49 total species extent is truncated

.Rbuildignore

@@ -4,3 +4,5 @@
 ^LICENSE\.md$
 ^data-raw$
 ^data_pipeline$
+^localtmp$
+^flow_debug.log

DESCRIPTION

@@ -18,7 +18,8 @@ Imports:
 Suggests: 
     testthat (>= 3.0.0),
     callthat,
-    httr
+    httr,
+    withr
 Config/testthat/edition: 3
 Remotes:
     birdflow-science/BirdFlowR,

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2025 UMass Amherst Center for Data Science & AI
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2025
+COPYRIGHT HOLDER: UMassCDS

NAMESPACE

@@ -1,7 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
 export(flow)
+export(get_s3_config)
 export(load_models)
 export(range_rescale)
 export(save_json_palette)
+export(set_s3_config)
 export(symbolize_raster_data)
+importFrom(stats,predict)

R/data.R

@@ -56,3 +56,6 @@
 #'   \item{"jitter_radius"}{Jitter radius in meters}
 #' }
 "counties_json"
+
+# Declare these as global variables so package check doesn't flag them
+utils::globalVariables(c("species", "flow_colors"))

R/flow.R

@@ -62,6 +62,7 @@ save_local_path <- "config/save_local.flag"
 #'    `legend`
 #'    `type`
 #' @export
+#' @importFrom stats predict
 flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE) {
   s3_cfg <- get_s3_config()
   s3_enabled <- !is.na(s3_cfg$bucket) && nzchar(s3_cfg$bucket)
@@ -195,6 +196,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
   combined <- NULL
   any_valid <- FALSE
 
+
   for (i in seq_along(target_species)) {
     sp <- target_species[i]
     bf <- models[[sp]]
@@ -215,13 +217,20 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
     start_proportion <- sum(initial_population_distr[location_i]) / 1
     abundance <- pred * species$population[species$species == sp] / prod(terra::res(bf) / 1000) * start_proportion
     this_raster <- BirdFlowR::rasterize_distr(abundance, bf = bf, format = "terra")
+
+    # Make NA zero (for adding)
+    this_raster[is.na(this_raster)] <- 0
+
     if (is.null(combined)) {
       combined <- this_raster
     } else {
       combined <- combined + this_raster
     }
   }
 
+  # Make zeros transparent
+  combined[combined == 0] <- NA
+
   if (!any_valid) {
     log_progress("No valid starting location. Returning error.")
     return(format_error("Invalid starting location", "outside mask"))

tests/testthat/setup.R

@@ -1,2 +1,13 @@
 load_models()
 set_s3_config()
+
+
+# Set the cache directory to a new tempdir for the duration of the tests.
+# and delete it after tests complete.
+# If running individual tests manually don't run this code.
+original_local_temp <- get_s3_config()$local_temp
+local_temp <- withr::local_tempdir("cache", .local_envir = teardown_env())
+s3_config$local_temp <- local_temp
+withr::defer(
+  s3_config$local_temp <- original_local_temp, envir = teardown_env()
+  )

tests/testthat/test-flow.R

@@ -113,3 +113,29 @@ test_that("result contents are valid (inflow)", {
     expect_true(row$type == "inflow")
   }
 })
+
+
+
+test_that("total is not constrained by individual taxa NAs", {
+  params <- standard_flow_input()
+
+  # Make a total projection
+  params$taxa <- "total"
+  expect_no_error(total_result <- do.call(flow, params))
+  total <- terra::rast(total_result$geotiff)
+
+  # Same start but for american black duck
+  params$taxa <- "ambduc"
+  expect_no_error(ambduc_result <- do.call(flow, params))
+  ambduc <- terra::rast(ambduc_result$geotiff)
+
+  # There should be more NA's in the American black duck result than in the total
+  ambduc_nas <- terra::values(ambduc) |> is.na() |> sum()
+  total_nas <- terra::values(total) |> is.na() |> sum()
+  expect_true(ambduc_nas > total_nas)
+
+  # The total should not be NA anywhere that ambduc is not NA
+  n_wrong <- (is.na(total) & !is.na(ambduc)) |> terra::values() |> sum()
+  expect_equal(n_wrong, 0)
+
+})