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nhcooper123 committed Apr 19, 2023
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Expand Up @@ -143,118 +143,118 @@ For reproducibility purposes, here is the output of `devtools::session_info()` u
broom * 1.0.3 2023-01-25 [1] CRAN (R 4.2.0)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.0)
cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0)
clusterGeneration 1.3.7 2020-12-15 [1] CRAN (R 4.2.0)
coda * 0.19-4 2020-09-30 [1] CRAN (R 4.2.0)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0)
combinat 0.0-8 2012-10-29 [1] CRAN (R 4.2.0)
corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.2.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
cubature 2.0.4.4 2022-03-22 [1] CRAN (R 4.2.0)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.2.0)
dplyr * 1.1.0 2023-01-29 [1] CRAN (R 4.2.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0)
expm 0.999-7 2023-01-09 [1] CRAN (R 4.2.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
fastmatch 1.1-3 2021-07-23 [1] CRAN (R 4.2.0)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.2.0)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.2.0)
fs 1.6.1 2023-02-06 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
ggfortify * 0.4.14 2022-01-03 [1] CRAN (R 4.2.0)
ggfun 0.0.9 2022-11-21 [1] CRAN (R 4.2.0)
ggnewscale * 0.4.8 2022-10-06 [1] CRAN (R 4.2.0)
ggplot2 * 3.4.1 2023-02-10 [1] CRAN (R 4.2.0)
ggplotify 0.1.0 2021-09-02 [1] CRAN (R 4.2.0)
ggtree * 3.6.2 2022-11-10 [1] Bioconductor
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0)
gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.2.0)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0)
here * 1.0.1 2020-12-13 [1] CRAN (R 4.2.0)
hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.0)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.0)
httpuv 1.6.6 2022-09-08 [1] CRAN (R 4.2.0)
igraph 1.3.5 2022-09-22 [1] CRAN (R 4.2.0)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.2.0)
jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.0)
knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0)
later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.2.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
lubridate * 1.9.2 2023-02-10 [1] CRAN (R 4.2.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
maps * 3.4.1 2022-10-30 [1] CRAN (R 4.2.0)
MASS 7.3-56 2022-03-23 [1] CRAN (R 4.2.0)
Matrix * 1.4-1 2022-03-23 [1] CRAN (R 4.2.0)
MCMCglmm * 2.34 2022-06-21 [1] CRAN (R 4.2.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
mnormt 2.1.1 2022-09-26 [1] CRAN (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
nlme 3.1-157 2022-03-25 [1] CRAN (R 4.2.0)
numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.2.0)
optimParallel 1.0-2 2021-02-11 [1] CRAN (R 4.2.0)
patchwork * 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
phangorn * 2.11.1 2023-01-23 [1] CRAN (R 4.2.0)
phytools * 1.5-1 2023-02-19 [1] CRAN (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.0)
plotrix 3.8-2 2021-09-08 [1] CRAN (R 4.2.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.0)
profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.0)
purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
quadprog 1.5-8 2019-11-20 [1] CRAN (R 4.2.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.0)
readr * 2.1.4 2023-02-10 [1] CRAN (R 4.2.0)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
RevGadgets * 1.1.0 2023-02-03 [1] Github (revbayes/RevGadgets@6f8491b)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.0)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
scatterplot3d 0.3-42 2022-09-08 [1] CRAN (R 4.2.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
shiny 1.7.3 2022-10-25 [1] CRAN (R 4.2.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0)
stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
tensorA 0.36.2 2020-11-19 [1] CRAN (R 4.2.0)
tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
tidyr * 1.3.0 2023-01-24 [1] CRAN (R 4.2.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
tidytree 0.4.2 2022-12-18 [1] CRAN (R 4.2.0)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.2.0)
timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.0)
treeio 1.22.0 2022-11-01 [1] Bioconductor
tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0)
vroom 1.6.1 2023-01-22 [1] CRAN (R 4.2.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
xfun 0.37 2023-01-31 [1] CRAN (R 4.2.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
yulab.utils 0.0.6 2022-12-20 [1] CRAN (R 4.2.0)

[1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0)
clusterGeneration 1.3.7 2020-12-15 [1] CRAN (R 4.2.0)
coda * 0.19-4 2020-09-30 [1] CRAN (R 4.2.0)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0)
combinat 0.0-8 2012-10-29 [1] CRAN (R 4.2.0)
corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.2.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
cubature 2.0.4.4 2022-03-22 [1] CRAN (R 4.2.0)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.2.0)
dplyr * 1.1.0 2023-01-29 [1] CRAN (R 4.2.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0)
expm 0.999-7 2023-01-09 [1] CRAN (R 4.2.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
fastmatch 1.1-3 2021-07-23 [1] CRAN (R 4.2.0)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.2.0)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.2.0)
fs 1.6.1 2023-02-06 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
ggfortify * 0.4.14 2022-01-03 [1] CRAN (R 4.2.0)
ggfun 0.0.9 2022-11-21 [1] CRAN (R 4.2.0)
ggnewscale * 0.4.8 2022-10-06 [1] CRAN (R 4.2.0)
ggplot2 * 3.4.1 2023-02-10 [1] CRAN (R 4.2.0)
ggplotify 0.1.0 2021-09-02 [1] CRAN (R 4.2.0)
ggtree * 3.6.2 2022-11-10 [1] Bioconductor
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0)
gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.2.0)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0)
here * 1.0.1 2020-12-13 [1] CRAN (R 4.2.0)
hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.0)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.0)
httpuv 1.6.6 2022-09-08 [1] CRAN (R 4.2.0)
igraph 1.3.5 2022-09-22 [1] CRAN (R 4.2.0)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.2.0)
jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.0)
knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0)
later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.2.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
lubridate * 1.9.2 2023-02-10 [1] CRAN (R 4.2.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
maps * 3.4.1 2022-10-30 [1] CRAN (R 4.2.0)
MASS 7.3-56 2022-03-23 [1] CRAN (R 4.2.0)
Matrix * 1.4-1 2022-03-23 [1] CRAN (R 4.2.0)
MCMCglmm * 2.34 2022-06-21 [1] CRAN (R 4.2.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
mnormt 2.1.1 2022-09-26 [1] CRAN (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
nlme 3.1-157 2022-03-25 [1] CRAN (R 4.2.0)
numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.2.0)
optimParallel 1.0-2 2021-02-11 [1] CRAN (R 4.2.0)
patchwork * 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
phangorn * 2.11.1 2023-01-23 [1] CRAN (R 4.2.0)
phytools * 1.5-1 2023-02-19 [1] CRAN (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.0)
plotrix 3.8-2 2021-09-08 [1] CRAN (R 4.2.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.0)
profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.0)
purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
quadprog 1.5-8 2019-11-20 [1] CRAN (R 4.2.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.0)
readr * 2.1.4 2023-02-10 [1] CRAN (R 4.2.0)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
RevGadgets * 1.1.0 2023-02-03 [1] Github (revbayes/RevGadgets@6f8491b)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.0)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
scatterplot3d 0.3-42 2022-09-08 [1] CRAN (R 4.2.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
shiny 1.7.3 2022-10-25 [1] CRAN (R 4.2.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0)
stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
tensorA 0.36.2 2020-11-19 [1] CRAN (R 4.2.0)
tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
tidyr * 1.3.0 2023-01-24 [1] CRAN (R 4.2.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
tidytree 0.4.2 2022-12-18 [1] CRAN (R 4.2.0)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.2.0)
timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.0)
treeio 1.22.0 2022-11-01 [1] Bioconductor
tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0)
vroom 1.6.1 2023-01-22 [1] CRAN (R 4.2.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
xfun 0.37 2023-01-31 [1] CRAN (R 4.2.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
yulab.utils 0.0.6 2022-12-20 [1] CRAN (R 4.2.0)

[1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library

## Checkpoint for reproducibility
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:
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