Merge branch 'state_level_addSectors' into pop_downscaling

.github/workflows/build_fredi.yml

@@ -6,7 +6,7 @@
 ### For uploading artifacts:
 ###     "path:" is the output path where Pandoc will write the compiled PDF.
 ###      Note, this should be the same directory as the input paper.md
-name: Build FrEDI Package
+name: 4. Build FrEDI Package
 
 on: [workflow_dispatch]
 

.github/workflows/test_fredi.yml

@@ -6,22 +6,36 @@
 ### For uploading artifacts:
 ###     "path:" is the output path where Pandoc will write the compiled PDF.
 ###      Note, this should be the same directory as the input paper.md
-name: Test FrEDI Package
+name: 3. Test FrEDI Package
 
 # on: [workflow_dispatch]
 on:
   workflow_dispatch:
     inputs:
       run_tests:
         type: choice
-        description: Run general tests
+        description: Run general tests?
         required: true
         options:
         - no
         - yes
-      make_figures:
+      figH_results:
         type: choice
-        description: Create report figures
+        description: Fig H results?
+        required: true
+        options:
+        - no
+        - yes
+      make_appx_figs:
+        type: choice
+        description: Create appendix figures for report?
+        required: true
+        options:
+        - no
+        - yes
+      make_tots_figs:
+        type: choice
+        description: Make figures for impact type totals?
         required: true
         options:
         - no
@@ -40,7 +54,7 @@ jobs:
 
       - name: Send input status
         run: |
-          echo "${{ inputs.run_tests }} ${{ inputs.make_figures }}"
+          echo "${{ inputs.run_tests }} ${{ inputs.figH_results }} ${{ inputs.make_appx_figs }} ${{ inputs.make_tots_figs }}"
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
@@ -67,15 +81,12 @@ jobs:
               upgrade = "never",
               force   = TRUE,
               type    = "source"
-            )'
+            )
+            '
 
-      - name: Run create_DoW_results
+      - name: Run tests & create figures
         run: |
           Rscript -e '
-          ### Which tests to do
-          do_tests <- "${{ inputs.run_tests    }}" == "true"
-          do_figs  <- "${{ inputs.make_figures }}" == "true"
-
           ### Main repo path, FrEDI project path, scripts path
           rPath0   <- ".";
           pPath0   <- rPath0 |> file.path("FrEDI")
@@ -89,19 +100,36 @@ jobs:
           tFiles0 <- tPath0 |> list.files(full.names=TRUE)
           for(file_i in tFiles0){file_i |> source(); rm(file_i)}
 
+          ### Load source
+          sPath0 |> file.path("create_DoW_results.R") |> source()
+
+          ### Which tests to do
+          do_tests <- "${{ inputs.run_tests      }}" == "true"
+          do_figH  <- "${{ inputs.figH_results   }}" == "true"
+          do_appx  <- "${{ inputs.make_appx_figs }}" == "true"
+          do_tots  <- "${{ inputs.make_tots_figs }}" == "true"
+          do_figs  <- do_appx | do_tots
+
           ### Where to save results
           oPath0   <- pPath0 |> file.path("data_tests")
           oPath1   <- oPath0 |> file.path("general")
           oPath2   <- oPath0 |> file.path("report_figures")
 
+          ### Whether paths exist
+          exists0  <- oPath0 |> dir.exists()
+          exists1  <- oPath1 |> dir.exists()
+          exists2  <- oPath2 |> dir.exists()
+
+          ### Check if path exists and, if not, create it
+          if(!exists0){ oPath0 |> dir.create(recursive = TRUE)}
+          if(!exists1){ oPath1 |> dir.create(recursive = TRUE)}
+          if(!exists2){ oPath2 |> dir.create(recursive = TRUE)}
+
           ### Test results
           if(do_tests){
-            ### Check if path exists and, if not, create it
-            exists0 <- oPath1 |> dir.exists()
-            if(!exists0){oPath1 |> dir.create(recursive = TRUE)}
-
             ### Run FrEDI
             results0 <- run_fredi()
+
             ### Run tests
             tests0   <- results0 |> general_fredi_test(
               outPath   = oPath1,
@@ -115,35 +143,37 @@ jobs:
             save0       <- listResults |> save(file= oPath1 |> file.path("defaultScenarioTotals.rda")) |> try()
 
             ### Remove results
-            rm(results0, tests0, listResults)
-          }
+            rm(exists0, results0, tests0, listResults, save0)
+          } ### End if(do_tests)
 
-          ### Create report results
+          ### Create Fig H results
+          if(do_figH){
+            ### Figure H results
+            results0 <- run_fredi(aggLevels=c("modelaverage", "national", "impactYear"))
+            results0 <- results0 |> filter(year %in% seq(2010, 2090, by=5))
+            save0    <- results0 |> write.csv(file=oPath2 |> file.path("FigH_results.csv"), row.names=F) |> try()
+
+            ### Remove reslts
+            rm(results0, save0)
+          } ### End if(do_figH)
+
+          ### Create report figures
           if(do_figs){
             ### Load source
             sPath0 |> file.path("create_DoW_results.R") |> source()
 
-            ### Check if path exists and, if not, create it
-            exists0 <- oPath2 |> dir.exists()
-            if(!exists0){oPath2 |> dir.create(recursive = TRUE)}
-
-
             ### Create report figures
             reports0 <- create_DoW_results(
               outPath  = oPath2,
               saveFile = TRUE,
               loadCode = "project",
+              totals   = do_tots,
               silent   = FALSE,
               testing  = TRUE,
               return   = FALSE,
               fpath    = pPath0
             )
-
-            ### Figure H results
-            results0 <- run_fredi(aggLevels=c("modelaverage", "national", "impactYear"))
-            results0 <- results0 |> filter(year %in% seq(2010, 2090, by=5))
-            save0    <- results0 |> write.csv(file=oPath2 |> file.path("FigH_results.csv"), row.names=F) |> try()
-          }
+          } ### End if(do_figs)
           '
 
       - name: Upload Tests
@@ -156,12 +186,32 @@ jobs:
             ./FrEDI/data_tests/general/defaultScenarioTotals.rda
             ./FrEDI/data_tests/general/testResults_fredi_general.xlsx
 
-      - name: Upload Report Figures
+
+      - name: Upload FigH Results
+        if: |
+          inputs.figH_results == 'true'
+        uses: actions/upload-artifact@v3
+        with:
+          name: FigH results
+          path: |
+            ./FrEDI/data_tests/report_figures/
+
+
+      - name: Upload Report Appendix Figures
+        if: |
+          inputs.make_appx_figs == 'true'
+        uses: actions/upload-artifact@v3
+        with:
+          name: Report appendix figures & data
+          path: |
+            ./FrEDI/data_tests/report_figures/
+
+      - name: Upload Report Fig7 Figures
         if: |
-          inputs.make_figures == 'true'
+          inputs.make_tots_figs == 'true'
         uses: actions/upload-artifact@v3
         with:
-          name: Report Data
+          name: Fig7 report figures & data
           path: |
             ./FrEDI/data_tests/report_figures/
 #            ./FrEDI/data_tests/general/FigH_results.csv

.github/workflows/update_base_data.yml

@@ -1,4 +1,4 @@
-name: Update Base System Data
+name: 1. Update Base System Data
 
 on:
   workflow_dispatch:

.github/workflows/update_sv_impactsList.yml

@@ -1,4 +1,4 @@
-name: Update SV ImpactsList Data
+name: 2. Update SV ImpactsList Data (as needed)
 
 on:
   workflow_dispatch:

FrEDI/R/FrEDI-package.R

@@ -2,61 +2,77 @@
 #' README
 #' FrEDI: The Framework for Evaluating Damages and Impacts
 #'
-#' [FrEDI] is an R package being developed by the U.S. Environmental Protection Agency (EPA). The functions and data provided by this package can be used to estimate climate change impacts for the contiguous United States (CONUS) using the Framework for Evaluating Damages and Impacts (FrEDI), developed as part of EPA's [Climate Change Impacts and Risk Analysis](https://epa.gov/cira/) (CIRA) project. [FrEDI] contains R code that implement FrEDI and allow users to project impacts from climate change and sea level rise for a selected set of sectors.
 #'
-#' For help getting started with [FrEDI], visit <https://usepa.github.io/FrEDI/articles/manual.html>.
+#' FrEDI is an R package being developed by the U.S. Environmental Protection Agency (EPA). The functions and data provided by this package can be used to estimate climate change impacts for the contiguous United States (CONUS) using the [Framework for Evaluating Damages and Impacts (FrEDI)](https://epa.gov/cira/FrEDI/), developed as part of EPA's [Climate Change Impacts and Risk Analysis](https://epa.gov/cira/) (CIRA) project. FrEDI contains R code that implement FrEDI and allow users to project impacts from climate change and sea level rise for a selected set of sectors.
+#'
+#'
+#'
+#' For help getting started with FrEDI, visit <https://usepa.github.io/FrEDI/articles/manual.html>.
 #'
 #' For additional package documentation, see <https://usepa.github.io/FrEDI/index.html>.
 #'
 #' For more information on the Framework and the CIRA project, visit <https://epa.gov/cira/>, especially <https://epa.gov/cira/FrEDI/>.
 #'
+#'
+#'
 #' @section Overview of Functions:
-#' The function [FrEDI::run_fredi()] provided in this package is the primary function implementing the [`FrEDI`](https://epa.gov/cira/FrEDI/) developed by the U.S. EPA for projecting annual climate impacts. The main inputs to [FrEDI::run_fredi()] are climate scenarios (temperature in degrees Celsius, global mean sea level rise in centimeters) and socioeconomic scenarios (U.S. gross domestic product, state population).
 #'
-#' [FrEDI] also contains functions to assist in the pre-processing of input scenarios and the post-processing of outputs.
+#' The function [FrEDI::run_fredi()] provided in this package is the primary function implementing the [Framework for Evaluating Damages and Impacts (FrEDI)](https://epa.gov/cira/FrEDI/), developed by the U.S. EPA for projecting annual climate impacts. The main inputs to [FrEDI::run_fredi()] are climate scenarios (temperature in degrees Celsius, global mean sea level rise in centimeters) and socioeconomic scenarios (U.S. gross domestic product, state population).
+#'
+#' FrEDI also contains functions to assist in the pre-processing of input scenarios and the post-processing of outputs.
 #'
 #' * Pre-processing functions include [FrEDI::get_sectorInfo()], [FrEDI::import_inputs()], [FrEDI::convertTemps()], [FrEDI::temps2slr()].
 #'      * [FrEDI::get_sectorInfo()] allows users to access a list of sectors within `FrEDI` and related sector information.
 #'      * [FrEDI::import_inputs()] helps users in importing custom scenarios from user-specified comma-separated value (CSV) files.
 #'      * [FrEDI::convertTemps()] helps users to convert between global mean temperature and temperatures for the contiguous United States (CONUS) (both in degrees Celsius).
 #'      * [FrEDI::temps2slr()] helps users to estimate global mean sea level rise (GMSL, in centimeters) from global mean temperature in degrees Celsius.
 #'
-#' [FrEDI::aggregate_impacts()] is a post-processing helper function that helps users to aggregate and summarize the outputs of [FrEDI]. [FrEDI::aggregate_impacts()] can be used to calculate national totals, model averages, sum over impact types, and interpolate between multiple impact years (note that [FrEDI::run_fredi()] will automatically run [FrEDI::aggregate_impacts()] before returning outputs if the `aggLevels` argument is not `"none"`).
+#' [FrEDI::aggregate_impacts()] is a post-processing helper function that helps users to aggregate and summarize the outputs of FrEDI. [FrEDI::aggregate_impacts()] can be used to calculate national totals, model averages, sum over impact types, and interpolate between multiple impact years (note that [FrEDI::run_fredi()] will automatically run [FrEDI::aggregate_impacts()] before returning outputs if the `aggLevels` argument is not `"none"`).
 #'
 #' Versions 2.3.0 and above include the `FrEDI` Social Vulnerability (SV) module for estimating impacts on socially vulnerable populations for select sectors. [FrEDI::get_sv_sectorInfo()] allows users to access a list of sectors within the FrEDI SV module and related sector information. The function [FrEDI::run_fredi_sv()] is the main function for the `FrEDI` SV module. [FrEDI::run_fredi_sv()] is designed to calculate impacts for a single sector at a time for a custom population scenario or one or more custom temperature or sea level rise scenarios. For more information on the data underlying the `FrEDI` SV module, see <https://www.epa.gov/cira/social-vulnerability-report/>.
 #'
-#'  @section Overview of Package Contents:
-#' [FrEDI] consists of files in the following directories:
+#'
+#'
+#' @section Overview of Package Contents:
+#'
+#' FrEDI consists of files in the following directories:
 #' * __R__. Contains function definitions (files ending in `".R"`) and configuration files (ending in `".rda"`).
 #' * __data__. Contains R Data files ending in `".rdb"`, `".rds"`, and `".rdx"`, containing data included with the package.
 #' * __help__ and __html__. Contain documentation for functions available to the user, including function descriptions, lists of arguments and outputs, and examples. See `"html/00Index.html"` or the individual R help functions for more information about individual functions.
 #' * __Meta__. Contains RDS files (ending in `".rds"`) with information about the package contents.
 #' * __extdata__. __extdata/scenarios__ Contains four CSV files for users to test the function for importing data. For more information on importing scenarios for use with [FrEDI::run_fredi()], refer to documentation for the function [FrEDI::import_inputs()].
-#'      * `"GCAM_scenario.csv"` contains a set of temperature scenarios that can be used with [FrEDI], including the default temperature scenario used by both [FrEDI::run_fredi()] and [FrEDI::run_fredi_sv()] (labeled `"description="Hector_GCAM_v5.3_ECS_3.0_REF"` in `"slr_from_GCAM.csv"` and `"ECS_3.0_ref_0"` in the [FrEDI::gcamScenarios] dataset)). Also see the documentation for the [FrEDI::gcamScenarios] dataset for more information.
+#'      * `"GCAM_scenario.csv"` contains a set of temperature scenarios that can be used with FrEDI, including the default temperature scenario used by both [FrEDI::run_fredi()] and [FrEDI::run_fredi_sv()] (labeled `"description="Hector_GCAM_v5.3_ECS_3.0_REF"` in `"slr_from_GCAM.csv"` and `"ECS_3.0_ref_0"` in the [FrEDI::gcamScenarios] dataset)). Also see the documentation for the [FrEDI::gcamScenarios] dataset for more information.
 #'      * `"State ICLUS Population.csv"` and `"Region ICLUS Population.csv"` contain the default population scenarios used by [FrEDI::run_fredi()] and [FrEDI::run_fredi_sv()], respectively (see [FrEDI::popScenario] and [FrEDI::popScenario_sv]).
 #'      * `"slr_from_GCAM.csv"` contains global mean sea level rise heights in centimeters (created from the reference temperature scenario).
 #'  * __extdata/sv__ Contains files used by the `FrEDI` SV module to calculate impacts.
 #'
-#' The `FrEDI` package contains a loadable dataset with default results `defaultResults`, which contains annual impacts produced by [FrEDI::run_fredi()] for the with the default options and default default scenarios (i.e., default temperature, GDP and regional population trajectories). Other loadable datasets provided by [FrEDI] are a set of driver scenarios ([FrEDI::gcamScenarios]), a state-level population scenario ([FrEDI::popScenario]) for use with [FrEDI::run_fredi()], and a region-level `popScenario_sv` for use with [FrEDI::run_fredi_sv()]. These data can be loaded into the workspace using the `data()` function.
+#' The `FrEDI` package contains a loadable dataset with default results `defaultResults`, which contains annual impacts produced by [FrEDI::run_fredi()] for the with the default options and default scenarios (i.e., default temperature, GDP, and state population trajectories). Other loadable datasets provided by FrEDI are a set of driver scenarios ([FrEDI::gcamScenarios]), a state population scenario ([FrEDI::popScenario]) for use with [FrEDI::run_fredi()] or [FrEDI::import_inputs()], and a regional population scenario (`popScenario_sv`) for use with [FrEDI::run_fredi_sv()]. These data can be loaded into the workspace using the `data()` function.
 #'
 #' Typical use will involve `library(FrEDI)` or `require(FrEDI)`.
 #'
 #'
+#'
 #' @section Status:
 #' Disclaimer: All code in this repository is being provided in a "draft" state and has not been reviewed or cleared by U.S. EPA. This status will be updated as models are reviewed.
 #'
+#'
+#'
 #' @section Dependencies:
-#' [FrEDI] requires R (>= 4.2.0).
+#' FrEDI requires R (>= 4.2.0).
 #'
 #'
-#' [FrEDI] depends on:
+#' FrEDI depends on:
 #' * [tidyverse] (Easily Install and Load the 'Tidyverse'). The official documentation for [tidyverse] can be found [here](https://cran.r-project.org/web/packages/tidyverse/index.html). [tidyverse] can be installed using `install.packages("tidyverse")`, or see [link](https://tidyverse.tidyverse.org/) for more information.
 #' * [ggpubr] ('ggplot2' Based Publication Ready Plots). The official documentation for [ggpubr] can be found [here](https://cran.r-project.org/web/packages/ggpubr/index.html). [ggpubr] can be installed using `install.packages("ggpubr")`, or see [link](https://rpkgs.datanovia.com/ggpubr/) for more information.
 #' * [openxlsx] (Read, Write and Edit `xlsx` Files). The official documentation for [openxlsx] can be found [here](https://cran.r-project.org/web/packages/openxlsx/index.html). [openxlsx] can be installed using `install.packages("openxlsx")`.
 #'
+#'
+#'
 #' @section License:
 #' This repository is released under the MIT License.
 #'
+#'
+#'
 #' @section EPA Disclaimer:
 #' The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.
 #'