Merge pull request #12 from pascal-sauer/master

major cleanup

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '72254000'
+ValidationKey: '7948400'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.gitignore

@@ -2,4 +2,3 @@
 .Rhistory
 .RData
 .Ruserdata
-/man/

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: 'luplot: Landuse Plot Library'
-version: 3.64.0
-date-released: '2024-05-07'
+version: 4.0.0
+date-released: '2024-05-28'
 abstract: Some useful functions to plot data such as a map plot function for MAgPIE
   objects.
 authors:
@@ -40,6 +40,9 @@ authors:
 - family-names: Chen
   given-names: David
   email: [email protected]
+- family-names: Sauer
+  given-names: Pascal
+  email: [email protected]
 license: LGPL-3.0
 repository-code: https://github.com/pik-piam/luplot
 

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: luplot
 Title: Landuse Plot Library
-Version: 3.64.0
-Date: 2024-05-07
+Version: 4.0.0
+Date: 2024-05-28
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
     person("Jan Philipp", "Dietrich", , "[email protected]", role = "aut"),
@@ -14,35 +14,31 @@ Authors@R: c(
     person("David", "Klein", , "[email protected]", role = "aut"),
     person("Susanne", "Rolinski", , "[email protected]", role = "aut"),
     person("Xiaoxi", "Wang", , "[email protected]", role = "aut"),
-    person("David", "Chen", , "[email protected]", role = "aut")
+    person("David", "Chen", , "[email protected]", role = "aut"),
+    person("Pascal", "Sauer", , "[email protected]", role = "aut")
   )
 Maintainer: Benjamin Bodirsky <[email protected]>
 Description: Some useful functions to plot data such as a map plot
     function for MAgPIE objects.
 License: LGPL-3 | file LICENSE
 URL: https://github.com/pik-piam/luplot
 Depends:
-    R (>= 2.15.1),
-    magclass
+    magclass,
+    R (>= 2.15.1)
 Imports:
-    RColorBrewer,
     data.table,
-    dplyr,
-    fields,
     ggplot2,
-    grDevices,
     graphics,
-    luscale,
+    grDevices,
+    gridExtra,
     lusweave,
-    magpiesets,
     mip,
+    mstools (>= 0.6.0),
     quitte,
+    RColorBrewer,
     reshape2,
     rworldmap (>= 1.3.8),
-    sp,
-    xml2,
-    gridExtra,
-    mstools (>= 0.6.0)
+    utils
 Suggests: 
     covr
 Encoding: UTF-8

NAMESPACE

@@ -1,49 +1,27 @@
 # Generated by roxygen2: do not edit by hand
 
-export(aggregate_for_plot)
-export(alloc_plot)
+export(aggregateForPlot)
 export(as.ggplot)
-export(comparisonplot)
 export(deco_plot)
-export(get_layout_parameters)
-export(gg.reg.x.crop)
 export(gginput)
-export(histoplot)
-export(histoplot2)
-export(magpie2ggplot)
 export(magpie2ggplot2)
-export(magpie2map)
-export(map2image)
-export(mipAreaOverlapFirstNameFacetSecondNameStacked)
 export(nice_colors)
-export(nitrogen_sankey)
-export(performancePlot)
 export(plotCorrHist2D)
-export(plotNbudget)
 export(plotRegionMapping)
-export(plotRegions)
-export(plotUtilization)
 export(plotcountrymap)
-export(plotmap)
 export(plotmap2)
-export(plotmap_discrete)
 export(plotregionscluster)
 export(qualityMeasure)
-export(scratch_legend)
-export(scratch_plot)
 export(showcolors)
 export(swoutput)
 export(whereplot)
 import(magclass)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(data.table,data.table)
-importFrom(dplyr,bind_rows)
-importFrom(fields,image.plot)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,annotate)
-importFrom(ggplot2,annotation_raster)
 importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,coord_fixed)
 importFrom(ggplot2,coord_flip)
@@ -71,13 +49,11 @@ importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,guide_colorbar)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
-importFrom(ggplot2,label_wrap_gen)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,rel)
 importFrom(ggplot2,scale_alpha_continuous)
 importFrom(ggplot2,scale_alpha_discrete)
 importFrom(ggplot2,scale_color_manual)
-importFrom(ggplot2,scale_fill_brewer)
 importFrom(ggplot2,scale_fill_gradient)
 importFrom(ggplot2,scale_fill_gradient2)
 importFrom(ggplot2,scale_fill_gradientn)
@@ -88,46 +64,23 @@ importFrom(ggplot2,scale_x_discrete)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,scale_y_date)
 importFrom(ggplot2,scale_y_discrete)
-importFrom(ggplot2,scale_y_log10)
-importFrom(ggplot2,scale_y_sqrt)
 importFrom(ggplot2,stat_summary)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_linedraw)
 importFrom(ggplot2,unit)
 importFrom(ggplot2,waiver)
-importFrom(ggplot2,xlab)
 importFrom(ggplot2,xlim)
 importFrom(ggplot2,ylim)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
-importFrom(grDevices,dev.new)
-importFrom(grDevices,dev.off)
 importFrom(grDevices,gray.colors)
-importFrom(grDevices,hcl)
 importFrom(grDevices,hsv)
-importFrom(grDevices,pdf)
-importFrom(grDevices,png)
 importFrom(grDevices,rgb)
 importFrom(grDevices,rgb2hsv)
-importFrom(grDevices,terrain.colors)
-importFrom(graphics,abline)
 importFrom(graphics,axis)
-importFrom(graphics,barplot)
-importFrom(graphics,grid)
-importFrom(graphics,image)
-importFrom(graphics,layout)
-importFrom(graphics,legend)
-importFrom(graphics,lines)
-importFrom(graphics,mtext)
-importFrom(graphics,par)
-importFrom(graphics,plot)
-importFrom(graphics,points)
 importFrom(graphics,polygon)
-importFrom(graphics,text)
-importFrom(graphics,title)
 importFrom(gridExtra,marrangeGrob)
-importFrom(luscale,superAggregate)
 importFrom(lusweave,swfigure)
 importFrom(lusweave,swtable)
 importFrom(magclass,"getNames<-")
@@ -136,39 +89,30 @@ importFrom(magclass,"getSets<-")
 importFrom(magclass,"getYears<-")
 importFrom(magclass,as.data.frame)
 importFrom(magclass,collapseNames)
-importFrom(magclass,dimSums)
 importFrom(magclass,fulldim)
 importFrom(magclass,getCells)
 importFrom(magclass,getNames)
 importFrom(magclass,getRegions)
 importFrom(magclass,getYears)
 importFrom(magclass,is.magpie)
-importFrom(magclass,lowpass)
-importFrom(magclass,mbind)
 importFrom(magclass,ncells)
 importFrom(magclass,ndata)
 importFrom(magclass,new.magpie)
 importFrom(magclass,nyears)
-importFrom(magclass,read.magpie)
 importFrom(magclass,setCells)
 importFrom(magclass,setNames)
 importFrom(magclass,setYears)
 importFrom(magclass,where)
-importFrom(magpiesets,findset)
-importFrom(magpiesets,reportingnames)
 importFrom(mip,plotstyle)
 importFrom(mstools,toolGetMappingCoord2Country)
 importFrom(quitte,as.quitte)
 importFrom(reshape2,melt)
-importFrom(rworldmap,addMapLegendBoxes)
 importFrom(rworldmap,joinCountryData2Map)
 importFrom(rworldmap,mapCountryData)
-importFrom(sp,plot)
 importFrom(stats,as.formula)
 importFrom(stats,cor)
 importFrom(stats,cor.test)
 importFrom(stats,na.omit)
-importFrom(stats,quantile)
 importFrom(stats,reshape)
 importFrom(stats,weighted.mean)
 importFrom(utils,data)
@@ -177,8 +121,3 @@ importFrom(utils,methods)
 importFrom(utils,read.csv)
 importFrom(utils,tail)
 importFrom(utils,write.csv2)
-importFrom(xml2,"xml_attr<-")
-importFrom(xml2,read_xml)
-importFrom(xml2,write_xml)
-importFrom(xml2,xml_attr)
-importFrom(xml2,xml_find_all)

R/aggregate_for_plot.R → R/aggregateForPlot.R

@@ -1,15 +1,15 @@
-#' aggregate_for_plot
+#' aggregateForPlot
 #' 
 #' Aggregates Data for an area chart. The value of all underlying
 #' regions/years/timesteps are added to the value of the current
 #' region/year/timestep.
 #' 
 #' 
-#' @usage aggregate_for_plot(plotdata,
-#' dimension="region",region_plotorder=NULL)
+#' @usage aggregateForPlot(plotdata,
+#' dimension="region",regionPlotorder=NULL)
 #' @param plotdata An MAgPIE object
 #' @param dimension by "region", "name" or "year"
-#' @param region_plotorder allows to change the order of the regions by giving
+#' @param regionPlotorder allows to change the order of the regions by giving
 #' a vector with the order
 #' @return A MAgPIE object of the same dimensions as plotdata
 #' @author Benjamin Bodirsky
@@ -19,34 +19,34 @@
 #' #no aggregation
 #' scratch_plot(population_magpie[,,2])
 #' #aggregation
-#' scratch_plot(aggregate_for_plot(population_magpie[,,2],region_plotorder=c(10,1:9)))
+#' scratch_plot(aggregateForPlot(population_magpie[,,2],regionPlotorder=c(10,1:9)))
 #' }
 #' @export
 #' @importFrom magclass getRegions setCells getCells getNames<- getYears getYears<- getRegions<- getNames
 
-aggregate_for_plot<-function(plotdata, dimension="region", region_plotorder=NULL)
+aggregateForPlot<-function(plotdata, dimension="region", regionPlotorder=NULL)
 {
 #dimension="region"
 #data(population_magpie)
 #plotdata<-population_magpie
 #plot_order=NULL      
-#region_plotorder=c(1,3,4,5,6,7,8,9,10,2)           
-  if (is.null(region_plotorder)) {
-    region_plotorder=1:dim(plotdata)[1]
-  } else if(length(region_plotorder)!=dim(plotdata)[1]){stop("plotorder has to be vector with the length of dim(plotdata)[1]")}
+#regionPlotorder=c(1,3,4,5,6,7,8,9,10,2)           
+  if (is.null(regionPlotorder)) {
+    regionPlotorder=1:dim(plotdata)[1]
+  } else if(length(regionPlotorder)!=dim(plotdata)[1]){stop("plotorder has to be vector with the length of dim(plotdata)[1]")}
   if(magpieResolution(plotdata)=="cell") {stop("Cellular datasets are not supported")} 
   if (dimension=="region") {
     aggregateplotdata<-plotdata[1,,]*0 
     plotdata_out<-plotdata*0
-    dimnames(plotdata_out)[[1]]<-paste(getRegions(plotdata)[region_plotorder],1:dim(plotdata)[1],sep=".")
-    for (region_dimension in getRegions(plotdata)[region_plotorder]) {
+    dimnames(plotdata_out)[[1]]<-paste(getRegions(plotdata)[regionPlotorder],1:dim(plotdata)[1],sep=".")
+    for (region_dimension in getRegions(plotdata)[regionPlotorder]) {
       plotdata_out[region_dimension,,] <- setCells(aggregateplotdata,getCells(plotdata[region_dimension,,])) + plotdata[region_dimension,,]
       aggregateplotdata<-plotdata_out[region_dimension,,]
     }
   } else if (dimension=="name") {
     aggregateplotdata<-plotdata[,,1]*0 
     for (name_dimension in getNames(plotdata)) {
-      getNames(aggregate_for_plot) <- name_dimension
+      getNames(aggregateForPlot) <- name_dimension
       plotdata_out[,,name_dimension] <- aggregateplotdata + plotdata[,,name_dimension]
       aggregateplotdata<-plotdata_out[,,name_dimension]
     }
@@ -60,8 +60,8 @@ aggregate_for_plot<-function(plotdata, dimension="region", region_plotorder=NULL
   } else if (dimension=="region_name") {
     aggregateplotdata<-plotdata[1,,1]*0 
     plotdata_out<-plotdata*0
-    dimnames(plotdata_out)[[1]]<-paste(getRegions(plotdata)[region_plotorder],1:dim(plotdata)[1],sep=".")    
-    for (region_dimension in getRegions(plotdata)[region_plotorder]) {
+    dimnames(plotdata_out)[[1]]<-paste(getRegions(plotdata)[regionPlotorder],1:dim(plotdata)[1],sep=".")    
+    for (region_dimension in getRegions(plotdata)[regionPlotorder]) {
       getRegions(aggregateplotdata) <- region_dimension
       for (name_dimension in getNames(plotdata)) {
         plotdata_out[region_dimension,,name_dimension] <- setCells(aggregateplotdata,getCells(plotdata[region_dimension,,])) + plotdata[region_dimension,,name_dimension]