From 5f5d2e067905a0a144e7706a8fa4a4466edbce79 Mon Sep 17 00:00:00 2001
From: Jeffrey Hanson <jeffrey.hanson@uqconnect.edu.au>
Date: Tue, 2 Nov 2021 16:07:56 +1300
Subject: [PATCH] fix issue when upper elev < lower elev

---
 R/format_spp_data.R                       | 12 ++++
 tests/testthat/test_create_spp_aoh_data.R | 71 +++++++++++++++++++++++
 2 files changed, 83 insertions(+)

diff --git a/R/format_spp_data.R b/R/format_spp_data.R
index b9b047e6..276124c5 100644
--- a/R/format_spp_data.R
+++ b/R/format_spp_data.R
@@ -90,6 +90,18 @@ format_spp_data <- function(x,
   spp_summary_data$elevation_lower[idx] <- -Inf
   idx <- is.na(spp_summary_data$elevation_upper)
   spp_summary_data$elevation_upper[idx] <- Inf
+  ## ensure that lower elevation limit is <= upper elevation limit
+  idx <- which(
+    is.finite(spp_summary_data$elevation_lower) &
+    is.finite(spp_summary_data$elevation_upper)
+  )
+  if (length(idx) > 0) {
+    l <- spp_summary_data$elevation_lower[idx]
+    u <- spp_summary_data$elevation_upper[idx]
+    spp_summary_data$elevation_lower[idx] <- pmin(l, u)
+    spp_summary_data$elevation_upper[idx] <- pmax(l, u)
+    rm(l, u)
+  }
   ## extract relevant columns
   nms <- c("id_no", "elevation_lower", "elevation_upper")
   spp_summary_data <- spp_summary_data[, nms, drop = FALSE]
diff --git a/tests/testthat/test_create_spp_aoh_data.R b/tests/testthat/test_create_spp_aoh_data.R
index c1a41feb..c2e4aed4 100644
--- a/tests/testthat/test_create_spp_aoh_data.R
+++ b/tests/testthat/test_create_spp_aoh_data.R
@@ -134,6 +134,77 @@ test_that("some species missing habitat data", {
   unlink(output_dir2, recursive = TRUE)
 })
 
+test_that("species with reversed elevation limits", {
+  # skip if needed
+  skip_on_cran()
+  # specify file path
+  f <- system.file("testdata", "SIMULATED_SPECIES.zip", package = "aoh")
+  elevation_data <- terra::rast(
+    system.file("testdata", "sim_elevation_data.tif", package = "aoh")
+  )
+  habitat_data <- terra::rast(
+    system.file("testdata", "sim_habitat_data.tif", package = "aoh")
+  )
+  spp_habitat_data <- read.csv(
+    system.file("testdata", "sim_spp_habitat_data.csv", package = "aoh"),
+    sep = ",", header = TRUE
+  )
+  spp_summary_data <- read.csv(
+    system.file("testdata", "sim_spp_summary_data.csv", package = "aoh"),
+    sep = ",", header = TRUE
+  )
+  # load data
+  d <- read_spp_range_data(f)
+  # create copy of spp_summary_data with reversed elevation data
+  spp_summary_data_alt <- spp_summary_data
+  spp_summary_data_alt$elevation_lower <- spp_summary_data$elevation_upper
+  spp_summary_data_alt$elevation_upper <- spp_summary_data$elevation_lower
+  # create output dirs
+  output_dir1 <- tempfile()
+  output_dir2 <- tempfile()
+  dir.create(output_dir1, showWarnings = FALSE, recursive = TRUE)
+  dir.create(output_dir2, showWarnings = FALSE, recursive = TRUE)
+  # create objects
+  x1 <- create_spp_aoh_data(
+    x = d,
+    output_dir = output_dir1,
+    habitat_data = habitat_data,
+    elevation_data = elevation_data,
+    spp_habitat_data = spp_habitat_data,
+    spp_summary_data = spp_summary_data,
+    force = TRUE,
+    verbose = FALSE
+  )
+  x2 <- create_spp_aoh_data(
+    x = d,
+    output_dir = output_dir2,
+    habitat_data = habitat_data,
+    elevation_data = elevation_data,
+    spp_habitat_data = spp_habitat_data,
+    spp_summary_data = spp_summary_data_alt,
+    force = TRUE,
+    verbose = FALSE
+  )
+  # tests
+  expect_equal(
+    dplyr::select(x1, -path),
+    dplyr::select(x2, -path)
+  )
+  expect_equal(
+    lapply(
+      x1$path,
+      function(x) terra::values(terra::rast(x))
+    ),
+    lapply(
+      x2$path,
+      function(x) terra::values(terra::rast(x))
+    )
+  )
+  # clean up
+  unlink(output_dir1, recursive = TRUE)
+  unlink(output_dir2, recursive = TRUE)
+})
+
 test_that("GDAL processing", {
   # skip if needed
   skip_on_cran()