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monogeneaGM (version 1.1)

Geometric Morphometric Analysis of Monogenean Anchors

Description

Geometric morphometric and evolutionary biology analyses of anchor shape from four-anchored monogeneans.

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Version

Install

install.packages('monogeneaGM')

Monthly Downloads

2

Version

1.1

License

GPL (>= 2)

Maintainer

Tsung Fei Khang

Last Published

February 12th, 2016

Functions in monogeneaGM (1.1)

anglePolygon

Internal angles of a polygon
heatmapAnnot

Annotated heat map
shapeEvo

Statistical test of deviation from directional uniformity and estimation of average magnitude of directional change
procrustesFit

Generalized Procrustes Analysis
estimated_ancestral_va

Estimated Generalized Procrustes Analysis (GPA) coordinates of ventral anchors of root ancestor
pwdist

Pairwise Euclidean distances between landmarks
ligophorus_shape

Shape variable data for 13 Ligophorus species
anglecheck

Angle swept by a ray
colorBar

Add a color bar
pca2d

Principal component analyis
boxplotSort

Median-ordered box plot
plotCircular

Circular plot
plotLM

Scatter plot of Generalized Procrustes Analysis (GPA) coordinates of anchor landmarks
spcolmap

Species-color map
va_mean

Mean Generalized Procrustes Analysis (GPA) coordinates for ventral anchors of 13 Ligophorus species
procrustesFit.2

Mass Extraction of Generalized Procrustes Analysis Coordinates from Anchors
pcloadhm

Heat map representation of principal component loadings of shape variables
polyVis

Wireframe plot of monogenean anchor
ligophorus_tpsdata

Raw landmark coordinate data for 13 Ligophorus species
tpColorPlot3d

Color-annotated three-dimensional scatter plot with transparency control
stdLM

Standardization of landmark configuration by a reference landmark
matrix2list

Partitioning a matrix by row into objects of a list
ligotree

Maximum likelihood tree for 13 Ligophorus species
tpColorPlot2d

Color-annotated scatter plot with transparency control
liewi_gpa

Array data of Generalized Procrustes Analysis (GPA) coordinates of dorsal anchors of Ligophorus liewi samples
pwed_pd

Physical distance between landmarks in ventral and dorsal anchors of 13 Ligophorus species
hsplot

Scatter plot with marginal histograms
matrix2list.2

Partitioning a matrix by row labels into objects of a list
Qscore

Data quality control
tpsRead

Reading tps files into R