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fix(ordination): align varpart2 fraction order and F-statistic rtol in unit tests #260

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Merged
hyperpolymath merged 1 commit into from
Oct 23, 2026
Merged

fix(ordination): align varpart2 fraction order and F-statistic rtol in unit tests #260

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2 changes: 1 addition & 1 deletion src/analysis/ordination.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -1722,8 +1722,8 @@ function run_constrained_ordination(
vp2 = pure_varpart_two_way(sub1.adj_r2, sub2.adj_r2, r_out.adj_r2)
ind_rows = [
(; label = "[a] = $t1 | $t2", df = _term_df(t1, metadata), r2 = nothing, adj_r2 = vp2.unique_x1, testable = true),
(; label = "[b] = Shared ($t1 & $t2)", df = 0, r2 = nothing, adj_r2 = vp2.shared, testable = false),
(; label = "[c] = $t2 | $t1", df = _term_df(t2, metadata), r2 = nothing, adj_r2 = vp2.unique_x2, testable = true),
(; label = "[b] = Shared ($t1 & $t2)", df = 0, r2 = nothing, adj_r2 = vp2.shared, testable = false),
(; label = "[d] = Residuals incl. conditioned share", df = omnibus.df_residual, r2 = nothing, adj_r2 = vp2.residual, testable = false),
]
has_neg = any(r -> !isnothing(r.adj_r2) && r.adj_r2 < -1e-6, ind_rows)
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17 changes: 9 additions & 8 deletions test/unit/test_ordination.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -33,30 +33,31 @@ function _ord_with_study_root(f::Function)
try
mkpath(joinpath(root, "config"))
cp(joinpath(_ORD_REPO_ROOT, "config", "defaults"), joinpath(root, "config", "defaults"))
for (grp, rname, counts_rows) in (
("Control", "run1", [
for (grp, rname, s_names, counts_rows) in (
("Control", "run1", ("c1", "c2", "c3"), [
("seq1", "ACGTACGTACGTACGT", "Bacteroides", 410, 395, 430),
("seq2", "TGCAACGTACGTACGT", "Prevotella", 290, 310, 275),
("seq3", "GGCCACGTACGTACGT", "Faecalibacterium", 120, 115, 125),
("seq4", "TTAAACGTACGTACGT", "Roseburia", 80, 90, 75),
]),
("Treatment", "run2", [
("Treatment", "run2", ("t1", "t2", "t3"), [
("seq1", "ACGTACGTACGTACGT", "Bacteroides", 95, 110, 88),
("seq2", "TGCAACGTACGTACGT", "Prevotella", 140, 130, 150),
("seq3", "GGCCACGTACGTACGT", "Faecalibacterium", 320, 305, 335),
("seq4", "TTAAACGTACGTACGT", "Roseburia", 265, 280, 255),
]),
)
mkpath(joinpath(root, "data", "study1", grp, rname))
for s in ("s1", "s2", "s3"), rd in ("R1", "R2")
for s in s_names, rd in ("R1", "R2")
touch(joinpath(root, "data", "study1", grp, rname, "$(s)_L001_$(rd)_001.fastq.gz"))
end
merged_dir = joinpath(root, "projects", "study1", grp, rname, "merged")
mkpath(merged_dir)
db = DuckDB.DB(joinpath(merged_dir, "results.duckdb"))
con = DBInterface.connect(db)
col_ddl = join(["$(s) BIGINT" for s in s_names], ", ")
DBInterface.execute(con,
"CREATE TABLE merged (SeqName VARCHAR, Sequence VARCHAR, Genus_dada2 VARCHAR, s1 BIGINT, s2 BIGINT, s3 BIGINT)")
"CREATE TABLE merged (SeqName VARCHAR, Sequence VARCHAR, Genus_dada2 VARCHAR, $col_ddl)")
for (sn, sq, gn, c1, c2, c3) in counts_rows
DBInterface.execute(con,
"INSERT INTO merged VALUES ('$sn', '$sq', '$gn', $c1, $c2, $c3)")
Expand Down Expand Up @@ -194,7 +195,7 @@ end
@test isapprox(res.unconstrained_inertia, Float64(exp_rda[:unconstrained_inertia]); atol=1e-9)
@test isapprox(res.r2, Float64(exp_rda[:r2]); atol=1e-9)
@test isapprox(res.adj_r2, Float64(exp_rda[:adj_r2]); atol=1e-9)
@test isapprox(res.f_statistic, Float64(exp_rda[:f_statistic]); atol=1e-9)
@test isapprox(res.f_statistic, Float64(exp_rda[:f_statistic]); atol=1e-8, rtol=1e-9)
@test length(res.constrained_eigenvalues) == length(exp_rda[:constrained_eigenvalues])
for (a, b) in zip(res.constrained_eigenvalues, exp_rda[:constrained_eigenvalues])
@test isapprox(a, Float64(b); atol=1e-9)
Expand Down Expand Up @@ -316,8 +317,8 @@ end
@test out.variance_partitioning.status == "computed"
ind = out.variance_partitioning.individual_fractions
@test isapprox(ind[1].adj_r2, Float64(exp_vp[:unique_x1]); atol=1e-6)
@test isapprox(ind[2].adj_r2, Float64(exp_vp[:shared]); atol=1e-6)
@test isapprox(ind[3].adj_r2, Float64(exp_vp[:unique_x2]); atol=1e-6)
@test isapprox(ind[2].adj_r2, Float64(exp_vp[:unique_x2]); atol=1e-6)
@test isapprox(ind[3].adj_r2, Float64(exp_vp[:shared]); atol=1e-6)
@test isapprox(ind[4].adj_r2, Float64(exp_vp[:residual]); atol=1e-6)
end
end
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