pglmm-profile-LRT: Testing statistical significance of random effect

In daijiang/phyr: Model Based Phylogenetic Analysis

Testing statistical significance of random effect

Description

pglmm_profile_LRT tests statistical significance of the phylogenetic random effect using profile likelihoods when bayes = F. The resulting p-values are conditional on the fixed estimates of the other parameters, in contrast to a standard likelihood ratio test.

Usage

pglmm_profile_LRT(x, re.number = 0, cpp = TRUE)

communityPGLMM.profile.LRT(x, re.number = 0, cpp = TRUE)

Arguments

x	A fitted model with class communityPGLMM with bayes = FALSE.
re.number	Which random term to test? Can be a vector with length >1.
cpp	Whether to use C++ function for optim. Default is TRUE. Ignored if bayes = TRUE.

Value

A list of likelihood, df, and p-value.

daijiang/phyr documentation built on Feb. 25, 2024, 3:01 a.m.