Merge pull request #44 from pascal-sauer/master

replace speed_aggregate, remove luscale dependency

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '28963480'
+ValidationKey: '29179500'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: 2c9f875913ee60ca25ce70243dc24d5b6415598c  # frozen: v4.6.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: 7910e0323d7213f34275a7a562b9ef0fde8ce1b9  # frozen: v0.4.2
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

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: 'mrmagpie: madrat based MAgPIE Input Data Library'
-version: 1.46.0
-date-released: '2024-04-25'
+version: 1.47.0
+date-released: '2024-05-07'
 abstract: Provides functions for MAgPIE country and cellular input data generation.
 authors:
 - family-names: Karstens

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrmagpie
 Title: madrat based MAgPIE Input Data Library
-Version: 1.46.0
-Date: 2024-04-25
+Version: 1.47.0
+Date: 2024-05-07
 Authors@R: c(
     person("Kristine", "Karstens", , "[email protected]", role = c("aut", "cre")),
     person("Jan Philipp", "Dietrich", , "[email protected]", role = "aut"),
@@ -38,7 +38,6 @@ Imports:
     ggplot2,
     lpjclass,
     luplot (>= 3.56.0),
-    luscale,
     magpiesets,
     mstools,
     ncdf4,

NAMESPACE

@@ -35,7 +35,6 @@ importFrom(dplyr,select)
 importFrom(ggplot2,ggsave)
 importFrom(lpjclass,read.LPJ_input)
 importFrom(luplot,plotregionscluster)
-importFrom(luscale,speed_aggregate)
 importFrom(madrat,calcOutput)
 importFrom(madrat,getConfig)
 importFrom(madrat,readSource)

R/calcClusterKMeans.R

@@ -12,7 +12,7 @@
 #'                    for the cluster distribution, e.g. weight=c(AFR=3,EUR=0.5).
 #'                    weight > 1 will grant more cluster to a region and
 #'                    weight < 1 less cluster than by default.
-#' @param cpr         cells-per-region information as returned by cluster_per_region.
+#' @param cpr         cells-per-region information as returned by toolClusterPerRegionManual.
 #'                    Weight and ncluster are ignored in case that cpr is provided!
 #' @param seed        a single value, interpreted as an integer, or NULL, to define seed for random calculations
 #' @param clusterdata similarity data to be used to determine clusters: yield_airrig (current default)
@@ -21,7 +21,7 @@
 #' @return A mapping between regions and clusters
 #' @author Jan Philipp Dietrich
 #' @importFrom stats kmeans
-#' @seealso \code{\link{toolClusterPerRegion}}, \code{\link{calcClusterHierarchical}}
+#' @seealso \code{\link{toolClusterPerRegionManual}}, \code{\link{calcClusterHierarchical}}
 #' @export
 
 calcClusterKMeans <- function(regionscode, ncluster, weight = NULL, cpr = NULL, seed = 42,

R/calcClusterTreeHierarchical.R

@@ -20,16 +20,13 @@
 #' @author Jan Philipp Dietrich
 #' @importFrom magclass getCells ncells getRegions getItems
 #' @importFrom stats hclust cutree
-#' @seealso \code{\link{cluster_per_region}}, \code{\link{mag_kmeans}},
-#' \code{\link{clusterspam}}
 #' @export
-
 calcClusterTreeHierarchical <- function(regionscode, mode = "h", weight = NULL,
                                         lpjml = c(natveg = "LPJmL4", crop = "LPJmL5"), clusterdata = "yield_airrig") {
 
   # read in cluster base data
   cdata <- toolApplyRegionNames(cdata = calcOutput("ClusterBase", lpjml = lpjml,
-                                                  clusterdata = clusterdata, aggregate = FALSE),
+                                                   clusterdata = clusterdata, aggregate = FALSE),
                                 regionscode = regionscode)
   # transform to array
   cdata <- as.array(cdata)[, , ]

R/readMAPSPAM.R

@@ -4,7 +4,6 @@
 #' @author Edna J. Molina Bacca, Felicitas Beier
 #' @param subtype It can be either "harvested" or "physical" area
 #' @importFrom terra rast values crds aggregate
-#' @importFrom luscale speed_aggregate
 #' @importFrom mrcommons toolGetMappingCoord2Country
 #' @importFrom magpiesets findset
 #' @importFrom magclass new.magpie
@@ -128,8 +127,7 @@ readMAPSPAM <- function(subtype = "harvested") {
 
     .convertMag <- function(x) {
       spam2Magpie <- spam2Magpie[spam2Magpie$SPAM %in% getNames(x), ]
-      x           <- luscale::speed_aggregate(x, rel = spam2Magpie,
-                                              from = "SPAM", to = "Magpie", dim = 3)
+      x           <- toolAggregate(x, rel = spam2Magpie, from = "SPAM", to = "Magpie", dim = 3)
       return(x)
     }
 

README.md

@@ -1,6 +1,6 @@
 # madrat based MAgPIE Input Data Library
 
-R package **mrmagpie**, version **1.46.0**
+R package **mrmagpie**, version **1.47.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrmagpie)](https://cran.r-project.org/package=mrmagpie) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4319612.svg)](https://doi.org/10.5281/zenodo.4319612) [![R build status](https://github.com/pik-piam/mrmagpie/workflows/check/badge.svg)](https://github.com/pik-piam/mrmagpie/actions) [![codecov](https://codecov.io/gh/pik-piam/mrmagpie/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrmagpie) [![r-universe](https://pik-piam.r-universe.dev/badges/mrmagpie)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Kristine Karstens <karstens@pik-p
 
 To cite package **mrmagpie** in publications use:
 
-Karstens K, Dietrich J, Chen D, Windisch M, Alves M, Beier F, Köberle A, v. Jeetze P, Mishra A, Humpenoeder F, Sauer P (2024). _mrmagpie: madrat based MAgPIE Input Data Library_. doi:10.5281/zenodo.4319612 <https://doi.org/10.5281/zenodo.4319612>, R package version 1.46.0, <https://github.com/pik-piam/mrmagpie>.
+Karstens K, Dietrich J, Chen D, Windisch M, Alves M, Beier F, Köberle A, v. Jeetze P, Mishra A, Humpenoeder F, Sauer P (2024). _mrmagpie: madrat based MAgPIE Input Data Library_. doi:10.5281/zenodo.4319612 <https://doi.org/10.5281/zenodo.4319612>, R package version 1.47.0, <https://github.com/pik-piam/mrmagpie>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,8 +48,8 @@ A BibTeX entry for LaTeX users is
   title = {mrmagpie: madrat based MAgPIE Input Data Library},
   author = {Kristine Karstens and Jan Philipp Dietrich and David Chen and Michael Windisch and Marcos Alves and Felicitas Beier and Alexandre Köberle and Patrick {v. Jeetze} and Abhijeet Mishra and Florian Humpenoeder and Pascal Sauer},
   year = {2024},
-  note = {R package version 1.46.0},
-  doi = {10.5281/zenodo.4319612},
+  note = {R package version 1.47.0},
   url = {https://github.com/pik-piam/mrmagpie},
+  doi = {10.5281/zenodo.4319612},
 }
 ```