{ "_id": "6a197c95acfb0bcc41df65e1", "Package": "MRFcov", "Type": "Package", "Title": "Markov Random Fields with Additional Covariates", "Version": "1.0.39", "URL": "https://github.com/nicholasjclark/MRFcov", "Authors@R": "c(\nperson(\"Nicholas J\", \"Clark\", email = \"nicholas.j.clark1214@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Konstans\", \"Wells\", email = \"konswells@gmail.com\", role = \"aut\"),\nperson(\"Oscar\", \"Lindberg\", email = \"o.lindberg@gmail.com\", role = \"aut\"))", "Maintainer": "Nicholas J Clark ", "Description": "Approximate node interaction parameters of Markov Random\nFields graphical networks. Models can incorporate additional\ncovariates, allowing users to estimate how interactions between\nnodes in the graph are predicted to change across covariate\ngradients. The general methods implemented in this package are\ndescribed in Clark et al. (2018) .", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.2.1", "LazyData": "true", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev", "Repository": "https://nicholasjclark.r-universe.dev", "Date/Publication": "2024-03-27 02:28:25 UTC", "RemoteUrl": "https://github.com/nicholasjclark/mrfcov", "RemoteRef": "HEAD", "RemoteSha": "91d77124c07a7572c292d114a6ed2deca314596c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 10:35:40 UTC", "User": "root" }, "Author": "Nicholas J Clark [aut, cre],\nKonstans Wells [aut],\nOscar Lindberg [aut]", "MD5sum": "bcaba76113e8067047449d70f9482e57", "_user": "nicholasjclark", "_type": "src", "_file": "MRFcov_1.0.39.tar.gz", "_fileid": "c32857d9bed33e433856a2f08d531f52fa44e69b57025975f604c1f1e6129d3c", "_filesize": 1148934, "_sha256": "c32857d9bed33e433856a2f08d531f52fa44e69b57025975f604c1f1e6129d3c", "_created": "2026-05-29T10:35:40.000Z", "_published": "2026-05-29T11:46:29.907Z", "_distro": "noble", "_jobs": [ { "job": 78484439519, "time": 200, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7288761165" }, { "job": 78484439536, "time": 182, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7288756505" }, { "job": 78484439557, "time": 183, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7289865946" }, { "job": 78484439558, "time": 251, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7289886625" }, { "job": 78483898921, "time": 234, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288705598" }, { "job": 78484439522, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7288747512" }, { "job": 78484439546, "time": 460, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7288832567" }, { "job": 78484439570, "time": 452, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7288830782" }, { "job": 78484439538, "time": 489, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7288840407" } ], "_buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/nicholasjclark/mrfcov", "_commit": { "id": "91d77124c07a7572c292d114a6ed2deca314596c", "author": "Nicholas Clark ", "committer": "GitHub ", "message": "Update README.md", "time": 1711506505 }, "_maintainer": { "name": "Nicholas J Clark", "email": "nicholas.j.clark1214@gmail.com", "login": "nicholasjclark", "linkedin": "in/nicholasjoshuaclark", "twitter": "@nj_clark", "description": "Ecologist and quantitative geneticist, interested in multivariate statistics, genetic risk prediction, forecasting, and Bayesian decision theory", "uuid": 35205724 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.3", "role": "Depends" }, { "package": "glmnet", "role": "Depends" }, { "package": "purrr", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "sfsmisc", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "mgcv", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "nicholasjclark", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "conditional-random-fields", "graphical-models", "machine-learning", "markov-random-field", "multivariate-analysis", "multivariate-statistics", "network-analysis", "networks" ], "_stars": 25, "_contributors": [ { "user": "nicholasjclark", "count": 126, "uuid": 35205724 } ], "_userbio": { "uuid": 35205724, "type": "user", "name": "Nicholas Clark", "description": "Ecologist and quantitative geneticist, interested in multivariate statistics, genetic risk prediction, forecasting, and Bayesian decision theory" }, "_downloads": { "count": 218, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MRFcov" }, "_devurl": "https://github.com/nicholasjclark/mrfcov", "_searchresults": 30, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MRFcov.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/nicholasjclark/mrfcov", "_realowner": "nicholasjclark", "_cranurl": true, "_releases": [ { "version": "1.0.35", "date": "2018-08-24" }, { "version": "1.0.36", "date": "2018-11-26" }, { "version": "1.0.37", "date": "2019-04-10" }, { "version": "1.0.38", "date": "2021-03-18" }, { "version": "1.0.39", "date": "2023-04-06" } ], "_exports": [ "bootstrap_MRF", "cv_MRF_diag", "cv_MRF_diag_rep", "cv_MRF_diag_rep_spatial", "MRFcov", "MRFcov_spatial", "plotMRF_hm", "predict_MRF", "predict_MRFnetworks", "prep_MRF_covariates", "prep_MRF_covariates_spatial" ], "_datasets": [ { "name": "Bird.parasites", "title": "Blood parasite occurrences in New Caledonian birds.", "object": "Bird.parasites", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Hzosteropis", "Hkillangoi", "Plas", "Microfilaria", "scale.prop.zos" ], "rows": 449, "table": true, "tojson": true } ], "_help": [ { "page": "Bird.parasites", "title": "Blood parasite occurrences in New Caledonian birds.", "topics": [ "Bird.parasites" ] }, { "page": "bootstrap_MRF", "title": "Bootstrap observations to estimate MRF parameter coefficients", "topics": [ "bootstrap_MRF" ] }, { "page": "cv_MRF_diag", "title": "MRF cross validation and assessment of predictive performance", "topics": [ "cv_MRF_diag", "cv_MRF_diag_rep", "cv_MRF_diag_rep_spatial" ] }, { "page": "MRFcov", "title": "Markov Random Fields with covariates", "topics": [ "MRFcov" ] }, { "page": "MRFcov_spatial", "title": "Spatially structured Markov Random Fields with covariates", "topics": [ "MRFcov_spatial" ] }, { "page": "plotMRF_hm", "title": "Plot MRF interaction parameters as a heatmap", "topics": [ "plotMRF_hm" ] }, { "page": "predict_MRF", "title": "Predict training observations from fitted MRFcov models", "topics": [ "predict_MRF" ] }, { "page": "predict_MRFnetworks", "title": "Extract predicted network metrics for observations in a given dataset using equations from a fitted 'MRFcov' object", "topics": [ "predict_MRFnetworks" ] }, { "page": "prep_MRF_covariates", "title": "Cross-multiply response and covariate variables", "topics": [ "prep_MRF_covariates" ] }, { "page": "prep_MRF_covariates_spatial", "title": "Cross-multiply response and covariate variables and build spatial splines", "topics": [ "prep_MRF_covariates_spatial" ] } ], "_readme": "https://github.com/nicholasjclark/mrfcov/raw/HEAD/docs/README.md", "_rundeps": [ "caret", "class", "cli", "clock", "codetools", "cpp11", "data.table", "diagram", "digest", "dplyr", "e1071", "farver", "foreach", "future", "future.apply", "generics", "ggplot2", "glmnet", "globals", "glue", "gower", "gridExtra", "gtable", "hardhat", "igraph", "ipred", "isoband", "iterators", "KernSmooth", "labeling", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "mgcv", "ModelMetrics", "nlme", "nnet", "numDeriv", "parallelly", "pbapply", "pillar", "pkgconfig", "plyr", "pROC", "prodlim", "progressr", "proxy", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "recipes", "reshape2", "rlang", "rpart", "S7", "scales", "sfsmisc", "shape", "sparsevctrs", "SQUAREM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tzdb", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "Gaussian_Poisson_CRFs.Rmd", "filename": "Gaussian_Poisson_CRFs.html", "title": "Gaussian and Poisson CRFs", "engine": "knitr::rmarkdown", "headings": [], "created": "2018-08-27 04:04:16", "modified": "2023-01-12 02:12:15", "commits": 7 }, { "source": "Bird_Parasite_CRF.Rmd", "filename": "Bird_Parasite_CRF.html", "title": "MRFs and CRFs for Bird.parasites data", "engine": "knitr::rmarkdown", "headings": [ "<<<<<<< HEAD", "title: \"MRFs and CRFs for Bird.parasites data\"output: rmarkdown::html_vignettevignette: >%\\VignetteIndexEntry", "Running MRFs and visualising interaction coefficients", "Running CRFs using additional covariates", "Comparing fits of MRF and CRF models", "Bootstrapping the data and running models", "Exploring regression coefficients and interpreting results", "Accounting for possible spatial autocorrelation", "=======" ], "created": "2018-03-04 23:27:33", "modified": "2023-04-04 23:18:52", "commits": 11 }, { "source": "CRF_data_prep.Rmd", "filename": "CRF_data_prep.html", "title": "Prepping datasets for CRF models", "engine": "knitr::rmarkdown", "headings": [ "Running CRFs with categorical covariates requires expansion to model matrix format" ], "created": "2018-03-04 23:49:13", "modified": "2023-01-12 02:12:15", "commits": 4 } ], "_score": 6.051152522447381, "_indexed": true, "_nocasepkg": "mrfcov", "_universes": [ "nicholasjclark" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.39", "date": "2026-05-29T10:38:45.000Z", "distro": "noble", "commit": "91d77124c07a7572c292d114a6ed2deca314596c", "fileid": "9a223e0d201d793b3a4b6ea4499114b68a6f689cda2bf717aac75b18d9c17748", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838" }, { "r": "4.6.0", "os": "linux", "version": "1.0.39", "date": "2026-05-29T10:38:20.000Z", "distro": "noble", "commit": "91d77124c07a7572c292d114a6ed2deca314596c", "fileid": "a830686c0d3d921882872f1f8666aea7fdf6a8b5abcef000886a022405204fc8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838" }, { "r": "4.5.3", "os": "mac", "version": "1.0.39", "date": "2026-05-29T11:44:00.000Z", "commit": "91d77124c07a7572c292d114a6ed2deca314596c", "fileid": "5c8272af2189e501c9214ab8800cf4da1017d0a17c0a01369d4248e0b0361bcf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838" }, { "r": "4.6.0", "os": "mac", "version": "1.0.39", "date": "2026-05-29T11:45:10.000Z", "commit": "91d77124c07a7572c292d114a6ed2deca314596c", "fileid": "a50a5518c5ce59211f0bab4c3c678ca4df2895b5f34b73baaa05997a8f17170f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.39", "date": "2026-05-29T10:38:33.000Z", "commit": "91d77124c07a7572c292d114a6ed2deca314596c", "fileid": "bfb24ba0832e157d06578cc95392e7ebf3651eec1a4d4502ac4c877f1872c4d9", "status": "success", "buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838" }, { "r": "4.7.0", "os": "win", "version": "1.0.39", "date": "2026-05-29T10:42:42.000Z", "commit": "91d77124c07a7572c292d114a6ed2deca314596c", "fileid": "d9ae22550ce2a180e99a58bafb7e01d3fb19b01b9ab18b53ef79905e0ecc114c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838" }, { "r": "4.5.3", "os": "win", "version": "1.0.39", "date": "2026-05-29T10:42:39.000Z", "commit": "91d77124c07a7572c292d114a6ed2deca314596c", "fileid": "340cec37883420df29c9be953449b4d1ac9314392a417d93006004a1669bb733", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838" }, { "r": "4.6.0", "os": "win", "version": "1.0.39", "date": "2026-05-29T10:43:13.000Z", "commit": "91d77124c07a7572c292d114a6ed2deca314596c", "fileid": "fc95bb4a6cf0a6eac0a24b840ef537778ce85bf4a0841bc573d1672a504f9cf3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nicholasjclark/actions/runs/26632283838" } ] }