Package: MorphoTools2 1.0.2.1

MorphoTools2: Multivariate Morphometric Analysis

Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package is described in Šlenker et al. 2022.

Authors:Marek Šlenker [aut, cre], Petr Koutecký [ctb], Karol Marhold [ctb]

MorphoTools2_1.0.2.1.tar.gz
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MorphoTools2.pdf |MorphoTools2.html✨
MorphoTools2/json (API)
NEWS

# Install 'MorphoTools2' in R:
install.packages('MorphoTools2', repos = c('https://marekslenker.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/marekslenker/morphotools2/issues

Datasets:
  • centaurea - 25 Morphological Characters of Three Species of the _Centaurea phrygia_ Complex

On CRAN:

4.95 score 6 stars 9 scripts 540 downloads 56 exports 102 dependencies

Last updated 2 months agofrom:2cb13b01c5. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winNOTENov 01 2024
R-4.5-linuxNOTENov 01 2024
R-4.4-winOKNov 02 2024
R-4.4-macOKNov 01 2024
R-4.3-winOKNov 01 2024
R-4.3-macOKNov 02 2024

Exports:boxMTestboxplotAllboxplotCharactercda.calccharactersclassif.knnclassif.ldaclassif.matrixclassif.qdaclassifSample.knnclassifSample.ldaclassifSample.qdaclustcormatcormatSignifTestdescrAlldescrPopulationdescrTaxonexportReshistAllhistCharacterkeepCharacterkeepPopulationkeepSamplekeepTaxonknn.selectmissingCharactersTablemissingSamplesTablenaMeanSubstnmds.calcpca.calcpcoa.calcplot3DpointsplotAddEllipsesplotAddLabels.charactersplotAddLabels.pointsplotAddLegendplotAddSpidersplotBiplotplotCharactersplotPointspopulationspopulOTUqqnormAllqqnormCharacterread.morphodataremoveCharacterremovePopulationremoveSampleremoveTaxonsamplesshapiroWilkTeststepdisc.calctaxatransformCharacterviewMorphodata

Dependencies:abindade4backportsbase64encbootbroombslibcachemcandisccarcarDataclasscliclustercolorspacecowplotcpp11DBIDerivdigestdoBydplyrellipseevaluatefansifarverfastmapfontawesomeFormulafsgenericsggplot2gluegtableheplotshighrhtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclelme4lpSolvemagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamisc3dmitoolsmodelrmunsellnlmenloptrnnetnumDerivpbkrtestpermutepillarpixmappkgconfigplot3DproxypurrrquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrglrlangrmarkdownsassscalesspSparseMStatMatchstringistringrsurveysurvivaltibbletidyrtidyselecttinytexutf8vctrsveganviridisLitewithrxfunyaml

\vspace{+2.0cm} MorphoTools2 version 1.0.2.0 tutorial \vspace{+2.0cm}

| 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

Rendered fromMorphoTools2_tutorial.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-09-26
Started: 2020-09-02

Readme and manuals

Help Manual

Help pageTopics
Box's M-test for Homogeneity of Covariance MatricesboxMTest
Box PlotsboxplotAll boxplotCharacter
Canonical Discriminant Analysiscda.calc
Class Cdadatacdadata
25 Morphological Characters of Three Species of the _Centaurea phrygia_ Complexcentaurea
List Morphological Characterscharacters
Classificatory Discriminant Analysisclassif.knn classif.lda classif.qda
Format the Classifdata to Summary Tableclassif.matrix
Class classifdataclassifdata
Classificatory Discriminant AnalysisclassifSample.knn classifSample.lda classifSample.qda
Hierarchical Clusteringclust
Correlations of Characterscormat cormatSignifTest
Descriptive StatisticsdescrAll descrPopulation descrTaxon
Export DataexportRes
Return the First or Last Parts of an Objecthead.classifdata head.morphodata tail.classifdata tail.morphodata
Histograms of CharactershistAll histCharacter
Keep Items (Taxa, Populations, Samples, Morphological Characters) in an Morphodata Object (and Remove Others)keepCharacter keepPopulation keepSample keepTaxon
Search for the Optimal K-nearest Neighboursknn.select
Summarize Missing DatamissingCharactersTable
Summarize Missing DatamissingSamplesTable
Class morphodatamorphodata
Replace Missing Data by Population AveragenaMeanSubst
Non-metric Multidimensional Scaling (NMDS)nmds.calc
Class nmdsdatanmdsdata
Principal Component Analysispca.calc
Class pcadatapcadata
Principal Coordinates Analysis (PCoA)pcoa.calc
Class pcoadatapcoadata
The Default Scatterplot 3D Functionplot3Dpoints
Add Prediction Ellipses to a PlotplotAddEllipses
Add Labels to a PlotplotAddLabels.characters
Add Labels to a PlotplotAddLabels.points
Add Legend to a PlotplotAddLegend
Add Spiders to a PlotplotAddSpiders
The Default Biplot FunctionplotBiplot
Draws Character's Contribution as ArrowsplotCharacters
The Default Scatterplot FunctionplotPoints
Population MeanspopulOTU
Quantile-Quantile PlotsqqnormAll qqnormCharacter
Data Input and Descriptionpopulations read.morphodata samples taxa
Remove Items (Taxa, Populations, Morphological Characters) from Morphodata ObjectremoveCharacter removePopulation removeSample removeTaxon
Shapiro-Wilk Normality TestshapiroWilkTest
Stepwise Discriminant Analysisstepdisc.calc
Object Summariessummary summary.cdadata summary.classifdata summary.morphodata summary.nmdsdata summary.pcadata summary.pcoadata
Transformation of CharactertransformCharacter
Invoke a Data ViewerviewMorphodata