more tests

KlausVigo · Oct 7, 2017 · fc2626c · fc2626c
1 parent 5e71cd0
commit fc2626c
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Showing 2 changed files with 13 additions and 8 deletions.
diff --git a/tests/testthat/test_phyDat.R b/tests/testthat/test_phyDat.R
@@ -13,17 +13,20 @@ phy_vec_dna <- phy_matrix[,1]
 phy_vec_user <- sample(c("0","1"), 26, replace=TRUE)
 names(phy_vec_user) <- letters
 phy_dnabin <- as.DNAbin(Laurasiatherian)
+phy_aabin <- as.AAbin(chloroplast)
 phy_align <- phyDat2alignment(Laurasiatherian)
 
 test_that("conversion work as expected", {
 ##    skip_on_cran()
     expect_is(phy_matrix, "matrix")
     expect_is(phy_df, "data.frame")
     expect_is(phy_dnabin, "DNAbin")
+    expect_is(phy_aabin, "AAbin")
     expect_is(phy_align, "alignment")
     expect_is(as.phyDat(phy_matrix), "phyDat")
     expect_is(as.phyDat(phy_df), "phyDat")
     expect_is(as.phyDat(phy_dnabin), "phyDat")
+    expect_equal(as.phyDat(phy_aabin), chloroplast)
     expect_is(phyDat(phy_vec_dna), "phyDat")
     expect_is(phyDat(phy_vec_user, type="USER", levels = c("0","1")), "phyDat")
     expect_is(as.phyDat(phy_dnabin), "phyDat")
@@ -33,14 +36,15 @@ test_that("conversion work as expected", {
 })
 
 
-#test_that("conversion with Biostrings work as expected", {
-#    skip_on_cran()
-#    library(Biostrings)
-#    expect_is(MA_AA <- as.MultipleAlignment(chloroplast), "AAMultipleAlignment")
-#    expect_equal(as.phyDat(MA_AA), chloroplast)
-#    expect_is(MA_DNA <- as.MultipleAlignment(Laurasiatherian), "DNAMultipleAlignment")
-#    expect_equal(as.phyDat(MA_DNA), Laurasiatherian)
-#})
+test_that("conversion with Biostrings work as expected", {
+    skip_on_cran()
+    if(require(Biostrings)){
+        expect_is(MA_AA <- as.MultipleAlignment(chloroplast), "AAMultipleAlignment")
+        expect_equal(as.phyDat(MA_AA), chloroplast)
+        expect_is(MA_DNA <- as.MultipleAlignment(Laurasiatherian), "DNAMultipleAlignment")
+        expect_equal(as.phyDat(MA_DNA), Laurasiatherian)
+    }    
+})
 
 
 test_that("subsetting and combining work as expected", {

diff --git a/tests/testthat/test_treeManipulation.R b/tests/testthat/test_treeManipulation.R
@@ -22,6 +22,7 @@ node_108 <- mrca.phylo(tree, node=desc_108)
 test_that("ancestor, mrca, descendants", {
     ## ancestor, mrca, descendants
     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_equal(lengths(Descendants(tree2, 101L:199, "all")), 2 * lengths(prop.part(tree2)) - 2L)