Merge branch 'develop' of github.com:magpiemodel/magpie into develop

CHANGELOG.md

@@ -11,7 +11,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 -
 
 ### added
--
+- **scripts** added a new validation_cell.R output script that generates a pdf with the comparison of magpie land use and crop type outputs with LUH and MAPSPAM historical data at cellular resolution.
 
 ### removed
 -

config/default.cfg

@@ -1960,7 +1960,9 @@ cfg$files2export$start <- c("input/info.txt",
                             "input/spamplot_*.pdf",
                             "input/regionmapping*.csv",
                             "input/kba_land_0.5.mz",
-                            "input/f58_peatland_area_0.5.mz")
+                            "input/f58_peatland_area_0.5.mz",
+                            "input/MAPSPAM_croparea_0.5.mz",
+                            "input/LUH2_croparea_0.5.mz")
 
 # Files that should be copied after the MAgPIE run is finished
 cfg$files2export$end <- NULL

scripts/output/validation_cell.R

@@ -0,0 +1,218 @@
+# |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+# |  authors, and contributors see CITATION.cff file. This file is part
+# |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
+# |  AGPL-3.0, you are granted additional permissions described in the
+# |  MAgPIE License Exception, version 1.0 (see LICENSE file).
+# |  Contact: [email protected]
+
+# --------------------------------------------------------------
+# description: Comparison at cellular level of land and crop types with LUH2 and MAPSPAM
+# comparison script: FALSE
+# ---------------------------------------------------------------
+
+library(magpie4)
+library(luscale)
+library(luplot)
+library(lusweave)
+library(magpiesets)
+
+############################# BASIC CONFIGURATION ##############################
+if (!file.exists(paste0(outputdir, "/LUH2_croparea_0.5.mz"))) stop("Cell validation is not possible. LUH2_croparea_0.5.mz and MAPSPAM_croparea_0.5.mz files are missing")
+map_file <- Sys.glob(file.path(outputdir, "/clustermap_*.rds"))
+gdx <- file.path(outputdir, "/fulldata.gdx")
+cfg <- gms::loadConfig(file.path(outputdir, "/config.yml"))
+crops <- c("maiz", "rice_pro", "soybean", "tece")
+mapping <- readRDS(map_file)
+################################################################################
+
+#### Folder for saving results
+out_dir <- paste0(outputdir, "/CellularValidation/")
+if (!dir.exists(out_dir)) dir.create(out_dir)
+
+######## Land use types comparison with LUH ########
+magpie_LU <- land(gdx, level = "cell")
+historical_LU <- readGDX(gdx, "f10_land")
+
+LU <- plotCorrHist2D(
+    x = historical_LU, y = magpie_LU, xlab = "LUH2 \n (mio.ha)", ylab = "MAgPIE \n (mio.ha)", bins = 35,
+    folder = out_dir, file = "/validationLUcell", breaks = c(1, 10, 100), nrows = 2, ncols = 2, axisFont = 10,
+    axisTitleFont = 11, TitleFontSize = 12, legendTitleFont = 10, legendTextFont = 8, statFont = 2, stat = FALSE, table = TRUE, tag = "year"
+)
+
+######## Crop types ("maiz","rice_pro","soybean","tece") comparison  with LUH ########
+magpie <- croparea(gdx, level = "cell", product_aggr = FALSE, water_aggr = TRUE)[, , crops]
+historical1 <- read.magpie(paste0(outputdir, "/LUH2_croparea_0.5.mz"))
+historical1 <- magpiesort((gdxAggregate(gdx, historical1, to = "cell", absolute = TRUE, dir = outputdir)))[, , crops]
+historical1 <- dimSums(historical1, dim = 3.1)
+
+intYears <- intersect(getYears(magpie, as.integer = TRUE), getYears(historical1, as.integer = TRUE))
+Crops <- plotCorrHist2D(
+    x = historical1[,intYears,], y = magpie[,intYears,], xlab = "LUH2 \n (mio.ha)", ylab = "MAgPIE \n (mio.ha)", bins = 35,
+    folder = out_dir, file = "/validationCropCell", breaks = c(1, 10, 50), nrows = 2, ncols = 2, axisFont = 10,
+    axisTitleFont = 11, TitleFontSize = 12, legendTitleFont = 10, legendTextFont = 8, statFont = 2, stat = FALSE, table = TRUE, tag = "year"
+)
+
+######## Crop types ("maiz","rice_pro","soybean","tece") comparison  with MAPSPAM ########
+historical <- read.magpie(paste0(outputdir, "/MAPSPAM_croparea_0.5.mz"))
+historical <- magpiesort(gdxAggregate(gdx, historical, to = "cell", absolute = TRUE, dir = outputdir))[,,crops] 
+historical <- dimSums(historical, dim = 3.2)
+intYears2 <- intersect(getYears(magpie, as.integer = TRUE), getYears(historical, as.integer = TRUE))
+
+CropsSPAM <- plotCorrHist2D(
+    x = historical, y = magpie[, intYears2, ], xlab = "MAPSPAM \n (mio.ha)", ylab = "MAgPIE \n (mio.ha)", bins = 35,
+    folder = out_dir, file = "/validationCropCellSPAM", breaks = c(1, 10, 50), nrows = 2, ncols = 2, axisFont = 10,
+    axisTitleFont = 11, TitleFontSize = 12, legendTitleFont = 10, legendTextFont = 8, statFont = 2, stat = FALSE, table = TRUE,
+    palette = "PiYG", tag = "year"
+)
+
+######################################### Generates document ##############################################
+template <- c(
+    "\\documentclass[a4paper, portrait ]{article}",
+    "\\setlength{\\parindent}{0in}",
+    "\\usepackage{float}",
+    "\\usepackage[bookmarksopenlevel=section]{hyperref}",
+    "\\hypersetup{bookmarks=true,pdfauthor={PIK Landuse group}}",
+    "\\usepackage{graphicx}",
+    "\\usepackage{rotating}",
+    "\\usepackage[strings]{underscore}",
+    "\\usepackage[margin=2cm]{geometry}",
+    "\\usepackage{fancyhdr}",
+    "\\pagestyle{fancy}",
+    "\\begin{document}",
+    "<<echo=false>>=",
+    "options(width=90)",
+    "@"
+)
+
+############################## Plots LUH vs. magpie land use types ####################################################
+x <- LU[[1]]
+y <- as.data.frame(LU[[2]])
+colnames(y) <- y[1, ]
+rownames(y) <- NULL
+y <- (y[2:(nrow(y)), ])
+y[, 3:ncol(y)] <- round(as.numeric(unlist(y[, 3:ncol(y)])), 3)
+colnames(y) <- c("Year", "Variable", "R2", "MAE", "MPE", "MAPE")
+
+tmpplot <- function(x, range) {
+    plotLU <- function(x, range) {
+        print(gridExtra::marrangeGrob(x[range], nrow = 3, ncol = 2, top = NULL))
+    }
+    a <- capture.output(plotLU(x, range))
+}
+
+namesReport <- as.character(magpiesets::reportingnames(getNames(magpie_LU)))
+
+sw <- swopen(outfile = paste0(outputdir, "/CellValidation.pdf"), template = template)
+swlatex(sw, c("\\title{MAgPIE Validation on Cellular level}", "\\maketitle", "\\tableofcontents"))
+swlatex(sw, "\\section{Land use between 1995-2020 compared to LUH2}")
+
+b <- 0
+
+for (i in 1:length(namesReport)) {
+    swlatex(sw, paste0("\\subsection{", namesReport[i], "}"))
+    a <- b + 1
+    b <- a + length(getYears(historical_LU)) - 1
+    swfigure(sw, tmpplot, x = x, c(a:b))
+    swtable(sw, collapseNames(as.magpie(y[a:b, ])),
+        table.placement = "H", caption.placement = "top",
+        transpose = FALSE, caption = paste0("Compilation of error measurements for ", namesReport[i], " data comparing MAgPIE outputs \\& the LUH2 set at cluster level"), vert.lines = 0, align = "c"
+    )
+    swlatex(sw, "\\newpage")
+}
+
+
+############################## Plots LUH vs. magpie crop types ##########################################################
+swlatex(sw, "\\section{", paste0("MAgPIE crop types compared to LUH2 (", intYears[1], "-", intYears[length(intYears)], ")"), "}")
+
+namesReport1 <- as.character(magpiesets::reportingnames(getNames(magpie)))
+x1 <- Crops[[1]]
+y1 <- as.data.frame(Crops[[2]])
+colnames(y1) <- y1[1, ]
+rownames(y1) <- NULL
+y1 <- (y1[2:(nrow(y1)), ])
+y1[, 3:ncol(y1)] <- round(as.numeric(unlist(y1[, 3:ncol(y1)])), 3)
+colnames(y1) <- c("Year", "Variable", "R2", "MAE", "MPE", "MAPE")
+
+tmpplot1 <- function(x1, range) {
+    plotLU1 <- function(x1, range) {
+        print(gridExtra::marrangeGrob(x1[range], nrow = 3, ncol = 2, top = NULL))
+    }
+    a <- capture.output(plotLU1(x1, range))
+}
+
+b1 <- 0
+for (i in 1:length(namesReport1)) {
+    swlatex(sw, paste0("\\subsection{", namesReport1[i], "}"))
+    a1 <- b1 + 1
+    b1 <- a1 + length(intYears) - 1
+    swfigure(sw, tmpplot1, x = x1, c(a1:b1))
+    swtable(sw, collapseNames(as.magpie(y1[a1:b1, ])),
+        table.placement = "H", caption.placement = "top",
+        transpose = FALSE, caption = paste0("Compilation of error measurements for ", namesReport1[i], " data comparing MAgPIE outputs \\& the LUH2 set at cluster level"), vert.lines = 0, align = "c"
+    )
+    swlatex(sw, "\\newpage")
+}
+
+
+############################## Plots MAPSPAM vs. magpie crop types ##########################################################
+
+
+    swlatex(sw, "\\newpage")
+    swlatex(sw, "\\section{", paste0("MAgPIE crop types compared to MAPSPAM (", intYears2[1], "-", intYears2[length(intYears2)], ")"), "}")
+
+    x2 <- CropsSPAM[[1]]
+    names(x2) <- paste0(names(x2), "MAP")
+    x3 <- Crops[[1]][names(CropsSPAM[[1]])]
+    y2 <- as.data.frame(CropsSPAM[[2]])
+    colnames(y2) <- y2[1, ]
+    rownames(y2) <- NULL
+    y2 <- (y2[2:(nrow(y2)), ])
+    y2[, 3:ncol(y2)] <- round(as.numeric(unlist(y2[, 3:ncol(y2)])), 3)
+    colnames(y2) <- c("Year", "Variable", "R2", "MAE", "MPE", "MAPE")
+
+    tmpplot2 <- function(x2, x3, range) {
+        plotLU2 <- function(x2, x3, range) {
+            print(gridExtra::marrangeGrob(c(x2[range], x3[range]), nrow = 3, ncol = 2, top = NULL))
+        }
+        a <- capture.output(plotLU2(x2, x3, range))
+    }
+
+    b2 <- 0
+    for (i in 1:length(namesReport1)) {
+        swlatex(sw, paste0("\\subsection{", namesReport1[i], "}"))
+        swlatex(sw, "\\qquad \\textbf{MAPSPAM} \\qquad \\qquad \\qquad \\qquad \\qquad \\qquad \\qquad \\qquad \\qquad \\qquad \\textbf{LUH2}")
+        a2 <- b2 + 1
+        b2 <- a2 + length(intYears2) - 1
+        swfigure(sw, tmpplot2, x2 = x2, x3 = x3, range = c(a2:b2))
+        swtable(sw, collapseNames(as.magpie(y2[a2:b2, ])),
+            table.placement = "H", caption.placement = "top",
+            transpose = FALSE, caption = paste0("Compilation of error measurements for ", namesReport[i], " data comparing MAgPIE outputs \\& the MAPSPAM set at cluster level"), vert.lines = 0, align = "c"
+        )
+        swlatex(sw, "\\newpage")
+    }
+
+########## Details about statistics ##########
+swlatex(sw, "\\newpage")
+swlatex(sw, "\\section{Details about statistical measuremens of error and goodness of fit}")
+swlatex(sw, "\\begin{itemize} \\item R2 represents the coefficient of determination. \\end{itemize}")
+swlatex(sw, "\\begin{itemize} \\item MAE stands for mean absolute error and is calculated as $MAE=\\frac{1}{n}\\sum(|error|)$. Where, error represents the difference between LUH/MAPSPAM values and MAgPIE Outputs.  \\end{itemize}")
+swlatex(sw, "\\begin{itemize} \\item MPE stands for mean percentage error (a measure of bias) and is calculated as $MPE=\\frac{100\\%}{n}\\sum(RE)$. Where, RE (relative error) represents the relative difference between LUH/MAPSPAM values and MAgPIE Outputs.  \\end{itemize}")
+swlatex(sw, "\\begin{itemize} \\item Finally, MAPE stands for mean absolute percentage error and is calculated as $MAPE=\\frac{100\\%}{n}\\sum(|RE|)$. Where, RE (relative error) represents the relative difference between LUH/MAPSPAM values and MAgPIE Outputs.  \\end{itemize}")
+
+####### Closes the pdf document
+swclose(sw, clean_output = FALSE, engine = "knitr")
+
+###########################################################################################################################
+
+##### Erase latex style and output files
+
+fileErase <- c(
+    Sys.glob(file.path(outputdir, "/CellValidation.*")),
+    Sys.glob(file.path(outputdir, "/Sweave.sty")),
+    Sys.glob(file.path(outputdir, "figure/*")),
+    Sys.glob(file.path(outputdir, "figure"))
+)
+fileErase <- fileErase[!(fileErase %in% paste0(outputdir, "//CellValidation.pdf"))]
+
+
+unlink(fileErase, recursive = TRUE)