calc_ordination: Calculate Point Coordinates in an Ordination

In leffj/mctoolsr: Microbial Community Data Analysis Tools

Calculate Point Coordinates in an Ordination

Description

Use to generate ordination axis scores to use when plotting ordination.

Usage

calc_ordination(dm, ord_type, metadata_map, constrain_factor)

Arguments

dm	Dissimilarity matrix.
ord_type	The type of ordination. 'NMDS', 'PCoA', or 'constrained' are the current accepted values.
metadata_map	Required if 'constrained' ord_type.
constrain_factor	Required if 'constrained' ord_type.

Details

Impliments nonmetric multidimensional scaling, principal coordinates analysis, or constrained ordination (via capscale in vegan).

Value

A data frame consisting of the coordinates.

Examples

dm = calc_dm(fruits_veggies$data_loaded)
ord = calc_ordination(dm, "nmds")

leffj/mctoolsr documentation built on Aug. 5, 2022, 1:27 a.m.