{ "_id": "6a17f264acfb0bcc41da7779", "Package": "StratPal", "Title": "Stratigraphic Paleobiology Modeling Pipelines", "Version": "0.7.1", "Authors@R": "person(\"Niklas\", \"Hohmann\", , \"N.H.Hohmann@uu.nl\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-1559-1838\"))", "Description": "The fossil record is a joint expression of ecological,\ntaphonomic, evolutionary, and stratigraphic processes (Holland\nand Patzkowsky, 2012, ISBN:978-0226649382). This package\nallowing to simulate biological processes in the time domain\n(e.g., trait evolution, fossil abundance, phylogenetic trees),\nand examine how their expression in the rock record\n(stratigraphic domain) is influenced based on age-depth models,\necological niche models, and taphonomic effects. Functions\nsimulating common processes used in modeling trait evolution,\nbiostratigraphy or event type data such as first/last\noccurrences are provided and can be used standalone or as part\nof a pipeline. The package comes with example data sets and\ntutorials in several vignettes, which can be used as a template\nto set up one's own simulation.", "License": "Apache License (>= 2)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "LazyData": "true", "URL": "https://mindthegap-erc.github.io/StratPal/ ,\nhttps://github.com/MindTheGap-ERC/StratPal", "BugReports": "https://github.com/MindTheGap-ERC/StratPal/issues", "Config/testthat/edition": "3", "Language": "en-US", "Repository": "https://mindthegap-erc.r-universe.dev", "Date/Publication": "2026-04-28 06:13:33 UTC", "RemoteUrl": "https://github.com/mindthegap-erc/stratpal", "RemoteRef": "HEAD", "RemoteSha": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 07:41:40 UTC", "User": "root" }, "Author": "Niklas Hohmann [aut, cre] (ORCID:\n)", "Maintainer": "Niklas Hohmann ", "MD5sum": "dc489d8b5db639bc8fa0ba3463abc234", "_user": "mindthegap-erc", "_type": "src", "_file": "StratPal_0.7.1.tar.gz", "_fileid": "4d066cf2e4717921bd32dd9afb8d279baa5eadf06a2c6c08d55803e52527edb9", "_filesize": 3095556, "_sha256": "4d066cf2e4717921bd32dd9afb8d279baa5eadf06a2c6c08d55803e52527edb9", "_created": "2026-05-28T07:41:40.000Z", "_published": "2026-05-28T07:44:36.827Z", "_distro": "noble", "_jobs": [ { "job": 78245815249, "time": 127, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7260369394" }, { "job": 78245815227, "time": 136, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7260371908" }, { "job": 78245815245, "time": 85, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7260355975" }, { "job": 78245815247, "time": 88, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7260356918" }, { "job": 78245355413, "time": 181, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7260328930" }, { "job": 78245815248, "time": 103, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7260361329" }, { "job": 78245815240, "time": 83, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7260355507" }, { "job": 78245815243, "time": 68, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7260351110" }, { "job": 78245815232, "time": 77, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7260353612" } ], "_buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/mindthegap-erc/stratpal", "_commit": { "id": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "author": "Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com>", "committer": "Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com>", "message": "update CI\n", "time": 1777356813 }, "_maintainer": { "name": "Niklas Hohmann", "email": "n.h.hohmann@uu.nl", "login": "niklashohmann", "mastodon": "@Niklas_Hohmann@ecoevo.social", "orcid": "0000-0003-1559-1838", "description": "PhD candidate @UtrechtUniversity ", "uuid": 67792281 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "admtools", "version": ">= 0.6.0", "role": "Imports" }, { "package": "paleoTS", "role": "Imports" }, { "package": "ape", "role": "Suggests" }, { "package": "FossilSim", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "mindthegap-erc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-35", "n": 4 }, { "week": "2025-48", "n": 1 }, { "week": "2025-49", "n": 4 }, { "week": "2026-18", "n": 2 } ], "_tags": [ { "name": "v0.6.0", "date": "2025-08-27" }, { "name": "v0.7.0", "date": "2025-11-24" } ], "_topics": [ "palaeobiology", "palaeontology", "paleobiology", "paleontology", "stratigraphic-paleobiology", "stratigraphy" ], "_stars": 2, "_contributors": [ { "user": "niklashohmann", "count": 256, "uuid": 67792281 }, { "user": "emiliajarochowska", "count": 2, "uuid": 18270548 } ], "_userbio": { "uuid": 127970444, "type": "organization", "name": "MindTheGap: Quantifying the completeness of the stratigraphic record and its role in reconstructing the tempo and mode of evolution", "description": "European Research Council Starting Grant" }, "_downloads": { "count": 150, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/StratPal" }, "_devurl": "https://github.com/mindthegap-erc/stratpal", "_pkgdown": "https://mindthegap-erc.github.io/StratPal/", "_searchresults": 35, "_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/StratPal.html", "manual.pdf" ], "_homeurl": "https://github.com/mindthegap-erc/stratpal", "_realowner": "mindthegap-erc", "_cranurl": true, "_releases": [ { "version": "0.1.1", "date": "2024-08-26" }, { "version": "0.2.0", "date": "2024-10-04" }, { "version": "0.3.0", "date": "2024-11-21" }, { "version": "0.3.1", "date": "2025-02-20" }, { "version": "0.4.0", "date": "2025-03-27" }, { "version": "0.5.0", "date": "2025-05-21" }, { "version": "0.6.0", "date": "2025-08-27" }, { "version": "0.7.0", "date": "2025-11-24" }, { "version": "0.7.1", "date": "2025-12-11" } ], "_exports": [ "all_preserved", "apply_niche", "apply_taphonomy", "as_char_mat", "bounded_niche", "discrete_gradient", "discrete_niche", "gradient_from_data", "is_char_mat", "last_occ", "ornstein_uhlenbeck", "ornstein_uhlenbeck_sl", "p3", "p3_var_rate", "perfect_preservation", "prob_remove", "random_walk", "random_walk_sl", "range_offset", "reduce_to_paleoTS", "rej_samp", "snd_niche", "stasis", "stasis_sl", "strat_filter", "strict_stasis_sl", "thin", "trivial_gradient", "trivial_niche" ], "_datasets": [ { "name": "scenarioA", "title": "example data, emulates scenario A from Hohmann et al. (2024)", "object": "scenarioA", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "all_preserved", "title": "Indestructible fossils", "topics": [ "all_preserved" ] }, { "page": "apply_niche", "title": "apply niche model", "topics": [ "apply_niche" ] }, { "page": "apply_taphonomy", "title": "model taphonomic effects", "topics": [ "apply_taphonomy" ] }, { "page": "as_char_mat", "title": "construct character matrix", "topics": [ "as_char_mat" ] }, { "page": "bounded_niche", "title": "define niche from boundaries", "topics": [ "bounded_niche" ] }, { "page": "discrete_gradient", "title": "construct discretized gradient", "topics": [ "discrete_gradient" ] }, { "page": "discrete_niche", "title": "niche from discrete data", "topics": [ "discrete_niche" ] }, { "page": "gradient_from_data", "title": "gradient or taphonomic conditions from data", "topics": [ "gradient_from_data" ] }, { "page": "is_char_mat", "title": "validity of character matrices", "topics": [ "is_char_mat" ] }, { "page": "last_occ", "title": "last occurrence of taxon", "topics": [ "last_occ" ] }, { "page": "ornstein_uhlenbeck", "title": "simulate ornstein-uhlenbeck (OU) process", "topics": [ "ornstein_uhlenbeck" ] }, { "page": "ornstein_uhlenbeck_sl", "title": "simulate ornstein-uhlenbeck (OU) process (specimen level)", "topics": [ "ornstein_uhlenbeck_sl" ] }, { "page": "p3", "title": "simulate Poisson point process", "topics": [ "p3" ] }, { "page": "p3_var_rate", "title": "simulate variable rate Poisson point process", "topics": [ "p3_var_rate" ] }, { "page": "perfect_preservation", "title": "perfect taphonomic conditions", "topics": [ "perfect_preservation" ] }, { "page": "plot.pre_paleoTS", "title": "plot pre-paleoTS objects", "topics": [ "plot.pre_paleoTS" ] }, { "page": "prob_remove", "title": "probabilistic removal of elements", "topics": [ "prob_remove" ] }, { "page": "random_walk", "title": "simulate (un)biased random walk", "topics": [ "random_walk" ] }, { "page": "random_walk_sl", "title": "simulate (un)biased random walk (specimen level)", "topics": [ "random_walk_sl" ] }, { "page": "range_offset", "title": "range offset of taxon", "topics": [ "range_offset" ] }, { "page": "reduce_to_paleoTS", "title": "reduce pre-paleoTS format to paleoTS", "topics": [ "reduce_to_paleoTS" ] }, { "page": "rej_samp", "title": "random numbers from rejection sampling", "topics": [ "rej_samp" ] }, { "page": "scenarioA", "title": "example data, emulates scenario A from Hohmann et al. (2024)", "topics": [ "scenarioA" ] }, { "page": "snd_niche", "title": "simple niche model", "topics": [ "snd_niche" ] }, { "page": "stasis", "title": "simulate phenotypic stasis", "topics": [ "stasis" ] }, { "page": "stasis_sl", "title": "simulate phenotypic stasis (specimen level)", "topics": [ "stasis_sl" ] }, { "page": "strat_filter", "title": "generate basic stratigraphic filter", "topics": [ "strat_filter" ] }, { "page": "strict_stasis_sl", "title": "simulate strict phenotypic stasis (specimen level)", "topics": [ "strict_stasis_sl" ] }, { "page": "thin", "title": "thin a series of events (e.g. fossil occurrences)", "topics": [ "thin" ] }, { "page": "trivial_gradient", "title": "model absence of environmental gradients", "topics": [ "trivial_gradient" ] }, { "page": "trivial_niche", "title": "trivial niche model", "topics": [ "trivial_niche" ] } ], "_readme": "https://github.com/mindthegap-erc/stratpal/raw/HEAD/README.md", "_rundeps": [ "admtools", "ape", "codetools", "digest", "doParallel", "foreach", "iterators", "lattice", "mnormt", "nlme", "paleoTS", "Rcpp" ], "_vignettes": [ { "source": "advanced_functionality.Rmd", "filename": "advanced_functionality.html", "title": "Advanced Functionality and Writing Extensions", "engine": "knitr::rmarkdown", "headings": [ "Different forward models", "Empirical age-depth models", "Other ecological gradients and niche definitions", "Different models of phenotypic evolution", "Different models of event type data", "Transforming data from the stratigraphic domain to the time domain", "Taphonomy", "Transform different types of data", "References" ], "created": "2024-07-19 08:14:05", "modified": "2025-12-04 06:51:57", "commits": 10 }, { "source": "StratPal_docs.Rmd", "filename": "StratPal_docs.html", "title": "Documentation of defined S3 classes", "engine": "knitr::rmarkdown", "headings": [ "S3 class pre_paleoTS", "Structure", "Construction", "Modification", "Transformation into other S3 classes", "Plotting", "S3 class char_mat" ], "created": "2024-10-03 07:11:58", "modified": "2025-12-04 06:51:57", "commits": 4 }, { "source": "stratigraphic_architecture.Rmd", "filename": "stratigraphic_architecture.html", "title": "Example Stratigraphic Architecture", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Stratigraphic Context", "Dataset structure", "Simulation settings", "Platform visualization", "References" ], "created": "2025-12-04 06:51:57", "modified": "2025-12-04 06:51:57", "commits": 1 }, { "source": "FossilSim_integration.Rmd", "filename": "FossilSim_integration.html", "title": "Integration with the FossilSim and paleotree packages", "engine": "knitr::rmarkdown", "headings": [ "Integration with the FossilSim package", "Stratigraphic basis", "Trees with fossils", "Ecological effects", "Stratigraphic effects", "Combined stratigraphic and ecological effects", "Technical notes", "Integration with paleotree", "References" ], "created": "2025-03-20 19:15:03", "modified": "2025-08-27 09:28:27", "commits": 3 }, { "source": "StratPal.Rmd", "filename": "StratPal.html", "title": "Introduction to the StratPal package", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Installation", "CRAN", "GitHub", "Dependencies", "Example data", "Piping", "Motivation and usage", "Advanced usage", "Age-depth models", "Defining age-depth models", "Plotting", "Extracting information", "Transforming data", "Getting started", "References" ], "created": "2024-07-15 10:21:59", "modified": "2025-12-04 06:51:57", "commits": 17 }, { "source": "event_data.Rmd", "filename": "event_data.html", "title": "Stratigraphic Paleobiology for Event Data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Modeling fossil occurrences and first/last fossil occurrences", "Age-depth models", "Stratigraphic distortions of \"event\" type data", "Fossil specimens", "First/Last occurrences of common taxa", "Range offset", "Niche modeling", "Taphonomic effects", "Further reading", "References" ], "created": "2024-07-19 06:13:20", "modified": "2025-12-04 06:51:57", "commits": 14 }, { "source": "phenotypic_evolution.Rmd", "filename": "phenotypic_evolution.html", "title": "Stratigraphic Paleobiology for Phenotypic Evolution", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Modes of evolution in the time domain", "Implemented modes of evolution", "Visualization", "Stratigraphic domain", "Age-depth models", "Stratigraphic expression of phenotypic evolution", "Prescribing a sampling strategy", "Further reading", "References" ], "created": "2024-07-19 06:13:20", "modified": "2025-01-14 10:26:00", "commits": 9 }, { "source": "paleoTS_functionality.Rmd", "filename": "paleoTS_functionality.html", "title": "Usage with the paleoTS and evoTS package", "engine": "knitr::rmarkdown", "headings": [ "Quick summary", "Motivation", "Modeling trait evolution on specimen level, complexity reduction, and plotting", "Modeling of ecological, taphonomic, and stratigraphic effects", "References" ], "created": "2024-10-03 08:42:11", "modified": "2025-01-14 10:26:00", "commits": 4 } ], "_score": 6.049218022670182, "_indexed": true, "_nocasepkg": "stratpal", "_universes": [ "mindthegap-erc", "niklashohmann" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.7.1", "date": "2026-05-28T07:43:51.000Z", "distro": "noble", "commit": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "fileid": "59145b1beec9d1761d6fe0dc003cf05539077d32c7c651668706c20c9ebc8e94", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296" }, { "r": "4.6.0", "os": "linux", "version": "0.7.1", "date": "2026-05-28T07:43:58.000Z", "distro": "noble", "commit": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "fileid": "804d26c601f45fcbc1b3152144e5304151868be3dfac0d67559a6f0e413c4305", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296" }, { "r": "4.5.3", "os": "mac", "version": "0.7.1", "date": "2026-05-28T07:43:15.000Z", "commit": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "fileid": "d98c64d809109a9b7f75659da126acbb0c092a7b5923266c53936184fc10189b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296" }, { "r": "4.6.0", "os": "mac", "version": "0.7.1", "date": "2026-05-28T07:43:16.000Z", "commit": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "fileid": "ac950531b02c14f53872d6a2a0822f82dda3e0b7621fb560a1c541085b914f6f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296" }, { "r": "4.6.0", "os": "wasm", "version": "0.7.1", "date": "2026-05-28T07:43:42.000Z", "commit": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "fileid": "5d9e9f2b585d5b915fae1b58e34762ca6a80ad3ae36c2374581b2b3118c02420", "status": "success", "buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296" }, { "r": "4.7.0", "os": "win", "version": "0.7.1", "date": "2026-05-28T07:43:01.000Z", "commit": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "fileid": "a6cd0b09563ddbca853ce101314faa8d74f1e62f6010597c0fa386aceb09c921", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296" }, { "r": "4.5.3", "os": "win", "version": "0.7.1", "date": "2026-05-28T07:42:49.000Z", "commit": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "fileid": "28daefe1e7ad4566de64a2db0a255e1be0304c186f22c6fabeac60e8b325a0ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296" }, { "r": "4.6.0", "os": "win", "version": "0.7.1", "date": "2026-05-28T07:42:55.000Z", "commit": "f18bef06db3f6fc1d9b31bc2b0dbc128e14272b0", "fileid": "d739b7d09b3848ce0d3fe313d8849a6ce9ffc9e006b59446065cc92bdb0aec25", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mindthegap-erc/actions/runs/26561476296" } ] }