Merge pull request #494 from fbenke-pik/convergence

Add nash analysis markdown

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '222064080'
+ValidationKey: '222106326'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
@@ -9,5 +9,6 @@ AcceptedNotes:
 - Imports includes .* non-default packages.
 - unable to verify current time
 - checking installed package size
+- Namespace in Imports field not imported from: ‘htmltools’
 AutocreateReadme: yes
 allowLinterWarnings: yes

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: 'remind2: The REMIND R package (2nd generation)'
-version: 1.127.0
-date-released: '2023-12-13'
+version: 1.127.1
+date-released: '2023-12-15'
 abstract: Contains the REMIND-specific routines for data and model output manipulation.
 authors:
 - family-names: Rodrigues

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: remind2
 Title: The REMIND R package (2nd generation)
-Version: 1.127.0
-Date: 2023-12-13
+Version: 1.127.1
+Date: 2023-12-15
 Authors@R: c(
     person("Renato", "Rodrigues", , "[email protected]", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", role = "aut"),
@@ -42,7 +42,6 @@ URL: https://github.com/pik-piam/remind2
 Depends:
     magclass (>= 3.37)
 Imports:
-    RColorBrewer,
     abind,
     assertr,
     data.table,
@@ -52,10 +51,9 @@ Imports:
     gdxrrw,
     ggplot2,
     gms,
-    highcharter,
+    htmltools,
     iamc,
     knitr,
-    lubridate,
     lucode2 (>= 0.43.0),
     luplot,
     luscale,
@@ -72,7 +70,6 @@ Imports:
     rlang,
     rmarkdown,
     rmndt,
-    scales,
     tibble,
     tidyr,
     tidyselect,

NAMESPACE

@@ -18,7 +18,6 @@ export(convGDX2MIF_LCOE)
 export(convGDX2MIF_REMIND2MAgPIE)
 export(convergenceCheck)
 export(createVarListHtml)
-export(dashboard)
 export(deletePlus)
 export(gdx.copy)
 export(getCfgDefaultPath)
@@ -30,6 +29,7 @@ export(getRunsMIFGDX)
 export(get_total_efficiencies)
 export(loadCs2Data)
 export(loadModeltest)
+export(nashAnalysis)
 export(plotCDR)
 export(plotLCOE)
 export(plotNashConvergence)
@@ -55,11 +55,9 @@ export(readTimeStepWeight)
 export(readTrade)
 export(reportCapacity)
 export(reportCapitalStock)
-export(reportCharts)
 export(reportCosts)
 export(reportCrossVariables)
 export(reportDIETER)
-export(reportDiagnosis)
 export(reportEDGETransport)
 export(reportEmi)
 export(reportEmiAirPol)
@@ -86,7 +84,6 @@ export(toolRegionSubsets)
 export(validationREMIND)
 export(variablesAsList)
 import(magclass)
-importFrom(RColorBrewer,brewer.pal)
 importFrom(abind,abind)
 importFrom(assertr,assert)
 importFrom(assertr,not_na)
@@ -110,7 +107,6 @@ importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
 importFrom(dplyr,coalesce)
 importFrom(dplyr,distinct)
-importFrom(dplyr,do)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
@@ -136,28 +132,19 @@ importFrom(gdxrrw,gdxInfo)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_)
 importFrom(ggplot2,coord_cartesian)
-importFrom(ggplot2,coord_flip)
-importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)
-importFrom(ggplot2,expand_limits)
 importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_area)
-importFrom(ggplot2,geom_bar)
-importFrom(ggplot2,geom_boxplot)
 importFrom(ggplot2,geom_col)
 importFrom(ggplot2,geom_errorbar)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_rect)
-importFrom(ggplot2,geom_text)
-importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
-importFrom(ggplot2,labeller)
 importFrom(ggplot2,labs)
-importFrom(ggplot2,position_stack)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_fill_brewer)
 importFrom(ggplot2,scale_fill_discrete)
@@ -173,24 +160,11 @@ importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_minimal)
 importFrom(ggplot2,unit)
 importFrom(ggplot2,xlab)
-importFrom(ggplot2,ylab)
 importFrom(gms,getLine)
 importFrom(gms,readDefaultConfig)
 importFrom(grDevices,colorRampPalette)
-importFrom(grDevices,rgb)
-importFrom(highcharter,hc_add_series_list)
-importFrom(highcharter,hc_mapNavigation)
-importFrom(highcharter,hc_plotOptions)
-importFrom(highcharter,hc_tooltip)
-importFrom(highcharter,highchart)
-importFrom(highcharter,list_parse)
 importFrom(iamc,iamCheck)
 importFrom(knitr,knit)
-importFrom(lubridate,day)
-importFrom(lubridate,hour)
-importFrom(lubridate,minute)
-importFrom(lubridate,second)
-importFrom(lubridate,seconds_to_period)
 importFrom(lucode2,getScenNames)
 importFrom(luplot,magpie2ggplot2)
 importFrom(luplot,plotcountrymap)
@@ -237,11 +211,9 @@ importFrom(magclass,setItems)
 importFrom(magclass,setNames)
 importFrom(magclass,setYears)
 importFrom(magclass,write.report)
-importFrom(mip,mipArea)
 importFrom(mip,mipBarYearData)
 importFrom(mip,mipLineHistorical)
 importFrom(mip,plotstyle)
-importFrom(mip,shorten_legend)
 importFrom(openxlsx,addStyle)
 importFrom(openxlsx,addWorksheet)
 importFrom(openxlsx,createStyle)
@@ -253,7 +225,6 @@ importFrom(plotly,config)
 importFrom(plotly,ggplotly)
 importFrom(plotly,hide_legend)
 importFrom(plotly,layout)
-importFrom(plotly,style)
 importFrom(plotly,subplot)
 importFrom(quitte,as.quitte)
 importFrom(quitte,calcCumulatedDiscount)
@@ -283,15 +254,9 @@ importFrom(rmarkdown,render)
 importFrom(rmndt,approx_dt)
 importFrom(rmndt,readMIF)
 importFrom(rmndt,writeMIF)
-importFrom(scales,pretty_breaks)
-importFrom(stats,IQR)
-importFrom(stats,as.formula)
-importFrom(stats,lag)
-importFrom(stats,quantile)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(tibble,tribble)
-importFrom(tidyr,"%>%")
 importFrom(tidyr,complete)
 importFrom(tidyr,crossing)
 importFrom(tidyr,drop_na)

R/checkVsCalibData.R

@@ -18,10 +18,11 @@
 #' }
 #' @export
 checkVsCalibData <- function(gdx, outputDir = getwd(), outputFile = "Check_vs_CalibData.pdf") {
+
   yamlParams <- list(gdx = normalizePath(gdx, mustWork = TRUE))
 
   rmarkdown::render(
-    system.file("markdown/checkVsCalibData/rc_main.Rmd", package = "remind2"),
+    system.file("markdown", "checkVsCalibrationData.Rmd", package = "remind2"),
     output_dir = outputDir,
     output_file = outputFile,
     output_format = "pdf_document",

R/compareCalibrationTargets.R

@@ -26,7 +26,7 @@ compareCalibrationTargets <- function(gdxPaths, outputDir = getwd(),
     gdxPathNames = names(gdxPaths)
   )
   rmarkdown::render(
-    system.file("markdown/compareCalibrationTargets/cct_main.Rmd", package = "remind2"),
+    system.file("markdown/compareCalibrationTargets.Rmd", package = "remind2"),
     output_dir = outputDir,
     output_file = outputFile,
     output_format = "html_document",

R/nashAnalysis.R

@@ -0,0 +1,28 @@
+#' @title Nash Analysis
+#' @description Create plots visualizing nash convergence of a given REMIND run
+#'
+#' @author Falk Benke
+#'
+#' @param gdx a GDX object as created by readGDX, or the path to a gdx
+#' @param outputDir \code{character(1)}. The directory where the output document
+#'   and intermediary files are created.
+#' @param outputFile \code{character(1)}. File name (without extension) of the
+#'   output document to be created.
+#' @return The value returned by \code{\link[rmarkdown:render]{rmarkdown::render()}}.
+#'
+#' @importFrom rmarkdown render
+#'
+#' @export
+nashAnalysis <- function(gdx = "fulldata.gdx", outputDir = getwd(), outputFile = "Nash Analysis.html") {
+
+
+  yamlParams <- list(gdx = normalizePath(gdx, mustWork = TRUE))
+
+  rmarkdown::render(
+    system.file("markdown", "nashAnalysis.Rmd", package = "remind2"),
+    output_dir = outputDir,
+    output_file = outputFile,
+    output_format = "html_document",
+    params = yamlParams
+  )
+}