BNPR: Bayesian nonparametric phylodynamic reconstruction. In phylodyn: Statistical Tools for Phylodynamics

Description

Bayesian nonparametric phylodynamic reconstruction.

Usage

 ```1 2 3 4 5 6 7``` ```BNPR(data, lengthout = 100, pref = FALSE, prec_alpha = 0.01, prec_beta = 0.01, beta1_prec = 0.001, fns = NULL, log_fns = TRUE, simplify = TRUE, derivative = FALSE, forward = TRUE) BNPR_PS(data, lengthout = 100, prec_alpha = 0.01, prec_beta = 0.01, beta1_prec = 0.001, fns = NULL, log_fns = TRUE, simplify = TRUE, derivative = FALSE, forward = TRUE) ```

Arguments

 `data` `phylo` object or list containing vectors of coalescent times `coal_times`, sampling times `samp_times`, and number sampled per sampling time `n_sampled`. `lengthout` numeric specifying number of grid points. `pref` logical. Should the preferential sampling model be used? `prec_alpha, prec_beta` numerics specifying gamma prior for precision τ. `beta1_prec` numeric specifying precision for normal prior on β_1. `fns` list containing functions of covariates. `log_fns` logical whether or not to to apply a log-transformation to the output of the functions in `fns`. `simplify` logical whether to fully bucket all Poisson points. `derivative` logical whether to calculate estimates of the log-derivative. `forward` logical whether to use the finite difference approximations of the log-derivative as a forward or backward derivative.

Value

Phylodynamic reconstruction of effective population size at grid points. `result` contains the INLA output, `data` contains the information passed to INLA, `grid` contains the grid end points, `x` contains the grid point centers, `effpop` contains a vector of the posterior median effective population size estimates, `effpop025` and `effpop975` contain the 2.5th and 97.5th posterior percentiles, `summary` contains a data.frame of the estimates, and `derivative` (if `derivative = TRUE`) contains a data.frame summarizing the log-derivative.

Functions

• `BNPR_PS`: Uses preferential sampling model.

Examples

 ```1 2 3 4 5``` ```data("NY_flu") if (requireNamespace("INLA", quietly = TRUE)) { res = BNPR(NY_flu) plot_BNPR(res) } ```

phylodyn documentation built on May 29, 2017, 1:28 p.m.