Merge branch 'master' of github.com:pik-piam/remind2 into ecemf

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '218545744'
+ValidationKey: '219049404'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

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: 1.115.2
-date-released: '2023-08-28'
+version: 1.117.2
+date-released: '2023-09-07'
 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: 1.115.2
-Date: 2023-08-28
+Version: 1.117.2
+Date: 2023-09-07
 Authors@R: c(
     person("Renato", "Rodrigues", , "[email protected]", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", role = "aut"),

NAMESPACE

@@ -7,6 +7,7 @@ export(calcPrice)
 export(calcTimeSeriesStats)
 export(calc_CES_marginals)
 export(calc_regionSubset_sums)
+export(checkVariableNames)
 export(checkVsCalibData)
 export(colorScenConf)
 export(compareCalibrationTargets)

R/checkVariableNames.R

@@ -0,0 +1,25 @@
+#' checkVariablesNames checks remind2 reporting on inconsistency in variable names
+#'
+#' Pass a vector of variable names including the units. Get warnings if inconsistencies are found
+#' for the reporting
+#' @param vars vector with variable names and units such as "PE (EJ)"
+#' @author Oliver Richters
+#' @export
+checkVariableNames <- function(vars) {
+
+  barspace <- grep("[\\| ]{2}|^[\\| ]|[\\| ]$", vars, value = TRUE)
+  if (length(barspace) > 0) {
+    warning("These variable names have wrong bars and spaces: ", paste(barspace, collapse = ", "))
+  }
+
+  NAvar <- grep("[\\|\\( ]NA[\\|\\) ]|^NA", vars, value = TRUE)
+  NAvar <- NAvar[! grepl("^Services and Products\\|Transport\\|non-LDV\\|S", NAvar)] # unit NA, but ok, see issue #408
+  if (length(NAvar) > 0) {
+    warning("These variables and units contain NA: ", paste(NAvar, collapse = ", "))
+  }
+
+  noUnit <- grep(" \\(.*\\)$", vars, value = TRUE, invert = TRUE)
+  if (length(noUnit) > 0) {
+    warning("These variables have no units: ", paste(noUnit, collapse = ", "))
+  }
+}

R/convGDX2MIF.R

@@ -115,10 +115,12 @@ convGDX2MIF <- function(gdx, gdx_ref = NULL, file = NULL, scenario = "default",
   output <- add_dimension(output,dim=3.1,add = "model",nm = "REMIND")
   output <- add_dimension(output,dim=3.1,add = "scenario",nm = scenario)
 
+  checkVariableNames(getNames(output, dim = 3))
+
   sumChecks <- piamInterfaces::checkSummations(
     mifFile = output, outputDirectory = NULL,
     summationsFile = "extractVariableGroups",
-    absDiff = 1.5e-8, relDiff = 1e-8, roundDiff = FALSE
+    absDiff = 1.5e-8, relDiff = 1e-8, roundDiff = TRUE
   ) %>% filter(abs(!!sym("diff")) >= 1.5e-8)
 
   # either write the *.mif or return the magpie object

R/reportEmi.R

@@ -262,8 +262,7 @@ reportEmi <- function(gdx, output = NULL, regionSubsetList = NULL, t = c(seq(200
     as.magpie(spatial = 2, temporal = 1, data = ncol(.)) %>%
     ifelse(is.finite(.), ., 0)   # replace NaN by 0
 
-  rm(vm_emiIndCCS_tibble, subsector_emissions, subsector_total_emissions,
-     pm_emifac_tibble)
+  rm(vm_emiIndCCS_tibble, subsector_total_emissions, pm_emifac_tibble)
 
   # utility functions ----
   # Convert a mixer table into a list that can be passed to mselect() to
@@ -672,6 +671,50 @@ reportEmi <- function(gdx, output = NULL, regionSubsetList = NULL, t = c(seq(200
           x[['variable']])
       }) %>%
         mbind())
+
+    # Baseline emission before CCS, corresponds to energy carbon content
+    out <- mbind(
+      # energy emissions
+      subsector_emissions %>%
+        mutate(
+          secInd37 = case_when(
+            'cement'    == .data$secInd37 ~ 'Cement',
+            'chemicals' == .data$secInd37 ~ 'Chemicals',
+            'steel'     == .data$secInd37 ~ 'Steel',
+            'otherInd'  == .data$secInd37 ~ 'Other Industry',
+            TRUE                          ~ NA_character_),
+          fety = case_when(
+            'fesos' == .data$fety ~ 'Solids',
+            'fehos' == .data$fety ~ 'Liquids',
+            'fegas' == .data$fety ~ 'Gases',
+            TRUE                  ~ NA_character_),
+          origin = case_when(
+            grepl('fos$', .data$sety) ~ 'Fossil',
+            grepl('bio$', .data$sety) ~ 'Biomass',
+            grepl('syn$', .data$sety) ~ 'Hydrogen',
+            TRUE                      ~ NA_character_)) %>%
+        assert(not_na, everything()) %>%
+        group_by(.data$t, .data$regi, .data$secInd37, .data$fety,
+                 .data$origin) %>%
+        summarise(value = sum(.data$subsector_emissions)
+                        * as.numeric(GtC_2_MtCO2),
+                  .groups = 'drop') %>%
+        mutate(d3 = paste0('Emi|CO2|pre-CCS|Energy|Demand|Industry|',
+                           .data$secInd37, '|', .data$fety, '|', .data$origin,
+                           ' (Mt CO2/yr)')) %>%
+        select('t', 'regi', 'd3', 'value') %>%
+        as.magpie(spatial = 2, temporal = 1, datacol = ncol(.)) %>%
+      `getSets<-`(fulldim = FALSE, value = getSets(out)),
+
+      # process emissions
+      readGDX(gdx, 'vm_macBaseInd', field = 'l', restore_zeros = FALSE) %>%
+      `[`(,,'co2cement_process.cement') %>%
+      `*`(as.numeric(GtC_2_MtCO2)) %>%
+      `getSets<-`(fulldim = FALSE, value = getSets(out)) %>%
+      `getNames<-`(
+        value = 'Emi|CO2|pre-CCS|Industrial Processes|Cement (Mt CO2/yr)'),
+
+      out)
   } else {
 
     # if o37_demFeIndSub not existing in GDX, calculate reporting parameter here, note: works for industry fixed_shares only

R/reportSE.R

@@ -179,9 +179,8 @@ reportSE <- function(gdx, regionSubsetList = NULL, t = c(seq(2005, 2060, 5), seq
     se.prod(vm_prodSe, dataoc, oc2te, entySe, "pecoal", "seel", te = "igcc",    name = "SE|Electricity|Coal|++|Gasification Combined Cycle w/o CC (EJ/yr)"),
     se.prod(vm_prodSe, dataoc, oc2te, entySe, "pecoal", "seel", te = "igccc",   name = "SE|Electricity|Coal|++|Gasification Combined Cycle w/ CC (EJ/yr)"),
     se.prod(vm_prodSe, dataoc, oc2te, entySe, "pecoal", "seel", te = "pc",      name = "SE|Electricity|Coal|++|Pulverised Coal w/o CC (EJ/yr)"),
-    se.prod(vm_prodSe, dataoc, oc2te, entySe, "pecoal", "seel", te = "pcc",     name = "SE|Electricity|Coal|++|Pulverised Coal w/ CC (EJ/yr)"),
     se.prod(vm_prodSe, dataoc, oc2te, entySe, "pecoal", "seel", te = "coalchp", name = "SE|Electricity|Coal|++|Combined Heat and Power w/o CC (EJ/yr)"),
-    se.prod(vm_prodSe, dataoc, oc2te, entySe, "pecoal", "seel", te = setdiff(pe2se$all_te, c("igcc", "igccc", "pcc", "pc", "coalchp")),
+    se.prod(vm_prodSe, dataoc, oc2te, entySe, "pecoal", "seel", te = setdiff(pe2se$all_te, c("igcc", "igccc", "pc", "coalchp")),
                                                                                 name = "SE|Electricity|Coal|++|Other (EJ/yr)"),
 
     se.prod(vm_prodSe, dataoc, oc2te, entySe, "pegas", "seel",                  name = "SE|Electricity|+|Gas (EJ/yr)"),
@@ -240,22 +239,22 @@ reportSE <- function(gdx, regionSubsetList = NULL, t = c(seq(2005, 2060, 5), seq
 
   ## Gases
   if (!(is.null(vm_macBase) & is.null(vm_emiMacSector))) {
-    ## correction for the reused gas from waste landfills
+    ## exogenous variable for representing reused gas from waste landfills (accounted in the model as segabio)
     MtCH4_2_TWa <- readGDX(gdx, "sm_MtCH4_2_TWa", react = "silent")
     if (is.null(MtCH4_2_TWa)) {
       MtCH4_2_TWa <- 0.001638
     }
     tmp1 <- mbind(tmp1,
-      setNames(MtCH4_2_TWa * (vm_macBase[, , "ch4wstl"] - vm_emiMacSector[, , "ch4wstl"]), "SE|Gases|+|Waste (EJ/yr)")
+      setNames(MtCH4_2_TWa * (vm_macBase[, , "ch4wstl"] - vm_emiMacSector[, , "ch4wstl"]), "SE|Gases|Biomass|Waste (EJ/yr)")
     )
   } else {
     tmp1 <- mbind(tmp1,
-      setNames(new.magpie(cells_and_regions = getRegions(dataoc), years = y, fill = 0), "SE|Gases|+|Waste (EJ/yr)")
+      setNames(new.magpie(cells_and_regions = getRegions(dataoc), years = y, fill = 0), "SE|Gases|Biomass|Waste (EJ/yr)")
     )
   }
 
   tmp1 <- mbind(tmp1,
-    setNames(se.prod(vm_prodSe, dataoc, oc2te, entySe, input_gas, se_Gas) + tmp1[, , "SE|Gases|+|Waste (EJ/yr)"], "SE|Gases (EJ/yr)"),
+    se.prod(vm_prodSe, dataoc, oc2te, entySe, input_gas, se_Gas,                name = "SE|Gases (EJ/yr)"),
     se.prod(vm_prodSe, dataoc, oc2te, entySe, pebio, se_Gas,                    name = "SE|Gases|+|Biomass (EJ/yr)"),
     se.prod(vm_prodSe, dataoc, oc2te, entySe, pebio, se_Gas, te = teccs,        name = "SE|Gases|Biomass|+|w/ CC (EJ/yr)"),
     se.prod(vm_prodSe, dataoc, oc2te, entySe, pebio, se_Gas, te = tenoccs,      name = "SE|Gases|Biomass|+|w/o CC (EJ/yr)"),

R/reportTechnology.R

@@ -105,7 +105,6 @@ reportTechnology <- function(gdx, output = NULL, regionSubsetList = NULL, t = c(
     "biochp" = "Electricity|Biomass|Combined Heat and Power w/o CC",
     "igccc" = "Electricity|Coal|Gasification Combined Cycle w/ CC",
     "igcc" = "Electricity|Coal|Gasification Combined Cycle w/o CC",
-    "pcc" = "Electricity|Coal|Pulverised Coal w/ CC",
     "pc" = "Electricity|Coal|Pulverised Coal w/o CC",
     "coalchp" = "Electricity|Coal|Combined Heat and Power w/o CC",
     "ngccc" = "Electricity|Gas|Combined Cycle w/ CC",

README.md

@@ -1,6 +1,6 @@
 # The REMIND R package (2nd generation)
 
-R package **remind2**, version **1.115.2**
+R package **remind2**, version **1.117.2**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/remind2)](https://cran.r-project.org/package=remind2)  [![R build status](https://github.com/pik-piam/remind2/workflows/check/badge.svg)](https://github.com/pik-piam/remind2/actions) [![codecov](https://codecov.io/gh/pik-piam/remind2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/remind2) [![r-universe](https://pik-piam.r-universe.dev/badges/remind2)](https://pik-piam.r-universe.dev/builds)
 
@@ -49,7 +49,7 @@ In case of questions / problems please contact Renato Rodrigues <renato.rodrigue
 
 To cite package **remind2** in publications use:
 
-Rodrigues R, Baumstark L, Benke F, Dietrich J, Dirnaichner A, Führlich P, Giannousakis A, Hasse R, Hilaire J, Klein D, Koch J, Kowalczyk K, Levesque A, Malik A, Merfort A, Merfort L, Morena-Leiva S, Pehl M, Pietzcker R, Rauner S, Richters O, Rottoli M, Schötz C, Schreyer F, Siala K, Sörgel B, Spahr M, Strefler J, Verpoort P (2023). _remind2: The REMIND R package (2nd generation)_. R package version 1.115.2, <https://github.com/pik-piam/remind2>.
+Rodrigues R, Baumstark L, Benke F, Dietrich J, Dirnaichner A, Führlich P, Giannousakis A, Hasse R, Hilaire J, Klein D, Koch J, Kowalczyk K, Levesque A, Malik A, Merfort A, Merfort L, Morena-Leiva S, Pehl M, Pietzcker R, Rauner S, Richters O, Rottoli M, Schötz C, Schreyer F, Siala K, Sörgel B, Spahr M, Strefler J, Verpoort P (2023). _remind2: The REMIND R package (2nd generation)_. R package version 1.117.2, <https://github.com/pik-piam/remind2>.
 
 A BibTeX entry for LaTeX users is
 
@@ -58,7 +58,7 @@ A BibTeX entry for LaTeX users is
   title = {remind2: The REMIND R package (2nd generation)},
   author = {Renato Rodrigues and Lavinia Baumstark and Falk Benke and Jan Philipp Dietrich and Alois Dirnaichner and Pascal Führlich and Anastasis Giannousakis and Robin Hasse and Jérome Hilaire and David Klein and Johannes Koch and Katarzyna Kowalczyk and Antoine Levesque and Aman Malik and Anne Merfort and Leon Merfort and Simón Morena-Leiva and Michaja Pehl and Robert Pietzcker and Sebastian Rauner and Oliver Richters and Marianna Rottoli and Christof Schötz and Felix Schreyer and Kais Siala and Björn Sörgel and Mike Spahr and Jessica Strefler and Philipp Verpoort},
   year = {2023},
-  note = {R package version 1.115.2},
+  note = {R package version 1.117.2},
   url = {https://github.com/pik-piam/remind2},
 }
 ```

inst/markdown/compareScenarios2/cs2_04_energy_supply.Rmd

@@ -311,8 +311,7 @@ items <- c(
   "SE|Gases|Biomass|w/o CC",
   "SE|Gases|Fossil|Coal|w/ CC",
   "SE|Gases|Fossil|Coal|w/o CC",
-  "SE|Gases|Hydrogen",
-  "SE|Gases|Waste")
+  "SE|Gases|Hydrogen")
 showAreaAndBarPlots(data, items, tot, scales = "fixed")
 ```
 

tests/testthat/test-checkVariableNames.R

@@ -0,0 +1,12 @@
+test_that("checkVariableNames works", {
+  fine <- c("PE (EJ)", "PE (NA/yr)", "FE|What (yr)", "FE|Electricity (EJ/yr)")
+  for (v in fine) {
+    expect_no_warning(checkVariableNames(v))
+  }
+  wrong <- c("PE", "PE| (EJ)", "PE||Elec (EJ)", "PE||Elec", "PE  (EJ)", "PE (NA)",
+             "NA|PE (EJ)", "PE|NA|What (EJ)", " PE (EJ)", "PE (EJ) ")
+  for (v in wrong) {
+    w <- capture_warnings(checkVariableNames(v))
+    expect_true(length(w) > 0)
+  }
+})

tests/testthat/test-convGDX2mif.R

@@ -10,22 +10,6 @@
 library(dplyr)
 library(gdx)
 
-checkVariableNames <- function(out) {
-
-  barspace <- grep("[\\| ]{2}", getNames(out, dim = 3), value = TRUE)
-
-  if (length(barspace) > 0) {
-    warning("These variable names have wrong bars and spaces: ", paste(barspace, collapse = ", "))
-  }
-
-  NAvar <- grep("[\\|\\( ]NA[\\|\\) ]|^NA", getNames(out, dim = 3), value = TRUE)
-  NAvar <- NAvar[! grepl("^Services and Products\\|Transport\\|non-LDV\\|S", NAvar)] # unit NA, but ok, see issue #408
-  if (length(NAvar) > 0) {
-    warning("These variables and units contain NA: ", paste(NAvar, collapse = ", "))
-  }
-}
-
-
 test_that("Test if REMIND reporting is produced as it should and check data integrity", {
   skip_if_not(as.logical(gdxrrw::igdx(silent = TRUE)), "gdxrrw is not initialized properly")
 
@@ -80,7 +64,7 @@ test_that("Test if REMIND reporting is produced as it should and check data inte
     message("Running convGDX2MIF(", gdxPath, ")...")
     mifContent <- convGDX2MIF(gdxPath, gdx_refpolicycost = gdxPath)
 
-    checkVariableNames(mifContent)
+    expect_no_warning(checkVariableNames(getNames(mifContent, dim = 3)))
 
     magclass::write.report(
       x = magclass::collapseNames(mifContent),