Merge pull request #421 from EDiLD/master

few tests

R/tax_agg.R

@@ -65,18 +65,18 @@
 
 tax_agg <- function(x, rank, db = 'ncbi', verbose=FALSE, ...)
 {
-  if(is.matrix(x))
-  {
-    if(is.null(colnames(x))) stop("The community data matrix must have named columns")
-    x <- data.frame(x, check.names=FALSE)
+  if (is.matrix(x)) {
+    if (is.null(colnames(x)))
+      stop("The community data matrix must have named columns")
+    x <- data.frame(x, check.names = FALSE)
   }
   # bring to long format
   x$rownames <- rownames(x)
   df_m <- melt(x, id = 'rownames')
 
   # aggregate to family level (by querying NCBI for taxonomic classification)
   uniq_tax <- as.character(unique(df_m$variable))
-  agg <- tax_name(uniq_tax, get = rank, db = db, verbose=verbose, ...)
+  agg <- tax_name(uniq_tax, get = rank, db = db, verbose = verbose, ...)
   lookup <- data.frame(variable = uniq_tax, agg = agg[ , 3], stringsAsFactors = FALSE)
 
   # merge lookup with orig.
@@ -87,7 +87,7 @@ tax_agg <- function(x, rank, db = 'ncbi', verbose=FALSE, ...)
 
   # bring back to long format and aggregate
   df_l <- dcast(df_merged, rownames ~ agg,
-                value.var='value', fun.aggregate = sum)
+                value.var = 'value', fun.aggregate = sum)
 
   rownames(df_l) <- df_l$rownames
   df_l$rownames <- NULL

tests/testthat/test-rankagg.R

@@ -0,0 +1,19 @@
+# tests for rankagg fxn in taxize
+context("rankagg")
+data(dune.taxon, package = 'vegan')
+dat <- dune.taxon
+set.seed(1234)
+dat$abundance <- round(rlnorm(n = nrow(dat), meanlog = 5, sdlog = 2), 0)
+out <- rankagg(data = dat, datacol = "abundance", rank = "Genus")
+
+
+test_that("rankagg throws error", {
+  expect_error(rankagg(datacol = "abundance", rank = "Genus"))
+  expect_error(rankagg(data = dat, datacol = "abundance"))
+})
+
+
+test_that("Correct result", {
+  expect_is(out, "data.frame")
+  expect_equal(out[1, 2], 13)
+})

tests/testthat/test-tax_agg.R

@@ -8,6 +8,9 @@ species <- c("Bellis perennis", "Empetrum nigrum", "Juncus bufonius", "Juncus ar
 "Aira praecox")
 colnames(take) <- species
 out_ncbi <- tax_agg(take, rank = 'family', db = 'ncbi', verbose = FALSE)
+take2 <- take
+colnames(take2) <- NULL
+
 
 
 test_that("tax_agg returns the correct class", {
@@ -21,6 +24,7 @@ test_that("tax_agg returns the correct value", {
   expect_that(nrow(out_ncbi$x), equals(nrow(take)))
   expect_that(nrow(out_ncbi$by), equals(length(unique(colnames(take)))))
   expect_that(out_ncbi$n_pre, equals(length(unique(colnames(take)))))
+  expect_error(tax_agg(as.matrix(take2), rank = 'family', db = 'ncbi', verbose = FALSE))
 })