Update plotCorrHist2D 67k and bugfixes

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '8098285'
+ValidationKey: '8245920'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -44,6 +44,13 @@ jobs:
           [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
           [ -f requirements.txt ] && pip install -r requirements.txt || true
 
+      - name: Run pre-commit checks
+        shell: bash
+        run: |
+          python -m pip install pre-commit
+          python -m pip freeze --local
+          pre-commit run --show-diff-on-failure --color=always --all-files
+
       - name: Verify validation key
         shell: Rscript {0}
         run: lucode2:::validkey(stopIfInvalid = TRUE)

.pre-commit-config.yaml

@@ -25,4 +25,4 @@ repos:
     -   id: readme-rmd-rendered
     -   id: use-tidy-description
 ci:
-    autoupdate_schedule: quarterly
+    autoupdate_schedule: weekly

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: 4.0.3
-date-released: '2025-01-07'
+version: 4.1.0
+date-released: '2025-01-24'
 abstract: Some useful functions to plot data such as a map plot function for MAgPIE
   objects.
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: luplot
 Title: Landuse Plot Library
-Version: 4.0.3
-Date: 2025-01-07
+Version: 4.1.0
+Date: 2025-01-24
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "bodirsky@pik-potsdam.de", role = c("aut", "cre")),
     person("Jan Philipp", "Dietrich", , "dietrich@pik-potsdam.de", role = "aut"),

R/plotCorrHist2D.R

@@ -12,7 +12,7 @@
 #' @param limx limits y axis (if NULL, fitting limits are calculated within the function)
 #' @param limy limits x axis (if NULL, fitting limits are calculated within the function)
 #' @param bins number of bins in histogram
-#' @param folder path in which to save the plots. if "." is used, it is saved 
+#' @param folder path in which to save the plots. if "." is used, it is saved
 #' in the current working directory. If NULL, no plots are saved.
 #' @param file name of file
 #' @param statFont font size r2-MAE label
@@ -21,13 +21,14 @@
 #' @param ncols number of columns in pdf file where plots are printed
 #' @param axisFont Font size of text of axis of the correlation plot
 #' @param axisTitleFont Font size of title of axis of the correlation plot
-#' @param TitleFontSize Font size of title of correlation plot
+#' @param titleFontSize Font size of title of correlation plot
 #' @param legendTitleFont Font size of the title of the legend
 #' @param legendTextFont Font size of legend
 #' @param table Conditional to include table with statistics in the output. TRUE (includes it), FALSE (it doesn't)
 #' @param stat Conditional to include R2 and MAE on the fiure. TRUE (includes it), FALSE (it doesn't)
 #' @param palette palette selection for heatd maps based on the RColorBrewer library
-#' @param tag for multiple items in the second and third dimensions of the magpie object, should the title include "year", "item", "year-item".
+#' @param tag for multiple items in the second and third dimensions of the magpie object,
+#' should the title include "year", "item", "year-item".
 #' @author Edna Molina Bacca
 #' @importFrom grDevices colorRampPalette
 #' @importFrom ggplot2 ggplot aes_ xlim ylim scale_fill_gradientn coord_fixed geom_abline geom_vline geom_hline
@@ -42,31 +43,39 @@
 #' x <- plotCorrHist2D(x, y, folder = ".")
 #' }
 #'
-plotCorrHist2D <- function(x, y, title = NULL, xlab = "x", ylab = "y", bins = 40, limx=NULL, limy=NULL,
-                           folder = NULL, file = "", breaks = waiver(),nrows=2, ncols=2, axisFont=13,
-                           axisTitleFont=13,TitleFontSize=15,legendTitleFont=12,legendTextFont=10,
-                           statFont=4, table=FALSE, stat=TRUE,palette="RdYlBu",tag=NULL) {
+plotCorrHist2D <- function(x, y, title = NULL, xlab = "x", ylab = "y", bins = 40, limx = NULL, limy = NULL,
+                           folder = NULL, file = "", breaks = waiver(), nrows = 2, ncols = 2, axisFont = 13,
+                           axisTitleFont = 13, titleFontSize = 15, legendTitleFont = 12, legendTextFont = 10,
+                           statFont = 4, table = FALSE, stat = TRUE, palette = "RdYlBu", tag = "year-item") {
 
 
   getNames(x) <- gsub(x = getNames(x), pattern = "\\.", replacement = "_")
   getNames(y) <- gsub(x = getNames(y), pattern = "\\.", replacement = "_")
 
+  if (length(getCells(x)) == 67420 && length(getCells(y)) == 67420) {
+    getCells(x) <- gsub(x = getCells(x), pattern = "\\.", replacement = "_")
+    getCells(y) <- gsub(x = getCells(y), pattern = "\\.", replacement = "_")
+  }
+
 
   if (!all(getCells(x) == getCells(y))) stop("Data sets don't have the same regional resolution")
   years <- if (!is.null(intersect(getYears(x), getYears(y)))) intersect(getYears(x, as.integer = TRUE),
                                                                         getYears(y, as.integer = TRUE)) else
-                                                                          stop("No common years between data sets")
+    stop("No common years between data sets")
   names <- if (!is.null(intersect(getNames(x), getNames(y)))) intersect(getNames(x),
                                                                         getNames(y)) else
-                                                                          stop("No common items between data sets")
+    stop("No common items between data sets")
+
 
   plotMagpie <- luplot::as.ggplot(mbind(setNames(x[, years, names], paste0(getNames(x), "_x")),
-                                setNames(y[, years, names],
-                                         paste0(getNames(x), "_y"))))[, c("Cell", "Region", "Year", "Data1", "Value")]
-  plotMagpie <- reshape(plotMagpie, direction = "wide", idvar = c("Cell", "Region", "Year"), timevar = "Data1")
+                                        setNames(y[, years, names],
+                                                 paste0(getNames(x), "_y"))))
+  cols <- colnames(plotMagpie)[colnames(plotMagpie) != "Scenario"]
+  plotMagpie <- reshape(plotMagpie[, cols], direction = "wide", idvar = cols[cols != "Data1" & cols != "Value"],
+                        timevar = "Data1")
 
   plots <- list()
-  corr <- c("Year","Variable", "r2", "MAE", "MPE", "MAPE")
+  corr <- c("Year", "Variable", "r2", "MAE", "MPE", "MAPE")
 
   rf <- colorRampPalette(rev(brewer.pal(11, palette)))
   r <- rf(32) # color palette
@@ -96,56 +105,58 @@ plotCorrHist2D <- function(x, y, title = NULL, xlab = "x", ylab = "y", bins = 40
 
       r2 <- round(cor(data[, valueX], data[, valueY])^2, 3)
       mae <- luplot::qualityMeasure(pd = data[, valueY], od = data[, valueX], measures = "MAE", p_value = FALSE)
-      
+
       relativeError <- (data[, valueY] - data[, valueX]) / data[, valueX]
       relativeError[!is.finite(relativeError)] <- NA
-      relativeError[data[, valueX] < 0.01 * max(data[, valueX])] <- NA      
+      relativeError[data[, valueX] < 0.01 * max(data[, valueX])] <- NA
       mpe <- sum(relativeError * 100, na.rm = TRUE) / length(relativeError[is.finite(relativeError)])
-      
+
       absoluteError <- abs((data[, valueY] - data[, valueX]) / data[, valueX])
       absoluteError[!is.finite(absoluteError)] <- NA
       absoluteError[data[, valueX] < 0.01 * max(data[, valueX])] <- NA
       mape <- round(sum(absoluteError * 100, na.rm = TRUE) / length(absoluteError[is.finite(absoluteError)]), 3)
 
-      all <- t(c(year,na, r2, mae, mpe, mape))
-  
+      all <- t(c(year, na, r2, mae, mpe, mape))
+
 
       corr <- rbind(corr, all)
       tag1 <- paste0(na, "-", year)
-      tagTitle <- if(tag=="year-item") tag1 else if(tag=="year") year else if(tag=="item") na
+      tagTitle <- if (tag == "year-item") tag1 else if (tag == "year") year else if (tag == "item") na
 
       plots[[tag1]] <- ggplot(data, aes_string(x = valueX, y = valueY)) + theme_bw()
       plots[[tag1]] <- plots[[tag1]] + geom_bin2d(bins = bins) + coord_fixed(ratio = 1) +
         geom_abline(intercept = 0, slope = 1) + geom_vline(xintercept = 0) + geom_hline(yintercept = 0)
       plots[[tag1]] <- plots[[tag1]] + labs(x = xlab, y = ylab, title = paste0(title, " ", "(", tagTitle, ")")) +
         scale_fill_gradientn(colours = r, trans = "log", breaks = breaks)
       plots[[tag1]] <- plots[[tag1]] + theme(axis.text.x = element_text(color = "grey20", size = axisFont),
-                                           axis.title.x = element_text(color = "grey20", size = axisTitleFont),
-                                           axis.text.y = element_text(color = "grey20", size = axisFont),
-                                           axis.title.y = element_text(color = "grey20", size = axisTitleFont),
-                                           plot.title = element_text(size = TitleFontSize, face = "bold"),
-                                           legend.text = element_text(size = legendTextFont),
-                                           legend.title = element_text(size = legendTitleFont),
-                                           legend.background = element_blank())
-
-      plots[[tag1]] <- if(stat) plots[[tag1]] + annotate("label", size = statFont, x = labelX, y = labelY,
-                                              label = paste0("R2 = ", r2), hjust = 1) else plots[[tag1]]
-      plots[[tag1]] <- if(stat) plots[[tag1]] + annotate("label", size = statFont, x = labelX, y = labelY2,
-                                              label = paste0("MAE = ", mae), hjust = 1) else plots[[tag1]]
-      plots[[tag1]] <- if (!is.null(limx)) plots[[tag1]] + scale_x_continuous(limits = limx) else plots[[tag1]] + scale_x_continuous(limits = limx1)
-      plots[[tag1]] <- if (!is.null(limy)) plots[[tag1]] + scale_y_continuous(limits = limy) else plots[[tag1]] + scale_y_continuous(limits = limy1)
-
+                                             axis.title.x = element_text(color = "grey20", size = axisTitleFont),
+                                             axis.text.y = element_text(color = "grey20", size = axisFont),
+                                             axis.title.y = element_text(color = "grey20", size = axisTitleFont),
+                                             plot.title = element_text(size = titleFontSize, face = "bold"),
+                                             legend.text = element_text(size = legendTextFont),
+                                             legend.title = element_text(size = legendTitleFont),
+                                             legend.background = element_blank())
+
+      plots[[tag1]] <- if (stat) plots[[tag1]] + annotate("label", size = statFont, x = labelX, y = labelY,
+                                                          label = paste0("R2 = ", r2), hjust = 1) else plots[[tag1]]
+      plots[[tag1]] <- if (stat) plots[[tag1]] + annotate("label", size = statFont, x = labelX, y = labelY2,
+                                                          label = paste0("MAE = ", mae), hjust = 1) else plots[[tag1]]
+      plots[[tag1]] <- if (!is.null(limx)) plots[[tag1]] + scale_x_continuous(limits = limx) else plots[[tag1]] +
+        scale_x_continuous(limits = limx1)
+      plots[[tag1]] <- if (!is.null(limy)) plots[[tag1]] + scale_y_continuous(limits = limy) else plots[[tag1]] +
+        scale_y_continuous(limits = limy1)
+
     }
   }
-  
-    if (!is.null(folder)) {
-      if (folder != "." && !dir.exists(folder)) dir.create(folder)
-      if(is.null(file)) stop("Please, write a file name")
-      ml<-gridExtra::marrangeGrob(plots, nrow = 2, ncol = 2)
-      ggsave(paste0(folder,file,".pdf"), ml)
-      write.csv2(corr,paste0(folder, file, "_stats.csv"))
-         }
-
-  out <- if (table) list(plots,corr) else plots
+
+  if (!is.null(folder)) {
+    if (folder != "." && !dir.exists(folder)) dir.create(folder)
+    if (is.null(file)) stop("Please, write a file name")
+    ml <- gridExtra::marrangeGrob(plots, nrow = nrows, ncol = ncols)
+    ggsave(paste0(folder, file, ".pdf"), ml)
+    write.csv2(corr, paste0(folder, file, "_stats.csv"))
+  }
+
+  out <- if (table) list(plots, corr) else plots
   return(out)
 }

README.md

@@ -1,6 +1,6 @@
 # Landuse Plot Library
 
-R package **luplot**, version **4.0.3**
+R package **luplot**, version **4.1.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/luplot)](https://cran.r-project.org/package=luplot) [![R build status](https://github.com/pik-piam/luplot/workflows/check/badge.svg)](https://github.com/pik-piam/luplot/actions) [![codecov](https://codecov.io/gh/pik-piam/luplot/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/luplot) [![r-universe](https://pik-piam.r-universe.dev/badges/luplot)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,15 +39,17 @@ In case of questions / problems please contact Benjamin Bodirsky <bodirsky@pik-p
 
 To cite package **luplot** in publications use:
 
-Bodirsky B, Dietrich J, Krause M, Stevanovic M, Humpenoeder F, Weindl I, Baumstark L, Klein D, Rolinski S, Wang X, Chen D, Sauer P (2025). "luplot: Landuse Plot Library - Version 4.0.3."
+Bodirsky B, Dietrich J, Krause M, Stevanovic M, Humpenoeder F, Weindl I, Baumstark L, Klein D, Rolinski S, Wang X, Chen D, Sauer P (2025). "luplot: Landuse Plot Library." Version: 4.1.0, <https://github.com/pik-piam/luplot>.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
 @Misc{,
-  title = {luplot: Landuse Plot Library - Version 4.0.3},
+  title = {luplot: Landuse Plot Library},
   author = {Benjamin Leon Bodirsky and Jan Philipp Dietrich and Michael Krause and Miodrag Stevanovic and Florian Humpenoeder and Isabelle Weindl and Lavinia Baumstark and David Klein and Susanne Rolinski and Xiaoxi Wang and David Chen and Pascal Sauer},
-  date = {2025-01-07},
+  date = {2025-01-24},
   year = {2025},
+  url = {https://github.com/pik-piam/luplot},
+  note = {Version: 4.1.0},
 }
 ```