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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.


Dependencies

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

  • 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

Execution

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.