support A. species for as.mo, cleanup

tests/testthat/test-misc.R

@@ -5,6 +5,9 @@ test_that("percentages works", {
   expect_equal(percent(0.5), "50%")
   expect_equal(percent(0.500, force_zero = TRUE), "50.0%")
   expect_equal(percent(0.1234), "12.3%")
+  # round up 0.5
+  expect_equal(percent(0.0054), "0.5%")
+  expect_equal(percent(0.0055), "0.6%")
 })
 
 test_that("size format works", {

tests/testthat/test-mo.R

@@ -195,6 +195,11 @@ test_that("as.mo works", {
 
   # TSN of prevalent and non prevalent ones
   expect_equal(mo_TSN(c("Gomphosphaeria aponina delicatula", "Escherichia coli")),
-                   c(717, 285))
+               c(717, 285))
+
+  expect_equal(mo_fullname(c("E. spp.",
+                             "E. spp",
+                             "E. species")),
+               rep("Escherichia species", 3))
 
 })

tests/testthat/test-read.4d.R

@@ -18,7 +18,7 @@ test_that("read 4D works", {
   tf <- tempfile()
   write.table(test1, file = tf, quote = F, sep = "\t")
 
-  x <- read.4D(tf, skip = 0)
+  x <- read.4D(tf, skip = 0, info = TRUE)
   unlink(tf)
 
   expect_equal(ncol(x), 11)