Geometric Morphometric Analysis of Monogenean Anchors

Documentation for package ‘monogeneaGM’ version 1.1

Help Pages

anglecheck	Angle swept by a ray
anglePolygon	Internal angles of a polygon
boxplotSort	Median-ordered box plot
colorBar	Add a color bar
estimated_ancestral_va	Estimated Generalized Procrustes Analysis (GPA) coordinates of ventral anchors of root ancestor
heatmapAnnot	Annotated heat map
hsplot	Scatter plot with marginal histograms
liewi_gpa	Array data of Generalized Procrustes Analysis (GPA) coordinates of dorsal anchors of _Ligophorus liewi_ samples
ligophorus_shape	Shape variable data for 13 _Ligophorus_ species
ligophorus_tpsdata	Raw landmark coordinate data for 13 _Ligophorus_ species
ligotree	Maximum likelihood tree for 13 _Ligophorus_ species
matrix2list	Partitioning a matrix by row into objects of a list
matrix2list.2	Partitioning a matrix by row labels into objects of a list
pca2d	Principal component analyis
pcloadhm	Heat map representation of principal component loadings of shape variables
plotCircular	Circular plot
plotLM	Scatter plot of Generalized Procrustes Analysis (GPA) coordinates of anchor landmarks
polyVis	Wireframe plot of monogenean anchor
procrustesFit	Generalized Procrustes Analysis
procrustesFit.2	Mass Extraction of Generalized Procrustes Analysis Coordinates from Anchors
pwdist	Pairwise Euclidean distances between landmarks
pwed_pd	Physical distance between landmarks in ventral and dorsal anchors of 13 _Ligophorus_ species
Qscore	Data quality control
shapeEvo	Statistical test of deviation from directional uniformity and estimation of average magnitude of directional change
spcolmap	Species-color map
stdLM	Standardization of landmark configuration by a reference landmark
tpColorPlot2d	Color-annotated scatter plot with transparency control
tpColorPlot3d	Color-annotated three-dimensional scatter plot with transparency control
tpsRead	Reading tps files into R
va_mean	Mean Generalized Procrustes Analysis (GPA) coordinates for ventral anchors of 13 _Ligophorus_ species