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fixing indentation
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tests/testthat/test--calculations.R

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,7 @@ test_that("Observation proportions", {
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result <- calc_obs_props(x, "tax_data", cols = 4:6)
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expect_equal(col_subset, colnames(result)[-1])
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result <- calc_obs_props(x, "tax_data",
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cols = startsWith(colnames(x$data$tax_data), "70001"))
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expect_equal(colnames(x$data$tax_data)[startsWith(colnames(x$data$tax_data), "70001")],
@@ -58,12 +58,12 @@ test_that("Observation proportions", {
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# Inlcuding specific columns in output
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result <- calc_obs_props(x, "tax_data", cols = col_subset,
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other_cols = 2:3)
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other_cols = 2:3)
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expect_true(all(c("otu_id", "lineage") %in% colnames(result)))
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# Rename output columns
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result <- calc_obs_props(x, "tax_data", cols = col_subset,
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out_names = c("a", "b", "c"))
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out_names = c("a", "b", "c"))
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expect_equal(colnames(result), c("taxon_id", "a", "b", "c"))
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})
@@ -77,7 +77,7 @@ test_that("Summing counts per taxon", {
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# Calculate the taxon abundance for a subset of columns
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expect_equal(calc_taxon_abund(x, "tax_data", cols = 4:5),
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calc_taxon_abund(x, "tax_data", cols = c("700035949", "700097855")))
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# Calculate the taxon abundance for groups of columns (e.g. treatments)
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# Note that we do not need to use the "cols" option for this since all
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# numeric columns are samples in this dataset. If there were numeric columns
@@ -108,8 +108,8 @@ test_that("Comparing groups of samples", {
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# Calculate difference between groups
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expect_warning(x$data$diff_table <- compare_treatments(x, dataset = "tax_table",
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cols = hmp_samples$sample_id,
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groups = hmp_samples$body_site))
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cols = hmp_samples$sample_id,
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groups = hmp_samples$body_site))
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expect_equal(nrow(x$data$diff_table),
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ncol(combn(length(unique(hmp_samples$body_site)), 2)) * nrow(x$data$tax_table))
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