Merge branch 'main' of https://github.com/bc3LC/rfasst

NAMESPACE

@@ -24,9 +24,10 @@ export(m3_get_daly_o3)
 export(m3_get_daly_pm25)
 export(m3_get_mort_o3)
 export(m3_get_mort_pm25)
+export(m3_get_mort_pm25_ecoloss)
+export(m3_get_o3_ecoloss_hcl)
 export(m3_get_o3_ecoloss_vsl)
 export(m3_get_pm25_ecoloss_gdpGrowth)
-export(m3_get_pm25_ecoloss_vsl)
 export(m3_get_yll_o3)
 export(m3_get_yll_pm25)
 export(m4_get_prod_loss)

R/m1_emissions_rescale.R

@@ -8,6 +8,7 @@
 #' @param query_path Path to the query file
 #' @param db_name Name of the GCAM database
 #' @param prj_name Name of the rgcam project. This can be an existing project, or, if not, this will be the name
+#' @param prj rgcam loaded project
 #' @param rdata_name Name of the RData file. It must contain the queries in a list
 #' @param scen_name Name of the GCAM scenario to be processed
 #' @param queries Name of the GCAM query file. The file by default includes the queries required to run rfasst
@@ -20,7 +21,7 @@
 #' @importFrom magrittr %>%
 #' @export
 
-m1_emissions_rescale<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name,
+m1_emissions_rescale<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name = NULL, prj = NULL,
                                rdata_name = NULL, scen_name, queries = "queries_rfasst.xml", final_db_year = 2100,
                                saveOutput = T, map = F, mapIndivPol = F, anim = T, recompute = F){
 
@@ -32,7 +33,8 @@ m1_emissions_rescale<-function(db_path = NULL, query_path = "./inst/extdata", db
     #----------------------------------------------------------------------
     # Assert that the parameters of the function are okay, or modify when necessary
 
-    #if (!endsWith(prj_name, '.dat')) prj_name = paste0(prj_name, '.dat')
+    if(!endsWith(prj_name, '.dat')) prj_name = paste0(prj_name, '.dat')
+    if(is.null(prj_name)) assertthat::assert_that(!is.null(prj), msg = 'Specify the project name or pass an uploaded project as parameter')
 
     #----------------------------------------------------------------------
     #----------------------------------------------------------------------
@@ -64,33 +66,37 @@ m1_emissions_rescale<-function(db_path = NULL, query_path = "./inst/extdata", db
       dplyr::rename(`ISO 3`=subRegionAlt,
                     `FASST Region`=fasst_region)
 
-    # Load the rgcam project:
-    if (!is.null(db_path) & !is.null(db_name)) {
-      rlang::inform('Creating project ...')
-      conn <- rgcam::localDBConn(db_path,
-                                 db_name,migabble = FALSE)
-      prj <- rgcam::addScenario(conn,
-                                prj_name,
-                                scen_name,
-                                paste0(query_path,"/",queries),
-                                saveProj = F)
-      prj <- fill_queries(prj, db_path, db_name, prj_name, scen_name,
-                          query_path, queries = 'queries_rfasst_nonCO2.xml')
-
-      rgcam::saveProject(prj, file = file.path('output',prj_name))
-
-      QUERY_LIST <- c(rgcam::listQueries(prj, c(scen_name)))
-    } else if (is.null(rdata_name)){
-      rlang::inform('Loading project ...')
-      prj <- rgcam::loadProject(prj_name)
-
-      QUERY_LIST <- c(rgcam::listQueries(prj, c(scen_name)))
-    } else {
-      rlang::inform('Loading RData ...')
-      if (!exists('prj_rd')) {
-        prj_rd = get(load(rdata_name))
-        QUERY_LIST <- names(prj_rd)
+    # Load the rgcam project if prj not passed as a parameter:
+    if (is.null(prj)) {
+      if (!is.null(db_path) & !is.null(db_name)) {
+        rlang::inform('Creating project ...')
+        conn <- rgcam::localDBConn(db_path,
+                                   db_name,migabble = FALSE)
+        prj <- rgcam::addScenario(conn,
+                                  prj_name,
+                                  scen_name,
+                                  paste0(query_path,"/",queries),
+                                  saveProj = F)
+        prj <- fill_queries(prj, db_path, db_name, prj_name, scen_name,
+                            query_path, queries = 'queries_rfasst_nonCO2.xml')
+
+        rgcam::saveProject(prj, file = file.path('output',prj_name))
+
+        QUERY_LIST <- c(rgcam::listQueries(prj, c(scen_name)))
+      } else if (is.null(rdata_name)){
+        rlang::inform('Loading project ...')
+        prj <- rgcam::loadProject(prj_name)
+
+        QUERY_LIST <- c(rgcam::listQueries(prj, c(scen_name)))
+      } else {
+        rlang::inform('Loading RData ...')
+        if (!exists('prj_rd')) {
+          prj_rd = get(load(rdata_name))
+          QUERY_LIST <- names(prj_rd)
+        }
       }
+    } else {
+      QUERY_LIST <- c(rgcam::listQueries(prj, c(scen_name)))
     }
     rlang::inform('Computing emissions ...')
 

R/m2_conc.R

@@ -1,13 +1,13 @@
 #' m2_get_conc_pm25
 #'
-#'
 #' Produce fine particulate matter (PM2.5) concentration levels for TM5-FASST regions based on re-scaled emission pathways.
 #' @keywords module_2, concentration, PM2.5
 #' @return Particulate matter (PM2.5) concentration levels for each TM5-FASST regions for all years (ug/m3).The list of countries that form each region and the full name of the region can be found in Table S2.2 in the TM5-FASST documentation paper: Van Dingenen, R., Dentener, F., Crippa, M., Leitao, J., Marmer, E., Rao, S., Solazzo, E. and Valentini, L., 2018. TM5-FASST: a global atmospheric source-receptor model for rapid impact analysis of emission changes on air quality and short-lived climate pollutants. Atmospheric Chemistry and Physics, 18(21), pp.16173-16211.
 #' @param db_path Path to the GCAM database
 #' @param query_path Path to the query file
 #' @param db_name Name of the GCAM database
 #' @param prj_name Name of the rgcam project. This can be an existing project, or, if not, this will be the name
+#' @param prj rgcam loaded project
 #' @param rdata_name Name of the RData file. It must contain the queries in a list
 #' @param scen_name Name of the GCAM scenario to be processed
 #' @param queries Name of the GCAM query file. The file by default includes the queries required to run rfasst
@@ -23,7 +23,7 @@
 #' @importFrom magrittr %>%
 #' @export
 
-m2_get_conc_pm25<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name,
+m2_get_conc_pm25<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name = NULL, prj = NULL,
                            rdata_name = NULL, scen_name, queries = "queries_rfasst.xml", final_db_year = 2100,
                            saveOutput = T, map = F, anim = T, recompute = F,
                            downscale = F, saveRaster_grid = F,
@@ -42,6 +42,7 @@ m2_get_conc_pm25<-function(db_path = NULL, query_path = "./inst/extdata", db_nam
     if(agg_grid == "NUTS3") assertthat::assert_that(downscale == T, msg = 'Set `downscale` to TRUE to aggregate the downscaled PM2.5 to NUTS3')
     if(save_AggGrid == T) assertthat::assert_that(agg_grid  == "NUTS3" & downscale == T,
                                                   msg = 'Set `downscale` to TRUE and agg_grid to `NUTS3` to save the aggregated raster grid')
+    if(is.null(prj_name)) assertthat::assert_that(!is.null(prj), msg = 'Specify the project name or pass an uploaded project as parameter')
 
 
     #----------------------------------------------------------------------
@@ -69,7 +70,7 @@ m2_get_conc_pm25<-function(db_path = NULL, query_path = "./inst/extdata", db_nam
       dplyr::rename(subRegion=fasst_region) %>%
       dplyr::mutate(subRegionAlt=as.factor(subRegionAlt))
 
-    em.list<-m1_emissions_rescale(db_path, query_path, db_name, prj_name, rdata_name, scen_name, queries, saveOutput = F, final_db_year, recompute = recompute)
+    em.list<-m1_emissions_rescale(db_path, query_path, db_name, prj_name, prj, rdata_name, scen_name, queries, saveOutput = F, final_db_year, recompute = recompute)
 
     #----------------------------------------------------------------------
     #----------------------------------------------------------------------
@@ -561,14 +562,14 @@ m2_get_conc_pm25<-function(db_path = NULL, query_path = "./inst/extdata", db_nam
 
 #' m2_get_conc_o3
 #'
-#'
 #' Produce ozone (O3) concentration levels based on re-scaled emission pathways.
 #' @keywords module_2, concentration, O3
 #' @return Produce ozone (O3) levels for each TM5-FASST regions for all years (ppb). The list of countries that form each region and the full name of the region can be found in Table S2.2 in the TM5-FASST documentation paper: Van Dingenen, R., Dentener, F., Crippa, M., Leitao, J., Marmer, E., Rao, S., Solazzo, E. and Valentini, L., 2018. TM5-FASST: a global atmospheric source-receptor model for rapid impact analysis of emission changes on air quality and short-lived climate pollutants. Atmospheric Chemistry and Physics, 18(21), pp.16173-16211.
 #' @param db_path Path to the GCAM database
 #' @param query_path Path to the query file
 #' @param db_name Name of the GCAM database
 #' @param prj_name Name of the rgcam project. This can be an existing project, or, if not, this will be the name
+#' @param prj rgcam loaded project
 #' @param rdata_name Name of the RData file. It must contain the queries in a list
 #' @param scen_name Name of the GCAM scenario to be processed
 #' @param queries Name of the GCAM query file. The file by default includes the queries required to run rfasst
@@ -581,13 +582,21 @@ m2_get_conc_pm25<-function(db_path = NULL, query_path = "./inst/extdata", db_nam
 #' @importFrom magrittr %>%
 #' @export
 
-m2_get_conc_o3<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name,
+m2_get_conc_o3<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name = NULL, prj = NULL,
                          rdata_name = NULL, scen_name, queries = "queries_rfasst.xml", final_db_year = 2100,
                          saveOutput = T, ch4_o3 = T, map = F, anim = T, recompute = F){
 
   if (!recompute & exists('m2_get_conc_o3.output')) {
     return(m2_get_conc_o3.output)
   } else {
+    #----------------------------------------------------------------------
+    #----------------------------------------------------------------------
+    # Assert that the parameters of the function are okay, or modify when necessary
+
+    if (is.null(prj_name)) assertthat::assert_that(!is.null(prj), msg = 'Specify the project name or pass an uploaded project as parameter')
+
+    #----------------------------------------------------------------------
+    #----------------------------------------------------------------------
 
     all_years<-all_years[all_years <= final_db_year]
 
@@ -810,6 +819,7 @@ m2_get_conc_o3<-function(db_path = NULL, query_path = "./inst/extdata", db_name
 #' @param query_path Path to the query file
 #' @param db_name Name of the GCAM database
 #' @param prj_name Name of the rgcam project. This can be an existing project, or, if not, this will be the name
+#' @param prj rgcam loaded project
 #' @param rdata_name Name of the RData file. It must contain the queries in a list
 #' @param scen_name Name of the GCAM scenario to be processed
 #' @param queries Name of the GCAM query file. The file by default includes the queries required to run rfasst
@@ -821,14 +831,21 @@ m2_get_conc_o3<-function(db_path = NULL, query_path = "./inst/extdata", db_name
 #' @importFrom magrittr %>%
 #' @export
 
-
-m2_get_conc_m6m<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name,
+m2_get_conc_m6m<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name = NULL, prj = NULL,
                           rdata_name = NULL, scen_name, queries = "queries_rfasst.xml", final_db_year = 2100,
                           saveOutput = T, map = F, anim = T, recompute = F){
 
   if (!recompute & exists('m2_get_conc_m6m.output')) {
     return(m2_get_conc_m6m.output)
   } else {
+    #----------------------------------------------------------------------
+    #----------------------------------------------------------------------
+    # Assert that the parameters of the function are okay, or modify when necessary
+
+    if(is.null(prj_name)) assertthat::assert_that(!is.null(prj), msg = 'Specify the project name or pass an uploaded project as parameter')
+
+    #----------------------------------------------------------------------
+    #----------------------------------------------------------------------
 
     all_years<-all_years[all_years <= final_db_year]
 
@@ -852,7 +869,7 @@ m2_get_conc_m6m<-function(db_path = NULL, query_path = "./inst/extdata", db_name
       dplyr::rename(subRegion=fasst_region) %>%
       dplyr::mutate(subRegionAlt=as.factor(subRegionAlt))
 
-    em.list<-m1_emissions_rescale(db_path,query_path,db_name,prj_name,rdata_name,scen_name,queries,saveOutput = F, final_db_year = final_db_year, recompute = recompute)
+    em.list<-m1_emissions_rescale(db_path,query_path,db_name,prj_name,prj,rdata_name,scen_name,queries,saveOutput = F, final_db_year = final_db_year, recompute = recompute)
 
     # First we load the base concentration and emissions, which are required for the calculations
     base_conc<-raw.base_conc %>%
@@ -1076,6 +1093,7 @@ m2_get_conc_m6m<-function(db_path = NULL, query_path = "./inst/extdata", db_name
 #' @param query_path Path to the query file
 #' @param db_name Name of the GCAM database
 #' @param prj_name Name of the rgcam project. This can be an existing project, or, if not, this will be the name
+#' @param prj rgcam loaded project
 #' @param rdata_name Name of the RData file. It must contain the queries in a list
 #' @param scen_name Name of the GCAM scenario to be processed
 #' @param queries Name of the GCAM query file. The file by default includes the queries required to run rfasst
@@ -1088,14 +1106,23 @@ m2_get_conc_m6m<-function(db_path = NULL, query_path = "./inst/extdata", db_name
 #' @export
 
 
-m2_get_conc_aot40<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name,
+m2_get_conc_aot40<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name = NULL, prj = NULL,
                             rdata_name = NULL, scen_name, queries = "queries_rfasst.xml", final_db_year = 2100,
                             saveOutput = T, map = F, anim = T, recompute = F){
 
   if (!recompute & exists('m2_get_conc_aot40.output')) {
     return(m2_get_conc_aot40.output)
   } else {
 
+    #----------------------------------------------------------------------
+    #----------------------------------------------------------------------
+    # Assert that the parameters of the function are okay, or modify when necessary
+
+    if(is.null(prj_name)) assertthat::assert_that(!is.null(prj), msg = 'Specify the project name or pass an uploaded project as parameter')
+
+    #----------------------------------------------------------------------
+    #----------------------------------------------------------------------
+
     all_years<-all_years[all_years <= final_db_year]
 
     # Create the directories if they do not exist:
@@ -1118,7 +1145,7 @@ m2_get_conc_aot40<-function(db_path = NULL, query_path = "./inst/extdata", db_na
       dplyr::rename(subRegion=fasst_region) %>%
       dplyr::mutate(subRegionAlt=as.factor(subRegionAlt))
 
-    em.list<-m1_emissions_rescale(db_path, query_path, db_name, prj_name, rdata_name, scen_name, queries, saveOutput = F, final_db_year = final_db_year, recompute = recompute)
+    em.list<-m1_emissions_rescale(db_path, query_path, db_name, prj_name, prj, rdata_name, scen_name, queries, saveOutput = F, final_db_year = final_db_year, recompute = recompute)
 
     # First we load the base concentration and emissions, which are required for the calculations
 
@@ -1509,6 +1536,7 @@ m2_get_conc_aot40<-function(db_path = NULL, query_path = "./inst/extdata", db_na
 #' @param query_path Path to the query file
 #' @param db_name Name of the GCAM database
 #' @param prj_name Name of the rgcam project. This can be an existing project, or, if not, this will be the name
+#' @param prj rgcam loaded project
 #' @param rdata_name Name of the RData file. It must contain the queries in a list
 #' @param scen_name Name of the GCAM scenario to be processed
 #' @param queries Name of the GCAM query file. The file by default includes the queries required to run rfasst
@@ -1520,15 +1548,23 @@ m2_get_conc_aot40<-function(db_path = NULL, query_path = "./inst/extdata", db_na
 #' @importFrom magrittr %>%
 #' @export
 
-
-m2_get_conc_mi<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name,
+m2_get_conc_mi<-function(db_path = NULL, query_path = "./inst/extdata", db_name = NULL, prj_name = NULL, prj = NULL,
                          rdata_name = NULL, scen_name, queries = "queries_rfasst.xml", final_db_year = 2100,
                          saveOutput = T, map = F, anim = T, recompute = F){
 
   if (!recompute & exists('m2_get_conc_mi.output')) {
     return(m2_get_conc_mi.output)
   } else {
 
+    #----------------------------------------------------------------------
+    #----------------------------------------------------------------------
+    # Assert that the parameters of the function are okay, or modify when necessary
+
+    if(is.null(prj_name)) assertthat::assert_that(!is.null(prj), msg = 'Specify the project name or pass an uploaded project as parameter')
+
+    #----------------------------------------------------------------------
+    #----------------------------------------------------------------------
+
     all_years<-all_years[all_years <= final_db_year]
 
     # Create the directories if they do not exist:
@@ -1551,7 +1587,7 @@ m2_get_conc_mi<-function(db_path = NULL, query_path = "./inst/extdata", db_name
       dplyr::rename(subRegion=fasst_region) %>%
       dplyr::mutate(subRegionAlt=as.factor(subRegionAlt))
 
-    em.list<-m1_emissions_rescale(db_path,query_path, db_name, prj_name, rdata_name, scen_name, queries, saveOutput = F, final_db_year = final_db_year, recompute = recompute)
+    em.list<-m1_emissions_rescale(db_path,query_path, db_name, prj_name, prj, rdata_name, scen_name, queries, saveOutput = F, final_db_year = final_db_year, recompute = recompute)
 
     # First we load the base concentration and emissions, which are required for the calculations