get.sd: Calculate Savage-Dickey ratio to test for significant rate...

In bstaggmartin/evorates: Evolving Rate Models of Continuous Trait Evolution

Calculate Savage-Dickey ratio to test for significant rate heterogeneity in a fitted evorates model

Description

This function calculates the Savage-Dickey Ratio (i.e., the ratio of posterior to prior probability density) at R_sig2 = 0 given an evorates_fit object. This is a relatively simple test statistic for determining whether the data exhibits evidence for trait evolution rate heterogeneity. The lower the ratio is, the more evidence for heterogeneity, with 1/3 typically being an appropriate threshold for "substantial evidence".

Usage

get.sd(fit)

Arguments

fit	An object of class "evorates_fit". Notably, this test is only applicable to fits with an unconstrained R_sig2 parameter!

Details

You can ensure your fitted evorates model has an unconstrained R_sig2 parameter by checking if fit$call$constrain.Rsig2 is TRUE. Attempting to use this function with a fit with a constrained R_sig2 parameter results in an error.

Unfortunately, we can only approximate the posterior density of R_sig2 about 0. Base R's density() function doesn't seem to do a good job here because R_sig2 posteriors are bounded to the left at 0 and often have fat tails that interact poorly with kernel-based approach of density(). We thus instead use penalized likelihood fitting of splines via the logspline package. This approach seems to better approximate densities of distributions with fat tails where sampling gets quite diffuse, and can handle bounded distributions to boot. The function divides the resulting approximate posterior density by the analytically known prior density given by dcauchy(0, 0, fit$call$Rsig2_prior_sig2).

Value

The Savage-Dickey ratio

See Also

logspline and dlogspline from the logspline package.

Examples

#get whale/dolphin evorates fit
data("cet_fit")

#get Savage-Dickey ratio
sdr <- get.sd(cet_fit) #substantial evidence since ratio is below 1/3!

#simulate some data on same tree evolving under Brownian Motion
sim <- sim.evorates(cet_fit$call$tree,
                    Rsig2 = 0, #no rate heterogeneity
                    R0 = mean(cet_fit %means% "bg_rate"), #set rate to estimated empirical background rate
                    Ysig2 = mean(cet_fit %means% "Y_sig2")) #set tip error to estimated empirical tip error
#fit simulated data with unconstrained R_sig2 (takes a few minutes)
fit <- fit.evorates(cet_fit$call$tree, sim$trait.data, chains = 1)
sdr <- get.sd(fit) #should almost always be over 1/3, though you might get the rare false positive
#ratios for BM simulations often exceed 3/1, indicating substantial evidence AGAINST rate heterogeneity!

#fit simulated data with contrained R_sig2 (takes a little bit)
fit <- fit.evorates(cet_fit$call$tree, sim$trait.data, constrain.Rsig2 = TRUE, chains = 1)
sdr <- get.sd(fit) #returns error

bstaggmartin/evorates documentation built on May 31, 2024, 5:56 a.m.