Merge pull request #83 from ropensci/fix/test-expected-fusions

Fix/test expected fusions

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "spatsoc" in publications use:'
 type: software
 license: GPL-3.0-only
 title: 'spatsoc: Group Animal Relocation Data by Spatial and Temporal Relationship'
-version: 0.2.4.9000
+version: 0.2.4.9001
 identifiers:
 - type: doi
   value: 10.32614/CRAN.package.spatsoc

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: spatsoc
 Title: Group Animal Relocation Data by Spatial and Temporal Relationship
-Version: 0.2.4.9000
+Version: 0.2.4.9001
 Authors@R: c(
     person("Alec L.", "Robitaille", , "robit.alec@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4706-1762")),

NEWS.md

@@ -1,3 +1,7 @@
+# v 0.2.4.9001
+
+* improve tests of `fusion_id` with tests for expected number of output fusionIDs [PR 83](https://github.com/ropensci/spatsoc/pull/83)
+
 # v 0.2.4.9000
 
 * (experimental) `fusion_id` function for flexibly identifying fission-fusion

R/fusion_id.R

@@ -19,9 +19,9 @@
 #' The \code{n_min_length} argument defines the minimum number of successive
 #' fixes that are required to establish a fusion event. The \code{n_max_missing}
 #' argument defines the the maximum number of allowable missing observations for
-#' either individual in a dyad within a fusion event. The \code{allow_split}
-#' argument defines if a single observation can be greater than the threshold
-#' distance without initiating fission event.
+#' the dyad within a fusion event. The \code{allow_split} argument defines if a
+#' single observation can be greater than the threshold distance without
+#' initiating fission event.
 #'
 #' @return \code{fusion_id} returns the input \code{edges} appended with a
 #'   \code{fusionID} column.
@@ -160,14 +160,6 @@ fusion_id <- function(edges = NULL,
                both_rleid := (both_rleid + seq.int(.N)) * -1,
                by = dyadID]
 
-  # Correct if (looking forward) the loc is part of a new fusion run
-  unique_edges[, both_rleid := data.table::fifelse(
-    timegroup - data.table::shift(timegroup, -1) == -1  &
-      within & !(tg_diff),
-    data.table::shift(both_rleid, -1),
-    both_rleid
-  ), by = dyadID]
-
   # If n minimum length > 0, check nrows and return NA if less than min
   if (n_min_length > 0) {
     unique_edges[!is.na(both_rleid), both_rleid := data.table::fifelse(

codemeta.json

@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/ropensci/spatsoc",
   "issueTracker": "https://github.com/ropensci/spatsoc/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.2.4.9000",
+  "version": "0.2.4.9001",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -190,7 +190,7 @@
     },
     "SystemRequirements": "GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0),\n    sqlite3"
   },
-  "fileSize": "1881.983KB",
+  "fileSize": "1884.503KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

tests/testthat/test-fusion-id.R

@@ -121,3 +121,143 @@ test_that('larger n_min_length returns less unique fusionID', {
     fusion_id(edges, n_min_length = 0)[, uniqueN(fusionID)]
   )
 })
+
+edges_expected <- data.table(
+  dyadID = rep('A-B', 11),
+  timegroup = seq.int(12)[-5],
+  distance = c(1, 50, 1, 1, 1, 50, 50, 1, 1, 50, 1)
+)
+threshold <- 25
+
+test_that('n_min_length returns expected number of unique fusionIDs', {
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 0
+    )[, uniqueN(fusionID,  na.rm = TRUE)],
+    5
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2
+    )[, uniqueN(fusionID,  na.rm = TRUE)],
+    2
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 3
+    )[, uniqueN(fusionID,  na.rm = TRUE)],
+    0
+  )
+
+})
+
+
+test_that('allow_split returns expected number of unique fusionIDs', {
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2,
+      allow_split = FALSE
+    )[, uniqueN(fusionID,  na.rm = TRUE)],
+    2
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2,
+      allow_split = FALSE
+    )[!is.na(fusionID), .N, fusionID][, max(N)],
+    2
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2,
+      allow_split = TRUE
+    )[, uniqueN(fusionID,  na.rm = TRUE)],
+    2
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2,
+      allow_split = TRUE
+    )[!is.na(fusionID), .N, fusionID][, max(N)],
+    4
+  )
+})
+
+
+test_that('n_max_missing returns expected number of unique fusionIDs', {
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 0,
+      n_max_missing = 1,
+      allow_split = FALSE
+    )[, uniqueN(fusionID,  na.rm = TRUE)],
+    4
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2,
+      n_max_missing = 1,
+      allow_split = FALSE
+    )[, uniqueN(fusionID,  na.rm = TRUE)],
+    2
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2,
+      n_max_missing = 1,
+      allow_split = FALSE
+    )[!is.na(fusionID), .N, fusionID][, max(N)],
+    3
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2,
+      n_max_missing = 1,
+      allow_split = TRUE
+    )[, uniqueN(fusionID,  na.rm = TRUE)],
+    2
+  )
+
+  expect_equal(
+    fusion_id(
+      edges_expected,
+      threshold = threshold,
+      n_min_length = 2,
+      n_max_missing = 1,
+      allow_split = TRUE
+    )[!is.na(fusionID), .N, fusionID][, max(N)],
+    5
+  )
+
+})