This is the repository containing the data and code for the article Contrasting modes of cultural evolution: Kra-Dai languages and weaving technologies, by Christopher D. Buckley, Emma Kopp, Thomas Pellard, Robin J. Ryder, and Guillaume Jacques.
The repository has the following structure:
.
├── kd-looms.Rproj # RStudio project file
├── README.md
├── data # Primary data
│ ├── images # Illusrative drawing of the looms
│ │ ├── BFcant.png
│ │ ├── BFcant.svg
│ │ ├── BFSRH.png
│ │ ├── BFSRH.svg
│ │ ├── BFYRH.png
│ │ ├── BFYRH.svg
│ │ ├── FBBS.png
│ │ ├── FBBS.svg
│ │ ├── FCBcant.png
│ │ ├── FCBcant.svg
│ │ ├── FCB.png
│ │ ├── FCB.svg
│ │ ├── FCBunique.png
│ │ └── FCBunique.svg
│ ├── kd-lgs # Linguistic data
│ │ ├── kd-lgs_datapoints.csv # Geographical coordinates of the languages
│ │ ├── kd-lgs_lx.csv # Matrix of lexical data
│ │ └── kd-lgs_bcov # BEAST input and output files
│ │ ├── kd-lgs_bcov.log
│ │ ├── kd-lgs_bcov.trees.zip
│ │ ├── kd-lgs_bcov.xml
│ │ └── kd-lgs.nex
│ └── kd-looms # Looms data
│ ├── kd-looms_data.ods # Raw data and sources for the looms
│ ├── kd-looms_datapoints.csv # Geographical coordinates of the looms
│ ├── kd-looms_characters.csv # Information about the looms characters
│ ├── kd-looms_matrix.csv # Raw character-state matrix for the looms
│ ├── kd-looms_bcov1000 # BEAST input and output files
│ │ ├── kd-looms_1000.nex
│ │ ├── kd-looms_bcov1000.log
│ │ ├── kd-looms_bcov1000.trees
│ │ └── kd-looms_bcov1000.xml
│ ├── kd-looms_bcov111 1 # BEAST input and output files
│ │ ├── kd-looms_1111.nex
│ │ ├── kd-looms_bcov1111.log
│ │ ├── kd-looms_bcov1111.trees
│ │ └── kd-looms_bcov1111.xml
│ ├── kd-looms_bcov8421 # BEAST input and output files
│ │ ├── kd-looms_8421.nex
│ │ ├── kd-looms_bcov8421.log
│ │ ├── kd-looms_bcov8421.trees
│ │ └── kd-looms_bcov8421.xml
│ ├── kd-looms_bcov_basic # BEAST input and output files
│ │ ├── kd-looms_basic.nex
│ │ ├── kd-looms_bcov_basic.log
│ │ ├── kd-looms_bcov_basic.trees
│ │ └── kd-looms_bcov_basic.xml
│ ├── kd-looms_bcov_patterns # BEAST input and output files
│ │ ├── kd-looms_bcov_patterns.log
│ │ ├── kd-looms_bcov_patterns.trees
│ │ ├── kd-looms_bcov_patterns.xml
│ │ └── kd-looms_patterns.nex
│ └── kd-looms_ctmc4 # BEAST input and output files
│ ├── kd-looms_ctmc4.log
│ ├── kd-looms_ctmc4.nex
│ ├── kd-looms_ctmc4.trees
│ └── kd-looms_ctmc4.xml
├── output # Output produced by running the R code files in src/
│ ├── data # Data summaries
│ │ ├── kd-lgs_ages.csv
│ │ ├── kd-lgs_ages_summary.csv
│ │ ├── kd-lgs_mu_summary.csv
│ │ ├── kd-looms_mu_bylevel.csv
│ │ └── kd-looms_mu_summary.csv
│ ├── figures # Figures for the analysis results
│ │ ├── kd_cophylo_plot.pdf
│ │ ├── kd-lgs_ages_plot.pdf
│ │ ├── kd-lgs_bcov_byconcept_cs_tree.pdf
│ │ ├── kd-lgs_bcov_cs_tree.pdf
│ │ ├── kd-lgs_map.pdf
│ │ ├── kd-lgs_mu_plot.pdf
│ │ ├── kd-looms_bcov1000_cs_tree.pdf
│ │ ├── kd-looms_bcov1111_cs_tree.pdf
│ │ ├── kd-looms_bcov8421_cs_tree.pdf
│ │ ├── kd-looms_bcov_basic_cs_tree.pdf
│ │ ├── kd-looms_bcov_patterns_cs_tree.pdf
│ │ ├── kd-looms_ctmc4_cs_tree.pdf
│ │ ├── kd-looms_map.pdf
│ │ ├── kd-looms_mu_plot.pdf
│ │ └── kd-looms_Tsw_map.pdf
│ ├── tables # Summary tables in LaTeX format
│ │ ├── kd-lgs_ages_summary.tex
│ │ └── kd-looms_mu_summary.tex
│ └── trees # Consensus trees
│ ├── kd-lgs_bcov_byconcept_consensus.tree
│ ├── kd-lgs_bcov_consensus.tree
│ ├── kd-looms_bcov1000_consensus.tree
│ ├── kd-looms_bcov1111_consensus.tree
│ ├── kd-looms_bcov8421_consensus.tree
│ ├── kd-looms_bcov_basic_consensus.tree
│ ├── kd-looms_bcov_patterns_consensus.tree
│ └── kd-looms_ctmc4_consensus.tree
└── src # R code files
├── 00_Preprocess.R
├── 01_Transform.R
└── 02_Visualise.R
- Preprocess data
- Run
00_Preprocess.Rto create the NEXUS files for languages and looms data, and to adjust and check the BEAST outputs.
- Run
- Transform data
- Run
01_Transform.Rto generate consensus trees, compute internal nodes depth and mutation rates when needed.
- Run
- Visualise data
- Run
02_Visualise.Rto generate the figures and tables used in the article.
- Run
The R packages listed below are needed to run the analysis, and they can be installed with the following command in R (https://www.r-project.org/):
install.packages(c(
"HDInterval",
"TreeTools",
"ggforce",
"ggnewscale",
"ggridges",
"ggspatial",
"ggstar",
"ggtext",
"ggthemes",
"here",
"kableExtra",
"knitr",
"patchwork",
"phangorn",
"phytools",
"rnaturalearth",
"sf",
"stringi",
"tidyverse",
"tracerer",
"utils"
))
if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("ggtree")The Noto Sans Condensed, Noto Sans SemiCondensed, and Noto Sans ExtraCondensed free fonts are also needed to produce the figures. They are available at https://notofonts.github.io/latin-greek-cyrillic/.
Phylogenetic analyses require the BEAST software v2.6.7 (https://www.beast2.org/). The additional packages Babel, CoupledMCMC, and SA for BEAST are also needed.
This dataset and code is licensed under a CC-BY-4.0 license (https://creativecommons.org/licenses/by/4.0/).