Little software

Some useful code to me:

images (1)

phenoselection 

Implementation in R of the equations from Lande and Arnold (1985)  to calculate natural selection on correlated traits (multivariate selection).

Since L&A proposed a solution by matricial algebra, I use a bootstrap procedure to assess the significance of selection.

DOI: http://dx.doi.org/10.5281/zenodo.61194


aGWA  

A number of scripts in python, R and bash for a Genome Wide Association analysis of phenotypes that does not remove population structure, but uses it. It re-purposes the output of chromosomepainter software to identify regions of the genome where ancestry origin is associated with a phenotype. The code includes a correction of p-values by an empirical p-value distribution.  It is basically what I used for this paper.


moiR

In this R package I store and document general functions that come quite handy in most of my analyses.

devtools::install_github('MoisesExpositoAlonso/moiR')

rbioclim

Ever wanted to use global climate databases? and from different times in history? This extends the “famous” getData funciton the raster R package to also retrieve historic datasets from worldclim.org  and in a recursive manner. Particularly, the available datasets to download correspond to the calendar dates of 22,000 years ago (Last Glacial Maximum), 6,000 years ago (Mid-Holocene), present (average 1960-1990), and two future time points (2050 and 2070) under several gas emission scenarios.

Install the package as:

devtools::install_github('MoisesExpositoAlonso/rbioclim')

Now get all data and start playing with it just with one command line:

library(raster)
library(rbioclim)
# To get the 19 bioclimatic variables for all available dates (past, present, future)
bioclim = recursive.getData(times="all") 

And for example, to plot a map of annual temperature and precipitation in summer. Present and future (2070 rcp8.5), just run:

plot(bioclim[["pres"]][["bio1]])
plot(bioclim[["CC8570"]][["bio18]])

Note: This repo is just making easier to get in R the awesome data that the people at www.worldclim.org and the developers of raster R package are producing and putting available.


hippo

A python module that wraps several image processing modules. It segments the green areas of plant images. It was used to produce this:f_video_s1

 

 

 

 

 

 

 

git clone https://github.com/MoisesExpositoAlonso/hippo
cd hippo
python countgreen_master.py # this will process example images