tests/testthat/test-SummarizeBM.R

In mvSLOUCH: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

## This file is part of mvSLOUCH

## This software comes AS IS in the hope that it will be useful WITHOUT ANY WARRANTY, 
## NOT even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
## Please understand that there may still be bugs and errors. Use it at your own risk. 
## We take no responsibility for any errors or omissions in this package or for any misfortune 
## that may befall you or others as a result of its use. Please send comments and report 
## bugs to Krzysztof Bartoszek at krzbar@protonmail.ch .

library(testthat)
context("mvSLOUCH: SummarizeBM")

library(mvSLOUCH)
library(PCMBase)

RNGversion(min(as.character(getRversion()),"3.6.1"))
set.seed(12345, kind = "Mersenne-Twister", normal.kind = "Inversion")
### We will first simulate a small phylogenetic tree using functions from ape.
### For simulating the tree one could also use alternative functions, e.g. sim.bd.taxa 
### from the TreeSim package
phyltree<-ape::rtree(5)

## The line below is not necessary but advisable for speed
phyltree<-phyltree_paths(phyltree)

### Define Brownian motion parameters to be able to simulate data 
### under the Brownian motion model.
BMparameters<-list(vX0=matrix(0,nrow=3,ncol=1),Sxx=rbind(c(1,0,0),c(0.2,1,0),c(0.3,0.25,1)))

### Now simulate the data.
BMdata<-simulBMProcPhylTree(phyltree,X0=BMparameters$vX0,Sigma=BMparameters$Sxx)
BMdata<-BMdata[phyltree$tip.label,,drop=FALSE]

### Summarize them.
BM.summary<-SummarizeBM(phyltree,BMdata,BMparameters,t=c(1),dof=9)

pcmbase_BM_model_box<-PCMBase::PCM(model="BM",k=3)
pcmbase_BM_model_box$X0[] <- BMparameters$vX0[,1]
pcmbase_BM_model_box$Sigma_x[,, 1] <-  BMparameters$Sxx
testthat::expect_equivalent(PCMBase::PCMLik(t(BMdata), phyltree, pcmbase_BM_model_box, log = TRUE),BM.summary$t_1$LogLik)
## should be -18.30802582542433754043