Nothing
context('estimate topic effects')
test_that('est.topics returns correct results for different formulae',{
skip_on_cran()
skip_on_travis()
DAT <- readRDS(system.file('testdata','otudata.rds',package='themetagenomics'))
set.seed(23)
x <- prepare_data(otu_table=DAT$OTU,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~DIAGNOSIS,
refs='Not IBD',
cn_normalize=TRUE,
drop=TRUE)
y <- find_topics(x,K=5,init_type='Spectral',tol=1e-03)
z1 <- est(y)
expect_identical(colnames(est(y)[[1]][[1]][[1]]),c('estimate','10%','90%'))
expect_identical(colnames(est(y,ui_level=.95)[[1]][[1]][[1]]),c('estimate','2.5%','97.5%'))
expect_identical(y$modelframe,z1$modelframe)
expect_error(est(y,metadata=DAT$META[1:7,],formula=~PCDAI))
x <- prepare_data(otu_table=DAT$OTU,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~PCDAI,
refs='Not IBD',
cn_normalize=TRUE,
drop=TRUE)
y <- find_topics(x,K=5,init_type='Spectral',tol=1e-03)
expect_identical(y$modelframe,est(y)$modelframe)
expect_error(est(y,metadata=DAT$META[1:7,],formula=~DIAGNOSIS))
expect_warning(est(y,metadata=DAT$META,formula=~DIAGNOSIS))
z2 <- est(y,metadata=DAT$META,formula=~DIAGNOSIS,refs='Not IBD')
expect_identical(z1$modelframe[rownames(DAT$META)[!is.na(DAT$META$PCDAI)],],
z2$modelframe[rownames(DAT$META)[!is.na(DAT$META$PCDAI)],])
DAT <- readRDS(system.file('testdata','seqdata.rds',package='themetagenomics'))
set.seed(423)
x <- prepare_data(otu_table=DAT$ABUND,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~Site + Day,
refs='UBERON:saliva',
cn_normalize=FALSE,
drop=TRUE)
y <- find_topics(x,K=5,init_type='Spectral')
z1 <- est(y)
expect_identical(colnames(est(y)[[1]][[1]][[1]]),c('estimate','10%','90%'))
expect_identical(colnames(est(y,ui_level=.95)[[1]][[1]][[1]]),c('estimate','2.5%','97.5%'))
expect_identical(y$modelframe,z1$modelframe)
x <- prepare_data(otu_table=DAT$ABUND,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~Day + Site,
refs='UBERON:saliva',
cn_normalize=FALSE,
drop=TRUE)
y <- find_topics(x,K=5,init_type='Spectral',tol=1e-03)
z2 <- est(y)
expect_true(mean(abs(z1$topic_effects$`SiteUBERON:feces`$est[,1]-z2$topic_effects$`SiteUBERON:feces`$est[,1])) < .1)
expect_true(mean(abs(z1$topic_effects$Day$est[,1]-z2$topic_effects$Day$est[,1])) < .1)
set.seed(23)
x <- prepare_data(otu_table=DAT$ABUND,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~Site + s(Day),
refs='UBERON:saliva',
cn_normalize=FALSE,
drop=TRUE)
y <- find_topics(x,K=5,init_type='Spectral',tol=1e-03)
z1 <- est(y)
expect_identical(colnames(est(y)[[1]][[1]][[1]]),c('estimate','10%','90%'))
expect_identical(colnames(est(y,ui_level=.95)[[1]][[1]][[1]]),c('estimate','2.5%','97.5%'))
expect_identical(y$modelframe,z1$modelframe)
x <- prepare_data(otu_table=DAT$ABUND,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~s(Day) + Site,
refs='UBERON:saliva',
cn_normalize=FALSE,
drop=TRUE)
y <- find_topics(x,K=5,init_type='Spectral',tol=1e-03)
z2 <- est(y)
expect_true(mean(abs(z1$topic_effects$`SiteUBERON:feces`$est[,1]-z2$topic_effects$`SiteUBERON:feces`$est[,1])) < .1)
expect_true(mean(abs(z1$topic_effects$Day$est[,1]-z2$topic_effects$Day$est[,1])) < .1)
set.seed(23)
x <- prepare_data(otu_table=DAT$ABUND,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~Multi + s(Day),
refs='1',
cn_normalize=FALSE,
drop=TRUE)
y <- find_topics(x,K=5,init_type='Spectral',tol=1e-03)
z1 <- est(y)
expect_identical(colnames(est(y)[[1]][[1]][[1]]),c('estimate','10%','90%'))
expect_identical(colnames(est(y,ui_level=.95)[[1]][[1]][[1]]),c('estimate','2.5%','97.5%'))
expect_identical(y$modelframe,z1$modelframe)
x <- prepare_data(otu_table=DAT$ABUND,
rows_are_taxa=FALSE,
tax_table=DAT$TAX,
metadata=DAT$META,
formula=~s(Day) + Multi,
refs='1',
cn_normalize=FALSE,
drop=TRUE)
y <- find_topics(x,K=5,init_type='Spectral',tol=1e-03)
z2 <- est(y)
expect_true(mean(abs(z1$topic_effects$Multi2$est[,1]-z2$topic_effects$Multi2$est[,1])) < .1)
expect_true(mean(abs(z1$topic_effects$Multi3$est[,1]-z2$topic_effects$Multi3$est[,1])) < .1)
expect_true(mean(abs(z1$topic_effects$Day$est[,1]-z2$topic_effects$Day$est[,1])) < .1)
})
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