Merge pull request #182 from birdflow-science/fix-collection-index

fix bug in example data for rmarkdwon collection index
birdflow-science · May 15, 2024 · c99704a · c99704a
2 parents dddb54d + 4378ffc
commit c99704a
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Showing 6 changed files with 21 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,12 +3,14 @@ Title: Predict and Visualize Bird Movement
 Version: 0.1.0.9056
 Authors@R: 
     c(person("Ethan", "Plunkett",  email = "plunkett@umass.edu", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-4405-2251")))
+           comment = c(ORCID = "0000-0003-4405-2251")),
+      person("BirdFlow-Science", role = "cph"),
+      person("National Science Foundation", role = "fnd"))
 Description: BirdFlowR predicts bird movement and distribution from previously fitted models.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     BirdFlowModels (>= 0.0.2.9002),
     covr,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# Birdflow 0.1.0.9058
+2024-05-07
+
+* Fixed bug that prevented knitting example collection index without passed
+parameters.
 
 # Birdflow 0.1.0.9057
 2024-04-17

diff --git a/R/animate_distr.R b/R/animate_distr.R
@@ -28,8 +28,8 @@
 #' anim <- animate_distr(distr, bf,  show_dynamic_mask = TRUE)
 #'
 #' \dontrun{
-#' # Display it
-#' anim
+#'   # Display it
+#'   anim
 #' }
 #' ### Project a distribution
 #'
@@ -65,7 +65,7 @@
 #'   gif_file <- tempfile("animation", fileext = ".gif")
 #'   gganimate::save_animation(gif, gif_file)
 #'   file.remove(gif_file) # cleanup
-#'   }
+#' }
 animate_distr <- function(distr, bf, title = species(bf), ...) {
 
   p <- plot_distr(distr, bf, ...)

diff --git a/inst/markdown_templates/index_example.Rds b/inst/markdown_templates/index_example.Rds
diff --git a/man/animate_distr.Rd b/man/animate_distr.Rd
diff --git a/tests/testthat/test-as_distr.R b/tests/testthat/test-as_distr.R
@@ -55,10 +55,14 @@ test_that("as_distr works with raster objects", {
   expect_warning(d <- as_distr(r, bf)) # value lost both to cropping and masking
   expect_equal(sum(d), 1)
 
-  # Multiple layers
+  # Multiple layers in raster
   r2 <- c(r, r, r)
   expect_warning(d2 <- as_distr(r2, bf)) # value lost to cropping and masking
-  expect_true(all(apply(d2, 2, sum) == 1))
+  sums <- apply(d2, 2, sum)
+  for(i in seq_along(sums)) {
+    expect_equal(sums[i], 1)
+  }
+
   expect_equal(nrow(d2), n_active(bf))
   expect_equal(ncol(d2), 3)
   expect_equal(d2[, 1], d, ignore_attr = TRUE)