Resolve "Migrate from raster to terra"

.Rbuildignore

@@ -5,3 +5,4 @@
 ^\README.Rmd$
 ^dev_history\.R$
 ^\.github$
+^data-raw$

.gitignore

@@ -6,3 +6,4 @@ src/*.so
 src/*.dll
 README.html
 README.Rmd
+data-raw/*.RData

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: remote
 Title: Empirical Orthogonal Teleconnections in R
-Version: 1.2.3
-Authors@R:
+Version: 1.2.3.9004
+Authors@R: 
     c(person(given = "Tim",
              family = "Appelhans",
              role = c("cre", "aut"),
@@ -25,24 +25,29 @@ Description: Empirical orthogonal teleconnections in R.
     space and time, EOT analysis produces patterns that are orthogonal in
     either space or time.
 License: GPL (>= 3) | file LICENSE
-Depends:
+Depends: 
     Rcpp (>= 0.10.3),
     raster,
-    methods
-Imports:
+    methods,
+    R (>= 3.5)
+Imports: 
     grDevices,
     gridExtra,
     latticeExtra,
     mapdata,
     scales, 
     stats, 
+    terra,
     utils
-Suggests:
-    maps,
-    lattice,
+Suggests: 
+    checkmate,
     grid,
-    sp
+    lattice,
+    maps,
+    sp, 
+    tinytest
 LinkingTo: Rcpp
-RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
+Config/roxygen2/version: 8.0.0
+LazyData: true

NAMESPACE

@@ -32,6 +32,7 @@ import(methods)
 import(parallel)
 import(raster)
 import(scales)
+import(terra)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,hcl)
 importFrom(stats,cov.wt)

NEWS.md

@@ -1,3 +1,14 @@
+# remote 1.2.3.9004 (2026-07-15)
+
+#### ✨ features and improvements
+
+#### 🐛 bug fixes
+
+#### 💬 documentation etc
+
+#### 🍬 miscellaneous
+
+
 # remote 1.2.3 (2025-04-12)
 
 #### 💬 documentation etc

R/anomalize.R

@@ -1,41 +1,81 @@
-#' Create an anomaly RasterStack 
+methods::setGeneric(
+  "anomalize"
+  , function(x, ...) {
+    standardGeneric("anomalize")
+  }
+)
+
+#' Create an anomaly raster series 
 #' 
-#' @description
-#' The function creates an anomaly RasterStack either based on the
-#' overall mean of the original stack, or a supplied reference RasterLayer.
-#' For the creation of seasonal anomalies use [deseason()].
+#' @description The function creates an anomaly raster series either based on 
+#'   the overall mean of the original series, or a supplied reference raster. 
+#'   For the creation of seasonal anomalies use [deseason()].
 #' 
-#' @param x a RasterStack
-#' @param reference an optional RasterLayer to be used as the reference 
-#' @param ... additional arguments passed to [raster::calc()] (and, in turn, 
-#' [raster::writeRaster()]) which is used under the hood
+#' @param x A `SpatRaster` (or `Raster*`) series.
+#' @param reference An optional `SpatRaster` (or `RasterLayer`) to be used as 
+#'   the reference.
+#' @param ... Additional arguments passed to [terra::app()] when 'reference' is 
+#'   `NULL` (e.g. 'cores', 'filename'), or to the underlying `SpatRaster` method
+#'   for `Raster*` input.
 #' 
-#' @return an anomaly RasterStack
+#' @return An anomaly `SpatRaster` series.
 #' 
 #' @seealso
-#' [deseason()], [denoise()], [raster::calc()]
+#' [deseason()], [denoise()]
 #' 
 #' @export anomalize
+#' @name anomalize
 #' 
 #' @examples
-#' data(australiaGPCP)
-#' 
-#' aus_anom <- anomalize(australiaGPCP)
+#' pcp = terra::unwrap(australiaGPCP)
+#' pcp_anom = anomalize(pcp)
 #' 
-#' opar <- par(mfrow = c(1,2))
-#' plot(australiaGPCP[[10]], main = "original")
-#' plot(aus_anom[[10]], main = "anomalized")
+#' opar = par(mfrow = c(1,2))
+#' plot(pcp[[10]], main = "original")
+#' plot(pcp_anom[[10]], main = "anomalized")
 #' par(opar)
-anomalize <- function(x, 
-                      reference = NULL, 
-                      ...) {
-
-  if (is.null(reference)) {
-    mn <- raster::calc(x, fun = mean, ...)
-  } else {
-    mn <- reference
+
+
+################################################################################
+### function using 'RasterStackBrick' ##########################################
+#' @aliases anomalize,RasterStackBrick-method
+#' @rdname anomalize
+methods::setMethod(
+  "anomalize"
+  , signature(x = "RasterStackBrick")
+  , function(
+    x
+    , ...
+  ) {
+    anomalize(
+      terra::rast(x)
+      , ...
+    )
+  }
+)
+
+
+################################################################################
+### function using 'SpatRaster' ################################################
+#' @aliases anomalize,SpatRaster-method
+#' @rdname anomalize
+methods::setMethod(
+  "anomalize"
+  , signature(x = "SpatRaster")
+  , function(
+    x
+    , reference = NULL
+    , ...
+  ) {
+
+    if (is.null(reference)) {
+      reference = terra::app(
+        x
+        , fun = mean
+        , ...
+      )
+    }
+
+    return(x - reference)
   }
-
-  return(x - mn)
-
-}
+)

R/calcVar.R

@@ -1,33 +1,70 @@
-#' Calculate space-time variance of a RasterStack or RasterBrick
+methods::setGeneric(
+  "calcVar"
+  , function(x, ...) {
+    standardGeneric("calcVar")
+  }
+)
+
+#' Calculate space-time variance of a raster series
 #' 
-#' @description
-#' The function calculates the (optionally standardised) space-time 
-#' variance of a RasterStack or RasterBrick. 
+#' @description The function calculates the (optionally standardised) space-time 
+#'   variance of a raster series. 
 #' 
-#' @param x a RasterStack or RasterBrick
-#' @param standardised logical. 
-#' @param ... currently not used
+#' @param x A `SpatRaster` (or `Raster*`) series.
+#' @param standardised `logical`, defaults to `FALSE`. 
+#' @param ... For `SpatRaster` input: currently not used. For `Raster*` input: 
+#'   arguments passed to the underlying `SpatRaster` method.
 #' 
-#' @return the mean (optionally standardised) space-time variance.
+#' @return The mean (optionally standardised) space-time variance as `numeric`.
 #' 
 #' @export calcVar
+#' @name calcVar
 #' 
-#' @examples 
-#' data("pacificSST")
+#' @examples
+#' sst = terra::unwrap(pacificSST)
 #' 
-#' calcVar(pacificSST)
-calcVar <- function(x, standardised = FALSE, ...) {
-
-  if (!standardised) {
-    t <- mean(apply(raster::getValues(x), 1, var, na.rm = TRUE), 
-              na.rm = TRUE)
-    s <- mean(apply(raster::getValues(x), 2, var, na.rm = TRUE), 
-              na.rm = TRUE)
-    vrnc <- t + s
-  } else {
-    vrnc <- var(as.vector(raster::getValues(x)), na.rm = TRUE)
+#' calcVar(sst) # default non-standardised
+#' calcVar(sst, standardised = TRUE)
+
+
+################################################################################
+### function using 'RasterStackBrick' ##########################################
+#' @aliases calcVar,RasterStackBrick-method
+#' @rdname calcVar
+methods::setMethod(
+  "calcVar"
+  , signature(x = "RasterStackBrick")
+  , function(
+    x
+    , ...
+  ) {
+    calcVar(
+      terra::rast(x)
+      , ...
+    )
   }
+)
+
+
+################################################################################
+### function using 'SpatRaster' ################################################
+#' @aliases calcVar,SpatRaster-method
+#' @rdname calcVar
+methods::setMethod(
+  "calcVar"
+  , signature(x = "SpatRaster")
+  , function(x, standardised = FALSE, ...) {
 
-  return(vrnc)
-
-}
+    if (!standardised) {
+      # compute variance across time and space, leveraging c++ functions for 
+      # speed (see `?terra::app` for details)
+      t <- mean(terra::values(terra::app(x, "sd", na.rm = TRUE)^2)[, 1L])
+      s <- mean((terra::global(x, fun = "sd", na.rm = TRUE)[, 1L])^2)
+      vrnc <- t + s
+    } else {
+      vrnc <- var(as.vector(terra::values(x)), na.rm = TRUE)
+    }
+
+    return(vrnc)
+  }
+)