{ "_id": "6a105447acfb0bcc41ca208a", "Package": "ecospat", "Version": "4.1.3", "Title": "Spatial Ecology Miscellaneous Methods", "Authors@R": "c(\nperson(\"Olivier\", \"Broennimann\", role = c(\"cre\",\"aut\",\"ctb\"), email = \"olivier.broennimann@unil.ch\"),\nperson(\"Valeria\", \"Di Cola\", role = c(\"aut\",\"ctb\"), email = \"valeriadicola@gmail.com\"),\nperson(\"Blaise\", \"Petitpierre\", role = \"ctb\"),\nperson(\"Frank\", \"Breiner\", role = \"ctb\"),\nperson(\"Daniel\", \"Scherrer\", role = \"ctb\"),\nperson(\"Manuela\", \"D`Amen\", role = \"ctb\"),\nperson(\"Christophe\", \"Randin\", role = \"ctb\"),\nperson(\"Robin\", \"Engler\", role = \"ctb\"),\nperson(\"Wim\", \"Hordijk\", role = \"ctb\", email = \"wimhor@gmail.com\"),\nperson(\"Heidi\", \"Mod\", role = \"ctb\"),\nperson(\"Julien\", \"Pottier\", role = \"ctb\"),\nperson(\"Mirko\", \"Di Febbraro\", role = \"ctb\"),\nperson(\"Loic\", \"Pellissier\", role = \"ctb\"),\nperson(\"Dorothea\", \"Pio\", role = \"ctb\"),\nperson(\"Ruben\", \"Garcia Mateo\", role = \"ctb\"),\nperson(\"Anne\", \"Dubuis\", role = \"ctb\"),\nperson(\"Luigi\", \"Maiorano\", role = \"ctb\"),\nperson(\"Achilleas\", \"Psomas\", role = \"ctb\"),\nperson(\"Charlotte\", \"Ndiribe\", role = \"ctb\"),\nperson(\"Nicolas\", \"Salamin\", role = \"ctb\"),\nperson(\"Niklaus\", \"Zimmermann\", role = \"ctb\"),\nperson(\"Flavien\", \"Collart\", role = \"ctb\"),\nperson(\"Valentin\", \"Verdon\", role = \"ctb\"),\nperson(\"Tyler\", \"Smith\", role = \"ctb\", email = \"tyler@plantarum.ca\"),\nperson(\"Antoine\", \"Guisan\", role = \"aut\", email = \"antoine.guisan@unil.ch\"))", "Author": "Olivier Broennimann [cre, aut, ctb], Valeria Di Cola [aut,\nctb], Blaise Petitpierre [ctb], Frank Breiner [ctb], Daniel\nScherrer [ctb], Manuela D`Amen [ctb], Christophe Randin [ctb],\nRobin Engler [ctb], Wim Hordijk [ctb], Heidi Mod [ctb], Julien\nPottier [ctb], Mirko Di Febbraro [ctb], Loic Pellissier [ctb],\nDorothea Pio [ctb], Ruben Garcia Mateo [ctb], Anne Dubuis\n[ctb], Luigi Maiorano [ctb], Achilleas Psomas [ctb], Charlotte\nNdiribe [ctb], Nicolas Salamin [ctb], Niklaus Zimmermann [ctb],\nFlavien Collart [ctb], Valentin Verdon [ctb], Tyler Smith\n[ctb], Antoine Guisan [aut]", "Maintainer": "Olivier Broennimann ", "VignetteBuilder": "knitr", "LazyData": "true", "URL": "https://www.unil.ch/ecospat/home/menuguid/ecospat-resources.html", "Description": "Collection of R functions and data sets for the support of\nspatial ecology analyses with a focus on pre, core and post\nmodelling analyses of species distribution, niche\nquantification and community assembly. Written by current and\nformer members and collaborators of the ecospat group of\nAntoine Guisan, Department of Ecology and Evolution (DEE) and\nInstitute of Earth Surface Dynamics (IDYST), University of\nLausanne, Switzerland. Read Di Cola et al. 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"ecospat.Cscore" ] }, { "page": "ecospat.cv.gbm", "title": "GBM Cross Validation", "topics": [ "ecospat.cv.gbm" ] }, { "page": "ecospat.cv.glm", "title": "GLM Cross Validation", "topics": [ "ecospat.cv.glm" ] }, { "page": "ecospat.cv.me", "title": "Maxent Cross Validation", "topics": [ "ecospat.cv.me" ] }, { "page": "ecospat.cv.rf", "title": "RandomForest Cross Validation", "topics": [ "ecospat.cv.rf" ] }, { "page": "ecospat.Epred", "title": "Prediction Mean", "topics": [ "ecospat.Epred" ] }, { "page": "ecospat.ESM.EnsembleEvaluation", "title": "Ensemble of Small Models: Evaluation via the Pooling procedure", "topics": [ "ecospat.ESM.EnsembleEvaluation" ] }, { "page": "ecospat.ESM.EnsembleModeling", "title": "Ensemble of Small Models: Evaluates and Averages Simple Bivariate Models To ESMs", "topics": [ "ecospat.ESM.EnsembleModeling" ] }, { "page": "ecospat.ESM.EnsembleProjection", "title": "Ensemble of Small Models: Projects Calibrated ESMs Into New Space Or Time.", "topics": [ "ecospat.ESM.EnsembleProjection" ] }, { "page": "ecospat.ESM.Modeling", "title": "Ensemble of Small Models: Calibration of Simple Bivariate Models", "topics": [ "ecospat.ESM.Modeling" ] }, { "page": "ecospat.ESM.Projection", "title": "Ensemble of Small Models: Projects Simple Bivariate Models Into New Space Or Time", "topics": [ "ecospat.ESM.Projection" ] }, { "page": "ecospat.ESM.responsePlot", "title": "Produce response plots for ESMs", "topics": [ "ecospat.ESM.responsePlot" ] }, { "page": "ecospat.ESM.threshold", "title": "Thresholds for Ensemble of Small Models", "topics": [ "ecospat.ESM.threshold" ] }, { "page": "ecospat.ESM.VarContrib", "title": "Variable contribution in ESM", "topics": [ "ecospat.ESM.VarContrib" ] }, { "page": "ecospat.grid.clim.dyn", "title": "Dynamic Occurrence Densities Grid", "topics": [ "ecospat.grid.clim.dyn" ] }, { "page": "ecospat.mantel.correlogram", "title": "Mantel Correlogram", "topics": [ "ecospat.mantel.correlogram" ] }, { "page": "ecospat.margin", "title": "Delineation of the distribution's margin and its uncertainty", "topics": [ "ecospat.margin" ] }, { "page": "ecospat.max.kappa", "title": "Maximum Kappa", "topics": [ "ecospat.max.kappa" ] }, { "page": "ecospat.max.tss", "title": "Maximum TSS", "topics": [ "ecospat.max.tss" ] }, { "page": "ecospat.maxentvarimport", "title": "Maxent Variable Importance", "topics": [ "ecospat.maxentvarimport" ] }, { "page": "ecospat.mdr", "title": "Minimum Dispersal Routes)", "topics": [ "ecospat.mdr" ] }, { "page": "ecospat.mess", "title": "MESS", "topics": [ "ecospat.mess" ] }, { "page": "ecospat.meva.table", "title": "Model Evaluation For A Given Threshold Value", "topics": [ "ecospat.meva.table" ] }, { "page": "ecospat.mpa", "title": "Minimal Predicted Area", "topics": [ "ecospat.mpa" ] }, { "page": "ecospat.niche.dyn.index", "title": "Niche Pioneering, Expansion, Stability, Unfilling and Abandonment", "topics": [ "ecospat.niche.dyn.index" ] }, { "page": "ecospat.niche.dynIndexProjGeo", "title": "Projection of niche dynamic indices to the Geography", "topics": [ "ecospat.niche.dynIndexProjGeo" ] }, { "page": "ecospat.niche.equivalency.test", "title": "Niche Equivalency Test", "topics": [ "ecospat.niche.equivalency.test" ] }, { "page": "ecospat.niche.overlap", "title": "Calculate Niche Overlap", "topics": [ "ecospat.niche.overlap" ] }, { "page": "ecospat.niche.similarity.test", "title": "Niche Similarity Test", "topics": [ "ecospat.niche.similarity.test" ] }, { "page": "ecospat.niche.zProjGeo", "title": "Projection of Occurrence Densities to the Geography", "topics": [ "ecospat.niche.zProjGeo" ] }, { "page": "ecospat.nicheNBmean", "title": "Niche position and niche breadth)", "topics": [ "ecospat.nicheNBmean" ] }, { "page": "ecospat.nichePOSNB", "title": "Niche position and niche breadth)", "topics": [ "ecospat.nichePOSNB" ] }, { "page": "ecospat.npred", "title": "Number Of Predictors", "topics": [ "ecospat.npred" ] }, { "page": "ecospat.occ.desaggregation", "title": "Species Occurrences Desaggregation", "topics": [ "ecospat.occ.desaggregation" ] }, { "page": "ecospat.occupied.patch", "title": "Extract occupied patches of a species in geographic space.)", "topics": [ "ecospat.occupied.patch" ] }, { "page": "ecospat.permut.glm", "title": "GLM Permutation Function", "topics": [ "ecospat.permut.glm" ] }, { "page": "ecospat.plot.contrib", "title": "Plot Variables Contribution", "topics": [ "ecospat.plot.contrib" ] }, { "page": "ecospat.plot.kappa", "title": "Plot Kappa", "topics": [ "ecospat.plot.kappa" ] }, { "page": "ecospat.plot.mess", "title": "Plot MESS", "topics": [ "ecospat.plot.mess" ] }, { "page": "ecospat.plot.niche", "title": "Plot Niche", "topics": [ "ecospat.plot.niche" ] }, { "page": "ecospat.plot.niche.dyn", "title": "Plot of categories of Niche dynamics and Species Density", "topics": [ "ecospat.plot.niche.dyn" ] }, { "page": "ecospat.plot.overlap.test", "title": "Plot Overlap Test", "topics": [ "ecospat.plot.overlap.test" ] }, { "page": "ecospat.plot.tss", "title": "Plot True skill statistic (TSS)", "topics": [ "ecospat.plot.tss" ] }, { "page": "ecospat.poolingEvaluation", "title": "Evaluation of species distribution models using the pooling procedure", "topics": [ "ecospat.poolingEvaluation" ] }, { "page": "ecospat.rand.pseudoabsences", "title": "Sample Pseudo-Absences", "topics": [ "ecospat.rand.pseudoabsences" ] }, { "page": "ecospat.rangesize", "title": "Quantification of the range size of a species using habitat suitability maps and IUCN criteria)", "topics": [ "ecospat.rangesize" ] }, { "page": "ecospat.rcls.grd", "title": "Reclassifying grids function", "topics": [ "ecospat.rcls.grd" ] }, { "page": "ecospat.recstrat_prop", "title": "Random Ecologically Stratified Sampling of propotional numbers", "topics": [ "ecospat.recstrat_prop" ] }, { "page": "ecospat.recstrat_regl", "title": "Random Ecologically Stratified Sampling of equal numbers", "topics": [ "ecospat.recstrat_regl" ] }, { "page": "ecospat.sample.envar", "title": "Sample Environmental Variables", "topics": [ "ecospat.sample.envar" ] }, { "page": "ecospat.SESAM.prr", "title": "SESAM Probability Ranking Rule", "topics": [ "ecospat.SESAM.prr" ] }, { "page": "ecospat.shift.centroids", "title": "Draw Centroid Arrows", "topics": [ "ecospat.shift.centroids" ] }, { "page": "ecospat.testData", "title": "Test Data For The Ecospat package", "topics": [ "ecospat.testData" ] }, { "page": "ecospat.testEnvRaster", "title": "Test Environmental SpatRasters for The Ecospat package", "topics": [ "ecospat.testEnv" ] }, { "page": "ecospat.testMdr", "title": "Test Data For The ecospat.mdr function", "topics": [ "ecospat.testMdr" ] }, { "page": "ecospat.testNiche", "title": "Test Data For The Niche Overlap Analysis", "topics": [ "ecospat.testNiche" ] }, { "page": "ecospat.testNiche.inv", "title": "Test Data For The Niche Dynamics Analysis In The Invaded Range Of A Hypothetical Species", "topics": [ "ecospat.testNiche.inv" ] }, { "page": "ecospat.testNiche.nat", "title": "Test Data For The Niche Dynamics Analysis In The Native Range Of A Hypothetical Species", "topics": [ "ecospat.testNiche.nat" ] }, { "page": "ecospat.testNichePOSNB", "title": "Test AVS Dataset For The Ecospat package", "topics": [ "ecospat.testNichePOSNB" ] }, { "page": "ecospat.testTree", "title": "Test Tree For The Ecospat package", "topics": [ "ecospat.testTree" ] }, { "page": "ecospat.varpart", "title": "Variation Partitioning For GLM Or GAM", "topics": [ "ecospat.varpart" ] } ], "_rundeps": [ "abind", "ade4", "adehabitatHR", "adehabitatLT", "adehabitatMA", "backports", "base64enc", "BH", "biomod2", "bslib", "cachem", "checkmate", "class", "classInt", "cli", "cluster", "codetools", "colorspace", "cpp11", "data.table", "digest", "dismo", "dplyr", "e1071", "ecodist", "evaluate", "farver", "fastmap", "FNN", "fontawesome", "foreach", "foreign", "Formula", "fs", "gbm", "generics", "ggplot2", "glue", "gridExtra", "gtable", "gtools", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "igraph", "isoband", "iterators", "jquerylib", "jsonlite", "kernlab", "KernSmooth", "knitr", "ks", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "matrixStats", "mclust", "memoise", "mgcv", "mime", "multicool", "mvtnorm", "nabor", "nlme", "nnet", "permute", "pillar", "pixmap", "pkgconfig", "plyr", "poibin", "pracma", "PresenceAbsence", "pROC", "proxy", "R6", "rappdirs", "raster", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "reshape", "reshape2", "rlang", "rmarkdown", "rpart", "rstudioapi", "S7", "sass", "scales", "sp", "stringi", "stringr", "survival", "terra", "tibble", "tidyselect", "tinytex", "utf8", "vctrs", "vegan", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "vignette_ecospat_package.Rmd", "filename": "vignette_ecospat_package.pdf", "title": "Vignette ecospat package", "engine": "knitr::rmarkdown", "headings": [ "08 November, 2017", "Load data", "Test data for the ecospat library", "Test data for the Niche Overlap Analysis", "Test tree for Phylogenetic Diversity Analysis", "Pre-Modelling Analysis", "Spatial Auto-correlation", "Mantel Correlogram with ecospat.mantel.correlogram()", "Predictor Variable Selection", "Number of Predictors with Pearson Correlation ecospat.npred()", "Number of Predictors with Spearman Correlation ecospat.npred()", "Climate Analogy Tools", "Climate Analogy with ecospat.climan()", "Extrapolation detection, creating a MESS object with ecospat.mess()", "Phylogenetic Diversity Measures", "Niche Quantification and Comparison with Ordination techniques", "Calculate the Occurrence Densities Grid with ecospat.grid.clim.dyn()", "Calculate Niche Overlap with ecospat.niche.overlap()", "Perform the Niche Equivalency Test with ecospat.niche.equivalency.test() according to Warren et al. (2008)", "Perform the Niche Similarity Test with ecospat.niche.similarity.test()", "Delimiting niche categories and quantifying niche dynamics in analogue climates with ecospat.niche.dyn.index()", "Visualizing niche categories, niche dynamics and climate analogy between ranges with ecospat.plot.niche.dyn()", "Plot the niche dynamics along one gradient (here temperature) with ecospat.plot.niche.dyn()", "Biotic Interactions", "Species Co-occurrences Analysis with a Presence-absence matrix using the function ecospat.co_occurrences()", "Pairwise co-occurrence Analysis with calculation of the C-score index using the function ecospat.Cscore()", "Data Preparation", "Correlation Plot of Variables with ecospat.cor.plot()", "Calibration And Evaluation Dataset", "Core Niche Modelling", "Model Evaluation", "Presence-only Evaluation Indices- Boyce Index", "Accuracy of Community Prediction", "Spatial Predictions and Projections", "ESM Ensemble of Small Models", "Spatial prediction of communities", "SESAM framework with ecospat.SESAM.prr()", "Post-Modelling", "Spatial Predictions of species assamblages", "Co-occurrence analysis & Environmentally Constrained Null Models" ], "created": "2016-10-25 08:11:34", "modified": "2024-06-11 12:45:43", "commits": 15 } ], "_score": 10.374364149851752, "_indexed": true, "_nocasepkg": "ecospat", "_universes": [ "ecospat" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.1.3", "date": "2026-05-09T08:38:13.000Z", "distro": "noble", "commit": "fab63156e37e319afcfc937b94c5ef4efd1daf29", "fileid": "adc25630f7a86d24111dc7a684f51ddd524a536de9507ff78512006e9b9f4518", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ecospat/actions/runs/25596551658" }, { "r": "4.6.0", "os": "linux", "version": "4.1.3", "date": "2026-05-09T08:38:14.000Z", "distro": "noble", "commit": "fab63156e37e319afcfc937b94c5ef4efd1daf29", "fileid": "9000f2716020fa3833ddfa822fa306b02706c7c0f0e43b6fc4a9469e9644dd68", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ecospat/actions/runs/25596551658" }, { "r": "4.5.3", "os": "mac", "version": "4.1.3", "date": "2026-05-09T08:42:18.000Z", "commit": "fab63156e37e319afcfc937b94c5ef4efd1daf29", "fileid": "870ab40969a83a42ab70f9f5d588bf9bcf81f53117f46c6cdedc5a1e346819c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ecospat/actions/runs/25596551658" }, { "r": "4.6.0", "os": "mac", "version": "4.1.3", "date": "2026-05-09T08:37:16.000Z", "commit": "fab63156e37e319afcfc937b94c5ef4efd1daf29", "fileid": "ca06d7f32ddf78fe59e59622fbca651cabb7aba798a8c9d9983409d22fd17754", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ecospat/actions/runs/25596551658" }, { "r": "4.7.0", "os": "win", "version": "4.1.3", "date": "2026-05-09T08:36:58.000Z", "commit": "fab63156e37e319afcfc937b94c5ef4efd1daf29", "fileid": "3a4b1bee9495855df1be15bc19df96f63a1bd6b75b21d5213e4bd5e19f0ffc5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ecospat/actions/runs/25596551658" }, { "r": "4.5.3", "os": "win", "version": "4.1.3", "date": "2026-05-09T08:37:07.000Z", "commit": "fab63156e37e319afcfc937b94c5ef4efd1daf29", "fileid": "1d89c15418aa1cdfcdd34883d25545b9020b0f487ec122e74f9dc51a193308ca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ecospat/actions/runs/25596551658" }, { "r": "4.6.0", "os": "win", "version": "4.1.3", "date": "2026-05-09T08:44:46.000Z", "commit": "fab63156e37e319afcfc937b94c5ef4efd1daf29", "fileid": "d2119905fce78f31606e22a6141af538cb58cb212effa7538abad89b89b3a532", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ecospat/actions/runs/25596551658" }, { "r": "4.6.0", "os": "wasm", "version": "4.1.3", "date": "2026-05-22T13:03:44.000Z", "commit": "fab63156e37e319afcfc937b94c5ef4efd1daf29", "fileid": "388a8c9a491b0887c7bb6d66830ba029459538385036d0f92b5df2ceba1371bd", "status": "success", "buildurl": "https://github.com/r-universe/ecospat/actions/runs/25596551658" } ] }