dd_SR_loglik
(Package: DDD) :
Loglikelihood for diversity-dependent diversification models with a shift in the parameters at time t = tshift
This function computes loglikelihood of a diversity-dependent diversification model for a given set of branching times and parameter values where the parameters are allowed to shift at time t = tshift
bd_ML
(Package: DDD) :
Maximization of the loglikelihood under the diversity-independent, possibly time-dependent diversification model
This function computes the maximum likelihood estimates of the parameters of a diversity-independent diversification model for a given set of phylogenetic branching times. It also outputs the corresponding loglikelihood that can be used in model comparisons.
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
Forthcoming: - High-precision arithmetic in numerically unstable regions of bd_loglik
dd_SR_ML
(Package: DDD) :
Maximization of the loglikelihood under a diversity-dependent diversification model with a shift in the parameters
This function computes the maximum likelihood estimates of the parameters of a diversity-dependent diversification model with shifting parameters at time t = tshift for a given set of phylogenetic branching times. It also outputs the corresponding loglikelihood that can be used in model comparisons.
dd_KI_ML
(Package: DDD) :
Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics
This function computes the maximum likelihood estimates of the parameters of a diversity-dependent diversification model with decoupling of the diversification dynamics of a subclade from the dynamics of the main clade for a given set of phylogenetic branching times of main clade and subclade and the time of splitting of the lineage that will form the subclade. It also outputs the corresponding loglikelihood that can be used in model comparisons.
dd_MS_sim
(Package: DDD) :
Function to simulate the macro-evolutionary succession process assuming diversity-dependent diversification
Simulating a diversity-dependent diversification process where at a given time a new clade emerges with different inherent speciation rate and extinction rate
dd_KI_loglik
(Package: DDD) :
Loglikelihood for diversity-dependent diversification models with decoupling of a subclade from a main clade at time t = t_d
This function computes loglikelihood of a diversity-dependent diversification model for a given set of branching times and parameter values where the diversity-dependent dynamics of a subclade decouple from the dynamics of the main clade at time t_d, potentially accompanied by a shift in parameters.
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