context("function effects")
Sys.setenv("R_TESTS" = "")
test_that('picrust results gives similar results for ml and hmc',{
skip_on_cran()
DAT <- readRDS(system.file('testdata','otufuncdata.rds',package='themetagenomics'))
overlap <- c('mu','phi','b_pw_sigma','b_topic_sigma','b_pwxtopic_sigma','b_pw','b_topic','b_pwxtopic','yhat')
ml <- suppressMessages(suppressWarnings(est(DAT,level=2,iters=5,method='ml')))
hmc <- suppressMessages(suppressWarnings(est(DAT,level=2,iters=50,chains=1,
return_summary=TRUE,
prior=c('t','t','normal'),
t_df=c(7,7),seed=123)))
hmc_summary <- suppressMessages(suppressWarnings(extract(hmc)))
resume_orig <- suppressMessages(suppressWarnings(resume(hmc,init_type='orig',iters=50,chains=1,return_summary=TRUE)))
resume_last <- suppressMessages(suppressWarnings(resume(hmc,init_type='last',iters=50,chains=1,return_summary=TRUE)))
expect_identical(unlist(lapply(hmc$model$summary[overlap],rownames)),
unlist(lapply(ml$model$summary[overlap],rownames)))
expect_identical(unlist(lapply(hmc$model$summary[overlap],rownames)),
unlist(lapply(hmc_summary$summary[overlap],rownames)))
expect_identical(unlist(lapply(hmc$model$summary[overlap],rownames)),
unlist(lapply(resume_orig$model$summary[overlap],rownames)))
expect_identical(unlist(lapply(hmc$model$summary[overlap],rownames)),
unlist(lapply(resume_last$model$summary[overlap],rownames)))
})
test_that('format_gene_table works for level 3',{
DAT <- readRDS(system.file('testdata','otufuncdata.rds',package='themetagenomics'))
gene_table2 <- format_gene_table(DAT,level=2)
gene_table3 <- format_gene_table(DAT,level=3)
expect_is(gene_table2,'data.frame')
expect_true(max(gene_table2$count) > 0)
expect_true(min(gene_table2$count) == 0)
expect_is(gene_table3,'data.frame')
expect_true(max(gene_table3$count) > 0)
expect_true(min(gene_table3$count) == 0)
expect_true(length(unique(gene_table3$pw)) > length(unique(gene_table2$pw)))
DAT <- readRDS(system.file('testdata','seqfuncdata.rds',package='themetagenomics'))
gene_table2 <- format_gene_table(DAT,level=2)
gene_table3 <- format_gene_table(DAT,level=3)
expect_is(gene_table2,'data.frame')
expect_true(max(gene_table2$count) > 0)
expect_true(min(gene_table2$count) == 0)
expect_is(gene_table3,'data.frame')
expect_true(max(gene_table3$count) > 0)
expect_true(min(gene_table3$count) == 0)
expect_true(length(unique(gene_table3$pw)) > length(unique(gene_table2$pw)))
})
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