use expect_length

KlausVigo · Dec 2, 2024 · 714b369 · 714b369
1 parent 1450571
commit 714b369
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Showing 4 changed files with 10 additions and 10 deletions.
diff --git a/inst/tinytest/test_add_edge_length.R b/inst/tinytest/test_add_edge_length.R
@@ -10,8 +10,8 @@ tree_unrooted <- allCompat(trees_unrooted, rooted=FALSE)
 tree_unrooted_el <- add_edge_length(tree_unrooted, trees_unrooted, rooted=FALSE)
 
 expect_null(tree_ultra$edge.length)
-expect_equal(length(tree_ultra_el$edge.length), nrow(tree_ultra_el$edge))
+expect_length(tree_ultra_el$edge.length, nrow(tree_ultra_el$edge))
 expect_true(is.ultrametric(tree_ultra_el))
 expect_null(tree_unrooted$edge.length)
-expect_equal(length(tree_unrooted_el$edge.length), nrow(tree_unrooted_el$edge))
+expect_length(tree_unrooted_el$edge.length, nrow(tree_unrooted_el$edge))
 expect_false(is.ultrametric(tree_unrooted_el))
diff --git a/inst/tinytest/test_pmlCluster.R b/inst/tinytest/test_pmlCluster.R
@@ -17,7 +17,7 @@ fit <- optim.pml(fit, control=pml.control(trace=0))
 sp <- pmlCluster( ~ edge + nni, fit, weight, p=1:3,
                      control=pml.control(epsilon=1e-08, maxit=10, trace=0))
 #    expect_equal( sp$Partition, c(1,1,1,2,2))
-expect_equal( all(sp$Partition ==  c(1,1,1,2,2)) ||
-                      all(sp$Partition ==  c(2,2,2,1,1)) , TRUE)
+expect_true(all(sp$Partition ==  c(1,1,1,2,2)) ||
+                      all(sp$Partition ==  c(2,2,2,1,1)))
 
 
diff --git a/inst/tinytest/test_splits.R b/inst/tinytest/test_splits.R
@@ -20,9 +20,9 @@ expect_true(inherits(Mat, "Matrix"))
 expect_equal(spl2tree , tree)
 # test generics
 c_spl <- c(tree2spl, tree2spl, tree2spl)
-expect_equal(length(c_spl) , 3L*length(tree2spl))
-expect_equal(length(unique(c_spl)) , length(tree2spl))
-expect_equal(length(distinct.splits(c_spl)) , length(tree2spl))
+expect_length(c_spl, 3L*length(tree2spl))
+expect_length(unique(c_spl), length(tree2spl))
+expect_length(distinct.splits(c_spl), length(tree2spl))
 spl <- allCircularSplits(6)
 spl <- ONEwise(spl)
 write.nexus.splits(spl, "tmp.nex")
@@ -59,7 +59,7 @@ expect_true(inherits(cnet, "networx"))
 net1$edge.length <- cnet$edge.length <- cnet$edge.labels <- NULL
 attr(cnet, "order") <- NULL
 expect_equal(cnet, net1)
-expect_equal(nrow(cnet$edge), length(as.splits(cnet)))
+expect_length(as.splits(cnet), nrow(cnet$edge))
 
 
 

diff --git a/inst/tinytest/test_treeManipulation.R b/inst/tinytest/test_treeManipulation.R
@@ -13,7 +13,7 @@ node_108 <- mrca.phylo(tree, node=desc_108)
 expect_equal(mrca.phylo(tree, node=desc_108), 108L)
 expect_equal(mrca(tree), mrca.phylo(tree))
 kids_108 <- Descendants(tree, 108, "children")
-expect_equal(length(Descendants(tree, 101L, "all")), 197L)
+expect_length(Descendants(tree, 101L, "all"), 197L)
 expect_equal(lengths(Descendants(tree2, 101L:199, "all")),
                  2 * lengths(prop.part(tree2)) - 2L)
 expect_equal(Ancestors(tree, kids_108, "parent"),
@@ -63,6 +63,6 @@ bs <- bootstrap.phyDat(Laurasiatherian,
                        FUN = function(x)NJ(dist.hamming(x)), bs=50)
 tree <- NJ(dist.hamming(Laurasiatherian))
 treeBS <- plotBS(tree, bs, type="none")
-expect_equal(length(treeBS$node.label), treeBS$Nnode)
+expect_length(treeBS$node.label, treeBS$Nnode)
 expect_true(all(treeBS$node.label >=0) )
 expect_true(all(treeBS$node.label <= 100) )