Clarke van Steenderen's repositories
CBC_Tutorials
A collection of phylogenetics tutorials delivered to colleagues at the Centre for Biological Control (CBC). Topics include producing Bayesian and Maximum Likelihood trees, haplotype networks, reading phylogenies into R, analysing ISSR and SSR data, and using STRUCTURE and SplitsTree.
map_shapefiles
R code and shapefiles to plot a map of South Africa's biomes, and plot GPS coordinates onto it.
spede_sampler_R
An R Shiny App that assesses sampling effects (e.g. sample size and BEAST parameters) on GMYC output for species delimitation.
beast_plotting
A short R script to plot the result of a dated BEAST phylogeny. Also, plotting character states alongside the phylogeny from the treeio package.
CBC_databases
R Shiny App skeleton for a database for the CBC
Clarke-van-Steenderen-CV
My CV to date, available to download as a PDF.
clarkevansteenderen.github.io
My personal website, with the template forked from mmistakes/minimal-mistakes
CodeChallenge
All my thinking about some code challenge and Free Code Camps
DZE_R_tutorials
R tutorials for the Department of Zoology and Entomology, Rhodes University
Inat_Images
Script to download images from inaturalist.org
M.Sc.-cochineal-barcoding
Masters thesis
PhD_files
PhD supplementary R code - Tetramesa genetic data
spede_sampler
A Python GUI that (1) randomly resamples Fasta files and (2) creates ML phylogenies for each using FastTree and/or RAxML. These output trees need to then be run in the R Shiny App to run GMYC analyses.
TetramesaID
An application to identify a Tetramesa wasp COI or 28S sequence
ThermalSampleR
ThermalSampleR R package
ThermalSampleR_Shiny
ThermalSampleR Shiny application
vizgradcam
vizgradcam is the fastest way to visualize GradCAM with your Keras models.