{ "_id": "6a1015c5acfb0bcc41c84277", "Package": "stelfi", "Type": "Package", "Title": "Hawkes and Log-Gaussian Cox Point Processes Using Template Model\nBuilder", "Version": "1.0.2", "Date": "2025-09-15", "Authors@R": "c(person(given = \"Charlotte M.\",\nfamily = \"Jones-Todd\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"c.jonestodd@auckland.ac.nz\",\ncomment = c(ORCID = \"0000-0003-1201-2781\",\n\"Charlotte Jones-Todd wrote and continued developmend of the main code.\")),\nperson(given = \"Alec\",\nfamily = \"van Helsdingen\",\nrole = \"aut\",\ncomment = \"Alec van Helsdingen wrote the Hawkes templates and extended self-exciting TMB templates\"),\nperson(given = \"Xiangjie\",\nfamily = \"Xue\",\nrole = \"ctb\",\ncomment = \"Xiangjie Xue worked the early spatio-temporal self-exciting TMB templates\"),\nperson(given = \"Joseph\",\nfamily = \"Reps\",\nrole = \"ctb\",\ncomment = \"Joseph Reps worked on the spatio-temporal self-exciting TMB templates\"),\nperson(given = \"Marsden Fund\",\nfamily = \"3723517\",\nrole = \"fnd\"),\nperson(given = \"Asian Office of Aerospace Research & Development\",\nfamily = \"FA2386-21-1-4028\",\nrole = \"fnd\"))", "Description": "Fit Hawkes and log-Gaussian Cox process models with\nextensions. Introduced in Hawkes (1971) a\nHawkes process is a self-exciting temporal point process where\nthe occurrence of an event immediately increases the chance of\nanother. We extend this to consider self-inhibiting process and\na non-homogeneous background rate. A log-Gaussian Cox process\nis a Poisson point process where the log-intensity is given by\na Gaussian random field. We extend this to a joint likelihood\nformulation fitting a marked log-Gaussian Cox model. In\naddition, the package offers functionality to fit self-exciting\nspatiotemporal point processes. Models are fitted via maximum\nlikelihood using 'TMB' (Template Model Builder). Where included\n1) random fields are assumed to be Gaussian and are integrated\nover using the Laplace approximation and 2) a stochastic\npartial differential equation model, introduced by Lindgren,\nRue, and Lindström. (2011)\n, is defined for the\nfield(s).", "License": "GPL (>= 3)", "URL": "https://github.com/cmjt/stelfi/", "BugReports": "https://github.com/cmjt/stelfi/issues", "LazyData": "TRUE", "LazyDataCompression": "xz", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibicu-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev", "Repository": "https://cmjt.r-universe.dev", "Date/Publication": "2025-09-15 01:54:21 UTC", "RemoteUrl": "https://github.com/cmjt/stelfi", "RemoteRef": "HEAD", "RemoteSha": "5b989108bc6900d2665160e73913fb3ddf07a262", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-14 09:18:46 UTC", "User": "root" }, "Author": "Charlotte M. Jones-Todd [aut, cre, cph] (ORCID:\n, Charlotte Jones-Todd wrote\nand continued developmend of the main code.),\nAlec van Helsdingen [aut] (Alec van Helsdingen wrote the Hawkes\ntemplates and extended self-exciting TMB templates),\nXiangjie Xue [ctb] (Xiangjie Xue worked the early spatio-temporal\nself-exciting TMB templates),\nJoseph Reps [ctb] (Joseph Reps worked on the spatio-temporal\nself-exciting TMB templates),\nMarsden Fund 3723517 [fnd],\nAsian Office of Aerospace Research & Development FA2386-21-1-4028 [fnd]", "Maintainer": "Charlotte M. Jones-Todd ", "MD5sum": "f43894ca9669535bf1c204d90ec08be5", "_user": "cmjt", "_type": "src", "_file": "stelfi_1.0.2.tar.gz", "_fileid": "162a5cae7de86e4aab42150a061bf5d32d656282e57e22df8bbfeb2488de12cd", "_filesize": 1257245, "_sha256": "162a5cae7de86e4aab42150a061bf5d32d656282e57e22df8bbfeb2488de12cd", "_created": "2026-05-14T09:18:46.000Z", "_published": "2026-05-22T08:37:25.557Z", "_distro": "noble", "_jobs": [ { "job": 77344834823, "time": 284, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7010808344" }, { "job": 77344834117, "time": 292, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6991270194" }, { "job": 77344834697, "time": 265, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7010804446" }, { "job": 77344834599, "time": 313, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6991276010" }, { "job": 77344834849, "time": 256, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7010981015" }, { "job": 77344834370, "time": 542, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "6991332622" }, { "job": 77344834371, "time": 281, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6991261407" }, { "job": 77344834466, "time": 467, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6991312385" }, { "job": 77344833849, "time": 372, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6991186778" }, { "job": 77344834026, "time": 190, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7156308673" }, { "job": 77344834121, "time": 366, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6991291835" }, { "job": 77344834317, "time": 305, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6991273886" }, { "job": 77344834335, "time": 311, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6991275507" } ], "_buildurl": "https://github.com/r-universe/cmjt/actions/runs/25852003118", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cmjt/stelfi", "_commit": { "id": "5b989108bc6900d2665160e73913fb3ddf07a262", "author": "cmjt ", "committer": "cmjt ", "message": "update dtae in DESC & add cran comments\n", "time": 1757901261 }, "_maintainer": { "name": "Charlotte M. Jones-Todd", "email": "c.jonestodd@auckland.ac.nz", "login": "cmjt", "orcid": "0000-0003-1201-2781", "uuid": 12936942 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "TMB", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "TMB", "version": ">= 1.9.6", "role": "Imports" }, { "package": "sf", "version": ">= 1.0.14", "role": "Imports" }, { "package": "fmesher", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4.3", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1.3", "role": "Imports" }, { "package": "gridExtra", "version": ">= 2.3", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.3.1", "role": "Imports" }, { "package": "testthat", "version": ">= 3.1.10", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "spatstat.utils", "role": "Suggests" }, { "package": "spatstat.geom", "role": "Suggests" }, { "package": "hawkesbow", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "cmjt", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-31", "n": 1 }, { "week": "2025-37", "n": 11 }, { "week": "2025-38", "n": 1 } ], "_tags": [], "_stars": 8, "_contributors": [ { "user": "cmjt", "count": 318, "uuid": 12936942 }, { "user": "abmvanhelsdingen", "count": 48, "uuid": 70261846 }, { "user": "farmgate-alec", "count": 11, "uuid": 93958558 }, { "user": "josephreps", "count": 2, "uuid": 37464482 }, { "user": "xiangjiexue", "count": 1, "uuid": 29616459 } ], "_userbio": { "uuid": 12936942, "type": "user", "name": "Charlotte M. Jones-Todd", "description": "`|=|'-" }, "_downloads": { "count": 461, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/stelfi" }, "_devurl": "https://github.com/cmjt/stelfi", "_searchresults": 4, "_topics": [ "cpp", "openmp" ], "_rbuild": "4.6.0", "_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/stelfi.html", "manual.pdf" ], "_homeurl": "https://github.com/cmjt/stelfi", "_realowner": "cmjt", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2022-11-03" }, { "version": "0.0.2", "date": "2023-04-06" }, { "version": "1.0.0", "date": "2023-09-28" }, { "version": "1.0.1", "date": "2023-10-24" }, { "version": "1.0.2", "date": "2025-09-15" } ], "_exports": [ "compensator_differences", "fit_hawkes", "fit_hawkes_cbf", "fit_lgcp", "fit_mhawkes", "fit_mlgcp", "fit_stelfi", "get_coefs", "get_fields", "get_weights", "mesh_2_sf", "meshmetrics", "show_field", "show_hawkes", "show_hawkes_GOF", "show_lambda", "show_multivariate_hawkes", "sim_hawkes", "sim_lgcp" ], "_datasets": [ { "name": "horse_mesh", "title": "Example Delaunay triangulation", "object": "horse_mesh", "class": [ "fm_mesh_2d", "inla.mesh" ], "fields": [], "table": false, "tojson": false }, { "name": "horse_sf", "title": "Example 'sf' 'POLYGON'", "object": "horse_sf", "class": [ "sfc_POLYGON", "sfc" ], "fields": [], "table": true, "tojson": true }, { "name": "iraq_terrorism", "title": "Terrorism in Iraq, 2013 - 2017", "object": "iraq_terrorism", "class": [ "sf", "data.frame" ], "fields": [ "iyear", "imonth", "iday", "country", "success", "nkill", "specificity", "gname", "x_coord", "y_coord", "z_coord", "popdensity", "luminosity", "tt", "utm_x", "utm_y", "geometry" ], "rows": 4208, "table": true, "tojson": true }, { "name": "marked", "title": "Example marked point pattern data set", "object": "marked", "class": [ "data.frame" ], "fields": [ "x", "y", "m1", "m2", "m3" ], "rows": 159, "table": true, "tojson": true }, { "name": "multi_hawkes", "title": "Example multivariate Hawkes dataset", "object": "multi_hawkes", "class": [ "data.frame" ], "fields": [ "times", "stream" ], "rows": 213, "table": true, "tojson": true }, { "name": "nz_earthquakes", "title": "Earthquakes in Canterbury, NZ, 2010 - 2014", "object": "nz_earthquakes", "class": [ "sf", "data.frame" ], "fields": [ "origintime", "magnitude", "depth", "geometry" ], "rows": 3824, "table": true, "tojson": true }, { "name": "nz_murders", "title": "Murders of NZ, 2004 - 2019", "object": "nz_murders", "class": [ "sf", "data.frame" ], "fields": [ "sex", "age", "date", "year", "cause", "killer", "name", "full_date", "month", "cause_cat", "region", "geometry" ], "rows": 967, "table": true, "tojson": true }, { "name": "retweets_niwa", "title": "Retweets of NIWA's viral leopard seal Tweet", "object": "retweets_niwa", "class": [ "POSIXct", "POSIXt" ], "fields": [], "table": false, "tojson": true }, { "name": "sasquatch", "title": "Sasquatch (bigfoot) sightings in the USA, 2000 - 2005", "object": "sasquatch", "class": [ "sf", "tbl_df", "tbl", "data.frame" ], "fields": [ "observed", "location_details", "county", "state", "season", "title", "date", "number", "classification", "geohash", "temperature_high", "temperature_mid", "temperature_low", "dew_point", "humidity", "cloud_cover", "moon_phase", "precip_intensity", "precip_probability", "precip_type", "pressure", "summary", "uv_index", "visibility", "wind_bearing", "wind_speed", "year", "geometry" ], "rows": 972, "table": true, "tojson": true }, { "name": "uk_serial", "title": "Serial killers of the UK, 1828 - 2015", "object": "uk_serial", "class": [ "data.frame" ], "fields": [ "number_of_kills", "years", "name", "aka", "year_start", "year_end", "date_of_first_kill", "population_million" ], "rows": 62, "table": true, "tojson": true }, { "name": "xyt", "title": "Self-exciting point pattern", "object": "xyt", "class": [ "stppp", "ppp" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "compensator_differences", "title": "Extract the compensator differences", "topics": [ "compensator_differences" ] }, { "page": "fit_hawkes", "title": "Self-exciting Hawkes process(es)", "topics": [ "fit_hawkes", "fit_hawkes_cbf", "fit_mhawkes" ] }, { "page": "fit_lgcp", "title": "Spatial or spatiotemporal log-Gaussian Cox process (LGCP)", "topics": [ "fit_lgcp" ] }, { "page": "fit_mlgcp", "title": "Marked spatial log-Gaussian Cox process (mLGCP)", "topics": [ "fit_mlgcp" ] }, { "page": "fit_stelfi", "title": "Modelling spatiotemporal self-excitement", "topics": [ "fit_stelfi" ] }, { "page": "get_coefs", "title": "Extract reported parameter estimates", "topics": [ "get_coefs" ] }, { "page": "get_fields", "title": "Estimated random field(s)", "topics": [ "get_fields" ] }, { "page": "get_weights", "title": "Mesh weights", "topics": [ "get_weights" ] }, { "page": "horse_mesh", "title": "Example Delaunay triangulation", "topics": [ "horse_mesh" ] }, { "page": "horse_sf", "title": "Example 'sf' 'POLYGON'", "topics": [ "horse_sf" ] }, { "page": "iraq_terrorism", "title": "Terrorism in Iraq, 2013 - 2017", "topics": [ "iraq_terrorism" ] }, { "page": "marked", "title": "Example marked point pattern data set", "topics": [ "marked" ] }, { "page": "mesh_2_sf", "title": "Transform a 'fmesher::fm_mesh_2d' into a 'sf' object", "topics": [ "mesh_2_sf" ] }, { "page": "meshmetrics", "title": "Calculate a number of different geometric attributes of a Delaunay triangulation", "topics": [ "meshmetrics" ] }, { "page": "multi_hawkes", "title": "Example multivariate Hawkes dataset", "topics": [ "multi_hawkes" ] }, { "page": "nz_earthquakes", "title": "Earthquakes in Canterbury, NZ, 2010 - 2014", "topics": [ "nz_earthquakes" ] }, { "page": "nz_murders", "title": "Murders of NZ, 2004 - 2019", "topics": [ "nz_murders" ] }, { "page": "retweets_niwa", "title": "Retweets of NIWA's viral leopard seal Tweet", "topics": [ "retweets_niwa" ] }, { "page": "sasquatch", "title": "Sasquatch (bigfoot) sightings in the USA, 2000 - 2005", "topics": [ "sasquatch" ] }, { "page": "show_field", "title": "Plot the estimated random field(s) of a fitted LGCP", "topics": [ "show_field" ] }, { "page": "show_hawkes", "title": "Plot Hawkes intensity", "topics": [ "show_hawkes", "show_hawkes_GOF" ] }, { "page": "show_lambda", "title": "Plot the estimated intensity from a fitted LGCP model", "topics": [ "show_lambda" ] }, { "page": "show_multivariate_hawkes", "title": "Multivariate Hawkes fitted model plot", "topics": [ "show_multivariate_hawkes" ] }, { "page": "sim_hawkes", "title": "Simulate a self-exciting Hawkes process", "topics": [ "sim_hawkes" ] }, { "page": "sim_lgcp", "title": "Simulate a log-Gaussian Cox process (LGCP)", "topics": [ "sim_lgcp" ] }, { "page": "uk_serial", "title": "Serial killers of the UK, 1828 - 2015", "topics": [ "uk_serial" ] }, { "page": "xyt", 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