mm_diagnostics: Run a suite of diagnostic analyses.

In ehrlichd/moRphomenses: Geometric Morphometric Tools to Align, Scale, and Compare "Shape" of Menstrual Cycle Hormones

Run a suite of diagnostic analyses.

Description

Conduct a set of analyses to make shape-PCA results easier to interpret. Specifically, this will provide a table of eigen values (optional barplot), provide 5-number summary across each PC, conduct a naive Ward's clustering of PC scores (optional dendrogram, along with silhouette plot and scree plot of individual distance to the sample mean

Usage

mm_Diagnostics(dat, max_PC_viz = 10, max_PC_calc = NULL, hide_plots = FALSE)

Arguments

dat	A 3D array or a mmPCA object (output of mm_CalcShapespace).
max_PC_viz	Maximum number of PCs to include in visualizations (EG Eigenplots, or shape trends.
max_PC_calc	By default (NULL), all PCs will be included in calculations. However, if fewer PCs are required users may specify an integer, n, to get the first n PCS.
hide_plots	By default (FALSE), helpful visuals are plotted.

Value

Returns a list containing the results of:

• eigs - A table containing individual and cumulutive loadings for each PC

• PC_5_num - A data.frame containing the fivenum summary for each PC

• TREE - A dendrogram representing the results of a naive-Ward's clustering

ehrlichd/moRphomenses documentation built on Dec. 13, 2024, 8:36 a.m.