Deleted commented out peatlands code

pik-piam · Aug 7, 2023 · 322c00c · 322c00c
1 parent 17084f7
commit 322c00c
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Showing 5 changed files with 24 additions and 40 deletions.
diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '232954400'
+ValidationKey: '232973976'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

diff --git a/CITATION.cff b/CITATION.cff
@@ -2,7 +2,7 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'magpie4: MAgPIE outputs R package for MAgPIE version 4.x'
-version: 1.190.0
+version: 1.190.1
 date-released: '2023-08-07'
 abstract: Common output routines for extracting results from the MAgPIE framework
   (versions 4.x).

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: magpie4
 Title: MAgPIE outputs R package for MAgPIE version 4.x
-Version: 1.190.0
+Version: 1.190.1
 Date: 2023-08-07
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),

diff --git a/R/reportEmissions.R b/R/reportEmissions.R
@@ -145,7 +145,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
             }
         }
 
-        # # No lowpass filter applied to peatland emissions
+        # No lowpass filter applied to peatland emissions
         co2Emissions <- Emissions(gdx, level = "regglo", type = "co2", unit = "gas",
                                   subcategories = TRUE, inorg_fert_split = TRUE,
                                   lowpass = NULL, cumulative = .cumulative)
@@ -159,22 +159,6 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
             total        <- total + peatland
             landuseTotal <- landuseTotal + peatland
         }
-
-
-        # # Never apply lowpass filter on peatland emissions
-        # peatland <- PeatlandEmissions(gdx, level = "regglo", unit = "gas", cumulative = .cumulative)
-        # if (!is.null(peatland)) {
-
-        #     peatland <- collapseNames(peatland[, , "co2"])
-
-        #     if (.cumulative) {
-        #         peatland <- peatland / 1000
-        #     }
-
-        #     total        <- total + peatland
-        #     landuseTotal <- landuseTotal + peatland
-        # }
-
 
         # Generate return list
         if (.raw) {
@@ -224,7 +208,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
 
     yearlyCO2 <- .calcCO2(.lowpass = 3, .cumulative = FALSE)
 
-    # nolint
+    # nolint start
     emissionsReport <- with(yearlyCO2, 
       mbind(
         setNames(total,                     "Emissions|CO2|Land (Mt CO2/yr)"), # all human-induced land-related CO2 emissions
@@ -265,15 +249,15 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
           )
         )
     } 
-    # end nolint
+    # nolint end
 
 
     # -----------------------------------------------------------------------------------------------------------------
     # RAW yearly CO2 emissions, lowpass = 0
 
     rawYearlyCO2 <- .calcCO2(.lowpass = 0, .cumulative = FALSE, .raw = TRUE)
 
-    # nolint
+    # nolint start
     emissionsReport <- with(rawYearlyCO2,
       mbind(
           emissionsReport, 
@@ -282,15 +266,15 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
           setNames(climateChange, "Emissions|CO2|Land RAW|+|Indirect RAW (Mt CO2/yr)")
       )
     )
-    # end nolint
+    # nolint end
 
 
     # -----------------------------------------------------------------------------------------------------------------
     # Cumulative CO2 emissions, lowpass = 3
 
     cumulativeCO2 <- .calcCO2(.lowpass = 3, .cumulative = TRUE)
 
-    # nolint
+    # nolint start
     emissionsReport <- with(cumulativeCO2, 
       mbind(
           emissionsReport,
@@ -327,7 +311,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
           )
         )
     }
-    # end nolint  
+    # nolint end  
 
 
     # -----------------------------------------------------------------------------------------------------------------
@@ -390,7 +374,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
 
     landCarbonSink <- .calcLandCarbonSink()
 
-    # nolint
+    # nolint start
     emissionsReport <- with(landCarbonSink, 
       mbind(
           emissionsReport,
@@ -411,15 +395,15 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
           setNames(unmanagedLandOther,         "Emissions|CO2|Land Carbon Sink|LPJmL|Unmanaged Land|+|Other Land (Mt CO2/yr)")
       )
     )
-    # end nolint
+    # nolint end
 
 
     # -----------------------------------------------------------------------------------------------------------------
     # Cumulative indirect CO2 emissions from land-use change (land-carbon sink) reporting
 
     cumulativeLandCarbonSink <- .calcLandCarbonSink(.cumulative = TRUE)
 
-    # nolint
+    # nolint start
     emissionsReport <- with(cumulativeLandCarbonSink, 
       mbind(
           emissionsReport,
@@ -440,7 +424,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
           setNames(unmanagedLandOther,         "Emissions|CO2|Land Carbon Sink|Cumulative|LPJmL|Unmanaged Land|+|Other Land (Gt CO2)")
       )
     )
-    # end nolint
+    # nolint end
 
 
     # -----------------------------------------------------------------------------------------------------------------
@@ -481,7 +465,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
         }
 
 
-        # nolint
+        # nolint start
         .x <- mbind(
             .createReport(nEmissions, c(agriculture, burn, peatland_n2o)), 
             .createReport(nEmissions, agriculture,                                                     "|+|Agriculture"), 
@@ -498,7 +482,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
             .createReport(nEmissions, burn,                                                            "|+|Biomass Burning"), 
             .createReport(nEmissions, c("resid_burn"),                                                 "|Biomass Burning|+|Burning of Crop Residues")
         )
-        # end nolint
+        # nolint end
 
         # Old versions of MAgPIE may not include peatlands
         if ("peatland" %in% getItems(nEmissions, dim = 3.1)) {
@@ -540,7 +524,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
         ch4 <- mbind(ch4, peatlandEmissions)
     }
 
-    # nolint
+    # nolint start
     emissionsReport <- mbind(
         emissionsReport,
         setNames(dimSums(ch4[, , c(agricult_ch4, burn_ch4, peatland_ch4)], dim = 3), "Emissions|CH4|Land (Mt CH4/yr)"),
@@ -553,7 +537,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
         setNames(dimSums(ch4[, , c(peatland_ch4)], dim = 3),                         "Emissions|CH4|Land|+|Peatland (Mt CH4/yr)"),
         setNames(dimSums(ch4[, , c("peatland")], dim = 3),                           "Emissions|CH4|Land|Peatland|+|Managed (Mt CH4/yr)")
     )
-    # end nolint
+    # nolint end
 
 
     # -----------------------------------------------------------------------------------------------------------------
@@ -572,7 +556,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
             return(setNames(t, n))
         }
 
-        # nolint
+        # nolint start
         .x <- mbind(
             .createReport(c(agriculture, "resid_burn", "peatland")),
             .createReport(c(agriculture),                                                   "|+|Agriculture"),
@@ -590,7 +574,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
             .createReport(c("peatland"),                                                    "|+|Peatland"),
             .createReport(c("peatland"),                                                    "|Peatland|+|Managed")
         )
-        # end nolint
+        # nolint end
 
         return(.x)
     }
@@ -615,7 +599,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
             return(setNames(t, n))
         }
 
-        # nolint
+        # nolint start
         .x <- mbind(
             .createReport(c("rice", "awms", "ent_ferm", "resid_burn", "peatland")),
             .createReport(c("rice", "awms", "ent_ferm"),                            "|+|Agriculture"),

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # MAgPIE outputs R package for MAgPIE version 4.x
 
-R package **magpie4**, version **1.190.0**
+R package **magpie4**, version **1.190.1**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/magpie4)](https://cran.r-project.org/package=magpie4) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1158582.svg)](https://doi.org/10.5281/zenodo.1158582) [![R build status](https://github.com/pik-piam/magpie4/workflows/check/badge.svg)](https://github.com/pik-piam/magpie4/actions) [![codecov](https://codecov.io/gh/pik-piam/magpie4/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/magpie4) [![r-universe](https://pik-piam.r-universe.dev/badges/magpie4)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Benjamin Leon Bodirsky <bodirsky@
 
 To cite package **magpie4** in publications use:
 
-Bodirsky B, Humpenoeder F, Dietrich J, Stevanovic M, Weindl I, Karstens K, Wang X, Mishra A, Beier F, Breier J, Yalew A, Chen D, Biewald A, Wirth S, von Jeetze P, Leip D, Crawford M, Alves M (2023). _magpie4: MAgPIE outputs R package for MAgPIE version 4.x_. doi: 10.5281/zenodo.1158582 (URL: https://doi.org/10.5281/zenodo.1158582), R package version 1.190.0, <URL: https://github.com/pik-piam/magpie4>.
+Bodirsky B, Humpenoeder F, Dietrich J, Stevanovic M, Weindl I, Karstens K, Wang X, Mishra A, Beier F, Breier J, Yalew A, Chen D, Biewald A, Wirth S, von Jeetze P, Leip D, Crawford M, Alves M (2023). _magpie4: MAgPIE outputs R package for MAgPIE version 4.x_. doi: 10.5281/zenodo.1158582 (URL: https://doi.org/10.5281/zenodo.1158582), R package version 1.190.1, <URL: https://github.com/pik-piam/magpie4>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {magpie4: MAgPIE outputs R package for MAgPIE version 4.x},
   author = {Benjamin Leon Bodirsky and Florian Humpenoeder and Jan Philipp Dietrich and Miodrag Stevanovic and Isabelle Weindl and Kristine Karstens and Xiaoxi Wang and Abhijeet Mishra and Felicitas Beier and Jannes Breier and Amsalu Woldie Yalew and David Chen and Anne Biewald and Stephen Wirth and Patrick {von Jeetze} and Debbora Leip and Michael Crawford and Marcos Alves},
   year = {2023},
-  note = {R package version 1.190.0},
+  note = {R package version 1.190.1},
   doi = {10.5281/zenodo.1158582},
   url = {https://github.com/pik-piam/magpie4},
 }