Nothing
# test_file('~/dev/HTSSIP/tests/testthat/test-qSIP_atom_excess.R')
test_that('qSIP_BD_shift working', {
skip_on_cran()
data(physeq_rep3)
data(physeq_rep3_qPCR)
physeq_rep3_t = OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)
# BD shift (Z) & atom excess (A)
atomX = qSIP_atom_excess(physeq_rep3_t,
control_expr='Treatment=="12C-Con"',
treatment_rep='Replicate')
# output object formatted correctly
expect_is(atomX, 'list')
expect_false(is.null(atomX$A$Z))
expect_false(is.null(atomX$A$A))
expect_equal(atomX$A$OTU %>% length,
atomX$A$OTU %>% unique %>% length)
## W variance among gradient replicates is > 0
min_var = atomX$W %>%
dplyr::group_by(IS_CONTROL, OTU) %>%
dplyr::summarize(W_var = var(W)) %>%
.$W_var %>% min
expect_gt(min_var, 0)
})
test_that('bootstrap iteration is working', {
data(physeq_rep3)
data(physeq_rep3_qPCR)
physeq_rep3_t = OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)
# BD shift (Z) & atom excess (A)
atomX = qSIP_atom_excess(physeq_rep3_t,
control_expr='Treatment=="12C-Con"',
treatment_rep='Replicate')
# bootstrap
atomX_boot = .qSIP_bootstrap(atomX)
expect_is(atomX_boot, 'data.frame')
expect_false(is.null(atomX_boot$Z))
expect_false(is.null(atomX_boot$A))
expect_gt(atomX_boot$bootstrap_id %>% min, 0)
})
test_that('bootstrap in parallel working', {
skip_on_cran()
data(physeq_rep3)
data(physeq_rep3_qPCR)
physeq_rep3_t = OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)
# BD shift (Z) & atom excess (A)
atomX = qSIP_atom_excess(physeq_rep3_t,
control_expr='Treatment=="12C-Con"',
treatment_rep='Replicate')
doParallel::registerDoParallel(2)
# qSIP with bootstrapping
df_atomX_boot = qSIP_bootstrap(atomX, parallel=TRUE, n_boot=20)
# output formatted correctly
expect_is(df_atomX_boot, 'data.frame')
# gte zero CI ranges
CI_diff = df_atomX_boot$A_CI_high - df_atomX_boot$A_CI_low
expect_gt(CI_diff %>% min, 0)
# A in CI(A)
CI_in = df_atomX_boot$A_CI_high >= df_atomX_boot$A &
df_atomX_boot$A_CI_low <= df_atomX_boot$A
expect_true(CI_in %>% all)
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.