Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution
This repository contains all the code and data used in our paper
All these files are also available in zenodo
To cite the paper:
Püschel, H. P., Bertrand, O. C., O’Reilly, J. E., Bobe, R., & Püschel, T. A. (2021). Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution. Nature Ecology & Evolution, 1–12. https://doi.org/10.1038/s41559-021-01431-1
Corresponding authors:
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Hans P. Püschel
affiliation: University of Edinburgh
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Thomas A. Püschel
affiliation: University of Oxford
journal: Nature Ecology & Evolution
url: https://www.nature.com/articles/s41559-021-01431-1
doi: https://dx.doi.org/10.1038/s41559-021-01431-1
Publication date: 01/04/2021
Data and analyses used in Püschel et al. 2021, Nature Ecology and Evolution, doi: https://dx.doi.org/10.1038/s41559-021-01431-1
These are the files necessary to replicate the study “Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution” by Hans P. Püschel, Ornella C. Bertrand, Joseph E. O’Reilly, René Bobe & Thomas A. Püschel
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The
Nexus_filesfolder contains all the nexus files necessary to replicate the TED analyses in MrBayes for the four topological hypothesis tested in our paper (see the methods section for more details). -
The
.con.trefiles correspond to the majority rule consensus trees obtained in the TED analyses for the four topological hypotheses. These files are necessary to run the R scripts contained inR_scripts_TED_hominin.Rmd. These files can also be obtained if the full analysis is replicated using the nexus files in MrBayes. -
The
.csvfiles correspond to tables with information about body mass, brain mass and PEQ for each one of the taxa analysed in our paper. These files are necessary to run the R scripts contained inR_scripts_TED_hominin.Rmd. -
The
post_tc_trees.txtfiles contained the 9002 time-calibrated posterior trees sampled for each one of the four analyses. These are necessary to run the fifth section of the script inR_scripts_TED_hominin.Rmd. These files can also be obtained if the full analysis is replicated using the nexus files in MrBayes, and then using the code available in the fifth section ofR_scripts_TED_hominin.Rmdwith the.tand.p files. -
The
R_scripts_TED_hominin.Rmdfile contains all the scripts necessary to replicate this study.
For reproducibility purposes, here is the output of devtools::session_info() used to perform the analyses in the publication.
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os macOS 10.16
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/London
date 2021-03-01
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
AICcmodavg * 2.3-1 2020-08-26 [1] CRAN (R 4.0.2)
ape * 5.4-1 2020-08-13 [1] CRAN (R 4.0.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
boot 1.3-25 2020-04-26 [1] CRAN (R 4.0.2)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2)
caper 1.0.1 2018-04-17 [1] CRAN (R 4.0.0)
cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.2)
clusterGeneration 1.3.7 2020-12-15 [1] CRAN (R 4.0.2)
coda * 0.19-4 2020-09-30 [1] CRAN (R 4.0.2)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.0.2)
colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.2)
combinat 0.0-8 2012-10-29 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
deSolve 1.28 2020-03-08 [1] CRAN (R 4.0.0)
devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
dplyr 1.0.3 2021-01-15 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
expm 0.999-6 2021-01-13 [1] CRAN (R 4.0.2)
fansi 0.4.2 2021-01-15 [1] CRAN (R 4.0.2)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
fastmatch 1.1-0 2017-01-28 [1] CRAN (R 4.0.0)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
geiger * 2.0.7 2020-06-02 [1] CRAN (R 4.0.0)
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.2)
geoscale * 2.0 2015-05-14 [1] CRAN (R 4.0.1)
ggmap * 3.0.0 2019-02-05 [1] CRAN (R 4.0.1)
ggplot2 * 3.3.3 2020-12-30 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.2)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
igraph 1.2.6 2020-10-06 [1] CRAN (R 4.0.2)
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.0)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.2)
KernSmooth 2.23-18 2020-10-29 [1] CRAN (R 4.0.2)
knitr 1.31 2021-01-27 [1] CRAN (R 4.0.2)
ks 1.11.7 2020-02-11 [1] CRAN (R 4.0.0)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
lme4 1.1-26 2020-12-01 [1] CRAN (R 4.0.2)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
maps * 3.3.0 2018-04-03 [1] CRAN (R 4.0.0)
MASS 7.3-53 2020-09-09 [1] CRAN (R 4.0.2)
Matrix 1.3-2 2021-01-06 [1] CRAN (R 4.0.2)
mclust 5.4.7 2020-11-20 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
minqa 1.2.4 2014-10-09 [1] CRAN (R 4.0.0)
mnormt 2.0.2 2020-09-01 [1] CRAN (R 4.0.2)
motmot * 2.1.3 2019-11-25 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
mvtnorm 1.1-1 2020-06-09 [1] CRAN (R 4.0.0)
nlme * 3.1-151 2020-12-10 [1] CRAN (R 4.0.2)
nloptr 1.2.2.2 2020-07-02 [1] CRAN (R 4.0.2)
nortest * 1.0-4 2015-07-30 [1] CRAN (R 4.0.2)
numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.0)
paleotree * 3.3.25 2019-12-12 [1] CRAN (R 4.0.0)
phangorn 2.5.5 2019-06-19 [1] CRAN (R 4.0.0)
phytools * 0.7-70 2020-09-19 [1] CRAN (R 4.0.2)
pillar 1.4.7 2020-11-20 [1] CRAN (R 4.0.2)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
plotrix * 3.7-8 2020-04-16 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.2)
ps 1.5.0 2020-12-05 [1] CRAN (R 4.0.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
quadprog 1.5-8 2019-11-20 [1] CRAN (R 4.0.0)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
raster 3.4-5 2020-11-14 [1] CRAN (R 4.0.2)
Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.2)
RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
RgoogleMaps 1.4.5.3 2020-02-12 [1] CRAN (R 4.0.1)
rjson 0.2.20 2018-06-08 [1] CRAN (R 4.0.0)
rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.2)
rmarkdown 2.6 2020-12-14 [1] CRAN (R 4.0.2)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2)
rr2 * 1.0.2 2019-05-09 [1] CRAN (R 4.0.2)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
scatterplot3d 0.3-41 2018-03-14 [1] CRAN (R 4.0.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
sp 1.4-5 2021-01-10 [1] CRAN (R 4.0.2)
statmod 1.4.35 2020-10-19 [1] CRAN (R 4.0.2)
strap * 1.4 2014-11-05 [1] CRAN (R 4.0.0)
stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
subplex 1.6 2020-02-23 [1] CRAN (R 4.0.0)
survival 3.2-7 2020-09-28 [1] CRAN (R 4.0.2)
testthat 3.0.1 2020-12-17 [1] CRAN (R 4.0.2)
tibble * 3.0.5 2021-01-15 [1] CRAN (R 4.0.2)
tidyr 1.1.2 2020-08-27 [1] CRAN (R 4.0.2)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
tmvnsim 1.0-2 2016-12-15 [1] CRAN (R 4.0.0)
unmarked 1.0.1 2020-07-02 [1] CRAN (R 4.0.2)
usethis 2.0.0 2020-12-10 [1] CRAN (R 4.0.2)
vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.2)
VGAM 1.1-5 2021-01-14 [1] CRAN (R 4.0.2)
withr 2.4.0 2021-01-16 [1] CRAN (R 4.0.2)
xfun 0.21 2021-02-10 [1] CRAN (R 4.0.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
To rerun all the analyses with the packages as they existed on CRAN at the time of our analyses, we suggest using the checkpoint package, and running the following code before carrying out the analysis:
checkpoint("2020-03-01")