Prepping v1.4.0 for CRAN submission. This version migrates the package to use the new QS2 format for saving and loading simulation results. Not backward compatible with QS.

Author: japilo

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: poems
 Type: Package
 Title: Pattern-Oriented Ensemble Modeling System
-Version: 1.3.3
+Version: 1.4.0
 Authors@R: c(
     person("Sean", "Haythorne", email = "[email protected]", role = "aut"),
     person("Damien", "Fordham", email = "[email protected]", role = "aut"),
@@ -30,7 +30,7 @@ Imports:
     trend (>= 1.1.4),
     truncnorm (>= 1.0),
     gdistance,
-    qs
+    qs2
 Collate: 
     'GenericClass.R'
     'Region.R'

NAMESPACE

@@ -41,6 +41,6 @@ importFrom(gdistance,geoCorrection)
 importFrom(gdistance,transition)
 importFrom(lhs,randomLHS)
 importFrom(metRology,qtri)
-importFrom(qs,qread)
+importFrom(qs2,qs_read)
 importFrom(trend,sens.slope)
 importFrom(truncnorm,qtruncnorm)

NEWS.md

@@ -1,3 +1,7 @@
+# version 1.4.0
+
+The R package `qs` will be deprecated soon, so `poems` has updated its `qs` dependency to `qs2`. Please note that `qs2` is not backward-compatible, so `poems` will no longer be able to handle `qs` data files. 
+
 # version 1.3.3
 ## Bug fixes
 - Fixed a bug that caused the `population_density` function to fail when population density was logistic and there were no growth rates (that is, a stagnant population).

R/Generator.R

@@ -81,7 +81,7 @@
 #'
 #' @importFrom R6 R6Class
 #' @importFrom metRology qtri
-#' @importFrom qs qread
+#' @importFrom qs2 qs_read
 #' @include SpatialModel.R
 #' @include GenerativeTemplate.R
 #' @export Generator
@@ -388,7 +388,7 @@ Generator <- R6Class(
     #' @param path_params Array of the names of the simulation sample
     #' parameters to be substituted (in order) into the path template.
     #' @param file_type File type raster \emph{"GRD"} (default), \emph{"TIF"},
-    #'  \emph{"RData/RDS"}, \emph{"QS"}, or \emph{"CSV"} to be read.
+    #'  \emph{"RData/RDS"}, \emph{"QS2"}, or \emph{"CSV"} to be read.
     add_file_template = function(
       param,
       path_template,
@@ -408,12 +408,12 @@ Generator <- R6Class(
               toupper(file_type) == "RDS" ||
               toupper(file_type) == "CSV" ||
               toupper(file_type) == "TIF" ||
-              toupper(file_type) == "QS"
+              toupper(file_type) == "QS2"
           ) {
             self$file_templates[[param]]$file_type <- toupper(file_type)
           } else {
             stop(
-              "The file type should be GRD (raster), TIF (raster), RDS, QS, or CSV",
+              "The file type should be GRD (raster), TIF (raster), RDS, QS2, or CSV",
               call. = FALSE
             )
           }
@@ -617,8 +617,8 @@ Generator <- R6Class(
             } else if (self$file_templates[[param]]$file_type == "RDS") {
               # RDS (RData)
               value_list[[param]] <- readRDS(file = file_path)
-            } else if (self$file_templates[[param]]$file_type == "QS") {
-              value_list[[param]] <- qread(file = file_path)
+            } else if (self$file_templates[[param]]$file_type == "QS2") {
+              value_list[[param]] <- qs_read(file = file_path)
             } else {
               # raster
               value_list[[param]] <- raster::brick(file_path)
@@ -687,10 +687,12 @@ Generator <- R6Class(
         sample_names <- names(sample)
         if (is.list(sample) && all(sample_names %in% c("mid", "window"))) {
           # window-based
-          if (is.character(sample$mid))
+          if (is.character(sample$mid)) {
             sample$mid <- self$get_attribute(sample$mid)
-          if (is.character(sample$window))
+          }
+          if (is.character(sample$window)) {
             sample$window <- self$get_attribute(sample$window)
+          }
           if (is.numeric(sample$mid) && is.numeric(sample$window)) {
             sample <- c(
               max(sample$mid - sample$window / 2, 0),

codemeta.json

@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/GlobalEcologyLab/poems",
   "issueTracker": "https://github.com/GlobalEcologyLab/poems/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "1.3.3",
+  "version": "1.4.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.5.0 (2025-04-11)",
+  "runtimePlatform": "R version 4.5.1 (2025-06-13)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -295,19 +295,19 @@
     },
     "13": {
       "@type": "SoftwareApplication",
-      "identifier": "qs",
-      "name": "qs",
+      "identifier": "qs2",
+      "name": "qs2",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://CRAN.R-project.org/package=qs"
+      "sameAs": "https://CRAN.R-project.org/package=qs2"
     },
     "SystemRequirements": null
   },
-  "fileSize": "6407.82KB",
+  "fileSize": "5287.888KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -357,7 +357,7 @@
       }
     }
   ],
-  "releaseNotes": "https://github.com/GlobalEcologyLab/poems/blob/master/NEWS.md",
+  "releaseNotes": "https://github.com/GlobalEcologyLab/poems/blob/main/NEWS.md",
   "readme": "https://github.com/GlobalEcologyLab/poems/blob/main/README.md",
   "contIntegration": ["https://app.codecov.io/gh/GlobalEcologyLab/poems?branch=main", "https://github.com/GlobalEcologyLab/poems/actions/workflows/R-CMD-check.yaml"],
   "developmentStatus": "https://www.repostatus.org/#active",

cran-comments.md

@@ -1,18 +1,25 @@
 ## Test environments
-* local macOS 15 install, Intel chip, R 4.5.0
+* local macOS 15.6.1 install, Apple Silicon chip, R 4.5.1
 * Windows, R-devel (via win-builder)
 * macOS, Apple Silicon chip, R 4.5.0 (via mac-builder)
 * Ubuntu 24.04, R-devel (via Github Actions)
-* Ubuntu 24.04, R 4.5.0 (via Github Actions)
+* Ubuntu 24.04, R 4.5.2 (via Github Actions)
 * Ubuntu 24.04, R 4.4.3 (via Github Actions)
 
 ## R CMD check results
 
 0 ERRORs, 0 WARNINGs, 0 NOTEs.
 
-## Past R CMD check results
+## Changes in this version
 
-`poems` did not have a dependency on R 4.1.0 as it should have. I have now updated the DESCRIPTION file.
+This version (1.4.0) updates the dependency from the deprecated `qs` package to `qs2`. 
+
+**Important note**: `qs2` is not backward-compatible with `qs`. Users with existing `qs` data files will need to convert them to `qs2` format or continue using an older version of `poems`.
+
+New features:
+* Added support for reading `.qs2` files in the Generator class via the file_type = "QS2" parameter
+* Added comprehensive test coverage for QS2 file handling (21 new test assertions)
+* Updated all documentation to reflect the qs2 migration
 
 ## Other notes
 

man/Generator.Rd

@@ -198,6 +198,136 @@ test_that("file template reading raster", {
   )
 })
 
+test_that("file template reading QS2 data frame", {
+  TEST_DIRECTORY <- test_path("test_inputs")
+  coordinates <- data.frame(x = c(1:4, 4:2), y = c(1, 1:4, 4:3))
+  occupancy_mask <- array(c(1, 1, 0, 0, 1, 1, 1))
+  generator <- Generator$new(
+    description = "Test generator", decimals = 4,
+    region = Region$new(coordinates = coordinates, use_raster = FALSE),
+    occupancy_mask = occupancy_mask
+  )
+  generator$set_attributes(attr1 = 1, attr2 = 2)
+  # Test QS2 data frame reading
+  generator$add_file_template("attr3",
+    path_template = file.path(TEST_DIRECTORY, "Test_%s_%s_df.qs2"),
+    path_params = c("attr1", "attr2"), file_type = "QS2"
+  )
+  test_data <- generator$read_file("attr3")
+  expect_is(test_data, "data.frame")
+  expect_equal(generator$attached$attr3, test_data)
+  expect_equal(generator$file_templates$attr3$file_type, "QS2")
+  generator$attached$attr3 <- test_data * 2
+  expect_equal(generator$get_attribute("attr3"), test_data * 2)
+  generator$attached$attr3 <- NULL # clear
+  expect_equal(generator$get_attribute("attr3"), test_data)
+  expect_equal(generator$attached$attr3, test_data)
+  generator$attached$attr3 <- NULL # clear
+  generator$outputs <- "attr3"
+  expect_equal(generator$get_attribute("attr3"), round(test_data * occupancy_mask, 4))
+  generator$attached$attr3 <- NULL # clear
+  generator$occupancy_mask <- array(1, c(7, 10))
+  generator$occupancy_mask[3:4, 5:8] <- 0
+  expect_equal(generator$get_attribute("attr3"), round(test_data * generator$occupancy_mask, 4))
+  generator$attached$attr3 <- NULL # clear
+  # Via nested aliases
+  generator$set_attributes(attr0 = list(first = 1, second = 2), attr1 = NULL, attr2 = NULL)
+  generator$attribute_aliases <- list(a1 = "attr0$first", a2 = "attr0$second", a3 = "attr3", a3_1 = "attr3[1]")
+  generator$add_file_template("attr3",
+    path_template = file.path(TEST_DIRECTORY, "Test_%s_%s_df.qs2"),
+    path_params = c("a1", "a2"), file_type = "QS2"
+  )
+  expect_equal(generator$get_attribute("a3"), round(test_data * generator$occupancy_mask, 4))
+  generator$attached$attr3 <- NULL # clear
+  expect_equal(generator$get_attribute("a3_1"), test_data[1])
+  # Generate rasters from QS2 data frame
+  region <- Region$new(coordinates = coordinates, use_raster = TRUE)
+  generator <- Generator$new(
+    description = "Test generator", decimals = 4, outputs = "attr3",
+    region = region, occupancy_mask = region$raster_from_values(occupancy_mask)
+  )
+  generator$add_generative_requirements(attr3 = "file")
+  generator$add_file_template("attr3",
+    path_template = file.path(TEST_DIRECTORY, "Test_%s_%s_df.qs2"),
+    path_params = c("attr1", "attr2"), file_type = "QS2"
+  )
+  generator$set_attributes(attr1 = 1, attr2 = 2)
+  expect_equal(
+    unname(generator$get_attribute("attr3")[region$region_indices]),
+    unname(round(as.matrix(test_data * occupancy_mask), 4))
+  )
+})
+
+test_that("file template reading QS2 raster", {
+  TEST_DIRECTORY <- test_path("test_inputs")
+  coordinates <- data.frame(x = c(1:4, 4:2), y = c(1, 1:4, 4:3))
+  region <- Region$new(coordinates = coordinates, use_raster = TRUE)
+  occupancy_mask <- array(1, c(7, 10))
+  occupancy_mask[3:4, 5:8] <- 0
+  raster_occupancy_mask <- raster::stack(replicate(10, raster::raster(
+    vals = region$region_raster[],
+    nrows = 4, ncol = 4,
+    xmn = 0, xmx = 4000, ymn = 0, ymx = 4000,
+    crs = "+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs"
+  )))
+  raster_occupancy_mask[][region$region_indices, ] <- occupancy_mask[raster_occupancy_mask[][region$region_indices, 1], ]
+  raster::crs(raster_occupancy_mask) <- raster::crs(region$region_raster)
+  raster::extent(raster_occupancy_mask) <- raster::extent(region$region_raster)
+  generator <- Generator$new(
+    description = "Test generator", decimals = 4,
+    region = Region$new(coordinates = coordinates, use_raster = TRUE),
+    occupancy_mask = raster_occupancy_mask
+  )
+  generator$set_attributes(attr1 = 1, attr2 = 2)
+  # Via QS2
+  generator$add_file_template("attr3",
+    path_template = file.path(TEST_DIRECTORY, "Test_%s_%s.qs2"),
+    path_params = c("attr1", "attr2"), file_type = "QS2"
+  )
+  test_raster <- generator$read_file("attr3")
+  expect_is(test_raster, "RasterBrick")
+  expect_equal(generator$file_templates$attr3$file_type, "QS2")
+  expect_equal(generator$attached$attr3[], test_raster[])
+  generator$attached$attr3 <- test_raster * 2
+  expect_equal(generator$get_attribute("attr3")[], test_raster[] * 2)
+  generator$attached$attr3 <- NULL # clear
+  expect_equal(generator$get_attribute("attr3")[], test_raster[])
+  generator$attached$attr3 <- NULL # clear
+  # Via nested aliases
+  generator$set_attributes(attr0 = list(first = 1, second = 2))
+  generator$attribute_aliases <- list(
+    a1 = "attr0$first", a2 = "attr0$second", a3 = "attr3", a3_8 = "attr3[8]",
+    a3_X5 = "attr3[][, 5]"
+  )
+  generator$add_file_template("attr3",
+    path_template = file.path(TEST_DIRECTORY, "Test_%s_%s.qs2"),
+    path_params = c("a1", "a2"), file_type = "QS2"
+  )
+  generator$outputs <- "attr3"
+  expect_equal(generator$get_attribute("a3")[], (round(test_raster, 4) * raster_occupancy_mask)[])
+  generator$attached$attr3 <- NULL # clear
+  expect_equal(generator$get_attribute("a3_8"), test_raster[8])
+  generator$attached$attr3 <- NULL # clear
+  expect_equal(generator$get_attribute("a3_X5"), test_raster[][, 5])
+  # Generate arrays from QS2 rasters
+  generator <- Generator$new(
+    description = "Test generator", decimals = 4, outputs = "attr3",
+    region = region, generate_rasters = FALSE,
+    occupancy_mask = raster_occupancy_mask
+  )
+  expect_equal(unname(generator$occupancy_mask), occupancy_mask)
+  generator$add_generative_requirements(attr3 = "file")
+  generator$add_file_template("attr3",
+    path_template = file.path(TEST_DIRECTORY, "Test_%s_%s.qs2"),
+    path_params = c("attr1", "attr2"), file_type = "QS2"
+  )
+  generator$set_attributes(attr1 = 1, attr2 = 2)
+  expect_equal(
+    unname(generator$get_attribute("attr3")),
+    unname(round(as.matrix(test_raster[region$region_indices] * occupancy_mask), 4))
+  )
+})
+
 test_that("function execution template", {
   TEST_DIRECTORY <- test_path("test_inputs")
   generator <- Generator$new(description = "Test generator", decimals = 4, outputs = "attr4")