Add tests

R/coerce.R

@@ -172,9 +172,9 @@ setMethod(
   signature = c(from = "CompositionMatrix"),
   definition = function(from) {
     data.frame(
-      codes = get_identifiers(from),
-      samples = get_samples(from),
-      groups = get_groups(from),
+      identifier = get_identifiers(from),
+      sample = get_samples(from),
+      group = get_groups(from),
       from,
       row.names = NULL
     )

R/replace.R

@@ -24,17 +24,17 @@ setMethod(
   }
 )
 
-zero_additive <- function(x, sigma) {
-  D <- length(x)
-
-  is_zero <- x == 0
-  Z <- sum(is_zero)
-
-  x[is_zero] <- (sigma * (Z + 1) * (D - Z)) / D^2
-  x[!is_zero] <- x[!is_zero] - (sigma * (Z + 1) * Z) / D^2
-
-  x
-}
+# zero_additive <- function(x, sigma) {
+#   D <- length(x)
+#
+#   is_zero <- x == 0
+#   Z <- sum(is_zero)
+#
+#   x[is_zero] <- (sigma * (Z + 1) * (D - Z)) / D^2
+#   x[!is_zero] <- x[!is_zero] - (sigma * (Z + 1) * Z) / D^2
+#
+#   x
+# }
 zero_multiplicative <- function(x, sigma) {
   is_zero <- x == 0 & !is.na(x)
   x[is_zero] <- sigma[is_zero]

inst/tinytest/test_coerce.R

@@ -1,6 +1,11 @@
+# Data with groups =============================================================
+data("slides")
+coda <- as_composition(slides, sample = 2, group = 1)
+expect_equal_to_reference(as_features(coda), file = "_snaps/features.rds")
+
+# Back transform to count ======================================================
 data("hongite")
 coda <- as_composition(hongite)
 
-# Back transform to count ======================================================
 count <- as_amounts(coda)
 expect_equal(as.data.frame(count), hongite)

inst/tinytest/test_pca.R

@@ -0,0 +1,4 @@
+data("hongite")
+coda <- as_composition(hongite)
+
+expect_error(pca(coda), "Transform your data first")