context('find topics')
test_that('find_topics returns correct results for different params',{
skip_on_cran()
DAT <- readRDS(system.file('testdata','otudata.rds',package='themetagenomics'))
set.seed(423)
x <- prepare_data(otu_table=DAT$OTU,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~DIAGNOSIS,
refs='Not IBD',
cn_normalize=TRUE,
drop=TRUE)
set.seed(1)
t1 <- find_topics(x,K=5,init_type='Spectral')
t2 <- find_topics(x,K=5,init_type='LDA')
t3 <- find_topics(x,K=5,init_type='Random')
expect_identical(names(t1),names(t2))
expect_identical(names(t1),names(t3))
expect_true(cor(sort(colSums(t1$fit$theta)),
sort(colSums(t2$fit$theta))) > .5)
expect_true(cor(sort(colSums(t1$fit$theta)),
sort(colSums(t3$fit$theta))) > .5)
x <- prepare_data(otu_table=DAT$OTU,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
cn_normalize=TRUE,
drop=TRUE)
set.seed(1)
t1 <- find_topics(x,K=5,init_type='Spectral')
t2 <- find_topics(x,K=5,init_type='LDA')
t3 <- find_topics(x,K=5,init_type='Random')
expect_identical(names(t1),names(t2))
expect_identical(names(t1),names(t3))
expect_true(cor(sort(colSums(t1$fit$theta)),
sort(colSums(t2$fit$theta))) > .5)
expect_true(cor(sort(colSums(t1$fit$theta)),
sort(colSums(t3$fit$theta))) > .5)
})
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