add prcomp method

DESCRIPTION

@@ -90,39 +90,40 @@ VignetteBuilder: knitr
 Encoding: UTF-8
 RoxygenNote: 7.3.1
 Collate: 
-    'init.R'
-    'stars.R'
-    'read.R'
-    'sf.R'
+    'aggregate.R'
+    'cubble.R'
+    'datasets.R'
     'dimensions.R'
-    'values.R'
-    'plot.R'
-    'tidyverse.R'
-    'transform.R'
-    'ops.R'
-    'write.R'
-    'raster.R'
-    'sp.R'
-    'spacetime.R'
+    'extract.R'
+    'factors.R'
+    'geom.R'
+    'gt.R'
+    'init.R'
+    'intervals.R'
+    'mdim.R'
+    'mosaic.R'
     'ncdf.R'
     'ncproxy.R'
+    'OpenStreetMap.R'
+    'ops.R'
+    'plot.R'
+    'prcomp.R'
     'proxy.R'
-    'factors.R'
     'rasterize.R'
+    'raster.R'
+    'read.R'
     'rotate.R'
+    'sample.R'
+    'sf.R'
+    'spacetime.R'
+    'spatstat.R'
+    'sp.R'
+    'stars.R'
     'subset.R'
+    'tidyverse.R'
+    'tile.R'
+    'transform.R'
+    'values.R'
     'warp.R'
-    'aggregate.R'
+    'write.R'
     'xts.R'
-    'intervals.R'
-    'geom.R'
-    'mosaic.R'
-    'spatstat.R'
-    'OpenStreetMap.R'
-    'sample.R'
-    'extract.R'
-    'datasets.R'
-    'tile.R'
-    'mdim.R'
-    'cubble.R'
-    'gt.R'

NAMESPACE

@@ -70,6 +70,8 @@ S3method(merge,stars_proxy)
 S3method(plot,nc_proxy)
 S3method(plot,stars)
 S3method(plot,stars_proxy)
+S3method(prcomp,stars)
+S3method(prcomp,stars_proxy)
 S3method(predict,stars)
 S3method(predict,stars_proxy)
 S3method(print,dimensions)
@@ -234,6 +236,7 @@ importFrom(stats,aggregate)
 importFrom(stats,complete.cases)
 importFrom(stats,na.omit)
 importFrom(stats,na.pass)
+importFrom(stats,prcomp)
 importFrom(stats,predict)
 importFrom(stats,quantile)
 importFrom(stats,runif)

NEWS.md

@@ -1,5 +1,7 @@
 # version 0.6-5
 
+* add `prcomp()` methods for `stars` and `stars_proxy` objects, working on attributes or last dimension
+
 * `st_rasterize()` with `align=TRUE` returns `NA` values where there are no data; #668
 
 * `read_mdim()` reads tables with composity type, returning a `data.frame` in that case; #659

R/init.R

@@ -1,7 +1,7 @@
 #' @importFrom graphics image.default image par plot title box text axis plot.new plot.window rasterImage layout lcm contour hist strwidth
 #' @importFrom grDevices dev.capabilities dev.size grey rgb col2rgb cm
 #' @importFrom utils head tail setTxtProgressBar txtProgressBar packageVersion methods modifyList
-#' @importFrom stats na.omit runif aggregate setNames predict quantile var complete.cases na.pass time
+#' @importFrom stats na.omit runif aggregate setNames predict quantile var complete.cases na.pass time prcomp
 #' @importFrom tools file_ext
 #' @importFrom methods as slotNames new slot
 #' @importFrom abind abind adrop asub

R/prcomp.R

@@ -0,0 +1,30 @@
+#' @name prcomp
+#' @param downsample see \link{st_as_stars}
+#' @export
+prcomp.stars_proxy = function(x, ..., downsample = 0) {
+	prcomp(st_as_stars(x, downsample = downsample), ...)
+}
+
+#' Principle components of stars object
+#'
+#' Compute principle components of stars object
+#' @param x object of class `stars` or `stars_proxy`
+#' @param quiet logical; if `TRUE`, suppress message that PCs will be computed on last dimension; see details
+#' @param ... see \link[stats]{prcomp}
+#' @details if `x` has only one attribute, principle components will be computed in the space of the last dimension of `x`
+#' to predict PC scores into a `stars` object, use \link{predict.stars}; see example below
+#' @name prcomp
+#' @value object of class `prcomp`, see \link[stats]{prcomp}
+#' @export
+#' @examples
+#' l7 = split(st_as_stars(L7_ETMs), 3) # use bands as features
+#' l7 |> prcomp() |> plot()
+#' l7 |> prcomp() |> predict(l7, model = _) |> merge() |> plot()
+prcomp.stars = function(x, ..., quiet = FALSE) {
+	if (length(x) == 1) {
+		if (!quiet)
+			message(paste0("computing PCs over dimension `", tail(names(dim(x)), 1), "'"))
+		x = split(x, length(dim(x)))
+	}
+	prcomp(as.data.frame(lapply(x, as.vector)), ...)
+}