{"action":"created","comment":{"url":"https://api.github.com/repos/JGCRI/gcamdata/pulls/comments/117266070","pull_request_review_id":38958070,"id":117266070,"diff_hunk":"@@ -43,80 +41,182 @@ module_emissions_L124.nonco2_unmgd_R_S_T_Y_DISABLED <- function(command, ...) {\n \n     # Load required inputs\n     iso_GCAM_regID <- get_data(all_data, \"common/iso_GCAM_regID\")\n-    EDGAR_nation <- get_data(all_data, \"emissions/EDGAR_nation\")\n-    EDGAR_sector <- get_data(all_data, \"emissions/EDGAR_sector\")\n-    L124.LC_bm2_R_Grass_Yh_GLU_adj <- get_data(all_data, \"L124.LC_bm2_R_Grass_Yh_GLU_adj\")\n-    L124.LC_bm2_R_UnMgdFor_Yh_GLU_adj <- get_data(all_data, \"L124.LC_bm2_R_UnMgdFor_Yh_GLU_adj\")\n-    EDGAR_SO2 <- get_data(all_data, \"emissions/EDGAR_SO2\")\n-    EDGAR_CO <- get_data(all_data, \"emissions/EDGAR_CO\")\n-    EDGAR_NOx <- get_data(all_data, \"emissions/EDGAR_NOx\")\n-    EDGAR_NMVOC <- get_data(all_data, \"emissions/EDGAR_NMVOC\")\n-    EDGAR_CH4 <- get_data(all_data, \"emissions/EDGAR_CH4\")\n-    EDGAR_N2O <- get_data(all_data, \"emissions/EDGAR_N2O\")\n-    GFED_ForestFire_SO2 <- get_data(all_data, \"emissions/GFED_ForestFire_SO2\")\n-    GFED_Deforest_SO2 <- get_data(all_data, \"emissions/GFED_Deforest_SO2\")\n-    GFED_ForestFire_CO <- get_data(all_data, \"emissions/GFED_ForestFire_CO\")\n-    GFED_Deforest_CO <- get_data(all_data, \"emissions/GFED_Deforest_CO\")\n-    GFED_ForestFire_NOx <- get_data(all_data, \"emissions/GFED_ForestFire_NOx\")\n-    GFED_Deforest_NOx <- get_data(all_data, \"emissions/GFED_Deforest_NOx\")\n+    EDGAR_sector <- get_data(all_data, \"emissions/EDGAR/EDGAR_sector\")\n+    L124.LC_bm2_R_Grass_Yh_GLU_adj <- get_data(all_data, \"temp-data-inject/L124.LC_bm2_R_Grass_Yh_GLU_adj\")\n+    L124.LC_bm2_R_UnMgdFor_Yh_GLU_adj <- get_data(all_data, \"temp-data-inject/L124.LC_bm2_R_UnMgdFor_Yh_GLU_adj\")\n+    EDGAR_gases <- get_data(all_data, \"EDGAR_gases\")\n+    GFED_ForestFire_SO2 <- get_data(all_data, \"emissions/GFED/GFED_ForestFire_SO2\")\n+    GFED_Deforest_SO2 <- get_data(all_data, \"emissions/GFED/GFED_Deforest_SO2\")\n+    GFED_ForestFire_CO <- get_data(all_data, \"emissions/GFED/GFED_ForestFire_CO\")\n+    GFED_Deforest_CO <- get_data(all_data, \"emissions/GFED/GFED_Deforest_CO\")\n+    GFED_ForestFire_NOx <- get_data(all_data, \"emissions/GFED/GFED_ForestFire_NOx\")\n+    GFED_Deforest_NOx <- get_data(all_data, \"emissions/GFED/GFED_Deforest_NOx\")\n \n-    # ===================================================\n-    # TRANSLATED PROCESSING CODE GOES HERE...\n-    #\n-    # If you find a mistake/thing to update in the old code and\n-    # fixing it will change the output data, causing the tests to fail,\n-    # (i) open an issue on GitHub, (ii) consult with colleagues, and\n-    # then (iii) code a fix:\n-    #\n-    # if(OLD_DATA_SYSTEM_BEHAVIOR) {\n-    #   ... code that replicates old, incorrect behavior\n-    # } else {\n-    #   ... new code with a fix\n-    # }\n-    #\n-    #\n-    # NOTE: there are 'match' calls in this code. You probably want to use left_join_error_no_match\n-    # For more information, see https://github.com/JGCRI/gcamdata/wiki/Name-That-Function\n-    # NOTE: This code uses vecpaste\n-    # This function can be removed; see https://github.com/JGCRI/gcamdata/wiki/Name-That-Function\n-    # NOTE: This code uses repeat_and_add_vector\n-    # This function can be removed; see https://github.com/JGCRI/gcamdata/wiki/Name-That-Function\n-    # ===================================================\n+    # Reformat temporary data -- Note: this can be removed after the upstream files are done\n+    L124.LC_bm2_R_Grass_Yh_GLU_adj %>%\n+      gather(year, value, -GCAM_region_ID, -Land_Type, -GLU) %>%\n+      mutate(year = as.integer(substr(year, 2, 5))) ->\n+      L124.LC_bm2_R_Grass_Yh_GLU_adj\n+\n+    L124.LC_bm2_R_UnMgdFor_Yh_GLU_adj %>%\n+      gather(year, value, -GCAM_region_ID, -Land_Type, -GLU) %>%\n+      mutate(year = as.integer(substr(year, 2, 5))) ->\n+      L124.LC_bm2_R_UnMgdFor_Yh_GLU_adj\n+\n+    # Prepare EDGAR emissions for use\n+    # Map in region ID and sector name; extrapolate to 2010; aggregate to sector & region; convert from Gg to Tg\n+    EDGAR_gases %>%\n+      left_join(EDGAR_sector, by = \"IPCC\") %>%                                          # Add GCAM sector from the sector mapping\n+      rename(sector = agg_sector) %>%\n+      mutate(iso = tolower( ISO_A3 ), ISO_A3 = NULL) %>%\n+      change_iso_code('rou', 'rom') %>%                                                 # Switch Romania iso code to its pre-2002 value\n+      left_join(iso_GCAM_regID, by = \"iso\") %>%                                         # Map in GCAM regions\n+      select(IPCC, Non.CO2, sector, iso, GCAM_region_ID, year, value) ->\n+      EDGAR_history\n+\n+    if(OLD_DATA_SYSTEM_BEHAVIOR) {\n+      # The old data system processed data in wide format. There was a na.omit() in the code that effectively removed\n+      # any region/sector combination where the time series was incomplete. We'd like to keep this information.\n+      # Additionally, the old data system never included NH3 in the processing. The emissions are small\n+      # but we should keep them.\n+      EDGAR_history %>%\n+        filter(Non.CO2 != \"NH3\" ) %>%                                                    # Remove NH3 for consistency with old data\n+        filter(year <= 2008) %>%                                                         # Old data didn't care if post-2008 data was missing so remove it here\n+        spread(year, value) %>%                                                          # Convert to wide format\n+        na.omit() %>%                                                                    # Remove any row with an NA (i.e., incomplete time series)\n+        gather(year, value, -GCAM_region_ID, -iso, -sector, -Non.CO2, -IPCC) %>%         # Convert back to long format\n+        mutate(year = as.integer( year )) ->                                             # Convert year back to integer form (not sure why this changes type)\n+        EDGAR_history\n+\n+    } else {\n+      #   ... new code with a fix\n+    }\n+\n+    # Prepare EDGAR emissions for use (continued)\n+    EDGAR_history %>%\n+      # Extrapolate using average of last five years --- 2010 is problematic here because of deforestation (i.e., we don't want to rely on 2005 as last year of data)\n+      filter(year %in% 2004:2008) %>%\n+      group_by(GCAM_region_ID, iso, sector, Non.CO2, IPCC) %>%\n+      summarize(value = mean(value)) %>%\n+      mutate(year = as.integer(2010)) %>%\n+      bind_rows(EDGAR_history) %>%                                                      # Bind extrapolated 2010 data to the rest of the EDGAR data\n+      group_by(GCAM_region_ID, sector, Non.CO2, year) %>%\n+      summarize(value = sum(value)) %>%                                                 # Aggregate by region, sector, gas, and year\n+      na.omit() %>%\n+      mutate(value = value * CONV_GG_TG) ->                                             # Convert to Tg\n+      EDGAR_history\n+\n+    # Part 1: Grassland burning\n+    # Downscale regional grassland burning emissions to GLU based on the share of land in each GLU\n+    L124.LC_bm2_R_Grass_Yh_GLU_adj %>%\n+      group_by(GCAM_region_ID, year) %>%\n+      mutate(land_share = value / sum(value)) %>%                                                           # Compute the share of regional grassland in each GLU\n+      select(-value) %>%\n+      left_join(filter(EDGAR_history, sector == \"grassland\"), by = c(\"GCAM_region_ID\", \"year\")) %>%         # Map in EDGAR grassland emissions\n+      mutate(value = value * land_share) %>%                                                                # Compute emissions by GLU using EDGAR totals and land shares\n+      na.omit() %>%\n+      select(-sector, -land_share) ->\n+      L124.nonco2_tg_R_grass_Y_GLU\n+\n+    # Part 2: Forest fires and deforestation\n+    # Calculate share of forest emissions from forest fires versus deforestation using GFED data.\n+    # Bind all GFED data together, aggregate by GCAM region/gas/year, calculate share of forest fire versus deforestation\n+    bind_rows(mutate(GFED_ForestFire_CO, Non.CO2 = \"CO\", type = \"ForestFire\"),\n+              mutate(GFED_Deforest_CO, Non.CO2 = \"CO\", type = \"Deforest\"),\n+              mutate(GFED_ForestFire_SO2, Non.CO2 = \"SO2\", type = \"ForestFire\"),\n+              mutate(GFED_Deforest_SO2, Non.CO2 = \"SO2\", type = \"Deforest\"),\n+              mutate(GFED_ForestFire_NOx, Non.CO2 = \"NOx\", type = \"ForestFire\"),\n+              mutate(GFED_Deforest_NOx, Non.CO2 = \"NOx\", type = \"Deforest\")) %>%\n+      # NMVOC is split into lots of inventories, so using CO for now.\n+      bind_rows(mutate(GFED_ForestFire_CO, Non.CO2 = \"NMVOC\", type = \"ForestFire\"),\n+                mutate(GFED_Deforest_CO, Non.CO2 = \"NMVOC\", type = \"Deforest\")) %>%\n+      # Use CO for other missing gases. Previous code did this implicitly in lines 162-166\n+      bind_rows(mutate(GFED_ForestFire_CO, Non.CO2 = \"CH4\", type = \"ForestFire\"),\n+                mutate(GFED_Deforest_CO, Non.CO2 = \"CH4\", type = \"Deforest\"),\n+                mutate(GFED_ForestFire_CO, Non.CO2 = \"N2O\", type = \"ForestFire\"),\n+                mutate(GFED_Deforest_CO, Non.CO2 = \"N2O\", type = \"Deforest\")) %>%\n+      gather(year, value, -Country, -Non.CO2, -type) %>%                                             # Convert from wide to long\n+      mutate(year = as.integer(year)) %>%\n+      spread(type, value) %>%                                                                        # Spread data so deforestation and forest fires are in columns\n+      mutate(iso = tolower( Country ), Country = NULL) %>%\n+      change_iso_code('rou', 'rom') %>%                                                              # Convert Romania iso code to pre-2002 value\n+      left_join(iso_GCAM_regID, by = \"iso\") %>%\n+      group_by(GCAM_region_ID, Non.CO2, year ) %>%\n+      summarize(ForestFire = sum(ForestFire), Deforest = sum(Deforest) ) %>%                         # Aggregate emissions by region, gas, and year\n+      na.omit() %>%\n+      mutate(PctForestFire = ForestFire / (ForestFire + Deforest)) %>%                               # Compute share of emissions from forest fires\n+      mutate(PctForestFire = if_else( is.na(PctForestFire), 1, PctForestFire )) %>%                  # Assume missing values mean 100% forest fires since these are easier to model in GCAM","path":"R/zchunk_L124.nonco2_unmgd_R_S_T_Y.R","position":203,"original_position":203,"commit_id":"b2054b13593f00c4098607e1a51813777c82a5f3","original_commit_id":"413deb08eba2248e1064b0eb022295ce26892c7a","user":{"login":"kvcalvin","id":11820268,"avatar_url":"https://avatars3.githubusercontent.com/u/11820268?v=3","gravatar_id":"","url":"https://api.github.com/users/kvcalvin","html_url":"https://github.com/kvcalvin","followers_url":"https://api.github.com/users/kvcalvin/followers","following_url":"https://api.github.com/users/kvcalvin/following{/other_user}","gists_url":"https://api.github.com/users/kvcalvin/gists{/gist_id}","starred_url":"https://api.github.com/users/kvcalvin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kvcalvin/subscriptions","organizations_url":"https://api.github.com/users/kvcalvin/orgs","repos_url":"https://api.github.com/users/kvcalvin/repos","events_url":"https://api.github.com/users/kvcalvin/events{/privacy}","received_events_url":"https://api.github.com/users/kvcalvin/received_events","type":"User","site_admin":false},"body":"We have NAs in the GCAM_region_ID prior to the na.omit because there are iso codes in the GFED data that don't exist in the iso_to_region mapping (\"ala\" \"ata\" \"atf\" \"blm\" \"bvt\" \"ggy\" \"hmd\" \"iot\" \"jey\" \"maf\" \"sgs\" \"umi\"). We have NAs after that mutate statement because there are places where the denominator (`ForestFire + Deforest`) is zero. I'll add comments to make this clearer.","created_at":"2017-05-18T14:38:50Z","updated_at":"2017-05-18T14:38:50Z","html_url":"https://github.com/JGCRI/gcamdata/pull/403#discussion_r117266070","pull_request_url":"https://api.github.com/repos/JGCRI/gcamdata/pulls/403","_links":{"self":{"href":"https://api.github.com/repos/JGCRI/gcamdata/pulls/comments/117266070"},"html":{"href":"https://github.com/JGCRI/gcamdata/pull/403#discussion_r117266070"},"pull_request":{"href":"https://api.github.com/repos/JGCRI/gcamdata/pulls/403"}}},"pull_request":{"url":"https://api.github.com/repos/JGCRI/gcamdata/pulls/403","id":120603635,"html_url":"https://github.com/JGCRI/gcamdata/pull/403","diff_url":"https://github.com/JGCRI/gcamdata/pull/403.diff","patch_url":"https://github.com/JGCRI/gcamdata/pull/403.patch","issue_url":"https://api.github.com/repos/JGCRI/gcamdata/issues/403","number":403,"state":"open","locked":false,"title":"Kate - L124_nonco2_unmgd","user":{"login":"kvcalvin","id":11820268,"avatar_url":"https://avatars3.githubusercontent.com/u/11820268?v=3","gravatar_id":"","url":"https://api.github.com/users/kvcalvin","html_url":"https://github.com/kvcalvin","followers_url":"https://api.github.com/users/kvcalvin/followers","following_url":"https://api.github.com/users/kvcalvin/following{/other_user}","gists_url":"https://api.github.com/users/kvcalvin/gists{/gist_id}","starred_url":"https://api.github.com/users/kvcalvin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kvcalvin/subscriptions","organizations_url":"https://api.github.com/users/kvcalvin/orgs","repos_url":"https://api.github.com/users/kvcalvin/repos","events_url":"https://api.github.com/users/kvcalvin/events{/privacy}","received_events_url":"https://api.github.com/users/kvcalvin/received_events","type":"User","site_admin":false},"body":"@bpbond: Note that I'm using `FLAG_SUM_TEST` for `L124.nonco2_tg_R_grass_Y_GLU`. When I remove this flag, it fails to match on row 1048. I am fairly convinced that this is a rounding issue, but let me know if you want me to do something different.\r\n\r\n#332 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