This function computes the maximum likelihood estimates of the parameters of a diversity-dependent diversification model where the diversity-dependent dynamics of an innovative subclade have different parameters from the dynamics of the main clade from time t_d, but both are governed by the same carrying capacity and experience each other's diversity. Required isa given set of phylogenetic branching times of main clade and subclade and the time of splitting of the lineage that will form the subclade. The function also outputs the corresponding loglikelihood that can be used in model comparisons.
dd_MS_ML(
brtsM,
brtsS,
tsplit,
initparsopt = c(0.5, 0.1, 2 * (1 + length(brtsM) + length(brtsS) + sum(missnumspec)),
(tsplit + max(brtsS))/2),
parsfix = NULL,
idparsopt = c(1:3, 6),
idparsfix = NULL,
idparsnoshift = (1:6)[c(-idparsopt, (-1)^(length(idparsfix) != 0) * idparsfix)],
res = 10 * (1 + length(c(brtsM, brtsS)) + sum(missnumspec)),
ddmodel = 1.3,
missnumspec = 0,
cond = 0,
soc = 2,
tol = c(0.001, 1e-04, 1e-06),
maxiter = 1000 * round((1.25)^length(idparsopt)),
changeloglikifnoconv = FALSE,
optimmethod = "subplex",
num_cycles = 1,
methode = "ode45",
correction = FALSE,
verbose = FALSE
)gives the maximum likelihood estimate of lambda of the main clade
gives the maximum likelihood estimate of mu of the main clade
gives the maximum likelihood estimate of K of the main clade
gives the maximum likelihood estimate of lambda of the subclade
gives the maximum likelihood estimate of mu of the subclade
gives the time of the key innovation event
gives the maximum loglikelihood
gives the number of estimated parameters, i.e. degrees of feedom
gives a message on convergence of optimization; conv = 0 means convergence
A set of branching times of the main clade in a phylogeny, all positive
A set of branching times of the subclade in a phylogeny, all positive
The branching time at which the lineage forming the subclade branches off, positive
The initial values of the parameters that must be optimized
The values of the parameters that should not be optimized
The ids of the parameters that must be optimized, e.g. 1:7
for all parameters. The ids are defined as follows:
id == 1 corresponds to lambda_M (speciation rate) of the main clade
id == 2 corresponds to mu_M (extinction rate) of the main clade
id == 3 corresponds to K_M (clade-level carrying capacity) of the main clade
id == 4 corresponds to
lambda_S (speciation rate) of the subclade
id == 5 corresponds to mu_S (extinction rate) of the subclade
id == 6 corresponds to t_d (the time of the key innovation)
The ids of the parameters that should not be optimized, e.g. c(1,3,4,6) if lambda and K should not be optimized, but only mu. In that case idparsopt must be c(2,5,7). The default is to fix all parameters not specified in idparsopt.
The ids of the parameters that should not shift; This can only apply to ids 4, 5 and 6, e.g. idparsnoshift = c(4,5) means that lambda and mu have the same values before and after tshift
sets the maximum number of species for which a probability must be computed, must be larger than 1 + max(length(brtsM),length(brtsS))
sets the model of diversity-dependence:
ddmodel == 1 : linear dependence in speciation rate with parameter K (= diversity
where speciation = extinction)
ddmodel == 1.3 : linear dependence in speciation rate with parameter K' (= diversity where speciation = 0)
ddmodel == 2 : exponential dependence in speciation rate with
parameter K (= diversity where speciation = extinction)
ddmodel == 2.1 : variant of exponential dependence in speciation rate with offset at
infinity
ddmodel == 2.2 : 1/n dependence in speciation rate
ddmodel == 2.3 : exponential dependence in speciation rate with
parameter x (= exponent)
ddmodel == 3 : linear dependence in extinction rate
ddmodel == 4 : exponential dependence in
extinction rate
ddmodel == 4.1 : variant of exponential dependence in extinction rate
with offset at infinity
ddmodel == 4.2 : 1/n dependence in extinction rate with offset at
infinity
The number of species that are in the clade but missing in the phylogeny. One can specify the sum of the missing species in main clade and subclade or a vector c(missnumspec_M,missnumspec_S) with missing species in main clade and subclade respectively.
Conditioning:
cond == 0 : no conditioning
cond == 1 :
conditioning on non-extinction of the phylogeny
Sets whether stem or crown age should be used (1 or 2); stem age only works when cond = 0
Sets the tolerances in the optimization. Consists of:
reltolx
= relative tolerance of parameter values in optimization
reltolf =
relative tolerance of function value in optimization
abstolx = absolute
tolerance of parameter values in optimization
Sets the maximum number of iterations in the optimization
if TRUE the loglik will be set to -Inf if ML does not converge
Method used in optimization of the likelihood. Current default is 'subplex'. Alternative is 'simplex' (default of previous versions)
the number of cycles of opimization. If set at Inf, it will do as many cycles as needed to meet the tolerance set for the target function.
The method used in the ode solver. This can be either 'analytical' for explicit matrix exponentation or any of the solvers in the deSolve package.
Sets whether the correction should be applied (TRUE) or not (FALSE)
Show the parameters and loglikelihood for every call to the loglik function
Rampal S. Etienne & Bart Haegeman
The output is a dataframe containing estimated parameters and maximum loglikelihood. The computed loglikelihood contains the factor q! m!/(q + m)! where q is the number of species in the phylogeny and m is the number of missing species, as explained in the supplementary material to Etienne et al. 2012.
- 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
dd_MS_loglik, dd_ML,
dd_KI_ML, dd_SR_ML,
cat("This will estimate parameters for two sets of branching times brtsM, brtsS\n")
cat("without conditioning.\n")
cat("The tolerance of the optimization is set high so runtime is fast in this example.\n")
cat("In real applications, use the default or more stringent settins for tol.\n")
brtsM = 4:10
brtsS = seq(0.1,3.5,0.7)
tsplit = 5
dd_MS_ML(brtsM = brtsM, brtsS = brtsS, tsplit = tsplit, idparsopt = c(1:3,6),
initparsopt = c(0.885, 2e-14, 10, 4.001), idparsfix = NULL, parsfix = NULL,
idparsnoshift = c(4,5), cond = 0, tol = c(3E-1,3E-1,3E-1))
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