{ "_id": "6a104248acfb0bcc41c9db1e", "Package": "MorphoTools2", "Type": "Package", "Title": "Multivariate Morphometric Analysis", "Version": "1.0.2.1", "Date": "2024-10-01", "Authors@R": "c(\nperson(\"Marek\", \"Šlenker\", email = \"marek.slenker@savba.sk\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5919-890X\")),\nperson(\"Petr\", \"Koutecký\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3455-850X\")),\nperson(\"Karol\", \"Marhold\", role = \"ctb\", comment = c(ORCID = \"0000-0002-7658-0844\"))\n)", "Maintainer": "Marek Šlenker ", "Description": "Tools for multivariate analyses of morphological data,\nwrapped in one package, to make the workflow convenient and\nfast. Statistical and graphical tools provide a comprehensive\nframework for checking and manipulating input data, statistical\nanalyses, and visualization of results. Several methods are\nprovided for the analysis of raw data, to make the dataset\nready for downstream analyses. Integrated statistical methods\ninclude hierarchical classification, principal component\nanalysis, principal coordinates analysis, non-metric\nmultidimensional scaling, and multiple discriminant analyses:\ncanonical, stepwise, and classificatory (linear, quadratic, and\nthe non-parametric k nearest neighbours). The philosophy of the\npackage is described in Šlenker et al. 2022.", "URL": "https://github.com/MarekSlenker/MorphoTools2", "BugReports": "https://github.com/MarekSlenker/MorphoTools2/issues", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfreetype6-dev libglu1-mesa-dev make\ntexlive libicu-dev libpng-dev libuv1-dev libgl1-mesa-dev\nzlib1g-dev", "Repository": "https://marekslenker.r-universe.dev", "Date/Publication": "2024-10-02 08:05:27 UTC", "RemoteUrl": "https://github.com/marekslenker/morphotools2", "RemoteRef": "HEAD", "RemoteSha": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 07:29:31 UTC", "User": "root" }, "Author": "Marek Šlenker [aut, cre] (ORCID:\n),\nPetr Koutecký [ctb] (ORCID: ),\nKarol Marhold [ctb] (ORCID: )", "MD5sum": "3ddfc8248a939823bbb64dc9717e90d3", "_user": "marekslenker", "_type": "src", "_file": "MorphoTools2_1.0.2.1.tar.gz", "_fileid": "39be2e6e5b7d2528058ec811397daa125110513f31e034e0db51daf6bed132fb", "_filesize": 1520083, "_sha256": "39be2e6e5b7d2528058ec811397daa125110513f31e034e0db51daf6bed132fb", "_created": "2026-05-11T07:29:31.000Z", "_published": "2026-05-22T11:47:20.834Z", "_distro": "noble", "_jobs": [ { "job": 77373095388, "time": 228, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6912701717" }, { "job": 77373095532, "time": 229, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6912701615" }, { "job": 77373095618, "time": 205, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6912686026" }, { "job": 77373095645, "time": 207, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6912686252" }, { "job": 77373095044, "time": 301, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6912627216" }, { "job": 77373094975, "time": 172, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159729050" }, { "job": 77373095719, "time": 129, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6912670688" }, { "job": 77373095940, "time": 133, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6912672181" }, { "job": 77373095861, "time": 136, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6912673159" } ], "_buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/marekslenker/morphotools2", "_commit": { "id": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "author": "Marek Šlenker <55733454+MarekSlenker@users.noreply.github.com>", "committer": "GitHub ", "message": "Update DESCRIPTION", "time": 1727856327 }, "_maintainer": { "name": "Marek Šlenker", "email": "marek.slenker@savba.sk", "login": "marekslenker", "uuid": 55733454, "orcid": "0000-0002-5919-890X" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "ade4", "role": "Imports" }, { "package": "candisc", "role": "Imports" }, { "package": "car", "role": "Imports" }, { "package": "class", "role": "Imports" }, { "package": "ellipse", "role": "Imports" }, { "package": "heplots", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "plot3D", "role": "Imports" }, { "package": "StatMatch", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "marekslenker", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 7, "_contributors": [ { "user": "marekslenker", "count": 240, "uuid": 55733454 }, { "user": "yihui", "count": 1, "uuid": 163582 } ], "_userbio": { "uuid": 55733454, "type": "user", "name": "Marek Šlenker" }, "_downloads": { "count": 413, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MorphoTools2" }, "_devurl": "https://github.com/marekslenker/morphotools2", "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MorphoTools2.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/marekslenker/morphotools2", "_realowner": "marekslenker", "_cranurl": true, "_releases": [ { "version": "0.9.0", "date": "2021-11-22" }, { "version": "0.9.1", "date": "2021-12-02" }, { "version": "0.9.1.1", "date": "2021-12-07" }, { "version": "0.9.1.2", "date": "2022-02-03" }, { "version": "1.0.0.0", "date": "2022-05-26" }, { "version": "1.0.1.0", "date": "2022-10-31" }, { "version": "1.0.1.1", "date": "2023-02-20" }, { "version": "1.0.2.0", "date": "2024-09-30" }, { "version": "1.0.2.1", "date": "2024-10-02" } ], "_exports": [ "boxMTest", "boxplotAll", "boxplotCharacter", "cda.calc", "characters", "classif.knn", "classif.lda", "classif.matrix", "classif.qda", "classifSample.knn", "classifSample.lda", "classifSample.qda", "clust", "cormat", "cormatSignifTest", "descrAll", "descrPopulation", "descrTaxon", "exportRes", "histAll", "histCharacter", "keepCharacter", "keepPopulation", "keepSample", "keepTaxon", "knn.select", "missingCharactersTable", "missingSamplesTable", "naMeanSubst", "nmds.calc", "pca.calc", "pcoa.calc", "plot3Dpoints", "plotAddEllipses", "plotAddLabels.characters", "plotAddLabels.points", "plotAddLegend", "plotAddSpiders", "plotBiplot", "plotCharacters", "plotPoints", "populations", "populOTU", "qqnormAll", "qqnormCharacter", "read.morphodata", "removeCharacter", "removePopulation", "removeSample", "removeTaxon", "samples", "shapiroWilkTest", "stepdisc.calc", "taxa", "transformCharacter", "viewMorphodata" ], "_datasets": [ { "name": "centaurea", "title": "25 Morphological Characters of Three Species of the _Centaurea phrygia_ Complex", "object": "centaurea", "class": [ "morphodata" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "boxMTest", "title": "Box's M-test for Homogeneity of Covariance Matrices", "topics": [ "boxMTest" ] }, { "page": "boxplotCharacter", "title": "Box Plots", "topics": [ "boxplotAll", "boxplotCharacter" ] }, { "page": "cda.calc", "title": "Canonical Discriminant Analysis", "topics": [ "cda.calc" ] }, { "page": "cdadata", "title": "Class Cdadata", "topics": [ "cdadata" ] }, { "page": "centaurea", "title": "25 Morphological Characters of Three Species of the _Centaurea phrygia_ Complex", "topics": [ "centaurea" ] }, { "page": "characters", "title": "List Morphological Characters", "topics": [ "characters" ] }, { "page": "classif.lda", "title": "Classificatory Discriminant Analysis", "topics": [ "classif.knn", "classif.lda", "classif.qda" ] }, { "page": "classif.matrix", "title": "Format the Classifdata to Summary Table", "topics": [ "classif.matrix" ] }, { "page": "classifdata", "title": "Class classifdata", "topics": [ "classifdata" ] }, { "page": "classifSample.lda", "title": "Classificatory Discriminant Analysis", "topics": [ "classifSample.knn", "classifSample.lda", "classifSample.qda" ] }, { "page": "clust", "title": "Hierarchical Clustering", "topics": [ "clust" ] }, { "page": "cormat", "title": "Correlations of Characters", "topics": [ "cormat", "cormatSignifTest" ] }, { "page": "descrTaxon", "title": "Descriptive Statistics", "topics": [ "descrAll", "descrPopulation", "descrTaxon" ] }, { "page": "exportRes", "title": "Export Data", "topics": [ "exportRes" ] }, { "page": "head.morphodata", "title": "Return the First or Last Parts of an Object", "topics": [ "head.classifdata", "head.morphodata", "tail.classifdata", "tail.morphodata" ] }, { "page": "histCharacter", "title": "Histograms of Characters", "topics": [ "histAll", "histCharacter" ] }, { "page": "keepTaxon", "title": "Keep Items (Taxa, Populations, Samples, Morphological Characters) in an Morphodata Object (and Remove Others)", "topics": [ "keepCharacter", "keepPopulation", "keepSample", "keepTaxon" ] }, { "page": "knn.select", "title": "Search for the Optimal K-nearest Neighbours", "topics": [ "knn.select" ] }, { "page": "missingCharactersTable", "title": "Summarize Missing Data", "topics": [ "missingCharactersTable" ] }, { "page": "missingSamplesTable", "title": "Summarize Missing Data", "topics": [ "missingSamplesTable" ] }, { "page": "morphodata", "title": "Class morphodata", "topics": [ "morphodata" ] }, { "page": "naMeanSubst", "title": "Replace Missing Data by Population Average", "topics": [ "naMeanSubst" ] }, { "page": "nmds.calc", "title": "Non-metric Multidimensional Scaling (NMDS)", "topics": [ "nmds.calc" ] }, { "page": "nmdsdata", "title": "Class nmdsdata", "topics": [ "nmdsdata" ] }, { "page": "pca.calc", "title": "Principal Component Analysis", "topics": [ "pca.calc" ] }, { "page": "pcadata", "title": "Class pcadata", "topics": [ "pcadata" ] }, { "page": "pcoa.calc", "title": "Principal Coordinates Analysis (PCoA)", "topics": [ "pcoa.calc" ] }, { "page": "pcoadata", "title": "Class pcoadata", "topics": [ "pcoadata" ] }, { "page": "plot3Dpoints", "title": "The Default Scatterplot 3D Function", "topics": [ "plot3Dpoints" ] }, { "page": "plotAddEllipses", "title": "Add Prediction Ellipses to a Plot", "topics": [ "plotAddEllipses" ] }, { "page": "plotAddLabels.characters", "title": "Add Labels to a Plot", "topics": [ "plotAddLabels.characters" ] }, { "page": "plotAddLabels.points", "title": "Add Labels to a Plot", "topics": [ "plotAddLabels.points" ] }, { "page": "plotAddLegend", "title": "Add Legend to a Plot", "topics": [ "plotAddLegend" ] }, { "page": "plotAddSpiders", "title": "Add Spiders to a Plot", "topics": [ "plotAddSpiders" ] }, { "page": "plotBiplot", "title": "The Default Biplot Function", "topics": [ "plotBiplot" ] }, { "page": "plotCharacters", "title": "Draws Character's Contribution as Arrows", "topics": [ "plotCharacters" ] }, { "page": "plotPoints", "title": "The Default Scatterplot Function", "topics": [ "plotPoints" ] }, { "page": "populOTU", "title": "Population Means", "topics": [ "populOTU" ] }, { "page": "qqnormCharacter", "title": "Quantile-Quantile Plots", "topics": [ "qqnormAll", "qqnormCharacter" ] }, { "page": "read.morphodata", "title": "Data Input and Description", "topics": [ "populations", "read.morphodata", "samples", "taxa" ] }, { "page": "removeTaxon", "title": "Remove Items (Taxa, Populations, Morphological Characters) from Morphodata Object", "topics": [ "removeCharacter", "removePopulation", "removeSample", "removeTaxon" ] }, { "page": "shapiroWilkTest", "title": "Shapiro-Wilk Normality Test", "topics": [ "shapiroWilkTest" ] }, { "page": "stepdisc.calc", "title": "Stepwise Discriminant Analysis", "topics": [ "stepdisc.calc" ] }, { "page": "summary", "title": "Object Summaries", "topics": [ "summary", "summary.cdadata", "summary.classifdata", "summary.morphodata", "summary.nmdsdata", "summary.pcadata", "summary.pcoadata" ] }, { "page": "transformCharacter", "title": "Transformation of Character", "topics": [ "transformCharacter" ] }, { "page": "viewMorphodata", "title": "Invoke a Data Viewer", "topics": [ "viewMorphodata" ] } ], "_readme": "https://github.com/marekslenker/morphotools2/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "backports", "base64enc", "boot", "broom", "bslib", "cachem", "candisc", "car", "carData", "class", "cli", "cluster", "colorspace", "cowplot", "cpp11", "DBI", "Deriv", "digest", "doBy", "dplyr", "ellipse", "evaluate", "farver", "fastmap", "fontawesome", "forecast", "Formula", "fracdiff", "fs", "generics", "ggplot2", "glue", "gtable", "heplots", "highr", "htmltools", "htmlwidgets", "insight", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "lpSolve", "magrittr", "MASS", "Matrix", "MatrixModels", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "misc3d", "mitools", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "permute", "pillar", "pixmap", "pkgconfig", "plot3D", "proxy", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rgl", "rlang", "rmarkdown", "S7", "sass", "scales", "sp", "SparseM", "StatMatch", "stringi", "stringr", "survey", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "vegan", "viridisLite", "withr", "xfun", "yaml", "zoo" ], "_vignettes": [ { "source": "MorphoTools2_tutorial.Rmd", "filename": "MorphoTools2_tutorial.html", "title": "\\vspace{+2.0cm} MorphoTools2 version 1.0.2.0 tutorial \\vspace{+2.0cm}", "author": "| developed by Marek Šlenker\\footnotemark[2] \\footnotemark[3] \\footnotemark[1] \\vspace*{0.5pc} | with contributions from Petr Koutecký\\footnotemark[4]  and Karol Marhold\\footnotemark[2] \\footnotemark[3] \\vspace*{0.7pc} | \\vspace*{0.7pc} | https://github.com/MarekSlenker/MorphoTools2", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "2. Obtaining and installing the MorphoTools2 package", "3. Data import, checking and manipulation", "3.1 Data import", "3.2 Assessing normality of data", "3.2.1 Shapiro-Wilk test of normality", "3.2.2 Histograms", "3.2.3 Normal Q-Q plot", "3.3 Data transformation", "3.4 Box Plots", "3.5 Descriptive statistics", "3.6 Correlations of characters", "3.7 Populations as operational taxonomic units", "3.8 Missing data", "3.8.1 Removing items", "3.8.2 Replacing missing values", "4. Hierarchical clustering", "5. Principal component analysis (PCA)", "6. Principal coordinate analysis (PCoA)", "7. Non-metric multidimensional scaling (NMDS)", "8. Stepwise discriminant analysis", "9. Canonical discriminant analysis (CDA)", "Passive prediction of samples.", "10. Classificatory discriminant analysis", "10.1 Linear discriminant analysis (LDA)", "10.2 Quadratic discriminant analysis (QDA)", "10.3 K nearest neighbour classificatory DA", "10.4 Classification of sample individuals based on an independent training set.", "Further reading", "References" ], "created": "2020-09-02 14:00:33", "modified": "2024-09-26 12:54:19", "commits": 59 } ], "_score": 4.544068044350276, "_indexed": true, "_nocasepkg": "morphotools2", "_universes": [ "marekslenker" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2.1", "date": "2026-05-11T07:32:55.000Z", "distro": "noble", "commit": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "fileid": "f878be6430298e97a68dda14fe32e2cc76be8ee411ce096e0712bfdac2683646", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619" }, { "r": "4.6.0", "os": "linux", "version": "1.0.2.1", "date": "2026-05-11T07:32:54.000Z", "distro": "noble", "commit": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "fileid": "158be7e09c334a7ed01982499193f3614e0d0a45e9819e136c9719743a79ea52", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2.1", "date": "2026-05-11T07:32:18.000Z", "commit": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "fileid": "e98dc443951064cf08bb990b3fe66a1e2c0166bb2c1f6a0b17828cb149c3893e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619" }, { "r": "4.6.0", "os": "mac", "version": "1.0.2.1", "date": "2026-05-11T07:32:05.000Z", "commit": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "fileid": "eaa9513a8b35a05b9ffa0448886023a214737ec6e2ad2aceba0a691b2ee3f286", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619" }, { "r": "4.7.0", "os": "win", "version": "1.0.2.1", "date": "2026-05-11T07:31:04.000Z", "commit": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "fileid": "18c4f547b20d7e84f66e1ca491300df039dc4c27c2ce58273555bf1a756bb454", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619" }, { "r": "4.5.3", "os": "win", "version": "1.0.2.1", "date": "2026-05-11T07:31:03.000Z", "commit": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "fileid": "f8c8f387a49ad56f92dec59aed6d8dc3d1d7c0a3b693e494df3db42999ef299f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619" }, { "r": "4.6.0", "os": "win", "version": "1.0.2.1", "date": "2026-05-11T07:31:10.000Z", "commit": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "fileid": "eeb084b760109a3681e647b38583a311eed0377c6e159c3e865603264075d0ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2.1", "date": "2026-05-22T11:47:04.000Z", "commit": "2cb13b01c5ecd0392d21467f634650d0bbc0507f", "fileid": "a56d817fcbc537764f89c5deaee0184b475b17abf695e39408cee08406795059", "status": "success", "buildurl": "https://github.com/r-universe/marekslenker/actions/runs/25656258619" } ] }