inst/tests/testthat/test-8pfnullsim.R

In reptalex/phylofactor: phylofactor

context('checking pf.nullsim')


set.seed(2)
data("FTmicrobiome",package = 'phylofactor')
tree <- FTmicrobiome$tree
Taxonomy <- FTmicrobiome$taxonomy
tree <- ape::drop.tip(tree,setdiff(tree$tip.label,sample(tree$tip.label,20)))

Taxonomy <- Taxonomy[match(tree$tip.label,Taxonomy[,1]),]
X <- as.factor(c(rep(0,5),rep(1,5)))

### Simulate data ###
Factornodes <- c(37,27)
sigClades <- list(c(16,17),c(6,7,8,9,10,11,12,13,14,15))

Data <- matrix(rlnorm(20*10,meanlog = 8,sdlog = .5),nrow=20)
rownames(Data) <- tree$tip.label
colnames(Data) <- X
Data[sigClades[[1]],X==0] <- Data[sigClades[[1]],X==0]*9
Data[sigClades[[2]],X==1] <- Data[sigClades[[2]],X==1]*14
Bins <- bins(G=sigClades,set=1:20)[c(3,2,1)]

invisible(capture.output(PF <- PhyloFactor(Data,tree,X,nfactors=2)))

test_that('basic log-normal pf.nullsim works',
          expect_error(invisible(capture.output(phylofactor:::pf.nullsim(PF,reps=1))),NA))

test_that('setting seed in pf.nullsim works',
          expect_error(invisible(capture.output(phylofactor:::pf.nullsim(PF,reps=2,seed=1))),NA))

test_that('pf.nullsim method="Shuffle" works',
          expect_error(invisible(capture.output(phylofactor:::pf.nullsim(PF,reps=1,seed=1,nullsimFcn='shuffle'))),NA))

Z <- rbinom(20,1,.5)
pf <- twoSampleFactor(Z,tree,2)

test_that('pf.nullsim works for twoSample phylofactor objects',
          expect_error(invisible(capture.output(phylofactor:::pf.nullsim(pf,reps=1))),NA))