# Bayes Factors in support of a shift in diversification rates over a given time interval. This function computes the Bayes Factor in favor of a rate-shift between time t1 and t2 (t1 < t2). The default assumption (suitable to standard HSMRF and GMRF models) is that the prior probability of a shift is 0.5. ```r calculateShiftBayesFactor( rate_trace, time_trace, rate_name, time_name, t1, t2, prior_prob = 0.5, decrease = TRUE, return_2lnBF = TRUE ) ``` ## Arguments - `rate_trace`: (list; no default) The processed Rev output of the rate of interest through time for computation (output of readTrace()). - `time_trace`: (list; no default) The processed Rev output of the change/interval times of the rate of interest through time for computation (output of readTrace()). - `rate_name`: (character; no default) The name of the parameter (e.g. "speciation") for which Bayes Factor is to be calculated. - `time_name`: (character; no default) The name of the interval times (e.g. "interval_times) for the rate change times. - `t1`: (numeric; no default) Support will be assessed for a shift between time t1 and time t2 (t1 < t2). - `t2`: (numeric; no default) Support will be assessed for a shift between time t1 and time t2 (t1 < t2). - `prior_prob`: (numeric; 0.5) The prior probability of a shift over this interval (default of 0.5 applies to standard HSMRF- and GMRF-based models). - `decrease`: (logical; default TRUE) Should support be assessed for a decrease in the parameter (if TRUE) or an increase (if FALSE) between t1 and t2? - `return_2lnBF`: (logical; TRUE) Should the 2ln(BF) be returned (if TRUE) or simply the BF (if FALSE)? ## Returns The Bayes Factor. ## Examples ```r #' # download the example datasets to working directory url_times <- "https://revbayes.github.io/tutorials/intro/data/primates_EBD_speciation_times.log" dest_path_times <- "primates_EBD_speciation_times.log" download.file(url_times, dest_path_times) url_rates <- "https://revbayes.github.io/tutorials/intro/data/primates_EBD_speciation_rates.log" dest_path_rates <- "primates_EBD_speciation_rates.log" download.file(url_rates, dest_path_rates) # to run on your own data, change this to the path to your data file speciation_time_file <- dest_path_times speciation_rate_file <- dest_path_rates speciation_times <- readTrace(speciation_time_file, burnin = 0.25) speciation_rate <- readTrace(speciation_rate_file, burnin = 0.25) calculateShiftBayesFactor(speciation_rate, speciation_times, "speciation", "interval_times", 0.0,40.0, decrease=FALSE) # remove file # WARNING: only run for example dataset! # otherwise you might delete your data! file.remove(dest_path_times, dest_path_rates) ``` ## References Kass and Raftery (1995) Bayes Factors. **JASA**, 90 (430) , 773-795.

calculateShiftBayesFactor function