README.md

In pygmyperch/melfuR: A collection of ugly R functions for analysis of SNP and spatial data.

http://www.molecularecology.flinders.edu.au/            Chris Brauer     

melfuR

A collection of ugly R scripts for exploratory analysis of ddRAD data, spatial analyses and other (hopefully) useful utilities.

These are mostly just wrapper scripts to simplify running basic pop-gen analyses using a single format (adegenet: genind) \ The code is characteristically ugly :dizzy_face: but feel free to use/modify whatever you find useful

How to Install

The preferred way to install this package is using devtools:

First install devtools

install.packages("devtools")

Then install melfuR

devtools::install_github("pygmyperch/melfuR")

A quick overview of some of the key functions:

• rainbow.genind: An example genind object consisting of 500 loci and 249 individuals from 14 populations of Melanotaenia fluviatilis in the Murray-Darling Basin.

• rainbow.env: Environmental data for 14 populations of Melanotaenia fluviatilis in the Murray-Darling Basin.

• run.gINLAnd: A wrapper function to run gINLAnd GEA analysis on a genind object

• HWE_filter: filter loci for HWE by population using a genind object

• impute.data: impute missing genotypes in a genind object

• percent_poly: calculate the % polymorphic loci per population from a genind object

• diversity_stats: calculate basic genetic diversity stats from a genind object

• missing_data: calculate the % of missing genotypes per population from a genind object

• subset_snps: subset a structure file based on a list of loci

• xy2kml: deprecated function, use sf2KML instead

• viamaris: calculate pairwise oceanic distances from a set of XY coordinates

• extract_tri: extract upper or lower triangle from a square matrix

• sf2KML: convert a sf point object to a .kml file

pygmyperch/melfuR documentation built on April 19, 2024, 7:24 a.m.