{ "_id": "6a12c43aacfb0bcc41d1ee14", "Package": "mobsim", "Type": "Package", "Title": "Spatial Simulation and Scale-Dependent Analysis of Biodiversity\nChanges", "Version": "0.3.2", "Authors@R": "c(\nperson(\"Felix\", \"May\", email = \"felix.may@fu-berlin.de\",\nrole = c(\"aut\", \"cre\",\"cph\"),\ncomment = c(ORCID = \"0000-0002-1106-8188\")),\nperson(\"Alban\", \"Sagouis\", email = \"alban.sagouis@idiv.de\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-3827-1063\")),\nperson(\"German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig\",\nrole = \"fnd\", comment = c(ROR = \"01jty7g66\")),\nperson(\"Freie Universität Berlin\",\nrole = \"fnd\", comment = c(ROR = \"046ak2485\"))\n)", "Date": "2024-11-26", "Description": "Simulation, analysis and sampling of spatial biodiversity\ndata (May, Gerstner, McGlinn, Xiao & Chase 2017)\n. In the simulation tools user\ndefine the numbers of species and individuals, the species\nabundance distribution and species aggregation. Functions for\nanalysis include species rarefaction and accumulation curves,\nspecies-area relationships and the distance decay of\nsimilarity.", "License": "GPL (>= 3)", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Language": "en-GB", "Encoding": "UTF-8", "URL": "https://github.com/MoBiodiv/mobsim", "BugReports": "https://github.com/MoBiodiv/mobsim/issues", "Config/pak/sysreqs": "cmake", "Repository": "https://mobiodiv.r-universe.dev", "Date/Publication": "2025-05-29 15:45:24 UTC", "RemoteUrl": "https://github.com/mobiodiv/mobsim", "RemoteRef": "HEAD", "RemoteSha": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-24 09:18:35 UTC", "User": "root" }, "Author": "Felix May [aut, cre, cph] (ORCID:\n),\nAlban Sagouis [aut] (ORCID: ),\nGerman Centre for Integrative Biodiversity Research (iDiv)\nHalle-Jena-Leipzig [fnd] (ROR: ),\nFreie Universität Berlin [fnd] (ROR: )", "Maintainer": "Felix May ", "MD5sum": "7d74b10eebc94100eb49c5ab18830be2", "_user": "mobiodiv", "_type": "src", "_file": "mobsim_0.3.2.tar.gz", "_fileid": "a5a5858fb02aaa5f984e790634673d096f1df6a95fc48ab3d096ec67900b5fc9", "_filesize": 3036877, "_sha256": "a5a5858fb02aaa5f984e790634673d096f1df6a95fc48ab3d096ec67900b5fc9", "_created": "2026-05-24T09:18:35.000Z", "_published": "2026-05-24T09:45:59.199Z", "_distro": "noble", "_jobs": [ { "job": 77586521111, "time": 158, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7183984689" }, { "job": 77586521119, "time": 170, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7183985913" }, { "job": 77586521118, "time": 149, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7183983817" }, { "job": 77586521115, "time": 165, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7183985444" }, { "job": 77586521110, "time": 173, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7183983478" }, { "job": 77586521112, "time": 421, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7184006994" }, { "job": 77586521102, "time": 174, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7183983317" }, { "job": 77586521098, "time": 326, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7183999714" }, { "job": 77586306979, "time": 227, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7183967682" }, { "job": 77586521092, "time": 105, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7183979173" }, { "job": 77586521123, "time": 180, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7183986841" }, { "job": 77586521105, "time": 190, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7183987835" }, { "job": 77586521109, "time": 227, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7183991775" } ], "_buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/mobiodiv/mobsim", "_commit": { "id": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "author": "AlbanSagouis <25483578+AlbanSagouis@users.noreply.github.com>", "committer": "GitHub ", "message": "Added FU and iDiv ROR as funders\n\nROR is similar to ORCID for institutions", "time": 1748533524 }, "_maintainer": { "name": "Felix May", "email": "felix.may@fu-berlin.de", "login": "felixmay", "description": "", "uuid": 15672017, "orcid": "0000-0002-1106-8188" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "sads", "version": ">= 0.4.1", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spatstat.geom", "role": "Suggests" }, { "package": "spatstat.random", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "mockery", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "vctrs", "role": "Suggests" } ], "_owner": "mobiodiv", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-22", "n": 1 } ], "_tags": [], "_topics": [ "biodiversity", "macroecology", "point-pattern-analysis", "rarefaction", "simulation", "species", "species-abundance-distributions", "cpp" ], "_stars": 21, "_contributors": [ { "user": "albansagouis", "count": 94, "uuid": 25483578 }, { "user": "felixmay", "count": 39, "uuid": 15672017 }, { "user": "katharinagerstner", "count": 7, "uuid": 12099296 }, { "user": "dmcglinn", "count": 1, "uuid": 1190381 } ], "_userbio": { "uuid": 12683972, "type": "organization", "name": "Measurement of Biodiversity (MoB)", "description": "The repositories related to an iDiv working group examining best practices in the measurement of biodiversity" }, "_downloads": { "count": 249, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mobsim" }, "_devurl": "https://github.com/mobiodiv/mobsim", "_searchresults": 83, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mobsim.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/mobiodiv/mobsim", "_realowner": "mobiodiv", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2017-11-02" }, { "version": "0.2.0", "date": "2021-03-23" }, { "version": "0.3.1", "date": "2024-03-22" }, { "version": "0.3.2", "date": "2024-12-05" } ], "_exports": [ "abund_rect", "community", "community_to_sad", "dist_decay", "dist_decay_quadrats", "div_rand_rect", "div_rect", "divar", "rare_curve", "rThomas_rcpp", "sample_quadrats", "sampling_grids", "sampling_one_quadrat", "sampling_random_bruteforce", "sampling_random_overlap", "sampling_random_spatstat", "sampling_transects", "sim_poisson_community", "sim_poisson_coords", "sim_sad", "sim_thomas_community", "sim_thomas_coords", "spec_sample", "spec_sample_curve" ], "_help": [ { "page": "abund_rect", "title": "-------------------------- Get local species abundance distribution", "topics": [ "abund_rect" ] }, { "page": "community", "title": "Create spatial community object", "topics": [ "community" ] }, { "page": "community_to_sad", "title": "Get species abundance distribution from community object", "topics": [ "community_to_sad" ] }, { "page": "dist_decay", "title": "Distance decay of similarity", "topics": [ "dist_decay" ] }, { "page": "dist_decay_quadrats", "title": "Distance decay of similarity with user-defined quadrats", "topics": [ "dist_decay_quadrats" ] }, { "page": "div_rand_rect", "title": "Distribution of local diversity indices", "topics": [ "div_rand_rect" ] }, { "page": "div_rect", "title": "Get local diversity indices", "topics": [ "div_rect" ] }, { "page": "divar", "title": "Diversity-area relationships", "topics": [ "divar" ] }, { "page": "plot.community", "title": "Plot spatial community object", "topics": [ "plot.community" ] }, { "page": "plot.dist_decay", "title": "Plot distance decay of similarity", "topics": [ "plot.dist_decay" ] }, { "page": "plot.divar", "title": "-------------------------- Plot diversity-area relationships", "topics": [ "plot.divar" ] }, { "page": "plot.sad", "title": "Plot species abundance distributions", "topics": [ "plot.sad" ] }, { "page": "plot.spec_sample_curve", "title": "Plot species sampling curves", "topics": [ "plot.spec_sample_curve" ] }, { "page": "rare_curve", "title": "Species rarefaction curve", "topics": [ "rare_curve" ] }, { "page": "rThomas_rcpp", "title": "Thomas process individual distribution simulation for one species", "topics": [ "rThomas_rcpp" ] }, { "page": "sample_quadrats", "title": "Plot-based samples from a spatially-explicit census", "topics": [ "sample_quadrats" ] }, { "page": "sampling_grids", "title": "Creates square quadrats aligned on a regular grid", "topics": [ "sampling_grids" ] }, { "page": "sampling_one_quadrat", "title": "Creates one square quadrat randomly located in the landscape", "topics": [ "sampling_one_quadrat" ] }, { "page": "sampling_random_bruteforce", "title": "Creates coordinates (lower left corner of a quadrat) randomly distributed but without overlapping each other", "topics": [ "sampling_random_bruteforce" ] }, { "page": "sampling_random_overlap", "title": "Creates coordinates (lower left corner of a quadrat) randomly distributed that may overlap each other", "topics": [ "sampling_random_overlap" ] }, { "page": "sampling_random_spatstat", "title": "Creates coordinates (lower left corner of a quadrat) randomly distributed but without overlapping each other", "topics": [ "sampling_random_spatstat" ] }, { "page": "sampling_transects", "title": "Creates square quadrats aligned along a transect", "topics": [ "sampling_transects" ] }, { "page": "sim_poisson_community", "title": "Simulate community with random spatial positions.", "topics": [ "sim_poisson_community" ] }, { "page": "sim_poisson_coords", "title": "Simulate random spatial coordinates", "topics": [ "sim_poisson_coords" ] }, { "page": "sim_sad", "title": "Simulate species abundance distributions", "topics": [ "sim_sad" ] }, { "page": "sim_thomas_community", "title": "Simulate community with clumped spatial positions.", "topics": [ "sim_thomas_community" ] }, { "page": "sim_thomas_coords", "title": "Simulate clumped spatial coordinates", "topics": [ "sim_thomas_coords" ] }, { "page": "spec_sample", "title": "Sample species richness", "topics": [ "spec_sample" ] }, { "page": "spec_sample_curve", "title": "Non-spatial and spatially-explicit species sampling curves", "topics": [ "spec_sample_curve" ] }, { "page": "summary.community", "title": "Print summary of spatial community object", "topics": [ "summary.community" ] }, { "page": "summary.sad", "title": "Print summary of species abundance distribution object", "topics": [ "summary.sad" ] } ], "_readme": "https://github.com/mobiodiv/mobsim/raw/HEAD/README.md", "_rundeps": [ "bbmle", "bdsmatrix", "cluster", "GUILDS", "lattice", "MASS", "Matrix", "mgcv", "mvtnorm", "nlme", "nloptr", "numDeriv", "permute", "poilog", "poweRlaw", "pracma", "Rcpp", "sads", "vegan", "VGAM" ], "_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": "Biodiversity_Patterns.Rmd", "filename": "Biodiversity_Patterns.html", "title": "Analysis of biodiversity patterns", "author": "Felix May", "engine": "knitr::rmarkdown", "headings": [ "Simulate and explore data", "Non-spatial patterns", "Species abundance distribution (SAD)", "Rarefaction curve", "Spatial patterns", "Species-accumulation curve", "Diversity-area relationships", "Distance decay of community similarity", "References" ], "created": "2016-11-02 10:40:37", "modified": "2017-11-01 10:31:59", "commits": 9 }, { "source": "Biodiversity_Changes.Rmd", "filename": "Biodiversity_Changes.html", "title": "Changes of biodiversity components", "author": "Felix May", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Change in total number of individuals", "Change in the abundance distribution", "Change in spatial distributions" ], "created": "2016-11-02 10:40:37", "modified": "2024-03-21 15:55:57", "commits": 9 }, { "source": "Introduction_mobsim.Rmd", "filename": "Introduction_mobsim.html", "title": "Introduction to mobsim", "author": "Felix May", "engine": "knitr::rmarkdown", "headings": [ "An example application of mobsim", "Simulating communities", "Analysis of spatially-explicit community data", "Sampling spatially-explicit community data", "Analysis of plot-based community data", "Small scale analysis", "Large scale analysis", "Compare results across scales", "Conclusion" ], "created": "2017-05-02 08:31:59", "modified": "2024-03-21 15:55:57", "commits": 8 }, { "source": "Sampling_communities.Rmd", "filename": "Sampling_communities.html", "title": "Sampling communities with mobsim", "author": "Felix May", "engine": "knitr::rmarkdown", "headings": [ "Random sampling", "Transect sampling", "Grid sampling" ], "created": "2017-09-27 21:31:30", "modified": "2024-03-21 15:55:57", "commits": 5 }, { "source": "Simulating_communities.Rmd", "filename": "Simulating_communities.html", "title": "Simulating communities with mobsim", "author": "Felix May", "engine": "knitr::rmarkdown", "headings": [ "Biodiversity components", "Simulating species abundance distributions", "Simulate spatial distributions", "Random distributions", "Aggregated positions", "References" ], "created": "2017-07-29 11:37:37", "modified": "2024-03-21 15:55:57", "commits": 6 } ], "_score": 7.116358650501693, "_indexed": true, "_nocasepkg": "mobsim", "_universes": [ "mobiodiv", "felixmay" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.2", "date": "2026-05-24T09:20:53.000Z", "distro": "noble", "arch": "aarch64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "cf29083dd708ec9479c0f367a91043d4ad3a62f4c3ad07788849965c4349491b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.7.0", "os": "linux", "version": "0.3.2", "date": "2026-05-24T09:20:56.000Z", "distro": "noble", "arch": "x86_64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "bf78fdf5df9ccc06bd7ff6b42ab3c67737aad2d941d353b57d5711eb96c859d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.6.0", "os": "linux", "version": "0.3.2", "date": "2026-05-24T09:20:47.000Z", "distro": "noble", "arch": "aarch64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "0f58ade012c43ab72731c38e3304ce95a17cb5027292be6e51dcd4479b58ed97", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.6.0", "os": "linux", "version": "0.3.2", "date": "2026-05-24T09:20:54.000Z", "distro": "noble", "arch": "x86_64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "2bb8605d2e4de8ad151e92eba16e437b068574ab0fb423ce9d3f23d94388a500", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.5.3", "os": "mac", "version": "0.3.2", "date": "2026-05-24T09:20:56.000Z", "arch": "aarch64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "93049c08c46b5e224ae84ad9103efec9635ca40a6220adb652728f22ecb7c23f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.5.3", "os": "mac", "version": "0.3.2", "date": "2026-05-24T09:23:54.000Z", "arch": "x86_64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "56ddcee809f5b18ac18634ef70c2c0e49b7119208bd5a1eea997d278d9412566", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.6.0", "os": "mac", "version": "0.3.2", "date": "2026-05-24T09:20:47.000Z", "arch": "aarch64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "fba7415b85ec876264cd37e2c76e9b93ab79b3646b15e17694746a91d1f63e1c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.6.0", "os": "mac", "version": "0.3.2", "date": "2026-05-24T09:22:55.000Z", "arch": "x86_64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "77cfe5355da6e781357dce981817b2f97048d09514600915e8c62df0f349c17e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.2", "date": "2026-05-24T09:20:43.000Z", "arch": "emscripten", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "75886b784aabe180e774e4ffe12f5d39f5ccfa0dbcccdf522b3b8b975cdaf231", "status": "success", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.7.0", "os": "win", "version": "0.3.2", "date": "2026-05-24T09:20:47.000Z", "arch": "x86_64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "40e85ef98615fff23a6e5bca37f7837d3d9c7ca0436937108d17e005325eaa27", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.5.3", "os": "win", "version": "0.3.2", "date": "2026-05-24T09:20:53.000Z", "arch": "x86_64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "5b4a6dbb5f2912d9c44ad036e544a8c6bf8c5af5b4e4a6f4c5812d18b6e8c9dc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" }, { "r": "4.6.0", "os": "win", "version": "0.3.2", "date": "2026-05-24T09:21:30.000Z", "arch": "x86_64", "commit": "ef1e5ce9f99397838b5d8fbe51f81c6ae7bd4ad3", "fileid": "b2401578531694a9409ed4a6f02e947e26b292c60d98b902922d4f6026a5ee72", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mobiodiv/actions/runs/26357297115" } ] }