This repository contains code that reproduces the analyses of the following study:
Dimitrios - Georgios Kontopoulos, Thomas P. Smith, Timothy G. Barraclough, and Samraat Pawar: Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate. PLOS Biology. 2020.
The scripts are written in shell, Python 2.7.6, Perl 5.22.1, and R 3.4.4. Besides the interpreters, the following modules or packages are needed:
- For Python 2.7.6:
- bigfloat, version 0.2.1
- joblib, version 0.11
- lmfit, version 0.8.1
- numpy, version 1.14.1
- rpy2, version 2.8.2
- scipy, version 0.14.0
- For Perl 5.22.1:
- Statistics::R, version 0.34
- Statistics::R, version 0.34
- For R 3.4.4:
- ade4, version 1.7-13
- ape, version 5.2
- BAMMtools, version 2.1.6
- boot, version 1.3-20
- coda, version 0.19-2
- cowplot, version 0.9.3
- geiger, version 2.0.6.4
- MCMCglmm, version 2.26
- motmot.2.0, version 1.1.2
- msm, version 1.6.6
- phytools, version 0.6-60
- R.devices, version 2.16.1
- Rphylopars, version 0.2.12
- spptest, version 0.4
Other required software:
- BayesTraitsV3, version 3.0.2
- levolution
- stabletraits and stabletraitssum
Scripts have to be executed from within Code. For R scripts, in particular, some of them produce R objects that need to be manually examined. Thus, R scripts should generally be run from within R, using the source command. Data files needed for execution (see https://doi.org/10.6084/m9.figshare.12816140.v1) have to be placed in a Data directory, outside Code. Outputs will be written in a Results directory, outside Code.