Description

Measuring Morphological Diversity and Evolutionary Tempo.

Description

Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014) <doi:10.1016/j.cub.2014.08.034>, Close et al. (2015) <doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>, and MatrixDistances(), which implements multiple discrete character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>. Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree() implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and plot_morphospace_stack() implements Foote (1993) <doi:10.1017/S0094837300015864>. Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) <doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>.

README.md

cran.r-project.org

Claddis

Claddis is an R package designed to import cladistic-type data sets (#NEXUS format) into R and perform disparity analysis and rate tests.

Package status

Travis release version

Travis development version

CRAN

Version

Claddis is on CRAN (version 0.6.1) but is also being developed on GitHub. To get the absolute latest version you can use:

if(!require(devtools)) install.packages("devtools", dependencies = TRUE)
devtools::install_github("graemetlloyd/Claddis", ref = "master")

However, installing a development version of a package is only recommended for expert users.

Please also consult the CHANGELOG file for all updates (including new functions, features and bug fixes) to Claddis.

Installation

You can install Claddis in R via CRAN with:

install.packages("Claddis", dependencies = TRUE)

Or from GitHub with:

if(!require(devtools)) install.packages("devtools", dependencies = TRUE)
devtools::install_github("graemetlloyd/Claddis", ref = "CRAN")

And load it into memory using:

library(Claddis)

Help

Basic help can be found with:

?Claddis

And clicking on the Index link at the base of the help file will reveal links to every available function.

Tutorials

Note that I have previously linked to tutorials for the package here, but substantial reworking of the core code means these will no longer work and so currently the example code in each function's help file is the best substitute for this. New tutorials will eventually be produced and shared here.

Users should also be aware of the dispRity R package, that can form the end of a Claddis disparity pipeline.

Citation

The first formal paper describing Claddis was published as Lloyd (2016):

Lloyd, G. T., 2016. Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions. Biological Journal of the Linnean Society, 118, 131-151.

The effects of ancestral state estimation choices on phylomorphospaces was discussed in Lloyd (2018):

Lloyd, G. T., 2018. Journeys through discrete-character morphospace: synthesizing phylogeny, tempo, and disparity. Palaeontology, 61, 637-645.

r-Claddis

Claddis

Package status

Travis release version

Travis development version

CRAN

Version

Installation

Help

Tutorials

Citation

Version

License

Status

Source

Homepage

Platforms (77)

Claddis

Package status

Travis release version

Travis development version

CRAN

Version

Installation

Help

Tutorials

Citation

Version

License

Status

Source

Homepage

Platforms77 (77)

Platforms (77)