Merge pull request #165 from dsmith-unbc/issue-#142-Return-dist.mat-e…

…ven-if-it-is-invalid

Issue #142 return dist.mat even if it is invalid

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: actel
 Title: Acoustic Telemetry Data Analysis
-Version: 1.3.0.9017
+Version: 1.3.0.9018
 Authors@R: c(
     person("Hugo", "Flávio", role = c("aut", "cre"),
            email = "[email protected]", comment = c(ORCID = "0000-0002-5174-1197")),

NEWS.md

@@ -25,6 +25,7 @@ Enhancements:
   * New `plotDot()` function to help users inspect their spatial.txt files (issue [#55](https://github.com/hugomflavio/actel/issues/55)).
   * Improved internal mechanisms for message/warning/debug/stop reporting. new internal function `event()` replaces the old `appendTo()`, `stopAndReport()`, and `emergencyBreak()` (issue [#135](https://github.com/hugomflavio/actel/issues/135))
   * Added the ability to use output of `loadSpatial()` as 'starters' for `distancesMatrix()` when 'actel' is 'TRUE'. This allows a user to input their spatial.csv if located in a separate working directory (issue [#133](https://github.com/hugomflavio/actel/issues/133))
+  * Distance matrix is now retained in the output of `explore()`, `residency()`, and `migration()` analysis when invalid. Additionally, if the distance matrix is not available NA will be denoted in the output. (issue [#142](https://github.com/hugomflavio/actel/issues/142))
 
 ## actel 1.3.0
 

R/explore.R

@@ -520,12 +520,9 @@ explore <- function(
   if (decision == "y") { # nocov start
    event(type = c("screen", "report"),
          paste0("M: Saving results as '", resultsname, "'."))
-    if (attributes(dist.mat)$valid)
-      save(bio, detections, valid.detections, spatial, deployments, arrays,
-        movements, valid.movements, times, rsp.info, dist.mat, file = resultsname)
-    else
-      save(bio, detections, valid.detections, spatial, deployments, arrays,
-        movements, valid.movements, times, rsp.info, file = resultsname)
+   save(bio, detections, valid.detections, spatial, deployments, arrays,
+        movements, valid.movements, times, rsp.info, dist.mat, 
+        file = resultsname)
   } else {
    event(type = c("screen", "report"),
          paste0("M: Skipping saving of the results."))
@@ -688,10 +685,8 @@ explore <- function(
                  movements = movements,
                  valid.movements = valid.movements,
                  times = times,
-                 rsp.info = rsp.info)
-
-  if (attributes(dist.mat)$valid)
-    output$dist.mat <- dist.mat
+                 rsp.info = rsp.info,
+                 dist.mat = dist.mat)
 
  event(type = "Screen",
        "M: Analysis completed!")

R/migration.R

@@ -831,19 +831,11 @@ migration <- function(
     # in coding style (actel 2.0).
     section.movements <- secmoves
     intra.array.matrices <- intra_mats
-    if (attributes(dist.mat)$valid) {
-      save(detections, valid.detections, spatial, deployments, arrays,
-           movements, valid.movements, section.movements, status.df,
-           section.overview, group.overview, release.overview, matrices,
-           overall.CJS, intra.array.matrices, intra.array.CJS, times,
-           rsp.info, dist.mat, file = resultsname)
-    } else {
-      save(detections, valid.detections, spatial, deployments, arrays,
-           movements, valid.movements, section.movements, status.df,
-           section.overview, group.overview, release.overview, matrices,
-           overall.CJS, intra.array.matrices, intra.array.CJS, times,
-           rsp.info, file = resultsname)
-    }
+    save(detections, valid.detections, spatial, deployments, arrays,
+         movements, valid.movements, section.movements, status.df,
+         section.overview, group.overview, release.overview, matrices,
+         overall.CJS, intra.array.matrices, intra.array.CJS, times,
+         rsp.info, dist.mat, file = resultsname)
   } else { # nocov end
     event(type = c("screen", "report"),
           "M: Skipping saving of the results.")
@@ -1065,11 +1057,8 @@ migration <- function(
                  intra.array.matrices = intra_mats,
                  intra.array.CJS = intra.array.CJS,
                  times = times,
-                 rsp.info = rsp.info)
-
-  if (attributes(dist.mat)$valid) {
-    output$dist.mat <- dist.mat
-  }
+                 rsp.info = rsp.info,
+                 dist.mat = dist.mat)
 
   event(type = "screen",
         "M: Analysis completed!")

R/residency.R

@@ -660,16 +660,10 @@ residency <- function(
   if (decision == "y") {
     event(type = c("screen", "report"),
           "M: Saving results as '", resultsname, "'.")
-    if (attributes(dist.mat)$valid)
-      save(detections, valid.detections, spatial, deployments, arrays, movements, valid.movements,
-        section.movements, status.df, last.seen, array.times, section.times, intra.array.matrices,
-        residency.list, time.ratios, time.positions, global.ratios, group.ratios, efficiency,
-        intra.array.CJS, rsp.info, dist.mat, file = resultsname)
-    else
-      save(detections, valid.detections, spatial, deployments, arrays, movements, valid.movements,
-        section.movements, status.df, last.seen, array.times, section.times, intra.array.matrices,
-        residency.list, time.ratios, time.positions, global.ratios, group.ratios, efficiency,
-        intra.array.CJS, rsp.info, file = resultsname)
+    save(detections, valid.detections, spatial, deployments, arrays, movements, valid.movements,
+         section.movements, status.df, last.seen, array.times, section.times, intra.array.matrices,
+         residency.list, time.ratios, time.positions, global.ratios, group.ratios, efficiency,
+         intra.array.CJS, rsp.info, dist.mat, file = resultsname)
   } else {
     event(type = c("screen", "report"),
           "M: Skipping saving of the results.")
@@ -883,10 +877,8 @@ residency <- function(
                  global.ratios = global.ratios,
                  group.ratios = group.ratios,
                  last.seen = last.seen,
-                 rsp.info = rsp.info)
-
-  if (attributes(dist.mat)$valid)
-    output$dist.mat <- dist.mat
+                 rsp.info = rsp.info,
+                 dist.mat = dist.mat)
 
   event(type = "screen",
         "M: Analysis completed!")

tests/testthat/test_explore.R

@@ -187,7 +187,7 @@ test_that("explore is able to run speed and inactiveness checks.", {
 	file.remove("distances.csv")
 	output <- suppressWarnings(explore(tz = 'Europe/Copenhagen', report = TRUE, GUI = "never", speed.warning = 1000000, inactive.warning = 1000000))
 	expect_false(any(is.na(match(names(output), c('bio', 'detections', 'valid.detections', 'spatial', 'deployments', 'arrays',
-    'movements', 'valid.movements', 'times', 'rsp.info')))))
+    'movements', 'valid.movements', 'times', 'rsp.info', 'dist.mat')))))
 })
 # n
 # n

tests/testthat/test_migration.R

@@ -140,7 +140,7 @@ test_that("migration is able to run speed and inactiveness checks.", {
 			GUI = "never", speed.error = 1000000, inactive.error = 1000000),
 		"Running inactiveness checks without a distance matrix. Performance may be limited.", fixed = TRUE)
 
-	expect_false(any(is.na(match(names(output), c('arrays', 'deployments', 'detections', 'group.overview', 'intra.array.CJS',
+	expect_false(any(is.na(match(names(output), c('arrays', 'deployments', 'detections', 'dist.mat', 'group.overview', 'intra.array.CJS',
 	 'intra.array.matrices','matrices', 'movements', 'overall.CJS', 'release.overview', 'rsp.info', 'section.movements',
 	  'section.overview', 'spatial', 'status.df', 'times', 'valid.detections', 'valid.movements')))))
 })

tests/testthat/test_residency.R

@@ -51,7 +51,7 @@ test_that("residency is able to run speed and inactiveness checks.", {
 			GUI = "never", speed.error = 1000000, inactive.error = 1000000),
 		"Running inactiveness checks without a distance matrix. Performance may be limited.", fixed = TRUE)
 	expect_false(any(is.na(match(names(output), c('array.times', 'arrays', 'time.positions', 'time.ratios',
-		'deployments', 'detections', 'efficiency', 'global.ratios', 'group.ratios', 'intra.array.CJS', 'intra.array.matrices',
+		'deployments', 'detections', 'dist.mat', 'efficiency', 'global.ratios', 'group.ratios', 'intra.array.CJS', 'intra.array.matrices',
 		'last.seen', 'movements', 'residency.list', 'rsp.info', 'section.movements', 'section.times',
 		'spatial', 'status.df', 'valid.detections', 'valid.movements')))))
 })