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Diversitree specifications

Information


Unique identifier OMICS_12496
Name Diversitree
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.9-10
Stability Stable
Requirements
methods, stats, R(≥2.10), graphics, grDevices, ape, numDeriv, expm, geiger, deSolve(≥1.7), subplex, Rcpp(≥0.10.0), minqa, lubridate, caper
Source code URL https://cran.r-project.org/src/contrib/diversitree_0.9-10.tar.gz
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Richard G. FitzJohn

Publication for Diversitree

Diversitree citations

 (78)
call_split

Asynchronous evolution of interdependent nest characters across the avian phylogeny

2018
Nat Commun
PMCID: 5951845
PMID: 29760391
DOI: 10.1038/s41467-018-04265-x
call_split See protocol

[…] ans of log likelihoods to compare models, with a value larger than 5 indicating strong support for the ‘dependent’ model.We also used the MuSSE (Multi-State Speciation and Extinction) function of the diversitree package in R to test the effect of nest structure types on the speciation rates of avian lineages across the bird phylogeny and the detailed methods and results were shown in Supplementary […]

library_books

Binary state speciation and extinction method is conditionally robust to realistic violations of its assumptions

2018
BMC Evol Biol
PMCID: 5941815
PMID: 29739313
DOI: 10.1186/s12862-018-1174-5

[…] y surviving species from the root of the tree to the tip is thus the same regardless of how many branching events took place. This simulation is implicit in the assumptions of BiSSE as implemented in diversitree [], and is equivalent to “phyletic gradualism” sensu Eldredge and Gould [].The second (“punctuated”) type of simulation emulates cladogenetic character evolution in which state changes hap […]

call_split

Macroecology and macroevolution of the latitudinal diversity gradient in ants

2018
Nat Commun
PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4
call_split See protocol

[…] ition rates shift at some time point—the boundary between two epochs. In practice, the asymmetric epoch model was problematic to fit, so we excluded it (see Supplementary Note ).We used the R package diversitree to fit the models of trait evolution with maximum likelihood and reconstruct marginal ancestral state probabilities under the ML model. The two-epoch model was fit by sweeping across possi […]

library_books

chromploid: An R package for chromosome number evolution across the plant tree of life

2018
Appl Plant Sci
PMCID: 5895187
PMID: 29732267
DOI: 10.1002/aps3.1037

[…] l., ).Implementing chromosomal and ploidy evolution models in the R environment in chromploid allows users to leverage other tools for phylogenetic analyses, like ancestral state reconstruction using diversitree (FitzJohn, ) or phylomap (Irvahn and Minin, ), and to visualize character evolution across the tree using phytools (Revell, ). In the future, it will be straightforward to implement more s […]

call_split

Live bearing promotes the evolution of sociality in reptiles

2017
Nat Commun
PMCID: 5725568
PMID: 29229907
DOI: 10.1038/s41467-017-02220-w
call_split See protocol

[…] models and confirm that 99% of the distribution of simulated estimates for both β1 and s2 did not cross zero (Table ; Supplementary Fig. ).Second, we used MuSSE models,, implemented in the R package ‘diversitree’. MuSSE models provide estimates of transition rates between different character states while accounting for variation in speciation and extinction rates associated with each state. Accoun […]

library_books

Different diversity dependent declines in speciation rate unbalances species richness in terrestrial slugs

2017
Sci Rep
PMCID: 5700933
PMID: 29170460
DOI: 10.1038/s41598-017-16417-y

[…] ckage DDD that evaluates six different diversity-dependent models (see details in Supplementary Text S1). These models were tested using the following R-packages: laser v2.4 (function: “fitdAICrc”); diversitree V.0.9 (functions: “make.bd.split”, “make.bd.t”) and DDD v.3.4,, (functions: “dd_ML”, “dd_KI_ML”). (see Supplementary Text S1 for details). The best supported models were those with low Aka […]

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Diversitree institution(s)
Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
Diversitree funding source(s)
This work was supported by a University Graduate Fellowship from the University of British Columbia and a Vanier Commonwealth Graduate Scholarship from NSERC, and an NSERC discovery grant.

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