revert back broken code

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '233715440'
+ValidationKey: '233735047'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

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: 1.192.0
+version: 1.192.1
 date-released: '2023-09-07'
 abstract: Common output routines for extracting results from the MAgPIE framework
   (versions 4.x).

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: magpie4
 Title: MAgPIE outputs R package for MAgPIE version 4.x
-Version: 1.192.0
+Version: 1.192.1
 Date: 2023-09-07
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),

R/emisCO2.R

@@ -188,7 +188,7 @@ emisCO2 <- function(gdx, file = NULL, level = "cell", unit = "gas",
 
     # forestry land
     ####################
-      p32_land <- landForestry(gdx, level = "cell")
+    p32_land <- landForestry(gdx, level = "cell")
     if (is.null(p32_land)) {
       b[, , "forestry_plant"] <- 0
     } else {
@@ -261,14 +261,14 @@ emisCO2 <- function(gdx, file = NULL, level = "cell", unit = "gas",
   timestep_length <- readGDX(gdx, "im_years", react = "silent")
   if (is.null(timestep_length)) timestep_length <- timePeriods(gdx)
   stock <- carbonstock(gdx, level = "cell", sum_cpool = FALSE, sum_land = FALSE)
-#  a <- new.magpie(getCells(stock),getYears(stock),getNames(stock),fill = 0); a[,1,] <- NA; dummy <- a;
+  #  a <- new.magpie(getCells(stock),getYears(stock),getNames(stock),fill = 0); a[,1,] <- NA; dummy <- a;
   a <- stock
-a[, , ] <- 0
-a[, 1, ] <- NA
-dummy <- a
+  a[, , ] <- 0
+  a[, 1, ] <- NA
+  dummy <- a
   t <- 2:length(timestep_length)
   a[, t, ] <- (setYears(stock[, t - 1, ], getYears(a[, t, ])) - stock[, t, ]) /
-                                                   timestep_length[, t, ]
+    timestep_length[, t, ]
   emis_total <- a
 
   ### emis_cc
@@ -311,60 +311,6 @@ dummy <- a
   emis_degrad <- emis_degrad / timestep_length
   emis_degrad[, 1, ] <- NA
 
-  ## Emission deforestation ----
-  emis_deforestation <- emis_other_land <- dummy
-
-  ### Find changes in secdf ---
-  secdforest <- collapseNames(readGDX(gdx, "ov35_secdforest")[,, "level"])
-  secdforest_change <- secdforest[, 1,]
-  secdforest_change[secdforest_change!=0] <- 0
-  for (t in 2:nyears(secdforest)) {
-    temp <- setYears(secdforest[, t - 1, ], getYears(secdforest[, t, ])) - secdforest[, t, ]
-    temp[temp<0] <- 0 # age-classes which increased in future, it does not count as "deforestation"
-    secdforest_change <- mbind(secdforest_change,temp)
-  }
-
-  ### Find changes in primf ----
-  primforest <- collapseNames(readGDX(gdx, "ov_land")[,,"primforest"][,, "level"])
-  primforest_change <- primforest[, 1,]
-  primforest_change[primforest_change!=0] <- 0
-  for (t in 2:nyears(primforest)) {
-    temp <- setYears(primforest[, t - 1, ], getYears(primforest[, t, ])) - primforest[, t, ]
-    temp[temp<0] <- 0 # if primf increased in future, it does not count as "deforestation"
-    primforest_change <- mbind(primforest_change,temp)
-  }
-
-  ### Find changes in other land ----
-  other <- collapseNames(readGDX(gdx, "ov35_other")[,, "level"])
-  other_change <- other[, 1,]
-  other_change[other_change!=0] <- 0
-  for (t in 2:nyears(other)) {
-    temp <- setYears(other[, t - 1, ], getYears(other[, t, ])) - other[, t, ]
-    temp[temp<0] <- 0 # age-classes which increased in future, it does not count as "other land conversion"
-    other_change <- mbind(other_change,temp)
-  }
-
-  if (all(!is.null(secdforest_change),
-          !is.null(primforest_change))) {
-    agPools <- c("vegc", "litc")
-    pm_carbon_density_ac <- readGDX(gdx, "pm_carbon_density_ac")[, getYears(timestep_length), ]
-    emis_deforestation[, , "secdforest"][, , agPools] <- dimSums(pm_carbon_density_ac[, , agPools] * secdforest_change, dim = "ac")
-    fm_carbon_density <- readGDX(gdx, "fm_carbon_density")[, getYears(emis_deforestation), ]
-    names(dimnames(fm_carbon_density))[2] <- "t"
-    emis_deforestation[, , "primforest"][, , agPools] <- primforest_change * fm_carbon_density[, , "primforest"][, , agPools]
-  }
-  emis_deforestation <- emis_deforestation / timestep_length
-  emis_deforestation[, 1, ] <- NA
-
-  if (all(!is.null(other_change))) {
-    agPools <- c("vegc", "litc")
-    pm_carbon_density_ac <- readGDX(gdx, "pm_carbon_density_ac")[, getYears(timestep_length), ]
-    emis_other_land[, , "other"][, , agPools] <- dimSums(pm_carbon_density_ac[, , agPools] * other_change, dim = "ac")
-  }
-  emis_other_land <- emis_other_land / timestep_length
-  emis_other_land[, 1, ] <- NA
-
-
   # ### emis_harvest (wood)
   # emis_harvest <- dummy
   # ov_hvarea_forestry <- readGDX(gdx,"ov_hvarea_forestry",select = list(type="level"),react = "silent")
@@ -411,14 +357,8 @@ dummy <- a
   # emis_harvest <- add_dimension(emis_harvest, dim = 3.3,
   #                               nm = "lu_harvest", add = "type")
 
-  emis_deforestation    <- add_dimension(emis_deforestation, dim = 3.3,
-                                  nm = "lu_deforestation", add = "type")
-
-  emis_other_land       <- add_dimension(emis_other_land, dim = 3.3,
-                                  nm = "lu_other_conversion", add = "type")
-
   # bind together
-  a <- mbind(emis_total, emis_cc, emis_lu, emis_luc, emis_regrowth, emis_degrad, emis_deforestation, emis_other_land)
+  a <- mbind(emis_total, emis_cc, emis_lu, emis_luc, emis_regrowth, emis_degrad)
 
   # calc emis_total
   # calc emis_cc #vegc,litc,soilc #natural + indirect human effects
@@ -453,8 +393,8 @@ dummy <- a
 
   # unit conversion
   if (unit == "gas") {
-     a <- a * 44 / 12
-     } # from Mt C/yr to Mt CO2/yr
+    a <- a * 44 / 12
+  } # from Mt C/yr to Mt CO2/yr
 
   # years
   years <- getYears(a, as.integer = TRUE)