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| BBMV-package | Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape |
| ACE_FPK | Ancestral Character Estimation |
| add.ML.landscape.FPK | Plot macroevolutionary landscapes estimated by the FPK or BBM+V models |
| BBMV | Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape |
| charac_time | Characteristic time measurement |
| ConvProp_bounds | Convolution of the diffusion matrix with the trait density vector. |
| DiffMat_backwards | Diffusion matrix building |
| DiffMat_forward | Diffusion matrix building |
| find.mle_FPK | Maximum-likelihood estimation |
| find.mle_FPK_multiple_clades_same_V_different_sig2 | Maximum-likelihood estimation |
| find.mle_FPK_multiple_clades_same_V_same_sig2 | Maximum-likelihood estimation |
| fit_BBMV_multiple_clades_different_V_different_sig2 | Fit independent models in several clades. |
| fit_FPK_multiple_clades_different_V_different_sig2 | Fit independent models in several clades. |
| FormatTree_bounds | Tree formatting. |
| FPK_sim_traitgram | Simulations with traitgram |
| get.landscape.FPK | Plot macroevolutionary landscapes estimated by the FPK or BBM+V models |
| get.landscape.FPK.MCMC | Plot posterior distribution of macroevolutionary landscapes. |
| lnL_BBMV | Creation of the likelihood function |
| lnl_BBMV_multiclades_same_V_different_sig2 | Likelihood functions for multiple clades |
| lnl_BBMV_multiclades_same_V_same_sig2 | Likelihood functions for multiple clades |
| lnL_FPK | Creation of the likelihood function |
| lnl_FPK_multiclades_same_V_different_sig2 | Likelihood functions for multiple clades |
| lnl_FPK_multiclades_same_V_same_sig2 | Likelihood functions for multiple clades |
| LogLik_bounds | Likelihood of the FPK model |
| LogLik_bounds_est_root | Likelihood of the FPK model |
| log_prior_5pars_root_bounds | Prior function. |
| log_prior_nclades_plus_3_pars | Prior function. |
| MH_MCMC_FPK | MCMC estimation |
| MH_MCMC_FPK_multiclades | MCMC estimation on multiple clades |
| posterior_vs_prior | Posterior vs. prior comparison for the FPK model. |
| prep_mat_exp | Matrix exponential. |
| proposal_5pars_root_bounds | Parameter update for the MCMC function |
| proposal_nclades_plus_3_pars | Parameter update for the multiclade MCMC function |
| reformat_multiclade_results | Format the output of a multiclade fit |
| Sim_FPK | Simulation of the BBM+V process. |
| trans_from_fixed | Linear transformations |
| trans_to_fixed | Linear transformations |
| Uncertainty_FPK | Parameter uncertainty |
| VectorPos_bounds | Discretization of a continuous trait value into a probability vector. |