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MorphoTools2

The package MorphoTools2 is intended for multivariate analyses of morphological data. At the moment, various necessary tools are scattered across several R packages. This package wraps available statistical and graphical tools and provides a comprehensive framework for checking and manipulating input data, performing core statistical analyses and running a wide palette of functions designed to visualize results, making the workflow convenient and fast.

Installation

You can install the released version of MorphoTools2 from CRAN with:

install.packages("MorphoTools2")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("MarekSlenker/MorphoTools2")

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Version

Install

install.packages('MorphoTools2')

Monthly Downloads

268

Version

1.0.2.1

License

GPL-3

Issues

0

Pull Requests

0

Stars

7

Forks

0

Maintainer

Marek Slenker

Last Published

October 2nd, 2024

Functions in MorphoTools2 (1.0.2.1)

knn.select

Search for the Optimal K-nearest Neighbours
plot3Dpoints

The Default Scatterplot 3D Function
morphodata

Class morphodata
plotAddEllipses

Add Prediction Ellipses to a Plot
pcoadata

Class pcoadata
pcoa.calc

Principal Coordinates Analysis (PCoA)
plotAddLabels.characters

Add Labels to a Plot
plotAddLabels.points

Add Labels to a Plot
qqnormCharacter

Quantile-Quantile Plots
read.morphodata

Data Input and Description
naMeanSubst

Replace Missing Data by Population Average
stepdisc.calc

Stepwise Discriminant Analysis
plotBiplot

The Default Biplot Function
plotAddLegend

Add Legend to a Plot
plotAddSpiders

Add Spiders to a Plot
plotCharacters

Draws Character's Contribution as Arrows
summary

Object Summaries
shapiroWilkTest

Shapiro-Wilk Normality Test
removeTaxon

Remove Items (Taxa, Populations, Morphological Characters) from Morphodata Object
cormat

Correlations of Characters
pcadata

Class pcadata
transformCharacter

Transformation of Character
pca.calc

Principal Component Analysis
nmdsdata

Class nmdsdata
viewMorphodata

Invoke a Data Viewer
nmds.calc

Non-metric Multidimensional Scaling (NMDS)
plotPoints

The Default Scatterplot Function
populOTU

Population Means
cda.calc

Canonical Discriminant Analysis
boxMTest

Box's M-test for Homogeneity of Covariance Matrices
boxplotCharacter

Box Plots
classifdata

Class classifdata
classifSample.lda

Classificatory Discriminant Analysis
keepTaxon

Keep Items (Taxa, Populations, Samples, Morphological Characters) in an Morphodata Object (and Remove Others)
clust

Hierarchical Clustering
exportRes

Export Data
cdadata

Class Cdadata
descrTaxon

Descriptive Statistics
classif.lda

Classificatory Discriminant Analysis
classif.matrix

Format the Classifdata to Summary Table
head.morphodata

Return the First or Last Parts of an Object
histCharacter

Histograms of Characters
centaurea

25 Morphological Characters of Three Species of the Centaurea phrygia Complex
characters

List Morphological Characters
missingCharactersTable

Summarize Missing Data
missingSamplesTable

Summarize Missing Data