{ "_id": "6a129186acfb0bcc41d0af57", "Package": "bmstdr", "Type": "Package", "Title": "Bayesian Modeling of Spatio-Temporal Data with R", "Version": "0.8.1", "Authors@R": "c(person(given=\"Sujit K.\", family=\"Sahu\", email=\"S.K.Sahu@soton.ac.uk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2315-3598\")), person(given=\"Duncan P.\", family=\"Lee\",\nemail=\"Duncan.Lee@glasgow.ac.uk\", role=\"aut\"), person(given=\"K. Shuvo\", family=\"Bakar\",\nemail=\"shuvo.bakar@gmail.com\", role=\"aut\"))", "URL": "https://www.sujitsahu.com", "Description": "Fits, validates and compares a number of Bayesian models\nfor spatial and space time point referenced and areal unit\ndata. Model fitting is done using several packages: 'rstan',\n'INLA', 'spBayes', 'spTimer', 'spTDyn', 'CARBayes' and\n'CARBayesST'. Model comparison is performed using the DIC and\nWAIC, and K-fold cross-validation where the user is free to\nselect their own subset of data rows for validation. Sahu\n(2022) describes the methods in\ndetail.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "RdMacros": "Rdpack", "VignetteBuilder": "knitr", "SystemRequirements": "GNU make", "Additional_repositories": "https://inla.r-inla-download.org/R/stable", "BugReports": "https://github.com/sujit-sahu/bmstdr/issues", "Config/pak/sysreqs": "libabsl-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev libglpk-dev make libharfbuzz-dev libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev zlib1g-dev", "Repository": "https://sujit-sahu.r-universe.dev", "Date/Publication": "2025-03-31 15:56:16 UTC", "RemoteUrl": "https://github.com/sujit-sahu/bmstdr", "RemoteRef": "HEAD", "RemoteSha": "db2895cc0d347fff245ff9a4a617219703c48796", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-22 19:03:46 UTC", "User": "root" }, "Author": "Sujit K. 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Calculates parameter estimates, validation statistics, and estimated values of several Bayesian model choice criteria.", "topics": [ "Bspatial" ] }, { "page": "Bsptime", "title": "Bayesian regression model fitting for point referenced spatio-temporal data. Calculates parameter estimates, validation statistics, and estimated values of several Bayesian model choice criteria.", "topics": [ "Bsptime" ] }, { "page": "calculate_dic", "title": "Calculate DIC function. Has two arguments: (1) log full likelihood at thetahat and (2) vector of log-likelihood at the theta samples Calculate the DIC criteria values", "topics": [ "calculate_dic" ] }, { "page": "calculate_validation_statistics", "title": "Calculates the four validation statistics: RMSE, MAE, CRPS and coverage given the observed values and MCMC iterates.", "topics": [ "calculate_validation_statistics" ] }, { "page": "calculate_waic", "title": "Calculate WAIC function. Has the sole argument component wise likelihood at thetahat samples. v must be a matrix Calculate the WAIC criteria values", "topics": [ "calculate_waic" ] }, { "page": "coef.bmstdr", "title": "Prints and returns the estimates of the coefficients", "topics": [ "coef.bmstdr" ] }, { "page": "colpalette", "title": "The color palette used to draw maps to illustrate the package bmstdr, see Sahu (2022) It has the values in order: dodgerblue4, dodgerblue2, firebrick2, firebrick4 and purple.", "topics": [ "colpalette" ] }, { "page": "engdeaths", "title": "Number of weekly Covid-19 deaths and cases in the 313 local Local Authority Districts, Counties and Unitary Authorities (LADCUA) in England during the 20 peaks in the first peak from March 13 to July 31, 2020.", "topics": [ "engdeaths" ] }, { "page": "engtotals", "title": "Total number of weekly Covid-19 deaths and cases in the 313 local Local Authority Districts, Counties and Unitary Authorities (LADCUA) in England during the first peak from March 13 to July 31, 2020.", "topics": [ "engtotals" ] }, { "page": "fig11.13.plot", "title": "Draws a time series (ribbon) plot by combining fitted and predicted values", "topics": [ "fig11.13.plot" ] }, { "page": "fitted.bmstdr", "title": "Extract fitted values from bmstdr objects.", "topics": [ "fitted.bmstdr" ] }, { "page": "fnc.delete.map.XYZ", "title": "This function is used to delete values outside the state of New York", "topics": [ "fnc.delete.map.XYZ" ] }, { "page": "get_parameter_estimates", "title": "Obtains parameter estimates from MCMC samples", "topics": [ "get_parameter_estimates" ] }, { "page": "get_validation_summaries", "title": "Obtains suitable validation summary statistics from MCMC samples obtained for validation.", "topics": [ "get_validation_summaries" ] }, { "page": "getvalidrows", "title": "Returns a vector of row numbers for validation.", "topics": [ "getvalidrows" ] }, { "page": "gridnyspatial", "title": "Values of three covariates for 100 grid locations in New York averaged over the 62 days during the months of July and August, 2006.", "topics": [ "gridnyspatial" ] }, { "page": "gridnysptime", "title": "Values of three covariates for 100 grid locations in New York for the 62 days during the months of July and August, 2006.", "topics": [ "gridnysptime" ] }, { "page": "hitandfalsealarm", "title": "Calculate the hit and false alarm rates", "topics": [ "hitandfalsealarm" ] }, { "page": "is.bmstdr", "title": "Is it a bmstdr model fitted object?", "topics": [ "is.bmstdr" ] }, { "page": "materncov", "title": "Banerjee, Carlin and Gelfand (2015) Mat'ern covariance function", "topics": [ "materncov" ] }, { "page": "maternfun", "title": "Banerjee et al Mat'ern covariance function", "topics": [ "maternfun" ] }, { "page": "nyspatial", "title": "Average ozone concentration values and three covariates from 28 sites in New York.", "topics": [ "nyspatial" ] }, { "page": "nysptime", "title": "Daily 8-hour maximum ozone concentration values and three covariates from 28 sites in New York for the 62 days during the months of July and August, 2006.", "topics": [ "nysptime" ] }, { "page": "obs_v_pred_plot", "title": "Observed against predicted plot", "topics": [ "obs_v_pred_plot" ] }, { "page": "phichoice_sp", "title": "Grid search method for choosing phi Calculates the validation statistics using the spatial model with a given range of values of the decay parameter phi.", "topics": [ "phichoice_sp" ] }, { "page": "phichoicep", "title": "Calculates the validation statistics using the spatial model with a given range of values of the decay parameter phi.", "topics": [ "phichoicep" ] }, { "page": "plot.bmstdr", "title": "Plot method for bmstdr objects.", "topics": [ "plot.bmstdr" ] }, { "page": "print.bmstdr", "title": "Provides basic information regarding the fitted model.", "topics": [ "print.bmstdr" ] }, { "page": "residuals.bmstdr", "title": "Extract residuals from a bmstdr fitted object.", "topics": [ "residuals.bmstdr" ] }, { "page": "summary", "title": "Provides basic summaries of model fitting.", "topics": [ "summary.bmstdr" ] }, { "page": "terms.bmstdr", "title": "Prints the terms", "topics": [ "terms.bmstdr" ] }, { "page": "Weng", "title": "A 313 by 313 proximity matrix for the 313 LADCUAS in England. Each entry is either 0 or 1 and is 1 if the corresponding row and column LADCUAs share a common boundary.", "topics": [ "Weng" ] }, { "page": "ydata", "title": "Average air pollution values from 28 sites in New York.", "topics": [ "ydata" ] } ], "_readme": "https://github.com/sujit-sahu/bmstdr/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "base64enc", "BH", "boot", "brew", "broom", "bslib", "cachem", "callr", "car", "CARBayes", "CARBayesdata", "CARBayesST", "carData", "checkmate", "class", "classInt", "cli", "coda", "codetools", "colorspace", "corrplot", "cowplot", "cpp11", "crayon", "crosstalk", "DBI", "deldir", "Deriv", "desc", "digest", "distributional", "doBy", "dotCall64", "dplyr", "e1071", "evaluate", "evd", "extraDistr", "farver", "fastmap", "fmesher", "fontawesome", "forcats", "foreach", "forecast", "Formula", "fracdiff", "fs", "generics", "geojsonsf", "geometries", "GGally", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggstats", "glmnet", "glue", "gridExtra", "gtable", "gtools", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "igraph", "inlabru", "inline", "intervals", "isoband", "iterators", "jquerylib", "jsonify", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "leafem", "leaflet", "leaflet.providers", "leafpop", "lifecycle", "lme4", "lmtest", "loo", "magic", "magrittr", "mapview", "MASS", "Matrix", "MatrixModels", "matrixStats", "mcmc", "MCMCpack", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "mnormt", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "otel", "patchwork", "pbkrtest", "pillar", "pkgbuild", "pkgconfig", "plyr", "png", "polynom", "posterior", "prettyunits", "processx", "progress", "promises", "proxy", "ps", "purrr", "quantreg", "QuickJSR", "R6", "rapidjsonr", "rappdirs", "raster", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "Rdpack", "reformulas", "rlang", "rmarkdown", "rstan", "rstantools", "rstatix", "s2", "S7", "sass", "satellite", "scales", "servr", "sf", "sfheaders", "shape", "sp", "spacetime", "spam", "SparseM", "spBayes", "spData", "spdep", "splancs", "spTDyn", "spTimer", "StanHeaders", "stringi", "stringr", "survival", "svglite", "systemfonts", "tensorA", "terra", "textshaping", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "truncdist", "truncnorm", "units", "urca", "utf8", "uuid", "vctrs", "viridisLite", "withr", "wk", "xfun", "xts", "yaml", "zoo" ], "_sysdeps": [ { "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": "vigverysmall.Rmd", "filename": "vigverysmall.html", "title": "bmstdr: Bayesian Modeling of Space Time Data with R", "author": "Sujit K. Sahu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Point reference spatial data modeling", "Illustration data set nyspatial", "The Bspatial function for fitting spatial regression models", "Fitting independent error regression models", "Fitting linear models with spatial error distribution", "Fitting spatial models with nugget effect", "Illustrating the model validation statistics", "Point reference spatio-temporal data modeling", "Illustration data set nysptime", "The Bsptime function for fitting spatio-temporal models", "Modeling areal unit data", "Two illustration data sets on Covid-19 mortality from England", "The Bcartime function for fitting CAR models", "Modeling static areal unit data", "Logistic regression model for areal unit data", "Poisson regression model (disease mapping) for areal unit data", "Normal regression model for areal unit data", "Modeling temporal areal unit data", "Spatio-temporal GLM fitting with binomial distribution", "Spatio-temporal GLM fitting with Poisson distribution", "Spatio-temporal GLM fitting with normal distribution", "Discussion", "References" ], "created": "2023-12-19 14:27:10", "modified": "2023-12-19 14:27:10", "commits": 1 } ], "_score": 5.105510184769974, "_indexed": true, "_nocasepkg": "bmstdr", "_universes": [ "sujit-sahu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8.1", "date": "2026-05-24T05:42:37.000Z", "distro": "noble", "arch": "aarch64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "8694e6d7641b739f5d4353e40cbec9e264180ad4a30af2d9c06690325c5fc30c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" }, { "r": "4.7.0", "os": "linux", "version": "0.8.1", "date": "2026-05-22T19:10:59.000Z", "distro": "noble", "arch": "x86_64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "833f3e1ceb5cca43c88de1439751b7618447e5095f5e85931b7e7e80b268680d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" }, { "r": "4.6.0", "os": "linux", "version": "0.8.1", "date": "2026-05-24T05:42:33.000Z", "distro": "noble", "arch": "aarch64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "2126af070533fe4485f7e404272b03945af29fed41ea1226a13b4c1cd3ab5305", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" }, { "r": "4.6.0", "os": "linux", "version": "0.8.1", "date": "2026-05-22T19:10:54.000Z", "distro": "noble", "arch": "x86_64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "078aa5594fada8e0a6328fcbef24bb2d09a75716c6bff3b05ab5d4fb2a3bfaab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" }, { "r": "4.6.0", "os": "mac", "version": "0.8.1", "date": "2026-05-22T19:33:27.000Z", "arch": "aarch64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "67ee7394d9ee787767b3c7059757e81b38b24af547c89ffe8cbef7dc97a5b430", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" }, { "r": "4.6.0", "os": "mac", "version": "0.8.1", "date": "2026-05-22T19:20:10.000Z", "arch": "x86_64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "ed908b74f96759f4fbb5415fc4fc763ef124d83774cec09074790b614331781d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" }, { "r": "4.7.0", "os": "win", "version": "0.8.1", "date": "2026-05-22T19:09:32.000Z", "arch": "x86_64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "0b699469b092edfcd927f4b4414aa5d75f0a1f9d7b556660d21def06cdb2fbb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" }, { "r": "4.5.3", "os": "win", "version": "0.8.1", "date": "2026-05-22T19:09:30.000Z", "arch": "x86_64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "4f6cb1b15b64167259824cb9b10f6baddf2e6c1c33892940203b56c1e52d603e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" }, { "r": "4.6.0", "os": "win", "version": "0.8.1", "date": "2026-05-22T19:09:44.000Z", "arch": "x86_64", "commit": "db2895cc0d347fff245ff9a4a617219703c48796", "fileid": "a707beb38ed4b3d6a3564c1a7e5a0a956c37720b582013c995651a26099a7c71", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sujit-sahu/actions/runs/26281533470" } ] }