { "page": "mcem_cov_plot", "title": "Visualizing cross-correlations among factors.", "topics": [ "mcem_cov_plot" ] }, { "page": "mcem_parameter_setup", "title": "Parameters' setup and initial value assignment for the Monte Carlo Expectation Maximization (MCEM) algorithm.", "topics": [ "mcem_parameter_setup" ] }, { "page": "numerics_summary_do_not_need_alignment", "title": "Numerical summary for important continuous variables that do not need alignment.", "topics": [ "numerics_summary_do_not_need_alignment" ] }, { "page": "numerics_summary_need_alignment", "title": "Numerical summary for factor loadings and factor scores, which need alignment.", "topics": [ "numerics_summary_need_alignment" ] }, { "page": "sim_fcs_init", "title": "Initials values.", "topics": [ "sim_fcs_init" ] }, { "page": "sim_fcs_results_irregular_6_8", "title": "Results when people have irregularly observed time points (some 6 while others 8).", "topics": [ "sim_fcs_results_irregular_6_8" ] }, { "page": "sim_fcs_results_regular_8", "title": "Results when people are observed at common 8 time points.", "topics": [ "sim_fcs_results_regular_8" ] }, { "page": "sim_fcs_truth", "title": "Truth of simulated data.", "topics": [ "sim_fcs_truth" ] }, { "page": "subject_specific_objects", "title": "Constructing subject-specific objects required for Gibbs sampler (for subjects with incomplete observations only).", "topics": [ "subject_specific_objects" ] }, { "page": "table_generator", "title": "Generating a table listing all possible combinations of the binary variables for one gene.", "topics": [ "table_generator" ] } ], "_rundeps": [ "ash", "bitops", "cli", "cluster", "coda", "codetools", "colorspace", "combinat", "corrplot", "cpp11", "deldir", "deSolve", "doParallel", "dotCall64", "evaluate", "factor.switching", "farver", "fda", "fda.usc", "fds", "fields", "FNN", "foreach", "ggplot2", "glue", "GPFDA", "gtable", "HDInterval", "hdrcde", "highr", "interp", "isoband", "iterators", "kernlab", "KernSmooth", "knitr", "ks", "kSamples", "labeling", "lattice", "lifecycle", "locfit", "lpSolve", "maps", "MASS", "Matrix", "MatrixModels", "mclust", "mcmc", "MCMCpack", "mgcv", "multicool", "mvtnorm", "nlme", "pcaPP", "pheatmap", "pracma", "quantreg", "R6", "rainbow", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "rlang", "S7", "scales", "spam", "SparseM", "SuppDists", "survival", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "bsfadgp_irregular_data_example.Rmd", "filename": "bsfadgp_irregular_data_example.html", "title": "An Example of Irregular Data Analysis", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-05-17 16:03:21", "modified": "2023-06-26 10:37:55", "commits": 6 }, { "source": "bsfadgp_regular_data_example.Rmd", "filename": "bsfadgp_regular_data_example.html", "title": "An Example of Regular Data Analysis", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-05-17 16:03:21", "modified": "2023-06-26 10:37:55", "commits": 6 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "dgp4lcf", "_universes": [ "jcai-1122" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-22T10:00:29.000Z", "distro": "noble", "arch": "aarch64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "b50d2c12c6e9bf342c5364feb350f72372cf9bbb6c9985f0256cfeabb5bba264", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-22T10:00:24.000Z", "distro": "noble", "arch": "x86_64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "8f9ad2e4484ac818e58f695228ee95d6582e2d85bd05c6c58d64511d0e5c5b5d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-22T10:00:20.000Z", "distro": "noble", "arch": "aarch64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "0cf42947b4d4abbb0361834c5dc03c3b30a77e74e23bb29b17ae18d4ffe9c7e1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-22T10:00:15.000Z", "distro": "noble", "arch": "x86_64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "29e6e97e74ced7ff276e4aeee7063b8068016d9e750425af983d1aea40fcc3ec", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-22T10:00:50.000Z", "arch": "aarch64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "a81ba1443828f5897b292415dbee6d78d01d01deeb8efc54cccaa11afff25aed", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-22T10:03:02.000Z", "arch": "x86_64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "a63899a210a6fce67dab415aac32e2f8dc7e8cc1fb981f2aa78f7d1c061efd86", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-22T10:00:20.000Z", "arch": "aarch64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "46a16140b5d4b238f091935074568f4fa25383e7ee2a7fc05f35740477630cac", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-22T10:01:07.000Z", "arch": "x86_64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "2e4223f60dab0dfa5189538f319b3f34be199ca85a84313bc7eaf264364f758a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-22T09:59:35.000Z", "arch": "x86_64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "29bc93dee9ae47d85b71a81cc67159e47e540bd609bc7694ce7b2324a3588528", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-22T09:59:20.000Z", "arch": "x86_64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "d87264f6c0e3bc978e126d02f7346afd5691c36412d9f9851c75d3ed5b4660b3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-22T10:00:05.000Z", "arch": "x86_64", "commit": "b33082b0d412b6bdcd1751ba7ac1cbe27f5f3685", "fileid": "f777a9a1e80131df1b3a3778097522613a376f954889fd307fddab0c8f3d5a64", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/jcai-1122/actions/runs/26280999878" } ] }