From f658de0821d0ce14b77cf2ca040dabdf4e0f2f09 Mon Sep 17 00:00:00 2001
From: Johanna Paijmans <paijmans.jla@gmail.com>
Date: Thu, 28 Sep 2023 12:39:35 +0100
Subject: [PATCH 1/6] Detailed warning messages sampling pseudoabs

---
 R/sample_pseudoabs.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/sample_pseudoabs.R b/R/sample_pseudoabs.R
index d5caebd2..19cc9747 100644
--- a/R/sample_pseudoabs.R
+++ b/R/sample_pseudoabs.R
@@ -100,7 +100,7 @@ sample_pseudoabs <- function (data, raster, n, coords = NULL,
   if (length(cell_id)>n){
     cell_id <- sample(x= cell_id, size = n)
   } else {
-    warning("There are fewer available cells in the raster than the requested ", n, " points.\n",
+    warning("There are fewer available cells in raster for raster \"",time(sampling_raster),"\" (",nrow(xy_pres)," presences) than the requested ", n, " points.\n",
             "Only ", length(cell_id), " will be returned.")
   }
   pseudoabsences <- as.data.frame (terra::xyFromCell(sampling_raster, cell_id))

From 05b2bdb676d37c2c58fd5cbc40f2318a5874e09f Mon Sep 17 00:00:00 2001
From: Johanna Paijmans <paijmans.jla@gmail.com>
Date: Thu, 28 Sep 2023 12:46:07 +0100
Subject: [PATCH 2/6] Detailed warning messages sampling pseudoabs

---
 R/sample_pseudoabs.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/sample_pseudoabs.R b/R/sample_pseudoabs.R
index 19cc9747..4c373af8 100644
--- a/R/sample_pseudoabs.R
+++ b/R/sample_pseudoabs.R
@@ -100,8 +100,7 @@ sample_pseudoabs <- function (data, raster, n, coords = NULL,
   if (length(cell_id)>n){
     cell_id <- sample(x= cell_id, size = n)
   } else {
-    warning("There are fewer available cells in raster for raster \"",time(sampling_raster),"\" (",nrow(xy_pres)," presences) than the requested ", n, " points.\n",
-            "Only ", length(cell_id), " will be returned.")
+    warning("There are fewer available cells in raster for raster \"",time(sampling_raster),"\" (",nrow(xy_pres)," presences) than the requested ", n, " points. Only ", length(cell_id), " will be returned.\n")
   }
   pseudoabsences <- as.data.frame (terra::xyFromCell(sampling_raster, cell_id))
   # fix the coordinate names to be the same we started with

From 98cd3f862906d9f466765904fdde74e4f89bd7fc Mon Sep 17 00:00:00 2001
From: Johanna Paijmans <paijmans.jla@gmail.com>
Date: Wed, 4 Oct 2023 10:00:07 +0100
Subject: [PATCH 3/6] More detailed error message pseudoabs sampling

---
 tests/testthat/test_sample_pseudoabs.R |   2 +-
 tests/testthat/testthat-problems.rds   | Bin 0 -> 14510 bytes
 2 files changed, 1 insertion(+), 1 deletion(-)
 create mode 100644 tests/testthat/testthat-problems.rds

diff --git a/tests/testthat/test_sample_pseudoabs.R b/tests/testthat/test_sample_pseudoabs.R
index 4f828d7e..103eeae7 100644
--- a/tests/testthat/test_sample_pseudoabs.R
+++ b/tests/testthat/test_sample_pseudoabs.R
@@ -82,7 +82,7 @@ test_that("handling of data frames and sf objects", {
   expect_error(sample_pseudoabs(locations_sf, coords = c("x", "y"), raster = grid_raster),
                "There are no recognised coordinate columns")
   expect_warning(sample_pseudoabs(locations_sf, raster = grid_raster, n = 100),
-                 "There are fewer available cells in the raster than the requested 100 points")
+                 "There are fewer available cells in raster for raster 'NA' (3 presences) than the requested 100 points. Only 52 will be returned.")
   locations_sf <- locations_sf %>% dplyr::bind_cols(sf::st_coordinates(.))
   expect_no_error(sample_pseudoabs(locations_sf, coords = c("X", "Y"), raster = grid_raster, n = 25))
   locations_sf$X <- rep(0, 3)
diff --git a/tests/testthat/testthat-problems.rds b/tests/testthat/testthat-problems.rds
new file mode 100644
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From 235c55bf02f4633285d8429bf07cfad0469c1e82 Mon Sep 17 00:00:00 2001
From: Johanna Paijmans <paijmans.jla@gmail.com>
Date: Wed, 4 Oct 2023 10:01:15 +0100
Subject: [PATCH 4/6] More detailed error message pseudoabs sampling

---
 R/sample_pseudoabs.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/sample_pseudoabs.R b/R/sample_pseudoabs.R
index 4c373af8..edc16452 100644
--- a/R/sample_pseudoabs.R
+++ b/R/sample_pseudoabs.R
@@ -100,7 +100,7 @@ sample_pseudoabs <- function (data, raster, n, coords = NULL,
   if (length(cell_id)>n){
     cell_id <- sample(x= cell_id, size = n)
   } else {
-    warning("There are fewer available cells in raster for raster \"",time(sampling_raster),"\" (",nrow(xy_pres)," presences) than the requested ", n, " points. Only ", length(cell_id), " will be returned.\n")
+    warning("There are fewer available cells in raster for raster '",time(sampling_raster),"' (",nrow(xy_pres)," presences) than the requested ", n, " points. Only ", length(cell_id), " will be returned.\n")
   }
   pseudoabsences <- as.data.frame (terra::xyFromCell(sampling_raster, cell_id))
   # fix the coordinate names to be the same we started with

From 2974989f2a5a00ad0980d0d2a05852aa8ca13982 Mon Sep 17 00:00:00 2001
From: Johanna Paijmans <paijmans.jla@gmail.com>
Date: Wed, 4 Oct 2023 10:12:31 +0100
Subject: [PATCH 5/6] More detailed error message pseudoabs sampling

---
 R/sample_pseudoabs.R                   | 2 +-
 tests/testthat/test_sample_pseudoabs.R | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/sample_pseudoabs.R b/R/sample_pseudoabs.R
index edc16452..81fc952d 100644
--- a/R/sample_pseudoabs.R
+++ b/R/sample_pseudoabs.R
@@ -100,7 +100,7 @@ sample_pseudoabs <- function (data, raster, n, coords = NULL,
   if (length(cell_id)>n){
     cell_id <- sample(x= cell_id, size = n)
   } else {
-    warning("There are fewer available cells in raster for raster '",time(sampling_raster),"' (",nrow(xy_pres)," presences) than the requested ", n, " points. Only ", length(cell_id), " will be returned.\n")
+    warning("There are fewer available cells for raster '",time(sampling_raster),"' (",nrow(xy_pres)," presences) than the requested ", n, " points. Only ", length(cell_id), " will be returned.\n")
   }
   pseudoabsences <- as.data.frame (terra::xyFromCell(sampling_raster, cell_id))
   # fix the coordinate names to be the same we started with
diff --git a/tests/testthat/test_sample_pseudoabs.R b/tests/testthat/test_sample_pseudoabs.R
index 103eeae7..5d5c90f0 100644
--- a/tests/testthat/test_sample_pseudoabs.R
+++ b/tests/testthat/test_sample_pseudoabs.R
@@ -81,8 +81,7 @@ test_that("handling of data frames and sf objects", {
   locations_sf <-  sf::st_as_sf(locations, coords=c("lon","lat")) %>% sf::st_set_crs(4326)
   expect_error(sample_pseudoabs(locations_sf, coords = c("x", "y"), raster = grid_raster),
                "There are no recognised coordinate columns")
-  expect_warning(sample_pseudoabs(locations_sf, raster = grid_raster, n = 100),
-                 "There are fewer available cells in raster for raster 'NA' (3 presences) than the requested 100 points. Only 52 will be returned.")
+  expect_warning(sample_pseudoabs(locations_sf, raster = grid_raster, n = 100),                 "There are fewer available cells for raster 'NA' (3 presences) than the requested 100 points. Only 52 will be returned.")
   locations_sf <- locations_sf %>% dplyr::bind_cols(sf::st_coordinates(.))
   expect_no_error(sample_pseudoabs(locations_sf, coords = c("X", "Y"), raster = grid_raster, n = 25))
   locations_sf$X <- rep(0, 3)

From 97a7fd6148f3b873ba48c8c926162fe17b3fdc4a Mon Sep 17 00:00:00 2001
From: Johanna Paijmans <paijmans.jla@gmail.com>
Date: Wed, 4 Oct 2023 10:57:44 +0100
Subject: [PATCH 6/6] More detailed error message pseudoabs sampling

---
 R/sample_pseudoabs.R                   |   2 +-
 tests/testthat/test_sample_pseudoabs.R |   2 +-
 tests/testthat/testthat-problems.rds   | Bin 14510 -> 0 bytes
 3 files changed, 2 insertions(+), 2 deletions(-)
 delete mode 100644 tests/testthat/testthat-problems.rds

diff --git a/R/sample_pseudoabs.R b/R/sample_pseudoabs.R
index 81fc952d..3b55ec78 100644
--- a/R/sample_pseudoabs.R
+++ b/R/sample_pseudoabs.R
@@ -100,7 +100,7 @@ sample_pseudoabs <- function (data, raster, n, coords = NULL,
   if (length(cell_id)>n){
     cell_id <- sample(x= cell_id, size = n)
   } else {
-    warning("There are fewer available cells for raster '",time(sampling_raster),"' (",nrow(xy_pres)," presences) than the requested ", n, " points. Only ", length(cell_id), " will be returned.\n")
+    warning("There are fewer available cells for raster '",time(sampling_raster),"' (",nrow(xy_pres)," presences) than the requested ", n, " pseudoabsences. Only ", length(cell_id), " will be returned.\n")
   }
   pseudoabsences <- as.data.frame (terra::xyFromCell(sampling_raster, cell_id))
   # fix the coordinate names to be the same we started with
diff --git a/tests/testthat/test_sample_pseudoabs.R b/tests/testthat/test_sample_pseudoabs.R
index 5d5c90f0..9f2d03bd 100644
--- a/tests/testthat/test_sample_pseudoabs.R
+++ b/tests/testthat/test_sample_pseudoabs.R
@@ -81,7 +81,7 @@ test_that("handling of data frames and sf objects", {
   locations_sf <-  sf::st_as_sf(locations, coords=c("lon","lat")) %>% sf::st_set_crs(4326)
   expect_error(sample_pseudoabs(locations_sf, coords = c("x", "y"), raster = grid_raster),
                "There are no recognised coordinate columns")
-  expect_warning(sample_pseudoabs(locations_sf, raster = grid_raster, n = 100),                 "There are fewer available cells for raster 'NA' (3 presences) than the requested 100 points. Only 52 will be returned.")
+  expect_warning(sample_pseudoabs(locations_sf, raster = grid_raster, n = 100),                 "There are fewer available cells for raster 'NA' (3 presences) than the requested 100 pseudoabsences. Only 52 will be returned.", fixed=TRUE)
   locations_sf <- locations_sf %>% dplyr::bind_cols(sf::st_coordinates(.))
   expect_no_error(sample_pseudoabs(locations_sf, coords = c("X", "Y"), raster = grid_raster, n = 25))
   locations_sf$X <- rep(0, 3)
diff --git a/tests/testthat/testthat-problems.rds b/tests/testthat/testthat-problems.rds
deleted file mode 100644
index 21e673b530bae9f0c79e5ab5f1fe5ca67204abc2..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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