kkdey/ecostructure

Clustering and Visualization of species abundance patterns in ecological data

ecostructure

R package for Clustering and Visualization of structure in ecological data

This package is targeted at fitting STRUCTURE type model on ecological species abundance and presence-absence data both at local and large geographic scales - together with high quality visualizations of the fitted models.

Authors

• Kushal K Dey
• Alexander E White

Advised by

• Matthew Stephens
• Trevor Price

Citation

If you find ecostructure, please cite our papers

White, Alexander E. and Dey, Kushal K. and Mohan, Dhananjai and Stephens, Matthew and Price, Trevor D. Regional influences on community structure across the tropical-temperate divide. Nature Communications. 2019. 10 (1). 2646. 10.1038/s41467-019-10253-6.

White, Alexander E. and Dey, Kushal K. and and Stephens, Matthew and Price, Trevor D. Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace’s Line. Global Ecology and Biogeography. 2021. https://doi.org/10.1111/geb.13250

Installation

Install ecostructure following the instructions below.

install.packages(devtools)
install.packages("sf")
devtools::install_github("kkdey/methClust")
devtools::install_github("kkdey/maptpx"). # this is an updated version of CRAN package maptpx
devtools::install_github("kkdey/CountClust")
devtools::install_github("kkdey/ecostructure")

Then load ecostructure

library(ecostructure)

Demo

Some examples of produced using our ecostructure package

If you want to try ecostructure and replicate figures like this, please check our tutorial here.

Questions?

For any queries or concerns related to the software, you can open an issue here. Or you can contact us. Kushal Dey - [email protected] or Alex White - [email protected].

We thank Prof. Trevor D. Price and Dhananjai Mohan for data collection for our accompanying paper. We thank our mentors Prof. Matthew Stephens and Prof. Trevor Price for helpful suggestions and discussions.

You are also most welcome to contribute to ecostructure !!

ecostructure's Issues

ecostructure_fit returns NULL theta for binomial model fit

Incorporate the Kriging function

Incorporate the kriging function for the ordered topic model for functional motif detection

Block models networks

Climate, precipitation of top deciles for regional motifs

small typo

ecostructure/R/ecos_blocks.R

Line 20 in 6b9193f

#' RColorBrewwer::brewer.pal(9, "Set1").

Methods of Ecology and Evolution paper

Prepare the format for the methods of ecology and evolution paper

Phylogenetic tree building

Subset from a phylogenetic tree

Incorporate the data

Put the Himalayan bird abundance

• count data for sites vs species
• metadata for samples
• metadata for birds

Put the regional motif data into some remote repository like "dryad"..