This package is a likelihood-based statistical package to estimate parameters under diversity-dependent diversification models. New in version 0.3: - Models with shifts in the parameters at a time tshift. New in version 0.4: - Bug fix of prefactor in likelihood - bug did not affect parameter estimates. - There is an option to condition or not on non-extinction of the phylogeny. - The functions dd_loglik and dd_SR_loglik now accept untransformed parameters; the transformation is done in the auxiliary functions. - Improved help pages. - Auxiliary functions no longer in help pages. New in version 1.0: - Another bug fix of prefactor in likelihood - bug did not affect parameter estimates. - Models with key innovations defined as decoupling of diversity-dependent dynamics. - Option to compute the likelihood of a set of branching times or of the phylogeny; these differ by a constant factor. New in version 1.1: - A model with diversity-dependence in speciation and extinction rate, currently only available for the likelihood without shifts or decoupling. New in version 1.2: - Possibility of automatically exploring multiple initial conditons for the SR models - Suppressing unnecessary output - Flushing computed likelihood values immediately (even with buffer on) - Bug fix in default value of the initial time of decoupling New in version 1.3: - Fix of default length of idparsopt - Fix of conversion problems for small branching times - Default initial parameter values in dd_ML based on birth-death model New in version 1.4: - Bug fix for when there is a large number of missing species New in version 1.5: - Bug fix for returned output of functions when there are fixed parameters. Textual output of DDD was correct. - Return to Nelder-Mead optimization for dd_ML (was set to "nlm" in versions 1.3 & 1.4) - New format for output off all ML-functions (dd_ML, dd_SR_ML, dd_KI_ML) New in version 1.6 (not on CRAN) - Bug fix in returned result when optimization does not converge. - Works also when only branching times are entered in ascending order (previously error was reported) New in version 1.7 - Cleaning up code, fixing various small bugs - New optimization algorithm because of occasional strange results with optim package New in version 1.8 - Bug fix for missing number of species in KI model - Bug fix for optimization of one parameter (due to R's inconsistent handling of matrices) - Model 5 (dd_ML and dd_loglik) now also allows values of -1 < r < 0; i.e. when extinction also decreases with diversity but less so than speciation New in version 1.9 - Bug fix in optimizer (did not stop when likelihood was positive) - Bug fix for large numbers of missing species - Conv = -1 is now always reported when optimization is not started or does not converge - An error is reported when parameter values cause numerical problems (NA or NaN) in likelihood computation, e.g. when parameter values are very high; loglik is then set to -Inf - For dd_KI_loglik and dd_KI_ML: if the number of missing species in main clade and subclade is known, this can now be specified - Fixing K at Inf is now possible in SR and KI models New in version 1.10 - All non-convergences now get conv = -1 (this was conv = 1 for true nonconvergence and conv = -1 for optimization that did not start because of low likelihood values) - Likelihoods can also be computed for a tree with a stem age rather than only a crown age New in version 1.11 - Various small tweaks to make the code run faster and some bug fixes New in version 1.12 - Allows conditioning on survival of crown linages AND on the number of extant species by setting cond = 2 New in version 1.13 - Fast computation of dd_loglik for the case K = Inf New in version 1.14 - Fast computation of dd_loglik for the case mu = 0 - Allows time-dependence instead of diversity-dependence; exponential decline in speciation rate and/or extinction - Start of time-dependence can be specified to allow synchronisation across multiple clades - Removed link to LASER New in version 2.0 - Includes function to simulate trees under diversity-dependence New in version 2.1 - Fixes numerical problems with the convolve-function (used to deal with missing species) - Fixes a bug in dd_KI_loglik (ddep unknown) - Changed third element of the output of dd_sim, such that all speciation and extinction times are in Mya New in version 2.2 - Allows conditioning on the number of taxa only for dd_loglik, asssuming a uniform prior on stem age; this is now the default - An additional model of time-dependence, following deterministic logistic equation New in version 2.3 - Allows conditioning on the number of taxa only for dd_SR_loglik, assuming a uniform prior on stem age; this is now the default - Fix of bug for stem age (soc = 1), introduced in v2.2. - Allows Rabosky's exponential model, with la(n) = la_0 * n^(-x(la_0,mu,K)) as ddmodel = 2.1, mu(n) = mu_0 * n^x(la, mu_0, K) as ddmodel = 4.1 - Allows specific case of Rabosky's exponential model, with la(n) = la_0 * n^(-1), as ddmodel = 2.2, and mu(n) = mu_0 * n, as ddmodel = 4.2 New in version 2.4 - Fix of bug in dd_KI_loglik ('m' was not found) New in version 2.5 - Fix of bug in bd_loglik where NA was output to screen for a nonexistent parameter under diversity-dependence without extinction - Fix of bug in dd_KI_loglik when m is a two-element vector - Fix of bug in dd_KI_loglik, introduced in v2.3 New in version 2.6 - Allows linear dependence of speciation with parameter K' (= diversity where speciation = 0) New in version 2.7 - Fixes bugs in dd_KI_loglik, for cond = 0 introduced in v2.3, and for cond = 1 introduced in v2.0 - Solves (some) memory problems with dd_KI_ML and dd_KI_loglik when cond = 1 - Provides option to set loglikelihood to -Inf if optimization did not converge New in version 3.0 - Includes a model of macroevolutionary succession in which there is no decoupling of diversity-dependence but parameters may change - Computes LRb, a bootstrap version of the likelihood ratio - Allows use of alternative ODE solvers - Allows use of subplex as optimization algorithm. New in version 3.1 - Fixes bug with dd_sim and dd_KI_sim for ddmodel 1.3 (Thanks to Giovanni Laudanno) - Fixes bug with cond = 3 - Includes matrix exponentiation as an alternative to numerical ODE solvers New in version 3.2 - Fixes bug with dd_loglik when lambda becomes infinite - Changes default tolerance of subplex - Fixes tiny bug in p-value computation in dd_LR New in version 3.3 - Documentation for several previously internal functions that were used by other packages - Small bug fix of L2phylo function (previously digits could be dropped in conversion from numbers as characters to numeric) - Contains a function to simulate the SR model New in version 3.4 - Contains a function to convert the L table directly to branching times - Bug fix in dd_KI_loglik for stem age with no further branching in the main clade after the decoupling. New in version 3.5 - Fixes bug in dd_SR_sim New in version 3.6 - Fixes bug with missing species in dd_LR - Fixes bug with ddmodel = 5 New in version 3.7 - Fixes bug with specifying integration method in dd_LR - Faster integration by using compiled fortran code with deSolve - Uses expm instead of expoRkit because the latter is no longer supported on CRAN Forthcoming: - Computation of the likelihood according to a lineage-specific rate shift model under an otherwise constant-rate birth-death model. - High-precision arithmetic in numerically unstable regions of bd_loglik
| Package: | DDD |
| Type: | Package |
| Version: | 3.7 |
| Date: | 2018-4-17 |
| License: | GPL 3.0 |
bd_loglik compues the likelihood under the constant-rate birth-death model of several specific time-dependent birth-death models.
bd_ML finds the parameters that maximizes the likelihood computed by bd_loglik.
dd_loglik computes the likelihood of any of 4 different models of diversity-dependent diversification, given a set of parameters and a data set of phylogenetic branching times.
dd_ML finds the parameters that maximizes the likelihood computed by dd_loglik.
dd_SR_loglik is the same as dd_loglik except that it allows a shift in the parameters at time tshift.
dd_SR_ML finds the parameters that maximizes the likelihood computed by dd_SR_loglik.
dd_KI_loglik is the same as dd_loglik except that it allows decoupling of a subclade's dynamics from the main clade's dynamics potentially accompanied by a shift in parameters at time t_d.
dd_KI_ML finds the parameters that maximizes the likelihood computed by dd_KI_loglik.
dd_MS_loglik is the same as dd_KI_loglik except that the subclade's dynamics do not decouple from the main clade's dynamics but they do get different parameters at time t_d.
dd_MS_ML finds the parameters that maximizes the likelihood computed by dd_MS_loglik.
dd_sim, dd_SR_sim, dd_KI_sim and dd_MS_sim simulate the diversity-dependent process according to the simple, rate shift, key innovation and macro-evolutionary models respectively.
dd_LR performs a bootstrap likelihood ratio test of the standard diversity-dependent model against the constant-rates diversity-independent model.
- Etienne, R.S. et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439 - Etienne, R.S. & B. Haegeman 2012. Am. Nat. 180: E75-E89, doi: 10.1086/667574 - Etienne, R.S. et al. 2016, Meth. Ecol. Evol. 7: 1092-1099, doi: 10.1111/2041-210X.12565
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