Package: DDD 5.2.2

DDD: Diversity-Dependent Diversification

Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <doi:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <doi:10.1086/667574>, Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <doi:10.1111/2041-210X.12565> and Laudanno et al. 2021. Syst. Biol. 70: 389–407, <doi:10.1093/sysbio/syaa048>. Also contains functions to simulate the diversity-dependent process.

Authors:Rampal S. Etienne [aut, cre], Bart Haegeman [aut], Hanno Hildenbrandt [ctb], Giovanni Laudanno [ctb]

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DDD.pdf |DDD.html✨
DDD/json (API)

# Install 'DDD' in R:
install.packages('DDD', repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rsetienne/ddd/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

6.88 score 3 stars 7 packages 81 scripts 804 downloads 14 mentions 28 exports 40 dependencies

Last updated 1 years agofrom:7a1022986f. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-win-x86_64OKOct 27 2024
R-4.5-linux-x86_64OKOct 27 2024
R-4.4-win-x86_64OKOct 27 2024
R-4.4-mac-x86_64OKOct 27 2024
R-4.4-mac-aarch64OKOct 27 2024
R-4.3-win-x86_64OKOct 27 2024
R-4.3-mac-x86_64OKOct 27 2024
R-4.3-mac-aarch64OKOct 27 2024

Exports:bd_loglikbd_MLbrts2phyloconvdd_KI_loglikdd_KI_MLdd_KI_simdd_loglikdd_LRdd_MLdd_MS_loglikdd_MS_MLdd_MS_simdd_simdd_SR_loglikdd_SR_MLdd_SR_simL2brtsL2phylooptimizerphylo2Lrng_respecting_sampleroundnsample2simplextd_simtransform_parsuntransform_pars

Dependencies:apeBHcliclusterGenerationcodacodetoolscombinatcpp11DEoptimdeSolvedigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcppRcppEigenrlangscatterplot3dSparseMsubplexvctrs

Readme and manuals

Help Manual

Help pageTopics
Loglikelihood for diversity-independent diversification modelbd_loglik
Maximization of the loglikelihood under the diversity-independent, possibly time-dependent diversification modelbd_ML
Function to convert a set of branching times into a phylogeny with random topology This code is taken from the package TESS by Sebastian Hoehna, where the function is called tess.create.phylobrts2phylo
Function to do convolution of two vectorsconv
Loglikelihood for diversity-dependent diversification models with decoupling of a subclade from a main clade at time t = t_ddd_KI_loglik
Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamicsdd_KI_ML
Function to simulate a key innovation in macro-evolution with the innovative clade decoupling from the diversity-dependent diversification dynamics of the main cladedd_KI_sim
Loglikelihood for diversity-dependent diversification modelsdd_loglik
Bootstrap likelihood ratio test of diversity-dependent diversification modeldd_LR
Maximization of the loglikelihood under a diversity-dependent diversification modeldd_ML
Loglikelihood for macro-evolutionary succession under diversity-dependent diversification with the key innovation at time t = t_ddd_MS_loglik
Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamicsdd_MS_ML
Function to simulate the macro-evolutionary succession process assuming diversity-dependent diversificationdd_MS_sim
Loglikelihood for diversity-dependent diversification models with multiple decoupling (rate shift) eventsdd_multiple_KI_loglik
Function to simulate the diversity-dependent diversification processdd_sim
Loglikelihood for diversity-dependent diversification models with a shift in the parameters at time t = tshiftdd_SR_loglik
Maximization of the loglikelihood under a diversity-dependent diversification model with a shift in the parametersdd_SR_ML
Function to simulate the diversity-dependent diversification process with a shift in one or more of the parametersdd_SR_sim
Function to convert a table with speciation and extinction events to a set of branching timesL2brts
Function to convert a table with speciation and extinction events to a phylogenyL2phylo
Carries out optimization (finding a minimum)optimizer
Function to convert phylogeny to a table with speciation and extinction eventsphylo2L
Sampling in which zero probabilities are removedrng_respecting_sample
Rounds up in the usual mannerroundn
Takes samples in the usual mannersample2
Carries out optimization using a simplex algorithm (finding a minimum)simplex
Simulation of a diversity-dependent-like time-dependent processtd_sim
Transforming parameters from -Inf to Inf into parameters from -1 to 1transform_pars
Untransforming parameters from -1 to 1 into parameters from -Inf to Inf.untransform_pars