Code used for the paper "Reproductive dispersion and damping time scale with life-history speed" by Sha Jiang, Harman Jaggi, Wenyun Zuo, Madan K. Oli, Tim Coulson, Jean‐Michel Gaillard, and Shripad Tuljapurkar.
Below are the files needed for analyses and their brief descriptions. Please either open the R project ("Reproductive dispersion and damping time scale with life-history speed (data and code).Rproj") or edit the file path while running the scripts.
"[1] data processing and plotting for damping paper.R"
- This is the R code used for data cleanning, calculation and preliminary regression analyses.
"tulja_lab_master_com_p_adre.2.1.RData"
- This is the combined dataset from COMADRE (DOI:10.1111/1365-2656.12482) and COMPADRE (DOI:10.1111/1365-2745.12334) after data correction using original papers.
- See details for modified species/matrices in "COMADRE Mods.pdf".
- Descriptions of dataset can be found in their website (https://compadre-db.org/Data/Comadre).
"combined dataset of JMG and MO without duplicates.csv"
- This is the GO dataset complied by Jean-Michel Gaillard (DOI: 10.1016/j.tpb.2012.09.003) and Madan Oli (DOI: 10.1016/j.baae.2004.06.002).
- Descriptions of dataset can be found in "Description of JMG and MO dataset.xlsx".
"[2] phylogenetic analysis for damping paper.R"
- This is the R code used to produce figures in our paper, including results based on PGLS, PPCA, etc.
- Also note that this part of the analyses can be run directly using only the files below.
"final_tree_corrected_newversion v2.tre"
- This file contains the matched phylogenetic tree using the master phylognetic tree from Open Tree of Life version 12.3 (DOI: 10.5281/zenodo.3937741).
"match_list_uncorrected_newversion v2.csv"
- This file contains the species that can be matched with the master phylogenetic tree.
"full animal and plant data v2.csv"
- This file contains the results (life-history traits, such as generation time, reproductive disperson, damping time, etc.) from Part 1.