Man pages for josteist/Compadre
Analysis of Macroevolutionary Rates of Speciation, Extinction and Sampling using Capture-Mark-Recapture techniques
| Alroy_3timers | Function to calculate Alroy's three-timer rates of... |
| checkchains | A quick function to plot chains and calc ESS's for drivers... |
| colbottom | Simple function to add colorbars at the lower end of a plot.... |
| contMCMC_CMR | Function to continue sampling a fit, without adaptation. |
| doBML | Function to approximate Bayesian model probability using... |
| ESS | Function to extract effective sample sizes from a MCMC-CMR... |
| Foote_percap | Function to calculate Foote's rates of macroevolutionary... |
| getInit | A function to generate sensible initial values for MCMC... |
| HPDI | Function to extract highest posterior density intervals. HPDI... |
| make_BayesCMR | Function to construct one clade CMR-model. |
| make_BayesCMR_2clades | Function to construct two clade CMR-model. |
| make_unvd | Generate datavectors used in Pradel likelihood calculations. |
| MCMC_CMR | An adaptive Markov chain Monte Carlo sampler for estimating... |
| plot.cmr_simulation | Plots simulation output in Compadre. |
| plotDrivers | Function to make simple plot of estimated drivers (and... |
| plotfun_internal | internal plottingfunction export |
| plotRates | Extract and plot macroevolutionary rates from a CMR model... |
| pradel_unvd | Internal function used to calculate the likelihood of the... |
| pradel_unvd_gam | Internal function used to calculate the likelihood of the... |
| prob2rate | Function transform a probability into a rate for an interval |
| prob_ext | A function to calculate the probability of extinction for a... |
| rate2prob | A simple function to translate a rate into a probability. |
| remake_fosrec | Function to resample a fossil record from a simulated clade. |
| rescale_time | Functino to rescale between time-scales. |
| sampFosRec | Function to sample fossil from a lineage. |
| sim_BD | Function to simulate a birth-death-fossilization process. |
