add test

inst/tinytest/test_pml_generics.R

@@ -8,3 +8,24 @@ expect_true(BIC(fit) > AIC(fit))
 
 c_mat <- vcov(fit)
 expect_true( isSymmetric(c_mat, tol=1e-12) )
+
+# test write.pml
+write.pml(fit, save_rds = TRUE)
+fit2 <- readRDS("pml.rds")
+expect_equal(fit, fit2)
+
+
+
+#write.pml(fit, save_rds = FALSE)
+
+#tree <- read.tree("pml_tree.nwk")
+#align <- read.phyDat("pml_align.fasta", format="fasta")
+#fit3 <- pml(tree = tree, data = align, k = 1L, site.rate = "gamma", ASC = FALSE,
+#           bf = c(0.306541405706333, 0.261308281141267, 0.126026443980515,
+#                  0.306123869171886),
+#           Q = c(1, 23.0401288315219, 1, 1, 23.0401288315219, 1),
+#           inv = 0.850681761772363, model = "HKY")
+
+#fit$method <- NULL
+#expect_equal(fit, fit3)
+unlink(c("pml_align.fasta", "pml_tree.nwk", "pml.rds", "pml.txt"))