viz.yaml

info:
  id: how-gdp
  name: How USGS GDP Works 
  date: 2017-09-19
  publish-date: 
  path: /how-gdp
  analytics-id: 
  description: >-
    Explanation of how the USGS Geo Data Portal works.
  keywords: >-
    USGS, VIZLAB, GDP
  audience: GDP current and future users
  url: 
  twitter: "@USGS-R"
  thumbnail-facebook:
    url: 
    width: 1560
    height: 820
    alttext: ""
    type: image/png
  thumbnail-twitter:
    url: 
    width: 560
    height: 300
    alttext: ""
  thumbnail-landing:
    url: images/vizlab06.png
    width: 400
    height: 400
    alttext: ""
  required-packages:
    dplyr:
      repo: CRAN
      version: 0.7.2
    geoknife:
      repo: CRAN
      version: 1.5.5
    ggmap:
      repo: CRAN
      version: 2.6.1
    ggplot2:
      repo: CRAN
      version: 2.2.1
    maps:
      repo: CRAN
      version: 3.2.0
    maptools:
      repo: CRAN
      version: 0.9-2
    ncdf4:
      repo: CRAN
      version: 1.16
    raster:
      repo: CRAN
      version: 2.5-8
    rasterVis:
      repo: CRAN
      version: 0.41
    RColorBrewer:
      repo: CRAN
      version: 1.1-2
    rgdal:
      repo: CRAN
      version: 1.2-8
    rgeos:
      repo: CRAN
      version: 0.3-23
    sp: 
      repo: CRAN
      version: 1.2.5
    tidyr:
      repo: CRAN
      version: 0.7.1
    vizlab:
      repo: CRAN
      version: 0.3.3
contributors:
  - 
    name: Dave Blodgett
    email: dblodgett@usgs.gov
    affiliation: U.S. Geological Survey
  -
    name: Lindsay Carr
    email: lcarr@usgs.gov
    affiliation: U.S. Geological Survey
  -
    name: Jordan Read
    email: jread@usgs.gov
    affiliation: U.S. Geological Survey
  -
    name: David Watkins
    email: wwatkins@usgs.gov
    affiliation: U.S. Geological Survey
parameter:
  -
    id: storm_dates
    comment: dates to timebox storm for getting data
    start_date: "2008-06-02"
    end_date: "2008-06-13"
  -
    id: display_crs	
    comment: projecting into
    crs_str: "+init=epsg:4326" #needed to play nice w/ ggmap?
  - 
    id: geoknife_crs
    comment: needed to create a simplegeom for geoknife
    crs_str: "+proj=longlat +datum=WGS84"
  -
    id: example_dateTime
    comment: use one timestep to illustrate geoknife processing
    date: "2008-06-12 22:00:00"
    tz: "UTC"
  -
    id: timestep_precip_limits
    comment: min and max for cumulative precip scale
    min: 0
    max: 2
  -
    id: cumulative_precip_limits
    comment: min and max for cumulative precip scale
    min: 0
    max: 11
  - 
    id: "context_bbox"
    comment: bbox for context around watershed
    west: -89.97
    east: -88.74
    south: 42.89
    north: 43.81
  -
    id: "cell_size"
    comment: cell size in degrees for GDP subset algorithm
    value: 0.06
fetch:
  -
    id: page_text
    comment: identify yaml file w/ site text
    location: data/page_text.yaml
    reader: md
    mimetype: text/yaml
  -
    id: yahara_geom
    comment: get shapefile as R object
    location: cache/yahara.rds
    reader: rds
    fetcher: geom_shp
    scripts: scripts/fetch/fetch.geom_shp.R
    depends:
      transform_crs: "geoknife_crs"
    filepath: "data/yahara.shp"
    shp_crs: "+init=epsg:3857"
  - 
    id: yahara_geom_transposed
    comment: moves yahara north (more process than fetch, but precip fetch depends on this)
    location: cache/yahara_transposed.rds
    reader: rds
    fetcher: geom_transpose
    scripts: scripts/fetch/fetch.geom_transpose.R
    depends: 
      geom_sp: "yahara_geom"
    vertical_trans_va: 0.35
  -
    id: context_geom
    comment: create spatial object of area around yahara (maybe just make bbox)	
    location: cache/context_geom.rds
    reader: rds
    fetcher: bbox_geom
    scripts: scripts/fetch/fetch.bbox_geom.R
    depends: 
      crs: "geoknife_crs"
      bbox: "context_bbox"
  -
    id: yahara_precip_avg
    comment: use transposed yahara as stencil 
    location: cache/yahara_precip_avg.rds
    reader: rds
    fetcher: precip_data
    scripts: scripts/fetch/fetch.precip_data.R
    depends:
      geom_sp: "yahara_geom_transposed"
      date_range: "storm_dates"
    algorithm: "summary"
  -
    id: yahara_precip_orig_avg
    comment: use original yahara as stencil 
    location: cache/yahara_precip_orig_avg.rds
    reader: rds
    fetcher: precip_data
    scripts: scripts/fetch/fetch.precip_data.R
    depends:
      geom_sp: "yahara_geom"
      date_range: "storm_dates"
    algorithm: "summary"
  -
    id: yahara_precip
    comment: use transposed yahara, use subset algorithm
    location: cache/yahara_precip_raster.rds
    raw_netcdf: cache/yahara_precip.nc
    reader: rds
    fetcher: precip_data
    scripts: [scripts/fetch/fetch.precip_data.R, scripts/fetch/fetch_utils.R]
    depends:
      geom_sp: "yahara_geom_transposed"
      date: "example_dateTime"
      crs: "display_crs"
      cell_size: "cell_size"
    algorithm: "subset"
  -
    id: context_precip
    comment: subset data from gdp for area around yahara
    location: cache/context_precip_raster.rds
    reader: rds
    fetcher: precip_data
    scripts: [scripts/fetch/fetch.precip_data.R, scripts/fetch/fetch_utils.R]
    depends:
      geom_sp: "context_geom"
      date: "example_dateTime"
      crs: "display_crs"
      cell_size: "cell_size"
    algorithm: "subset"
    raw_netcdf: cache/context_precip.nc
process:
  -
    id: yahara_precip_avg_cumulative
    comment: get cumulative avg precip
    location: cache/yahara_precip_avg_cumulative.rds
    reader: rds
    processor: precip_cumulative
    scripts: scripts/process/process.precip_cumulative.R
    depends: 
      precip_data: "yahara_precip_avg"
  -
    id: yahara_precip_orig_avg_cumulative
    comment: get cumulative avg precip from original yahara
    location: cache/yahara_precip_orig_avg_cumulative.rds
    reader: rds
    processor: precip_cumulative
    scripts: scripts/process/process.precip_cumulative.R
    depends: 
      precip_data: "yahara_precip_orig_avg"
  -
    id: yahara_precip_avg_timestep
    comment: filter to get just one precip value of the averaged precip data
    location: cache/yahara_precip_avg_timestep.rds
    reader: rds
    processor: precip_timestep
    scripts: scripts/process/process.precip_timestep.R
    depends: 
      precip_data: "yahara_precip_avg"
      timestep: "example_dateTime"

visualize:
  - id: basemap
    comment: map that will sit underneath everything else to give context
    location: cache/basemap.rds
    reader: rds
    visualizer: create_basemap
    scripts: scripts/visualize/visualize.create_basemap.R
    depends:
      bbox: "context_bbox"
  -
    id: inputs_data	
    comment: raster map of subset gdp data at one timestep for area around yahara	
    location: figures/inputs_data.png
    mimetype: image/png
    visualizer: raster_map_precip
    scripts: scripts/visualize/visualize.raster_map_precip.R
    depends:
      raster_data: "context_precip"
      crs: "display_crs"
      bbox: "context_bbox"
      basemap: "basemap"
      precip_limits: "timestep_precip_limits"
    title: "Gridded precipitation from GDP."
    alttext: "Pre-processing gridded data for interested storm area."
  -
    id: inputs_geometry	
    comment: map of subset gdp transposed yahara data w. surrounding area for context	
    location: figures/inputs_geometry.png
    mimetype: image/png
    visualizer: map_geometry
    scripts: scripts/visualize/visualize.map_geometry.R
    depends:
      geom_feature: "yahara_geom_transposed"
      geom_context: "context_geom"
      basemap: "basemap"
    title: "Geometry of feature of interest"
    alttext: "Spatial extent of the data you're interested in"
  -
    id: yahara_precip_clip
    comment: raster map w. subset gdp transposed yahara data at one timestep	
    location: figures/yahara_precip_clip.png
    mimetype: image/png
    visualizer: raster_map_precip
    scripts: scripts/visualize/visualize.raster_map_precip.R
    depends:
      raster_data: "context_precip"
      crs: "display_crs"
      geom_feature: "yahara_geom_transposed"
      bbox: "context_bbox"
      basemap: "basemap"
      precip_limits: "timestep_precip_limits"
    title: "Gridded precipitation only shown for watershed shape"
    alttext: "Subset of gridded precipitation for only the transposed watershed boundary."
  -
    id: yahara_precip_melt
    comment: map w. avg gdp data for yahara transpose at one timestep	
    location: figures/yahara_precip_melt.png
    mimetype: image/png
    visualizer: map_precip
    scripts: scripts/visualize/visualize.map_precip.R
    depends:
      precip_data: "yahara_precip_avg_timestep"
      geom_sp: "yahara_geom_transposed"
      basemap: "basemap"
      precip_limits: "timestep_precip_limits"
    title: "Processed GDP results for one timestep"
    alttext: "Processed GDP results for one timestep"
  -
    id: storm_transpose	
    comment: map showing yahara shape w. cumulative yahara-shaped precip in transposed location	
    location: figures/storm_transpose.png
    mimetype: image/png
    visualizer: map_precip
    scripts: scripts/visualize/visualize.map_precip.R
    depends:
      precip_data: "yahara_precip_avg_cumulative"
      precip_orig_data: "yahara_precip_orig_avg_cumulative"
      geom_sp: "yahara_geom_transposed"
      geom_sp_orig: "yahara_geom"
      basemap: "basemap"
      precip_limits: "cumulative_precip_limits"
    title: "Storm transposition"
    alttext: "Original watershed with lower precipitation and transposed watershed with higher precipitation."
publish:  
  - 
    id: gdp_page
    name: index
    publisher: page
    template: fullpage
    depends: 
      header: "header_section"
      footer: "footer_section"
      gdp_css: "gdp_figure_css"
      header_css: "lib-header-css"
      footer_css: "lib-footer-css"
      font: "sourcesanspro"
      text_overview: "gdp_overview"
      section_process: "gdp_processing_section"
      section_algorithm: "gdp_algorithm_section"
      text_usecase: "use_case_intro"
      section_storm_transpose: "storm_transpose_section"
      section_data_input: "inputs_data_section"
      section_geometry_input: "inputs_geometry_section"
      section_clip_melt: "yahara_clip_melt_section"
      text_conclusion: "conclusion_text"
    context:
      header: "header"
      footer: "footer"
      resources: ["gdp_css", "header_css", "footer_css", "font"]
      sections: [ "text_overview", "section_process", "section_algorithm", "text_usecase",
                  "section_storm_transpose", "section_data_input",
                  "section_geometry_input", "section_clip_melt",
                  "text_conclusion" ]
  -
    id: processing_gif
    location: images/gdp_process.gif
    mimetype: image/gif
    export: true
    title: "GDP Processing Schematic"
    alttext: "GDP Processing Schematic"
  -
    id: algorithm_gif
    location: images/gdp_algorithm.gif
    mimetype: image/gif
    title: "GDP Algorithm Schematic"
    alttext: "GDP Algorithm Schematic"
  - 
    id: gdp_overview
    publisher: section
    template: layout/templates/gdp-text.mustache
    depends: "page_text"
    context:
      id: "gdp-text gdp-intro-text"
      text: page_text.gdp_overview
  - 
    id: gdp_processing_section
    publisher: section
    template: layout/templates/gdp-figure.mustache
    depends: ["processing_gif", "page_text"]
    context:
      id: gdp-fig
      title: "Bandwidth and processing savings with GDP"
      figure: processing_gif
      text-before: page_text.gdp_processing_before
      text-after: page_text.gdp_processing_after
      caption: page_text.gdp_processing_caption
  - 
    id: gdp_algorithm_section
    publisher: section
    template: layout/templates/gdp-figure.mustache
    depends: ["algorithm_gif", "page_text"]
    context:
      id: gdp-fig
      title: "GDP algorithm support"
      figure: algorithm_gif
      text-before: page_text.gdp_algorithm_before
      text-after: page_text.gdp_algorithm_after
      caption: page_text.gdp_algorithm_caption
  -
    id: use_case_intro
    publisher: section
    template: layout/templates/gdp-text.mustache
    depends: "page_text"
    context:
      id: gdp-text
      title: 
      text: page_text.use_case_intro
  -
    id: storm_transpose_section
    publisher: section
    template: layout/templates/gdp-figure.mustache
    depends: ["storm_transpose", "page_text"]
    context:
      id: gdp-fig
      figure: storm_transpose
      text-before: page_text.storm_transpose_before
      text-after: page_text.storm_transpose_after
      caption: page_text.storm_transpose_caption
  - 
    id: inputs_data_section
    publisher: section
    template: layout/templates/gdp-figure.mustache
    depends: ["inputs_data", "page_text"]
    context:
      id: gdp-fig
      title: "Precip overtime for original storm location"
      figure: inputs_data
      text-before: page_text.inputs_data_before
      caption: page_text.inputs_data_caption
  - 
    id: inputs_geometry_section
    publisher: section
    template: layout/templates/gdp-figure.mustache
    depends: ["inputs_geometry", "page_text"]
    context:
      id: gdp-fig
      figure: inputs_geometry
      text-before: page_text.inputs_geometry_before
      caption: page_text.inputs_geometry_caption
  -
    id: yahara_clip_melt_section
    publisher: section
    template: layout/templates/gdp-figure-sidebyside.mustache
    depends: ["yahara_precip_clip", "yahara_precip_melt", "page_text"]
    context:
      id: gdp-fig-two
      title:
      figure1: yahara_precip_clip
      figure2: yahara_precip_melt
      text-before: page_text.yahara_precip_before
      caption-one: page_text.yahara_precip_caption_one
      caption-two: page_text.yahara_precip_caption_two
  -
    id: conclusion_text
    publisher: section
    template: layout/templates/gdp-text.mustache
    depends: "page_text"
    context:
      id: gdp-text
      text: page_text.conclusion
  -  
    id: gdp_figure_css
    location: layout/css/gdp-figure.css
    mimetype: text/css
  -
    id: sourcesanspro
    publisher: googlefont
    family: Source Sans Pro
    weight: [300, 400, 600]
  - 
    id: header_section
    publisher: header
    template: header-template
    depends: "lib-header-css"
    context:
      title: How the USGS Geo Data Portal works
  -
    id: footer_section
    publisher: footer
    template: footer-template
    depends: "lib-footer-css"
    blogsInFooter: FALSE
    github-url: https://github.com/USGS-VIZLAB/how-to-gdp
    vizzies:
      - name: Hurricane Irma's Water Footprint
        org: USGS-VIZLAB
        repo: hurricane-irma