Merge pull request #51 from JGCRI/dev

HectorUI v2.0

.github/templates/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,20 @@
+## HectorUI `[version]`
+
+### Type of Change
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+### Highlights ✨
+
+Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
+
+-
+
+### Bug Fixes 👾
+- 
+
+### New Features 💡
+-

.github/workflows/pkgdown.yml

@@ -20,22 +20,14 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+      - name: Install libcurl
+        run: brew install openssl curl
 
       - name: Install dependencies
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
+          install.packages("remotes")
           remotes::install_deps(dependencies = TRUE)
           install.packages("pkgdown", type = "binary")
         shell: Rscript {0}

.github/workflows/rcmd.yml

@@ -19,10 +19,13 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
+      - uses: r-lib/actions/setup-pandoc@master
       - uses: actions/checkout@v2
       - uses: r-lib/actions/setup-r@master
 
       - name: Install dependencies
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
           install.packages(c("remotes", "rcmdcheck"), repos = "https://cloud.r-project.org")
           remotes::install_deps(dependencies = TRUE)

.github/workflows/test_coverage.yml

@@ -3,26 +3,41 @@ on: [push, pull_request]
 name: build
 
 jobs:
+
   build:
-    runs-on: macOS-latest
+
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
     strategy:
+      fail-fast: false
       matrix:
-        r: ['3.6']
+        config:
+          - {os: macos-latest, r: '3.6.1'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
     steps:
-      - uses: actions/checkout@v1
-      - uses: r-lib/actions/setup-r@master
-        with:
-          r-version: ${{ matrix.r }}
+
       - uses: r-lib/actions/setup-pandoc@master
-      - uses: r-lib/actions/setup-tinytex@master
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@master
+
       - name: Install dependencies
         env:
-          R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-        run: Rscript -e "install.packages(c('remotes', 'rcmdcheck', 'covr'))" -e "remotes::install_deps(dependencies = TRUE)"
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          install.packages(c("remotes", "rcmdcheck", "covr"), repos = "https://cloud.r-project.org")
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
       - name: Check
-        run: Rscript -e "rcmdcheck::rcmdcheck(error_on = 'error')"
+        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
+        shell: Rscript {0}
+
       - name: Test coverage
-        if: matrix.r == '3.6'
-        run: |
-          Rscript -e 'remotes::install_github("r-lib/covr@gh-actions")'
-          Rscript -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")'
+        run: covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
+        shell: Rscript {0}

.gitignore

@@ -77,3 +77,4 @@ rsconnect
 inst/shinyApp/temp.ini
 inst/shinyApp/test.ini
 packrat/lib*/
+inst/shinyApp/lhs.R

CITATION.cff

@@ -0,0 +1,26 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: HectorUI
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - family-names: Pennington
+    given-names: Stephanie
+    email: [email protected]
+    affiliation: Pacific Northwest National Laboratory
+    orcid: 'https://orcid.org/0000-0003-2685-1092'
+  - given-names: Chris R
+    family-names: Vernon
+    email: [email protected]
+    affiliation: Pacific Northwest National Laboratory
+    orcid: 'https://orcid.org/0000-0002-3406-6214'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.3603215
+license: GPL-3.0
+version: '2.0'
+date-released: '2022-04-01'

DESCRIPTION

@@ -1,19 +1,19 @@
 Package: hectorui
 Type: Package
 Title: A web-based interactive scenario builder and visualization application for the Hector climate model
-Version: 1.1.4
+Version: 2.0
 Authors@R: c(person("Stephanie", "Pennington", email = "[email protected]", role = c("aut", "cre")),
          person("Chris", "Vernon", email = "[email protected]", role = "aut"),
          person("Stephanie", "Waldhoff", email = "[email protected]", role = "aut"),
          person("Abigail", "Snyder", email = "[email protected]", role = "aut"),
          person("Jason", "Evanoff", email = "[email protected]", role = "aut"),
 	     person("Corinne", "Hartin", email = "[email protected]", role = "aut"))
 Maintainer: Stephanie Pennington <[email protected]>
-Description: Provides a simple visual, interactive web interface for the simple climate model Hector from JGCRI. 
+Description: Provides a simple visual, interactive web interface for the simple climate model Hector from JGCRI.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-Imports: 
+Imports:
     maps,
     remotes,
     shiny,
@@ -32,16 +32,14 @@ Imports:
 Depends:
     R (>= 3.6.0),
     hector,
-    fldgen,
-    ggthemr
+    fldgen
 Suggests:
     testthat (>= 2.1.0),
     knitr,
     rmarkdown,
     pkgdown
 Remotes:
-    github::JGCRI/[email protected],
-    github::JGCRI/[email protected],
-    github::cttobin/[email protected]
+    github::JGCRI/hector,
+    github::JGCRI/[email protected]
 RoxygenNote: 7.1.1
 VignetteBuilder: knitr

R/set_globals.R

@@ -16,7 +16,8 @@ get_globalVars <- function() {
 get_globalColorScales <- function() {
 
     globalColorScales <- vector()
-    globalColorScales <- c("RCP 2.6"="#db735c", "RCP 4.5"="#EFA86E", "RCP 6.0"="#9A8A76", "RCP 8.5"="#7A6752")
+    globalColorScales <- c("RCP 2.6" = "#5DBFDE", "RCP 4.5" = "#5CB95C", "RCP 6.0" = "#FBAB33", "RCP 8.5" ="#D7534E")
+
 
     return(globalColorScales)
 }
@@ -50,7 +51,7 @@ get_globalScenarios <- function() {
 #' @export
 get_globalScenarioColors <- function() {
 
-    return(c("RCP 2.6" = "#99cc33", "RCP 4.5" = "#FFFF00", "RCP 6.0" = "#ff9900", "RCP 8.5" = "#ff3333"))
+    return(c("RCP 2.6" = "#5DBFDE", "RCP 4.5" = "#5CB95C", "RCP 6.0" = "#FBAB33", "RCP 8.5" = "#D7534E"))
 }
 
 
@@ -623,10 +624,6 @@ get_globalCapabilities <- function() {
     globalCapabilities[['so2_a']] <- hector::EMISSIONS_SO2()
     attr(globalCapabilities[['so2_a']], 'longName') <- "Anthropogenic SO2"
 
-    # "Natural CH4 Emissions"
-    globalCapabilities[['so2_n_ch4']] <- hector::EMISSIONS_CH4()
-    attr(globalCapabilities[['so2_n_ch4']], 'longName') <- "Natural CH4 Emissions"
-
     # "Volcanic SO2"
     globalCapabilities[['so2_v']] <- hector::VOLCANIC_SO2()
     attr(globalCapabilities[['so2_v']], 'longName') <- "Volcanic SO2"

README.md

@@ -17,8 +17,10 @@ To navigate directly to the `hectorui` app **CLICK the following image**:
 
 To install hectorui as an R package for local use, please follow these steps in your R command line:
 
-- library(devtools)
-- devtools::install_github("JGCRI/hectorui")
+```R
+library(devtools)
+devtools::install_github("JGCRI/hectorui")
+```
 
 ## Developing Locally
 How you launch the app after installation depends on your R environment.  See the following.
@@ -38,7 +40,9 @@ Users familiar with R Shiny can add new features by working directly in the `hec
 
 ## Contributing to `hectorui`
 
-We welcome contributions to `hectorui` from the development community.  Please contact us if you want to collaborate!  The `hectorui` GitHub repository is accessible here:  [`hector-ui` GitHub Repository](https://github.com/JGCRI/hectorui)
+We welcome contributions to `hectorui` from the development community. Join in 
+on the conversation at the [`hector-ui` GitHub Discussions page](https://github.com/JGCRI/hectorui/discussions) or contact us if you want to
+collaborate!
 
 For more information about contributing, please contact Stephanie Pennington at [email protected] or Chris Vernon at [email protected]
 

inst/shinyApp/observers.r

@@ -304,22 +304,6 @@ openPage <- function(url) {
 
 }
 
-
-#' Change visual theme
-#'
-#' This function changes the RColorBrewer theme for the output components (graphs, maps) based on the input dropdown
-#'
-#' @return
-#' @export
-#'
-#' @examples
-changeTheme <- function()
-{
-  ggthemr::ggthemr(stringr::str_to_lower(input$set_theme), type = "outer")
-  loadGraph()
-}
-
-
 #' Update selected index of the downscaled map's available cores
 #'
 #' @return

inst/shinyApp/output.r

@@ -80,8 +80,9 @@ loadGraph <- function()
 
                     }
                     # Get the units for graph axis
+
                     x <- dplyr::distinct(hdata, units)
-                    ggplotGraph <- ggplot2::ggplot(data=df_total, ggplot2::aes(x=Year, y=Value, group=variable, color=Scenario)) +
+                    ggplotGraph <- ggplot2::ggplot(data=df_total, ggplot2::aes(x=Year, y=Value, group=Scenario, color=Scenario)) +
                       ggplot2::geom_line() +
                       ggplot2::labs(y=Hmisc::capitalize(x[[1]]), title =  attr(outputVariables[[i]], 'longName')) +
                       ggplot2::scale_color_manual(values = globalColorScales)
@@ -183,13 +184,15 @@ loadMap <- function()
             {
               mapFill <- "\u0394 Temperature \u00B0C"
               mapVar <- "deltaTemp"
+              mapPalette <- c("#fff7ec", "#fdbb84", "#fc8d59", "#ef6548", "#d7301f", "#b30000", "#7f0000")
             }
             else
             {
               mapFill <- "Temperature \u00B0C"
               mapVar <- "Temp"
+              mapPalette <-  c( "#4575b4", "#74add1", "#abd9e9","#e0f3f8", "#ffffbf",  "#fee090", "#fdae61", "#d73027")
             }
-            mapPalette <- "RdYlBu"
+
             mapDirection <- -1
               combined_data <- dplyr::mutate(coordinates, Temp = round(hector_annual_gridded_t[, as.numeric(input$mapYear)-1899], 2),
                                              deltaTemp = round(hector_annual_gridded_t[, as.numeric(input$mapYear)-1899] - hector_annual_gridded_t[, 1], 2),
@@ -200,18 +203,19 @@ loadMap <- function()
           # Build aesthetics based on if the compare to 1900 was checked
           if(input$input_map_compare)
           {
-            mapFill <- "\u0394 Precip. - g/m2/s"
+            mapFill <- "\u0394 Precip. - mm/day"
             mapVar <- "deltaPrecip"
+            mapPalette <- c("#bf812d", "#dfc27d", "white",  "#80cdc1", "#35978f", "#01665e", "#003c30")
           }
           else
           {
-            mapFill <- "Precip. - g/m2/s"
+            mapFill <- "Precip. - mm/day"
             mapVar <- "Precip"
+            mapPalette <- c("#fff7fb", "#67a9cf","#3690c0", "#02818a", "#016c59", "#014636")
           }
           mapDirection <- 1
-          mapPalette <- "Purples"
-          combined_data <- dplyr::mutate(coordinates, Precip = round(1000*hector_annual_gridded_t[, as.numeric(input$mapYear)-1899], 4),
-                                           deltaPrecip = round(1000*(hector_annual_gridded_t[, as.numeric(input$mapYear)-1899] - hector_annual_gridded_t[, 1]), 4),
+          combined_data <- dplyr::mutate(coordinates, Precip = round(86400*hector_annual_gridded_t[, as.numeric(input$mapYear)-1899], 4),
+                                           deltaPrecip = round(((hector_annual_gridded_t[, as.numeric(input$mapYear)-1899] - hector_annual_gridded_t[, 1]) / hector_annual_gridded_t[, 1]) * 100 , 2),
                                            Lon=round(lon, 2), Lat=round(lat,2), Neg = ifelse(deltaPrecip < 0, TRUE, FALSE))
         }
 
@@ -246,15 +250,13 @@ loadMap <- function()
         }
 
         # Create world map borders
-        mapWorld <- ggplot2::borders("world", fill = NA)
-
+        mapWorld <- ggplot2::borders("world")
         # Construct ggplot map object
         ggplotMap <- ggplot2::ggplot() +
           mapWorld +
           ggplot2::geom_raster(data = combined_data, ggplot2::aes_string(x="Lon", y = "Lat", fill=mapVar),interpolate = TRUE ) +
-          ggplot2::coord_fixed() +
-          ggplot2::scale_fill_distiller(palette = mapPalette,type = "div", direction = mapDirection, na.value = "Gray") + #, limits = c(-1,1)*max(abs(combined_data[[mapVar]]))) +
-          ggplot2::labs(x="\u00B0Longitude", y="\u00B0Latitude", title = paste0(input$mapCore, " - ", input$mapYear), fill = mapFill) +
+          ggplot2::scale_fill_gradientn(colors = mapPalette) + #, limits = c(-1,1)*max(abs(combined_data[[mapVar]]))) +
+          ggplot2::labs(x="\u00B0 Longitude", y="\u00B0 Latitude", title = paste0(input$mapCore, " - ", input$mapYear), fill = mapFill) +
           ggplot2::scale_y_continuous(limits=c(lat_min, lat_max), expand = c(0, 0), breaks=seq(-90,90,30))+
           ggplot2::scale_x_continuous(limits=c(lon_min, lon_max), expand = c(0, 0), breaks=seq(-180,180,30))