Man pages for BBMV
Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape

ACE_FPKAncestral Character Estimation
BBMV-packageModels for Continuous Traits Evolving in Macroevolutionary...
charac_timeCharacteristic time measurement
ConvProp_boundsConvolution of the diffusion matrix with the trait density...
DiffMat_backwardsDiffusion matrix building
DiffMat_forwardDiffusion matrix building
find.mle_FPKMaximum-likelihood estimation
find.mle_FPK_multiple_clades_same_V_different_sig2Maximum-likelihood estimation
fit_FPK_multiple_clades_different_V_different_sig2Fit independent models in several clades.
FormatTree_boundsTree formatting.
FPK_sim_traitgramSimulations with traitgram
get.landscape.FPKPlot Plot macroevolutionary landscapes estimated by the FPK...
get.landscape.FPK.MCMCPlot posterior distribution of macroevolutionary landscapes.
lnL_FPKCreation of the likelihood function
lnl_FPK_multiclades_same_V_different_sig2Likelihood functions for multiple clades
LogLik_boundsLikelihood of the FPK model
log_prior_5pars_root_boundsPrior function.
log_prior_nclades_plus_3_parsPrior function.
MH_MCMC_FPKMCMC estimation
MH_MCMC_FPK_multicladesMCMC estimation on multiple clades
prep_mat_expMatrix exponential.
proposal_5pars_root_boundsParameter update for the MCMC function
proposal_nclades_plus_3_parsParameter update for the multiclade MCMC function
reformat_multiclade_resultsFormat the output of a multiclade fit
Sim_FPKSimulation of the BBM+V process.
trans_from_fixedLinear transformations
Uncertainty_FPKParameter uncertainty
VectorPos_boundsDiscretization of a continuous trait value into a probability...
BBMV documentation built on Nov. 17, 2017, 7:02 a.m.