Merge branch 'master' of https://github.com/pik-piam/remind2 into Emi…

…Report

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '229425000'
+ValidationKey: '229962240'
 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: 1.150.0
-date-released: '2024-08-15'
+version: 1.152.0
+date-released: '2024-08-27'
 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: 1.150.0
-Date: 2024-08-15
+Version: 1.152.0
+Date: 2024-08-27
 Authors@R: c(
     person("Renato", "Rodrigues", , "renato.rodrigues@pik-potsdam.de", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", role = "aut"),
@@ -49,15 +49,12 @@ Imports:
     data.table,
     dplyr (>= 1.1.1),
     gdx (>= 1.53.0),
-    gdxdt,
     gdxrrw,
     ggplot2,
     gms,
-    htmltools,
-    knitr,
     lucode2 (>= 0.43.0),
     lusweave,
-    madrat (>= 3.11.3),
+    madrat (>= 3.13.0),
     mip (>= 0.149.2),
     openxlsx,
     piamInterfaces (>= 0.17.11),
@@ -70,17 +67,17 @@ Imports:
     reshape2,
     rlang,
     rmarkdown,
-    rmndt,
     tibble,
     tidyr,
     tidyselect,
     withr,
-    yaml,
     digest
 Suggests:
     covr,
     gridExtra,
+    htmltools,
     kableExtra,
+    knitr,
     testthat,
     tidyverse
 VignetteBuilder: 

NAMESPACE

@@ -55,7 +55,6 @@ export(reportClimate)
 export(reportCosts)
 export(reportCrossVariables)
 export(reportDIETER)
-export(reportEDGETransport)
 export(reportEmi)
 export(reportEmiAirPol)
 export(reportEmiForClimateAssessment)
@@ -84,16 +83,10 @@ importFrom(abind,abind)
 importFrom(assertr,assert)
 importFrom(assertr,not_na)
 importFrom(data.table,":=")
-importFrom(data.table,CJ)
-importFrom(data.table,as.data.table)
-importFrom(data.table,copy)
-importFrom(data.table,data.table)
 importFrom(data.table,fread)
 importFrom(data.table,frollmean)
 importFrom(data.table,fwrite)
-importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
-importFrom(data.table,setnames)
 importFrom(digest,digest)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
@@ -124,7 +117,6 @@ importFrom(dplyr,tibble)
 importFrom(dplyr,tribble)
 importFrom(dplyr,ungroup)
 importFrom(gdx,readGDX)
-importFrom(gdxdt,readgdx)
 importFrom(gdxrrw,gdxInfo)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_)
@@ -198,6 +190,7 @@ importFrom(magclass,read.report)
 importFrom(magclass,setItems)
 importFrom(magclass,setNames)
 importFrom(magclass,setYears)
+importFrom(magclass,unitsplit)
 importFrom(magclass,write.report)
 importFrom(mip,plotstyle)
 importFrom(openxlsx,addStyle)
@@ -242,9 +235,6 @@ importFrom(rlang,is_empty)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
 importFrom(rmarkdown,render)
-importFrom(rmndt,approx_dt)
-importFrom(rmndt,readMIF)
-importFrom(rmndt,writeMIF)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(tibble,tribble)

R/calc_CES_marginals.R

@@ -1,147 +1,148 @@
 #' Calculate CES Marginals
-#' 
+#'
 #' Calculate marginals on the REMIND CES function and combine them to prices.
-#' 
+#'
 #' Marginals are calculated analytically
-#' \deqn{\frac{\partial V_i}{\partial V_o} = \xi_i (\theta_i \delta_i)^{\rho_o} 
+#' \deqn{\frac{\partial V_i}{\partial V_o} = \xi_i (\theta_i \delta_i)^{\rho_o}
 #'       {V_o}^{1 - \rho_o} {V_i}^{\rho_o - 1}}
 #' and prices by recursively applying the chain rule
-#' \deqn{\pi_i = \frac{\partial V_i}{\partial V_o} \pi_o 
+#' \deqn{\pi_i = \frac{\partial V_i}{\partial V_o} \pi_o
 #'       \quad \forall (i,o) \in CES}
 #'
 #' @md
 #' @param gdxName Vector of paths to `.gdx` files.
-#' @param id If several `.gdx` files are read, an id column is appended to the 
+#' @param id If several `.gdx` files are read, an id column is appended to the
 #'        result; either `file`, with the paths of the originating `.gdx` files,
 #'        or `scenario`, with the content of `c_expname`.
 #'
 #' @return A `data frame` with columns `pf` (production factor), `t`, `regi`,
 #'         `marginal`, `price`, and `file` (path to originating `.gdx` file).
-#'         
+#'
 #' @importFrom quitte read.gdx
-#' @importFrom dplyr %>% left_join filter sym select rename mutate pull 
+#' @importFrom dplyr %>% left_join filter sym select rename mutate pull
+#' @importFrom data.table :=
 #' @importFrom tidyr pivot_wider drop_na
 #' @importFrom gdxrrw gdxInfo
 #' @importFrom rlang is_empty
 
 #' @export
 calc_CES_marginals <- function(gdxName, id = 'file') {
-  
+
   if (all(!is.null(id), !id %in% c('file', 'scenario'))) {
     warning('id must be either "file" or "scenario".  Defaulting to "file".')
     id <- 'file'
   }
-  
+
   gdxName <- path.expand(gdxName)
-  
+
   .calc_CES_marginals <- function(gdxName, id) {
     # ---- read required items from gdx ----
     pm_cesdata <- read.gdx(gdxName, 'pm_cesdata',
                            colNames = c('t', 'regi', 'pf', 'param', 'value'))
-    
+
     vm_effGr <- read.gdx(gdxName, 'vm_effGr',
                          colNames = c('t', 'regi', 'pf', 'effGr'))
-    
+
     vm_cesIO <- read.gdx(gdxName, 'vm_cesIO',
                          colNames = c('t', 'regi', 'pf', 'value'))
-    
+
     cesOut2cesIn <- read.gdx(gdxName, 'cesOut2cesIn',
                              colNames = c('pf.out', 'pf.in'))
-    
+
     # ---- calculate marginals ----
-    marginals <- cesOut2cesIn %>% 
+    marginals <- cesOut2cesIn %>%
       left_join(
-        pm_cesdata %>% 
-          filter(!!sym('param') %in% c('xi', 'eff')) %>% 
-          pivot_wider(names_from = 'param') %>% 
+        pm_cesdata %>%
+          filter(!!sym('param') %in% c('xi', 'eff')) %>%
+          pivot_wider(names_from = 'param') %>%
           drop_na(),
-        
+
         c('pf.in' = 'pf')
-      ) %>% 
+      ) %>%
       left_join(
-        pm_cesdata %>% 
-          filter('rho' == !!sym('param')) %>% 
+        pm_cesdata %>%
+          filter('rho' == !!sym('param')) %>%
           select(-'param', 'rho' = 'value'),
-        
+
         c('t', 'regi', 'pf.out' = 'pf')
-      ) %>% 
+      ) %>%
       left_join(
         vm_effGr,
-        
+
         c('t', 'regi', 'pf.in' = 'pf')
-      ) %>% 
+      ) %>%
       left_join(
-        vm_cesIO %>% 
-          rename('value.in' = 'value'), 
-        
+        vm_cesIO %>%
+          rename('value.in' = 'value'),
+
         c('t', 'regi', 'pf.in' = 'pf')
-      ) %>% 
+      ) %>%
       left_join(
-        vm_cesIO %>% 
+        vm_cesIO %>%
           rename('value.out' = 'value'),
-        
+
         c('t', 'regi', 'pf.out' = 'pf')
-      ) %>% 
+      ) %>%
       mutate(
         # ^ !!sym() doesn't work, so use the explicit function call
-        !!sym('marginal') := !!sym('xi') 
+        !!sym('marginal') := !!sym('xi')
                            * (!!sym('eff') * !!sym('effGr')) ^ (!!sym('rho'))
                            * `^`(!!sym('value.out'), 1 - !!sym('rho'))
                            * `^`(!!sym('value.in'),  !!sym('rho') - 1))
-    
+
     # ---- calculate prices recursively using the chain rule ----
     CES_root <- setdiff(cesOut2cesIn$pf.out, cesOut2cesIn$pf.in)
-    
-    prices <- marginals %>% 
-      filter(!!sym('pf.out') %in% CES_root) %>% 
+
+    prices <- marginals %>%
+      filter(!!sym('pf.out') %in% CES_root) %>%
       select('pf' = 'pf.in', 't', 'regi', 'price' = 'marginal')
-    
-    CES_root <- cesOut2cesIn %>% 
-      filter(!!sym('pf.out') %in% CES_root) %>% 
+
+    CES_root <- cesOut2cesIn %>%
+      filter(!!sym('pf.out') %in% CES_root) %>%
       pull('pf.in')
-    
+
     while (!is_empty(CES_root)) {
       prices <- bind_rows(
         prices,
-        
-        marginals %>% 
-          filter(!!sym('pf.out') %in% CES_root) %>% 
-          select('pf' = 'pf.in', 't', 'regi', 'price' = 'marginal') %>% 
-          left_join(cesOut2cesIn, c('pf' = 'pf.in')) %>% 
+
+        marginals %>%
+          filter(!!sym('pf.out') %in% CES_root) %>%
+          select('pf' = 'pf.in', 't', 'regi', 'price' = 'marginal') %>%
+          left_join(cesOut2cesIn, c('pf' = 'pf.in')) %>%
           left_join(
-            prices %>% 
-              rename('price.out' = 'price'), 
-            
+            prices %>%
+              rename('price.out' = 'price'),
+
             c('t', 'regi', 'pf.out' = 'pf')
-          ) %>% 
-          mutate(!!sym('price') := !!sym('price') * !!sym('price.out')) %>% 
+          ) %>%
+          mutate(!!sym('price') := !!sym('price') * !!sym('price.out')) %>%
           select('pf', 't', 'regi', 'price')
       )
-      
-      CES_root <- cesOut2cesIn %>% 
-        filter(!!sym('pf.out') %in% CES_root) %>% 
+
+      CES_root <- cesOut2cesIn %>%
+        filter(!!sym('pf.out') %in% CES_root) %>%
         pull('pf.in')
     }
-    
+
     # ---- bind marginals and prices together ----
     r <- bind_rows(
-      marginals %>% 
-        select('pf' = 'pf.in', 't', 'regi', 'value' = 'marginal') %>% 
+      marginals %>%
+        select('pf' = 'pf.in', 't', 'regi', 'value' = 'marginal') %>%
         mutate(!!sym('name') := 'marginal'),
-      
-      prices %>% 
-        rename('value' = 'price') %>% 
+
+      prices %>%
+        rename('value' = 'price') %>%
         mutate(!!sym('name') := 'price')
-    ) %>% 
+    ) %>%
       pivot_wider()
-    
+
     if (id) {
-      r <- r %>% 
-        mutate(!!sym('scenario') := read.gdx(gdxName, 'c_expname', 
-                                             colNames = 'c_expname') %>% 
+      r <- r %>%
+        mutate(!!sym('scenario') := read.gdx(gdxName, 'c_expname',
+                                             colNames = 'c_expname') %>%
                  pull('c_expname'))
     }
-    
+
     return(r)
   }
 
@@ -158,19 +159,19 @@ calc_CES_marginals <- function(gdxName, id = 'file') {
       }
     )
   }
-  
+
   # ---- bind results for all valid input files together ----
   r <- bind_rows(
     lapply(gdxName, function(gdxName) {
-      .calc_CES_marginals(gdxName, id = all(!is.null(id), id == 'scenario')) %>% 
+      .calc_CES_marginals(gdxName, id = all(!is.null(id), id == 'scenario')) %>%
         mutate(file = gdxName)
     })
   )
-  
+
   if (any(is.null(id), 'file' != id)) {
-    r <- r %>% 
+    r <- r %>%
       select(-file)
   }
-  
+
   return(r)
 }

R/plotNashConvergence.R

@@ -12,6 +12,7 @@
 #' @importFrom gdx readGDX
 #' @importFrom dplyr summarise group_by mutate filter distinct case_when
 #' @importFrom quitte as.quitte
+#' @importFrom data.table :=
 #' @importFrom mip plotstyle
 #' @importFrom ggplot2 scale_y_continuous scale_x_continuous scale_y_discrete
 #'              scale_fill_manual scale_color_manual coord_cartesian aes_ geom_rect

R/reportCosts.R

@@ -603,6 +603,9 @@ reportCosts <- function(gdx,output=NULL,regionSubsetList=NULL,t=c(seq(2005,2060,
   if (!is.null(regionSubsetList))
     tmp <- mbind(tmp, calc_regionSubset_sums(tmp, regionSubsetList))
 
+  # cannot be summed for aggregation
+  tmp[c("GLO", names(regionSubsetList)),,"Costs|Biomass|Adjfactor (unitless)"] <- NA
+
   getSets(tmp)[3] <- "variable"
   return(tmp)
 }

R/reportCrossVariables.R

@@ -23,6 +23,7 @@
 #' @importFrom magclass getYears getRegions mbind setNames mselect
 #' new.magpie setYears mcalc
 #' @importFrom tibble as_tibble
+#' @importFrom data.table :=
 #' @importFrom tidyselect everything
 #' @importFrom madrat toolAggregate
 #'
@@ -234,7 +235,7 @@ reportCrossVariables <- function(gdx, output = NULL, regionSubsetList = NULL,
     output[,,"FE|Transport|Liquids (EJ/yr)"] * output[,,"Price|Final Energy|Transport|Liquids (US$2005/GJ)"] +
     output[,,"FE|Transport|Hydrogen (EJ/yr)"] * output[,,"Price|Final Energy|Transport|Hydrogen (US$2005/GJ)"] +
     output[,,"FE|Transport|Electricity (EJ/yr)"] * output[,,"Price|Final Energy|Transport|Electricity (US$2005/GJ)"],
-                       "Expenditure|Transport|Fuel (billion $US/yr)"))
+                       "Expenditure|Transport|Fuel (billion US$2005/yr)"))
 
   # calculate intensities growth
   int_gr <- new.magpie(getRegions(tmp),getYears(tmp),c("Intensity Growth|GDP|Final Energy (% pa)","Intensity Growth|GDP|Final Energy to 2005 (% pa)",