Diversitree protocols

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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

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Maintainer


  • person_outline Richard G. FitzJohn <>

Publication for Diversitree

Diversitree in pipelines

 (3)
2014
PMCID: 4298941
PMID: 25481482
DOI: 10.1186/1471-2164-15-1075

[…] were selected from the alignment, and a tree built under the same parameters with 100 bootstrap replicates (additional file ). the circular phylogenetic tree and trait plot was visualised using the diversitree [] and ape [] packages in r. further investigation of the paths in the tree topology to define phylogroup b1, and expecs within phylogroup b2 and phylogroup d isolates was were achieved […]

2014
PMCID: 4366372
PMID: 25526369
DOI: 10.1038/ismej.2014.242

[…] 70% identity over greater than 80% to the translated nucleotide sequence of the genome in question. the distribution of the genes across the e. coli core-genome dendrogram was visualized using the diversitree package () implemented in r ()., for statistical analysis to take account of genes incorrectly labelled as ‘absent' because of the splitting of coding sequences across contigs, the lee […]

2010
PMCID: 2901258
PMID: 20515493
DOI: 10.1186/1471-2148-10-162

[…] johannes mueller, and jim regetz for helpful discussions on phylogenetic analyses and software. extra thanks also to rich fitzjohn, wayne maddison and andrew rambaut for answering my questions about diversitree, mesquite and beast, respectively. ammon corl, christy hipsley, and kathleen kay provided valuable editorial comments on the ms. this project was funded by nceas (the national center […]


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Diversitree in publications

 (54)
PMCID: 5951845
PMID: 29760391
DOI: 10.1038/s41467-018-04265-x

[…] 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 […]

PMCID: 5941815
PMID: 29739313
DOI: 10.1186/s12862-018-1174-5

[…] 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 […]

PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4

[…] 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 […]

PMCID: 5725568
PMID: 29229907
DOI: 10.1038/s41467-017-02220-w

[…] 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. […]

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

[…] 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 […]


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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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