version 1.3.1

GlobalEcologyLab · Sep 19, 2024 · e30c7ed · e30c7ed
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: poems
 Type: Package
 Title: Pattern-Oriented Ensemble Modeling System
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: c(
     person("Sean", "Haythorne", email = "[email protected]", role = "aut"),
     person("Damien", "Fordham", email = "[email protected]", role = "aut"),
@@ -22,14 +22,14 @@ Imports:
     abc (>= 2.1),
     doParallel (>= 1.0.16),
     foreach (>= 1.5.1),
-    geosphere (>= 1.5.10),
     fossil (>= 0.4.0),
     lhs (>= 1.1.1),
     metRology (>= 0.9.28.1),
     R6 (>= 2.5.0),
     raster (>= 3.6),
     trend (>= 1.1.4),
     truncnorm (>= 1.0),
+    gdistance,
     qs
 Collate: 
     'GenericClass.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -35,10 +35,10 @@ importFrom(doParallel,registerDoParallel)
 importFrom(doParallel,stopImplicitCluster)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
+importFrom(fossil,earth.dist)
 importFrom(gdistance,costDistance)
 importFrom(gdistance,geoCorrection)
 importFrom(gdistance,transition)
-importFrom(fossil,earth.dist)
 importFrom(lhs,randomLHS)
 importFrom(metRology,qtri)
 importFrom(qs,qread)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# version 1.3.1
+
+## Bug fixes
+- `poems` no longer depends on `geosphere`. I am hopeful that this will clear up the test failures on CRAN's m1mac.
+
 # version 1.3.0
 
 Every update is an enhancement this time around:

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,15 +1,15 @@
 ## Test environments
-* local macOS (13.5) install, Intel chip, R 4.3.3
+* local macOS 15 install, Intel chip, R 4.4.1
 * Windows, R-devel (via win-builder)
-* macOS, Apple Silicon chip, R 4.3.3 (via mac-builder)
+* macOS, Apple Silicon chip, R 4.4.1 (via mac-builder)
 
 ## R CMD check results
 
 0 ERRORs, 0 WARNINGs, 1 NOTE.
 
 ## Past R CMD check results
 
-Previously, `poems` was archived due to some tests failing on certain Apple Silicon systems due to a dependency on `geosphere`. We have revised those tests so they will pass on Apple Silicon. Tests on CRAN's mac-builder are passing.
+Previously, `poems` was archived due to some tests failing on certain Apple Silicon systems due to a dependency on `geosphere`. We have removed the dependency on `geosphere` altogether. Tests on CRAN's mac-builder are passing.
 
 `poems` has also been turned away from CRAN due to long vignette runtimes. I have cut down vignette runtime to a third of what it was previously, which should hopefully solve this issue.
 

diff --git a/tests/testthat/test_dispersal_friction.R b/tests/testthat/test_dispersal_friction.R
@@ -76,7 +76,7 @@ test_that("distance multiplier calculation errors", {
     "Distance multipliers calculation requires region/coordinates to be set first"
   )
   # Dispersal indices incorrect or not consistent with coordinates
-  distance_matrix <- geosphere::distm(coordinates, coordinates, fun = geosphere::distGeo)
+  distance_matrix <- fossil::earth.dist(coordinates, dist = FALSE)*1000
   dispersal_indices <- which(distance_matrix > 0 & distance_matrix <= 350000, arr.ind = TRUE)
   colnames(dispersal_indices) <- c("target_pop", "source_pop")
   dispersal_friction <- DispersalFriction$new(
@@ -130,7 +130,7 @@ test_that("distance multiplier calculation errors", {
 
 test_that("distance multiplier calculations", {
   coordinates <- data.frame(x = rep(1:4, 4), y = rep(1:4, each = 4))
-  distance_matrix <- fossil::earth.dist(coordinates) / 1000
+  distance_matrix <- fossil::earth.dist(coordinates, dist = FALSE)
   dispersal_indices <- which(distance_matrix > 1 & distance_matrix <= 350, arr.ind = TRUE)
   colnames(dispersal_indices) <- c("target_pop", "source_pop")
   conductance_matrix <- array(1, c(16, 10))
@@ -209,7 +209,7 @@ test_that("distance multiplier calculations", {
   # No conductance values uses region raster set to 1 for non-NA values
   coordinates <- coordinates[-c(2, 5, 6), ] # isolate (1, 1)
   region <- Region$new(coordinates = coordinates)
-  distance_matrix <- geosphere::distm(coordinates, coordinates, fun = geosphere::distGeo) / 1000
+  distance_matrix <- fossil::earth.dist(coordinates, dist = FALSE)
   dispersal_indices <- which(distance_matrix > 0 & distance_matrix <= 350, arr.ind = TRUE)
   colnames(dispersal_indices) <- c("target_pop", "source_pop")
   dispersal_friction <- DispersalFriction$new(region = region)

diff --git a/tests/testthat/test_dispersal_generator.R b/tests/testthat/test_dispersal_generator.R
@@ -259,7 +259,6 @@ test_that("calculate distance data with dispersal friction object", {
       breaks = c(1, seq(100, 400, 20), Inf)
     ))
   }
-  distance_data_changes[[2]] <- distance_data_changes[[2]][-c(13, 179), ] # > Dmax in both t = 1 and 2
   for (i in c(3, 5)) { # reverse changes
     distance_data_changes[[i]] <- distance_data_base[which(distance_multipliers[[i - 1]] != 1), ]
   }
@@ -333,7 +332,7 @@ test_that("calculate dispersals with dispersal friction", {
     region = region, distance_classes = seq(100, 400, 20),
     proportion = 0.4, breadth = 110, max_distance = 300
   )
-  distance_matrix <- fossil::earth.dist(coordinates, dist = F) # km
+  distance_matrix <- fossil::earth.dist(coordinates[-c(2, 5, 6), ], dist = F) # km
   distance_matrix[which(distance_matrix < 1)] <- 0 # ensure actual zero distance for self-referenced cells
   dispersal_gen$calculate_distance_data(distance_matrix = distance_matrix)
   dispersal_gen$calculate_dispersals()
@@ -383,7 +382,7 @@ test_that("cloning and generation", {
   dispersal_clone <- dispersal_gen$new_clone(breadth = 120)
   expect_true(dispersal_clone$generative_requirements_satisfied()[[1]])
   expect_is(dispersal_clone$dispersal_data[[1]], "data.frame") # generated
-  expect_equal(dim(dispersal_clone$dispersal_data[[1]]), c(228, 5))
+  expect_equal(dim(dispersal_clone$dispersal_data[[1]]), c(220, 5))
   expect_null(dispersal_clone$error_messages)
   # Generation
   expect_equal(

diff --git a/tests/testthat/test_population_dispersal_function.R b/tests/testthat/test_population_dispersal_function.R
@@ -549,7 +549,7 @@ test_that("density dependent dispersal", {
     distance_scale = 1000,
     distance_classes = seq(100, 400, 20)
   )
-  distance_matrix <- fossil::earth.dist(coordinates, dist = F)
+  distance_matrix <- fossil::earth.dist(region$coordinates, dist = F)
   distance_matrix[which(distance_matrix < 1)] <- 0 # ensure actual zero distance for self-referenced cells
   dispersal_gen$calculate_distance_data(distance_matrix = distance_matrix)
   dispersal_gen$calculate_dispersals(type = "matrix")

diff --git a/tests/testthat/test_spatial_correlation.R b/tests/testthat/test_spatial_correlation.R
@@ -37,7 +37,7 @@ test_that("initialization and parameter setting", {
 test_that("calculate distance matrix", {
   # Latitude/longitude coordinates
   coordinates1 <- array(c(1:4, 4:1), c(7, 2))
-  distance_matrix1 <- fossil::earth.dist(coordinates, dist = FALSE)*1000
+  distance_matrix1 <- fossil::earth.dist(coordinates1, dist = FALSE)*1000
   spatial_correlation <- SpatialCorrelation$new()
   expect_error(
     spatial_correlation$calculate_distance_matrix(),