{ "_id": "6a17e7c6acfb0bcc41da1bf2", "Package": "provenance", "Title": "Statistical Toolbox for Sedimentary Provenance Analysis", "Version": "4.5", "Date": "2025-07-01", "Authors@R": "person(\"Pieter\", \"Vermeesch\", , \"p.vermeesch@ucl.ac.uk\", role = c(\"aut\", \"cre\"))", "Description": "Bundles a number of established statistical methods to\nfacilitate the visual interpretation of large datasets in\nsedimentary geology. Includes functionality for adaptive kernel\ndensity estimation, principal component analysis,\ncorrespondence analysis, multidimensional scaling, generalised\nprocrustes analysis and individual differences scaling using a\nvariety of dissimilarity measures. Univariate provenance\nproxies, such as single-grain ages or (isotopic) compositions\nare compared with the Kolmogorov-Smirnov, Kuiper, Wasserstein-2\nor Sircombe-Hazelton L2 distances. Categorical provenance\nproxies such as chemical compositions are compared with the\nAitchison and Bray-Curtis distances,and count data with the\nchi-square distance. Varietal data can either be converted to\none or more distributional datasets, or directly compared using\nthe multivariate Wasserstein distance. Also included are tools\nto plot compositional and count data on ternary diagrams and\npoint-counting data on radial plots, to calculate the sample\nsize required for specified levels of statistical precision,\nand to assess the effects of hydraulic sorting on detrital\ncompositions. Includes an intuitive query-based user interface\nfor users who are not proficient in R.", "Author": "Pieter Vermeesch [aut, cre]", "Maintainer": "Pieter Vermeesch ", "URL": "https://pieter-vermeesch.es.ucl.ac.uk/provenance/", "License": "GPL-2", "LazyData": "true", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "NeedsCompilation": "no", "Repository": "https://pvermees.r-universe.dev", "Date/Publication": "2025-12-05 23:33:29 UTC", "RemoteUrl": "https://github.com/pvermees/provenance", "RemoteRef": "HEAD", "RemoteSha": "1e853e9ad6f640f6212576a022dcfe331de6088c", "Packaged": { "Date": "2026-05-28 06:52:37 UTC", "User": "root" }, "MD5sum": "56150cf3790392d160f439b95f2c93b5", "_user": "pvermees", "_type": "src", "_file": "provenance_4.5.tar.gz", "_fileid": "75b8aff96b2833c88a8c4469f9290fdf18d7a2fab973190190cbd0b6436abe32", "_filesize": 745734, "_sha256": "75b8aff96b2833c88a8c4469f9290fdf18d7a2fab973190190cbd0b6436abe32", "_created": "2026-05-28T06:52:37.000Z", "_published": "2026-05-28T06:59:18.131Z", "_distro": "noble", "_jobs": [ { "job": 78239090524, "time": 123, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7259524074" }, { "job": 78239090562, "time": 135, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7259527007" }, { "job": 78239090532, "time": 82, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7259536529" }, { "job": 78239090540, "time": 88, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7259586260" }, { "job": 78238777004, "time": 149, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259492096" }, { "job": 78239090526, "time": 92, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259516131" }, { "job": 78239090547, "time": 110, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7259521505" }, { "job": 78239090558, "time": 92, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7259516127" }, { "job": 78239090535, "time": 105, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7259519132" } ], "_buildurl": "https://github.com/r-universe/pvermees/actions/runs/26559484252", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/pvermees/provenance", "_commit": { "id": "1e853e9ad6f640f6212576a022dcfe331de6088c", "author": "Pieter Vermeesch ", "committer": "Pieter Vermeesch ", "message": "Bumped roxygen version\n", "time": 1764977609 }, "_maintainer": { "name": "Pieter Vermeesch", "email": "p.vermeesch@ucl.ac.uk", "login": "pvermees", "description": "", "uuid": 7851420 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "IsoplotR", "version": ">= 6.2", "role": "Depends" }, { "package": "MASS", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "transport", "role": "Suggests" }, { "package": "T4transport", "role": "Suggests" } ], "_owner": "pvermees", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-27", "n": 1 }, { "week": "2025-49", "n": 1 } ], "_tags": [], "_stars": 14, "_contributors": [ { "user": "pvermees", "count": 126, "uuid": 7851420 } ], "_userbio": { "uuid": 7851420, "type": "user", "name": "Pieter Vermeesch" }, "_downloads": { "count": 246, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/provenance" }, "_devurl": "https://github.com/pvermees/provenance", "_searchresults": 80, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/provenance.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/pvermees/provenance", "_realowner": "pvermees", "_cranurl": true, "_releases": [ { "version": "0.1", "date": "2015-05-26" }, { "version": "0.2", "date": "2015-06-05" }, { "version": "0.3", "date": "2015-08-13" }, { "version": "0.5", "date": "2015-09-16" }, { "version": "0.6", "date": "2015-09-21" }, { "version": "1.0", "date": "2015-12-10" }, { "version": "1.1", "date": "2016-01-03" }, { "version": "1.2", "date": "2016-01-21" }, { "version": "1.3", "date": "2016-02-12" }, { "version": "1.4", "date": "2016-03-01" }, { "version": "1.5", "date": "2016-04-22" }, { "version": "1.6", "date": "2017-05-03" }, { "version": "1.7", "date": "2017-05-18" }, { "version": "1.8", "date": "2017-11-22" }, { "version": "1.9", "date": "2018-01-03" }, { "version": "2.0", "date": "2018-04-24" }, { "version": "2.1", "date": "2018-08-03" }, { "version": "2.2", "date": "2018-10-06" }, { "version": "2.3", "date": "2019-06-06" }, { "version": "2.4", "date": "2020-03-20" }, { "version": "3.0", "date": "2021-02-24" }, { "version": "3.2", "date": "2021-04-03" }, { "version": "3.3", "date": "2021-05-04" }, { "version": "4.0", "date": "2022-06-18" }, { "version": "4.1", "date": "2023-03-03" }, { "version": "4.2", "date": "2023-08-28" }, { "version": "4.3", "date": "2024-05-04" }, { "version": "4.4", "date": "2025-01-12" } ], "_exports": [ "ALR", "amalgamate", "as.acomp", "as.compositional", "as.counts", "as.varietal", "botev", "bray.diss", "CA", "CLR", "combine", "get.f", "get.n", "get.p", "GPA", "indscal", "KDE", "KDEs", "KS.diss", "Kuiper.diss", "MDS", "minsorting", "PCA", "procrustes", "provenance", "read.compositional", "read.counts", "read.densities", "read.distributional", "read.varietal", "restore", "SH.diss", "summaryplot", "ternary", "ternary.ellipse", "varietal2distributional", "Wasserstein.diss" ], "_datasets": [ { "name": "densities", "title": "A list of rock and mineral densities", "object": "densities", "class": [ "data.frame" ], "fields": [ "Q", "KF", "P", "F", "Lvf", "Lvm", "Lcc", "Lcd", "Lp", "Lch", "Lms", "Lmv", "Lmf", "Lmb", "Lv", "Lc", "Ls", "Lm", "Lu", "Lu.1", "mica", "opaques", "FeOx", "turbids", "zr", "tm", "rt", "TiOx", "sph", "ap", "mon", "oth", "ep", "othLgM", "gt", "ctd", "st", "and", "ky", "sil", "amp", "px", "cpx", "opx", "ol", "spinel", "othHM" ], "rows": 1, "table": true, "tojson": true }, { "name": "endmembers", "title": "Petrographic end-member compositions", "object": "endmembers", "class": [ "compositional" ], "fields": [], "table": false, "tojson": false }, { "name": "Namib", "title": "An example dataset", "object": "Namib", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "SNSM", "title": "varietal data example", "object": "SNSM", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "ALR", "title": "Additive logratio transformation", "topics": [ "ALR", "ALR.compositional", "ALR.default" ] }, { "page": "amalgamate", "title": "Group components of a composition", "topics": [ "amalgamate", "amalgamate.compositional", "amalgamate.counts", "amalgamate.default", "amalgamate.SRDcorrected", "amalgamate.varietal" ] }, { "page": "as.acomp", "title": "create an 'acomp' object", "topics": [ "as.acomp" ] }, { "page": "as.compositional", "title": "create a 'compositional' object", "topics": [ "as.compositional" ] }, { "page": "as.counts", "title": "create a 'counts' object", "topics": [ "as.counts" ] }, { "page": "as.data.frame", "title": "create a 'data.frame' object", "topics": [ "as.data.frame", "as.data.frame.compositional", "as.data.frame.counts" ] }, { "page": "as.varietal", "title": "create a 'varietal' object", "topics": [ "as.varietal" ] }, { "page": "botev", "title": "Compute the optimal kernel bandwidth", "topics": [ "botev" ] }, { "page": "bray.diss", "title": "Bray-Curtis dissimilarity", "topics": [ "bray.diss", "bray.diss.compositional", "bray.diss.default" ] }, { "page": "CA", "title": "Correspondence Analysis", "topics": [ "CA" ] }, { "page": "central.counts", "title": "Calculate central compositions", "topics": [ "central.counts" ] }, { "page": "CLR", "title": "Centred logratio transformation", "topics": [ "CLR", "CLR.compositional", "CLR.default" ] }, { "page": "combine", "title": "Combine samples of distributional data", "topics": [ "combine" ] }, { "page": "densities", "title": "A list of rock and mineral densities", "topics": [ "densities" ] }, { "page": "diss", "title": "Calculate the dissimilarity matrix between two datasets of class 'distributional', 'compositional', 'counts' or 'varietal'", "topics": [ "diss.compositional", "diss.counts", "diss.distributional", "diss.varietal" ] }, { "page": "endmembers", "title": "Petrographic end-member compositions", "topics": [ "endmembers" ] }, { "page": "get.f", "title": "Calculate the largest fraction that is likely to be missed", "topics": [ "get.f" ] }, { "page": "get.n", "title": "Calculate the number of grains required to achieve a desired level of sampling resolution", "topics": [ "get.n" ] }, { "page": "get.p", "title": "Calculate the probability of missing a given population fraction", "topics": [ "get.p" ] }, { "page": "GPA", "title": "Generalised Procrustes Analysis of configurations", "topics": [ "GPA" ] }, { "page": "indscal", "title": "Individual Differences Scaling of provenance data", "topics": [ "indscal" ] }, { "page": "KDE", "title": "Create a kernel density estimate", "topics": [ "KDE" ] }, { "page": "KDEs", "title": "Generate an object of class 'KDEs'", "topics": [ "KDEs" ] }, { "page": "KS.diss", "title": "Kolmogorov-Smirnov dissimilarity", "topics": [ "KS.diss", "KS.diss.default", "KS.diss.distributional" ] }, { "page": "Kuiper.diss", "title": "Kuiper dissimilarity", "topics": [ "Kuiper.diss", "Kuiper.diss.default", "Kuiper.diss.distributional" ] }, { "page": "lines.ternary", "title": "Ternary line plotting", "topics": [ "lines.ternary" ] }, { "page": "MDS", "title": "Multidimensional Scaling", "topics": [ "MDS", "MDS.compositional", "MDS.counts", "MDS.default", "MDS.distributional", "MDS.varietal" ] }, { "page": "minsorting", "title": "Assess settling equivalence of detrital components", "topics": [ "minsorting" ] }, { "page": "Namib", "title": "An example dataset", "topics": [ "Namib" ] }, { "page": "PCA", "title": "Principal Component Analysis", "topics": [ "PCA" ] }, { "page": "plot.CA", "title": "Point-counting biplot", "topics": [ "plot.CA" ] }, { "page": "plot.compositional", "title": "Plot a pie chart", "topics": [ "plot.compositional" ] }, { "page": "plot.distributional", "title": "Plot continuous data as histograms or cumulative age distributions", "topics": [ "plot.distributional" ] }, { "page": "plot.GPA", "title": "Plot a Procrustes configuration", "topics": [ "plot.GPA" ] }, { "page": "plot.INDSCAL", "title": "Plot an INDSCAL group configuration and source weights", "topics": [ "plot.INDSCAL" ] }, { "page": "plot.KDE", "title": "Plot a kernel density estimate", "topics": [ "plot.KDE" ] }, { "page": "plot.KDEs", "title": "Plot one or more kernel density estimates", "topics": [ "plot.KDEs" ] }, { "page": "plot.MDS", "title": "Plot an MDS configuration", "topics": [ "plot.MDS" ] }, { "page": "plot.minsorting", "title": "Plot inferred grain size distributions", "topics": [ "plot.minsorting" ] }, { "page": "plot.PCA", "title": "Compositional biplot", "topics": [ "plot.PCA" ] }, { "page": "plot.ternary", "title": "Plot a ternary diagram", "topics": [ "plot.ternary" ] }, { "page": "points.ternary", "title": "Ternary point plotting", "topics": [ "lines", "points.ternary", "text" ] }, { "page": "procrustes", "title": "Generalised Procrustes Analysis of provenance data", "topics": [ "procrustes" ] }, { "page": "provenance", "title": "Menu-based interface for 'provenance'", "topics": [ "provenance-package", "provenance" ] }, { "page": "radialplot.counts", "title": "Visualise point-counting data on a radial plot", "topics": [ "radialplot.counts" ] }, { "page": "read.compositional", "title": "Read a .csv file with compositional data", "topics": [ "read.compositional" ] }, { "page": "read.counts", "title": "Read a .csv file with point-counting data", "topics": [ "read.counts" ] }, { "page": "read.densities", "title": "Read a .csv file with mineral and rock densities", "topics": [ "read.densities" ] }, { "page": "read.distributional", "title": "Read a .csv file with distributional data", "topics": [ "read.distributional" ] }, { "page": "read.varietal", "title": "Read a .csv file with varietal data", "topics": [ "read.varietal" ] }, { "page": "restore", "title": "Undo the effect of hydraulic sorting", "topics": [ "restore" ] }, { "page": "SH.diss", "title": "Sircombe and Hazelton distance", "topics": [ "SH.diss" ] }, { "page": "SNSM", "title": "varietal data example", "topics": [ "SNSM" ] }, { "page": "subset", "title": "Get a subset of provenance data", "topics": [ "subset", "subset.compositional", "subset.counts", "subset.distributional", "subset.varietal" ] }, { "page": "summaryplot", "title": "Joint plot of several provenance datasets", "topics": [ "summaryplot" ] }, { "page": "ternary", "title": "Define a ternary composition", "topics": [ "ternary" ] }, { "page": "ternary.ellipse", 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