README.md

In DevonDeRaad/species.clusteRs: Clustering-based Species Delimitation

species.clusteRs

species.clusteRs is an in-development package for performing clustering-based species delimitation on SNP data from natural populations.

Installation

You can install the development version from GitHub using the following code:

# install.packages("devtools")
devtools::install_github("DevonDeRaad/species.clusteRs")

Example

This is a basic example which shows you how to solve a common problem:

library(species.clusteRs)
## basic example code for unsupervised clustering using PCA for dimensionality reduction
pcs<-cluster_pca(vcfR = species.clusteRs::vcfR.example,
            popmap = species.clusteRs::popmap)
#> Loading required namespace: adegenet
#> Registered S3 method overwritten by 'spdep':
#>   method   from
#>   plot.mst ape

#basic example code for using tsne for dimensionality rection
tsne<-cluster_tsne(vcfR = species.clusteRs::vcfR.example,
            popmap = species.clusteRs::popmap)

#Does decreasing perplexity improve cluster discrimination?
tsne<-cluster_tsne(vcfR = species.clusteRs::vcfR.example,
            popmap = species.clusteRs::popmap,
            perplexity = 3)

DevonDeRaad/species.clusteRs documentation built on Dec. 17, 2021, 4:12 p.m.