Release:
Development (master):
CRAN:
if(!require(devtools)) install.packages("devtools")
library(devtools)
install_github("TGuillerme/dispRity", ref = "release")
library(dispRity)The following installs the latest release of dispRity (see patch notes below). For the piping hot development version (not recommended), replace the ref = "release" option with ref = "master".
If you're using the master branch, see the patch notes for the latest developments.
The package is available in the CRAN Task Views in Phylogenetics.
Can't install the latest version of
dispRityfrom the CRAN?
The latest dispRity package version 1.5 requires R 4.0 to run. If you don't have your R version updated to 4.0 you can either:
-
- update your R version to the latest; this is suggested: since the amazing R CRAN team always update their software for a good reason (and for free!);
-
- if for some reason you really can't update your R version, you can simply download the released github version of the package using:
devtools::install_github("TGuillerme/dispRity", ref = "release").
- if for some reason you really can't update your R version, you can simply download the released github version of the package using:
A detailed vignette is available online or as a pdf:
Otherwise, each functions has a detailed associated manual with examples in R (?which.function).
Additionally, you can learn more about the structure of dispRity objects here.
You can download the workshop follow-along sheet here(use right click > save link as...) or visualise it in html here.
Not sure what disparity metric to use?
Not sure what a disparity metric is in the first place?
Check out this pre-print on selecting the best metric for your specific question on biorXiv or the moms shiny app.
You can also find more information in the dispRity manual.
-
2020/09/25 v1.5 between groups
- New function:
multi.acefor performing fast ancestral character estimations on multiple matrices (based oncastor::asr_mk_model). - New function:
reduce.space, a function to modify trait spaces imported from themomsshiny app. This function comes with a new reduction algorithm: the "evenness" algorithm for flattening the curve (thanks to Gavin Thomas for the suggestion). - New function:
test.metric(and associatedplot,printandsummaryfunctions), to apply thereduce.spacefunction on a specific space and metric to test whether a metric is picking up specific changes in trait space. - the
dispRityfunction can now use"between.groups"metrics to calculate disparity between groups rather than within groups. Themake.metricfunction is now modified to allow detection of metrics that can be applied between groups. - New metric:
group.dist, a dimension level 1 metric for between groups that measures the distance between two groups. By default, this is the minimum distance but the function takes theprobsargument allowing the distance to be between, says, the 95% CI (probs = c(0.025, 0.975))) or between the centroids (probs = c(0.5)). - New metric:
point.dist, a dimension level 2 metric for between groups that measures the distance between the rows inmatrixto a point inmatrix2. That point is the centroid by default but thepointargument can take any function. - The
dispRitypackage now depends onR (>= 4.0.0). - Many updates to the
dispRitymanual. - Many minor speed improvements across the package
- Simplified syntax for the internal
plot.dispRityS3 methods (for a potentialggpRity?). These changes should not be apparent at the user level but see the two removed options below: - removed option in
plot.dispRity: thechrono.subsetsoption (TRUE/FALSE) has now been removed. The time-slicing-ness is now automatically detected or can be specified by the user normally throughxlab. - removed option in
plot.dispRity: theylim,ylab,xlabandcoloptions have now been removed. They are now handled through...as normal genericplot(...)arguments. - removed option in
plot.dispRity: theelements.pchoption has now been removed. Thepchof the plotted elements can now be passed like other options directly to elements (e.g.elements = list(pch = 15)). - removed option in
plot.dispRity: thedimensions,matrix,nclassandcoeffoptions have now been removed. Any options for dual class plots (randtest,dtt,model.test,type = "preview"etc...) are now handled through the genericspecific.argsargument. - New option in
dtt.dispRity:scale.timeallowing to scale the time axis (like ingeiger::dtt) or not. - when plotting
chrono.subsetsdispRityobjects, the x label ticks are now rounded if possible (for nicer looking plots!). - when using automatic
chrono.subsetstime slices, the name of the time slices (their age) is now rounded for aesthetics.
- New function:
Previous patch notes and notes for the next version can be seen here.
If you are using this package, please cite the paper:
- Guillerme, T. (2018) dispRity: a modular R package for measuring disparity. Methods in Ecology and Evolution. doi:10.1111/2041-210X.13022
Also don't forget to cite R and consider citing the ape package since dispRity heavily relies on it (and, generally, cite all the R packages you use!):
- Paradis E. & Schliep K. (2019). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.
- R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
To cite the dispRity manual, please use:
- Guillerme, T. & Cooper, N. (2018) dispRity manual. figshare. Preprint. 10.6084/m9.figshare.6187337.v1
To cite the time slicing method from the chrono.subsets function, please use:
- Guillerme, T. & Cooper, N. (2018) Time for a rethink: time sub‐sampling methods in disparity‐through‐time analyses. Palaeontology, 61: 481-493. doi:10.1111/pala.12364
Some ideas/functionalities/implementations in this package where implemented following the suggestions of Natalie Cooper, Graeme Lloyd, Dave Bapst, Andrew Jackson and Martin Brazeau.
The dispRity package was cited in these papers. Below is a list of specific papers using specific functionalities. These papers do not only use the functionalities highlighted here (and the author do much more awesome science!) but this is just a list of references if you want an independent guide on how to use these functions:
Ezcurra MD, Montefeltro FC, Pinheiro FL, Trotteyn MJ, Gentil AR, Lehmann OE, Pradelli LA. The stem-archosaur evolutionary radiation in South America. Journal of South American Earth Sciences. 2020 Oct 7:102935. Journal of South American Earth Sciences. 2020 DOI: 10.1016/j.jsames.2020.102935
