pbd_LR {PBD} | R Documentation |
Bootstrap likelihood ratio test of protracted birth-death model of diversification
Description
This function computes the maximum likelihood and the associated estimates of the parameters of a protracted birth-death model of diversification for a given set of phylogenetic branching times. It then performs a bootstrap likelihood ratio test of the protracted birth-death (PBD) model against the constant-rates (CR) birth-death model. Finally, it computes the power of this test.
Usage
pbd_LR(
brts,
initparsoptPBD,
initparsoptCR,
missnumspec,
outputfilename = NULL,
seed = 42,
endmc = 1000,
alpha = 0.05,
plotit = TRUE,
parsfunc = c(function(t,pars) {pars[1]},
function(t,pars) {pars[2]},
function(t,pars) {pars[3]},
function(t,pars) {pars[4]}),
cond = 1,
btorph = 1,
soc = 2,
methode = 'lsoda',
n_low = 0,
n_up = 0,
tol = c(1E-6,1E-6,1E-6),
maxiter = 2000,
optimmethod = 'subplex',
verbose = FALSE
)
Arguments
brts |
A set of branching times of a phylogeny, all positive |
initparsoptPBD |
The initial values of the parameters that must be optimized for the protracted birth-death (PBD) model: b, mu and lambda |
initparsoptCR |
The initial values of the parameters that must be optimized for the constant-rates (CR) model: b and mu |
missnumspec |
The number of species that are in the clade but missing in the phylogeny |
outputfilename |
The name (and location) of the file where the output will be saved. Default is no save. |
seed |
The seed for the pseudo random number generator for simulating the bootstrap data |
endmc |
The number of bootstraps |
alpha |
The significance level of the test |
plotit |
Boolean to plot results or not |
parsfunc |
Specifies functions how the rates depend on time, default functions are constant functions |
cond |
Conditioning: |
btorph |
Sets whether the likelihood is for the branching times (0) or the phylogeny (1) |
soc |
Sets whether stem or crown age should be used (1 or 2) |
methode |
The numerical method used to solve the master equation, such as 'lsoda' or 'ode45'. |
n_low |
Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default) |
n_up |
Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default) |
tol |
Sets the tolerances in the optimization. Consists of: |
maxiter |
Sets the maximum number of iterations in the optimization |
optimmethod |
Method used in optimization of the likelihood. Current default is 'subplex'. Alternative is 'simplex'. |
verbose |
if TRUE, explanatory text will be shown |
Details
The output is a list with 3 elements:
Value
brtsCR |
a list of sets of branching times generated under the constant-rates model using the ML parameters under the CR model |
brtsDD |
a list of sets of branching times generated under the protracted birth-death model using the ML parameters under the PBD model |
out |
a dataframe with the parameter estimates and maximum likelihoods for protracted birth-death and constant-rates models
|
pvalue |
p-value of the test |
LRalpha |
Likelihood ratio at the signifiance level alpha |
poweroftest |
power of the test for significance level alpha |
Author(s)
Rampal S. Etienne
References
- Etienne, R.S. et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, doi: 10.1111/2041-210X.12565