Author(s): Thomas Guillerme and Natalie Cooper
This repository contains all the code and data used in the manuscript.
To cite the paper:
Thomas Guillerme & Natalie Cooper. 2018. Time for a rethink: time sub-sampling methods in disparity-through-time analyses. Palaeontology, 61, 481-493. doi:10.1111/pala.12364
To cite this repo:
Thomas Guillerme & Natalie Cooper. 2018. GitHub: nhcooper123/time-slice: Release for publication. Zenodo. http://doi.org/10.5281/zenodo.1172000.
Many thanks to Dr Jones for the image :)
These analyses are based on data from four previous studies.
They can be accessed from the links below, but for reproducibility purposes the data can also be found in the data/ folder in this repo.
If you use the data please cite the Dryad data packages and papers they originally came from.
All code used to run analyses and make figures and tables is included in the analyses/ folder. Before starting remember to either set your working directory to the time-slice folder on your computer, or open an RStudio project from that folder.
All of these files are in RMarkdown format, so you can click the Knit button in RStudio and create HTML versions with the code and output.
This code is not as tidy or functionified as we would like as we were a bit pushed for time.
- 01-extract-data-for-analyses.Rmd This script takes the raw data from the papers and processes them for use in the disparity-through-time analyses. This includes manipulating matrices and phylogenetic trees. All data is saved so if you're pushed for time or computational power we recommend skipping this step and using the data in the
data/processedfolder. - 02-time-slice-analyses.Rmd This script performs disparity-through-time analyses on the processed data according to several scenarios and methods described in the paper.
- 03-statistical-analyses.Rmd This script uses the outputs from 02-time-slice-analyses.Rmd to determine how the different time sub-sampling methods influence biological conclusions about the datasets. It tests for systematic differences in disparity-through-time (paired Wilcoxon tests), changes in disparity peaks, and changes in conclusions about the effects of mass extinctions on disparity.
- 04-table-datasets.Rmd Reproduces Table 1 (except the references).
- 05-figure-dtt.Rmd Reproduces Figure 3.
- 06-table-wilcox.Rmd Reproduces Table 2, and Table A1.
- 07-figure-peaks.Rmd Reproduces Figure 4.
- 08-figure-extinction.Rmd Reproduces Figure 5.
- 09-appendix-trees-figures.Rmd Builds plots of phylogenies using the R package
strapto add stratigraphic information (Appendix S1: Figures A1-A4). - 10-appendix-figure-dtt.Rmd Reproduces Appendix S2: Figures A1 and A2.
- 11-appendix-figure-peaks.Rmd Reproduces Appendix S2: Figures A3 and A4.
- 12-appendix-disparity-tables.Rmd Produces the detailed disparity outputs tables. Currently not in the appendices as they are around 100 pages long!
functions/contains functions required by the code in theanalyses/folder.outputs/contains all the outputs from the code in theanalyses/folder except for the figures and tables which can be found inmanuscript/figuresandmanuscript/tables.manuscript/contains the LaTeX version of the manuscript and appendices, plus style template, bibliography, figures and tables.
To rerun all the code with packages as they existed on CRAN at time of our analyses we recommend using the checkpoint package, and running this code prior to the analysis:
checkpoint("2018-01-06")
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 3.4.3 (2017-11-30)
system x86_64, darwin15.6.0
ui RStudio (1.1.383)
language (EN)
collate en_IE.UTF-8
tz Europe/Dublin
date 2018-01-06
Packages --------------------------------------------------------------------------------
package * version date source
ade4 1.7-10 2017-12-15 cran (@1.7-10)
animation 2.5 2017-03-30 CRAN (R 3.4.0)
ape * 5.0 2017-10-30 CRAN (R 3.4.2)
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
base * 3.4.3 2017-12-07 local
bindr 0.1 2016-11-13 CRAN (R 3.4.0)
bindrcpp 0.2 2017-06-17 CRAN (R 3.4.0)
broom * 0.4.3 2017-11-20 CRAN (R 3.4.3)
cellranger 1.1.0 2016-07-27 CRAN (R 3.4.0)
Claddis * 0.2 2017-09-05 Github (TGuillerme/Claddis@43c717b)
cli 1.0.0 2017-11-05 CRAN (R 3.4.2)
cluster 2.0.6 2017-03-10 CRAN (R 3.4.3)
clusterGeneration 1.3.4 2015-02-18 CRAN (R 3.4.0)
coda 0.19-1 2016-12-08 CRAN (R 3.4.0)
colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)
combinat 0.0-8 2012-10-29 CRAN (R 3.4.0)
compiler 3.4.3 2017-12-07 local
crayon 1.3.4 2017-09-16 CRAN (R 3.4.1)
datasets * 3.4.3 2017-12-07 local
deSolve 1.20 2017-07-14 CRAN (R 3.4.1)
devtools * 1.13.4 2017-11-09 CRAN (R 3.4.2)
digest 0.6.13 2017-12-14 CRAN (R 3.4.3)
dispRity * 0.5 2017-12-20 Github (TGuillerme/dispRity@80f3e97)
dplyr * 0.7.4 2017-09-28 CRAN (R 3.4.2)
expm 0.999-2 2017-03-29 CRAN (R 3.4.0)
fastmatch 1.1-0 2017-01-28 CRAN (R 3.4.0)
forcats * 0.2.0 2017-01-23 CRAN (R 3.4.0)
foreign 0.8-69 2017-06-22 CRAN (R 3.4.3)
gdata 2.18.0 2017-06-06 CRAN (R 3.4.0)
geiger 2.0.6 2015-09-07 CRAN (R 3.4.0)
geometry 0.3-6 2015-09-09 cran (@0.3-6)
geoscale * 2.0 2015-05-14 CRAN (R 3.4.0)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.4.0)
glue 1.2.0 2017-10-29 CRAN (R 3.4.2)
graphics * 3.4.3 2017-12-07 local
grDevices * 3.4.3 2017-12-07 local
grid * 3.4.3 2017-12-07 local
gridExtra * 2.3 2017-09-09 CRAN (R 3.4.1)
gtable 0.2.0 2016-02-26 CRAN (R 3.4.0)
gtools 3.5.0 2015-05-29 CRAN (R 3.4.0)
haven 1.1.0 2017-07-09 CRAN (R 3.4.1)
hms 0.4.0 2017-11-23 CRAN (R 3.4.3)
htmltools 0.3.6 2017-04-28 cran (@0.3.6)
htmlwidgets 0.9 2017-07-10 cran (@0.9)
httpuv 1.3.5 2017-07-04 cran (@1.3.5)
httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
igraph 1.1.2 2017-07-21 CRAN (R 3.4.1)
jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
knitr 1.17 2017-08-10 CRAN (R 3.4.1)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.3)
lazyeval 0.2.1 2017-10-29 CRAN (R 3.4.2)
lubridate 1.7.1 2017-11-03 CRAN (R 3.4.2)
magic 1.5-6 2013-11-20 cran (@1.5-6)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
maps * 3.2.0 2017-06-08 CRAN (R 3.4.0)
MASS 7.3-47 2017-02-26 CRAN (R 3.4.3)
Matrix 1.2-12 2017-11-20 CRAN (R 3.4.3)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.3 2017-12-07 local
mgcv 1.8-22 2017-09-24 CRAN (R 3.4.3)
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mnormt 1.5-5 2016-10-15 CRAN (R 3.4.0)
modelr 0.1.1 2017-07-24 CRAN (R 3.4.1)
msm 1.6.5 2017-12-05 CRAN (R 3.4.3)
munsell 0.4.3 2016-02-13 CRAN (R 3.4.0)
mvtnorm 1.0-6 2017-03-02 CRAN (R 3.4.0)
nlme 3.1-131 2017-02-06 CRAN (R 3.4.3)
numDeriv 2016.8-1 2016-08-27 CRAN (R 3.4.0)
paleotree 3.0.0 2017-10-21 cran (@3.0.0)
parallel 3.4.3 2017-12-07 local
permute 0.9-4 2016-09-09 CRAN (R 3.4.0)
phangorn 2.3.1 2017-11-01 cran (@2.3.1)
phyclust 0.1-22 2017-12-02 cran (@0.1-22)
phytools * 0.6-44 2017-11-12 CRAN (R 3.4.2)
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
plotrix 3.7 2017-12-07 CRAN (R 3.4.3)
plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
psych 1.7.8 2017-09-09 CRAN (R 3.4.3)
purrr * 0.2.4 2017-10-18 CRAN (R 3.4.2)
quadprog 1.5-5 2013-04-17 CRAN (R 3.4.0)
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
Rcpp 0.12.14 2017-11-23 CRAN (R 3.4.3)
readr * 1.1.1 2017-05-16 CRAN (R 3.4.0)
readxl 1.0.0 2017-04-18 CRAN (R 3.4.0)
reshape2 1.4.3 2017-12-11 CRAN (R 3.4.3)
rgl * 0.98.22 2017-12-13 CRAN (R 3.4.3)
rlang 0.1.4 2017-11-05 CRAN (R 3.4.2)
rstudioapi 0.7 2017-09-07 CRAN (R 3.4.1)
rvest 0.3.2 2016-06-17 CRAN (R 3.4.0)
scales 0.5.0 2017-08-24 CRAN (R 3.4.1)
scatterplot3d 0.3-40 2017-04-22 CRAN (R 3.4.0)
shiny 1.0.5 2017-08-23 CRAN (R 3.4.1)
snow 0.4-2 2016-10-14 cran (@0.4-2)
splines 3.4.3 2017-12-07 local
stats * 3.4.3 2017-12-07 local
strap * 1.4 2014-11-05 cran (@1.4)
stringi 1.1.6 2017-11-17 CRAN (R 3.4.2)
stringr * 1.2.0 2017-02-18 CRAN (R 3.4.0)
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withr 2.1.1 2017-12-19 CRAN (R 3.4.3)
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xtable * 1.8-2 2016-02-05 cran (@1.8-2)
yaml 2.1.16 2017-12-12 CRAN (R 3.4.3)