Merge pull request #164 from pfuehrlich-pik/master

fix read.magpie for nc files

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '120989154'
+ValidationKey: '121045680'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'magclass: Data Class and Tools for Handling Spatial-Temporal Data'
-version: 6.13.1
-date-released: '2024-01-12'
+version: 6.13.2
+date-released: '2024-01-18'
 abstract: Data class for increased interoperability working with spatial-temporal
   data together with corresponding functions and methods (conversions, basic calculations
   and basic data manipulation). The class distinguishes between spatial, temporal

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: magclass
 Title: Data Class and Tools for Handling Spatial-Temporal Data
-Version: 6.13.1
-Date: 2024-01-12
+Version: 6.13.2
+Date: 2024-01-18
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "dietrich@pik-potsdam.de", role = c("aut", "cre")),
     person("Benjamin Leon", "Bodirsky", , "bodirsky@pik-potsdam.de", role = "aut"),

R/as.magpie.R

@@ -333,7 +333,8 @@ setMethod("as.magpie",
   crs <- NULL
   if (inherits(x, "SpatRaster")) {
     if (!requireNamespace("terra", quietly = TRUE)) stop("The package \"terra\" is required for raster conversions!")
-    df <- as.data.frame(x, na.rm = TRUE, xy = TRUE)
+    df <- as.data.frame(x, xy = TRUE)
+    df <- df[rowSums(is.na(df)) != ncol(df), ] # remove rows with all NAs
     df$x <- sub(".", "p", df$x, fixed = TRUE)
     df$y <- sub(".", "p", df$y, fixed = TRUE)
     idVars <- c("x", "y")

R/magclass-package.R

@@ -1,26 +1,15 @@
-
-
 #' Data Class and Tools for Handling Spatial-Temporal Data
-#' 
-#' Data class for increased interoperability working with spatial-temporal 
-#' data together with corresponding functions and methods (conversions, 
+#'
+#' Data class for increased interoperability working with spatial-temporal
+#' data together with corresponding functions and methods (conversions,
 #' basic calculations and basic data manipulation). The class distinguishes
 #' between spatial, temporal and other dimensions to facilitate the development
 #' and interoperability of tools build for it. Additional features are name-based
-#' addressing of data and internal consistency checks (e.g. checking for the 
+#' addressing of data and internal consistency checks (e.g. checking for the
 #' right data order in calculations).
-#' 
+#'
 #' @name magclass-package
 #' @aliases magclass-package magclass
-#' @docType package
-#' @author 
-#' Maintainer: Jan Philipp Dietrich <dietrich@@pik-potsdam.de>
-NULL
-
-
-
-
-
-
-
-
+#' @author
+#' Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
+"_PACKAGE"

R/read.magpie.R

@@ -119,15 +119,32 @@ read.magpie <- function(file_name, file_folder = "", file_type = NULL, # nolint:
       x <- terra::rast(fileName)
       if (all(grepl("Time=[0-9]+", names(x)))) {
         names(x) <- sub("(.+)_Time=([0-9]+)", "y\\2..\\1", names(x))
-      } else if (all(grepl("_", names(x)))) {
-        names(x) <- vapply(names(x), function(n) {
-          parts <- strsplit(n, "_")[[1]] # e.g. "AFR_3" where 3 means the third entry in terra::time(x)
-          year <- terra::time(x)[as.integer(parts[2])]
-          if (is.na(year)) {
-            year <- as.integer(parts[2])
+      } else {
+        parts <- strsplit(names(x), "_")
+        lastParts <- vapply(parts, function(p) p[length(p)], character(1))
+        timeIndices <- suppressSpecificWarnings(as.numeric(lastParts), "NAs introduced by coercion")
+
+        terraTime <- terra::time(x)
+
+        if (any(is.na(terraTime)) && requireNamespace("ncdf4", quietly = TRUE)) {
+          nc <- ncdf4::nc_open(fileName)
+          withr::defer(ncdf4::nc_close(nc))
+          if ("time" %in% names(nc$dim)) {
+            terraTime <- rep_len(nc$dim$time$vals, terra::nlyr(x))
+            if (terra::nlyr(x) %% nc$dim$time$len != 0) {
+              warning("Found ", terra::nlyr(x), " layers, but ",
+                      nc$dim$time$len, " time steps. Now using ",
+                      terraTime)
+            }
           }
-          return(paste0("y", year, "..", parts[1]))
-        }, character(1))
+        }
+
+        if (all(timeIndices %in% seq_along(terraTime))) {
+          names(x) <- paste0("y", terraTime[timeIndices], "..",
+                             vapply(parts, function(p) paste0(p[-length(p)], collapse = "_"), character(1)))
+        } else if (all(!is.na(terraTime))) {
+          names(x) <- paste0("y", terraTime, "..", names(x))
+        }
       }
 
       readMagpie <- clean_magpie(as.magpie(x))

README.md

@@ -1,6 +1,6 @@
 # Data Class and Tools for Handling Spatial-Temporal Data
 
-R package **magclass**, version **6.13.1**
+R package **magclass**, version **6.13.2**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/magclass)](https://cran.r-project.org/package=magclass) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1158580.svg)](https://doi.org/10.5281/zenodo.1158580) [![R build status](https://github.com/pik-piam/magclass/workflows/check/badge.svg)](https://github.com/pik-piam/magclass/actions) [![codecov](https://codecov.io/gh/pik-piam/magclass/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/magclass) [![r-universe](https://pik-piam.r-universe.dev/badges/magclass)](https://pik-piam.r-universe.dev/builds)
 
@@ -56,7 +56,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **magclass** in publications use:
 
-Dietrich J, Bodirsky B, Bonsch M, Humpenoeder F, Bi S, Karstens K, Leip D, Sauer P (2024). _magclass: Data Class and Tools for Handling Spatial-Temporal Data_. doi:10.5281/zenodo.1158580 <https://doi.org/10.5281/zenodo.1158580>, R package version 6.13.1, <https://github.com/pik-piam/magclass>.
+Dietrich J, Bodirsky B, Bonsch M, Humpenoeder F, Bi S, Karstens K, Leip D, Sauer P (2024). _magclass: Data Class and Tools for Handling Spatial-Temporal Data_. doi: 10.5281/zenodo.1158580 (URL: https://doi.org/10.5281/zenodo.1158580), R package version 6.13.2, <URL: https://github.com/pik-piam/magclass>.
 
 A BibTeX entry for LaTeX users is
 
@@ -65,8 +65,8 @@ A BibTeX entry for LaTeX users is
   title = {magclass: Data Class and Tools for Handling Spatial-Temporal Data},
   author = {Jan Philipp Dietrich and Benjamin Leon Bodirsky and Markus Bonsch and Florian Humpenoeder and Stephen Bi and Kristine Karstens and Debbora Leip and Pascal Sauer},
   year = {2024},
-  note = {R package version 6.13.1},
-  url = {https://github.com/pik-piam/magclass},
+  note = {R package version 6.13.2},
   doi = {10.5281/zenodo.1158580},
+  url = {https://github.com/pik-piam/magclass},
 }
 ```