Identifying priority survey sites for early-season milkweed conservation
Data files
May 28, 2024 version files 1.93 GB
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MEDS-SBBG-milkweed-data.zip
1.93 GB
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README.md
45.97 KB
Abstract
Monarch butterfly (Danaus plexippus) populations are experiencing decline due to habitat degradation and climate threats. In 2024, this iconic species became protected under the Endangered Species Act. Critical to the persistence of this species of cultural and ecological importance is milkweed (Asclepias spp.), which monarchs rely on as an essential resource for food and reproduction. Motivated by concerns over the loss of monarch habitat, the Santa Barbara Botanic Garden (SBBG) and local collaborators are working to identify potential restoration areas in the Los Padres National Forest (LPNF). However, the vast size and complex terrain of the LPNF pose a logistical challenge to surveying. Therefore, there is a need for a tool to aid in selecting sites to prioritize. Our team created a priority index for surveying milkweed within the LPNF by predicting the habitat suitability for four early-season milkweed species using Maximum Entropy (MaxEnt) species distribution modeling and creating a novel survey site accessibility index. We identified high priority sites for the team to survey based on high predicted suitability for each species of early-season milkweed and high physical accessibility. To communicate these results, we created an interactive web dashboard, which the SBBG team will use for field planning to support the ongoing monitoring of milkweed populations for monarch habitat restoration efforts within the LPNF.
https://doi.org/10.5061/dryad.2rbnzs7x4
This README file was generated on 2024-05-22 by Anna Ramji, Amanda Herbst, Sam Muir, and Melissa Widas for the UCSB Bren School of Environmental Science & Management’s MEDS Capstone Project: Identifying Priority Survey Sites for Early-Season Milkweed Conservation.
File structure of data archive
├── clean_data
│ ├── bioclim
│ │ └── wallace_bioclim.tif
│ ├── canopy_cover
│ │ └── canopy_cover_cleaned.tif
│ ├── dem
│ │ ├── eastness.tif
│ │ ├── lpnf_aspect.tif
│ │ ├── lpnf_dem.tif
│ │ ├── lpnf_slope.tif
│ │ └── northness.tif
│ ├── lpnf_boundary
│ │ ├── lpnf_boundary
│ │ │ ├── lpnf_boundary.shp
│ │ │ └── ...
│ │ ├── lpnf_boundary_buffered
│ │ │ ├── lpnf_boundary_buffered.shp
│ │ │ └── ...
│ │ ├── lpnf_boundary_north
│ │ │ ├── lpnf_boundary_north.shp
│ │ │ └── ...
│ │ ├── lpnf_boundary_north_buffered
│ │ │ ├── lpnf_boundary_north_buffered.shp
│ │ │ └── ...
│ │ ├── lpnf_boundary_south
│ │ │ ├── lpnf_boundary_south.csv
│ │ │ ├── lpnf_boundary_south.shp
│ │ │ └── ...
│ │ └── lpnf_boundary_south_buffered
│ │ ├── lpnf_boundary_south_buffered.shp
│ │ └── ...
│ ├── lpnf_land_ownership
│ │ ├── lpnf_land_ownership.shp
│ │ └── ...
│ ├── milkweed_data
│ │ ├── sdm_milkweed_points
│ │ │ ├── californica_points.csv
│ │ │ ├── eriocarpa_points.csv
│ │ │ ├── erosa_points.csv
│ │ │ └── vestita_points.csv
│ │ └── survey_location_centroids
│ │ ├── all_species_points.shp
│ │ └── ...
│ ├── sdm_env_stack
│ │ ├── env_stack.tif
│ │ └── ... # .gri and .grd files associated with raster stack
│ ├── site_accessibility
│ │ ├── roads_distance_raster.tif
│ │ ├── template_raster.tif
│ │ └── trails_distance_raster.tif
│ └── trails_and_roads
│ └── forest_watch
│ ├── forest_open_roads_south.shp
│ ├── ...
│ ├── forest_open_trails_south.shp
│ ├── ...
│ ├── forest_roads_south.shp
│ ├── ...
│ ├── forest_trails_south.shp
│ └── ...
├── outputs
│ ├── priority_sites_outputs
│ │ ├── californica_priority.tif
│ │ ├── eriocarpa_priority.tif
│ │ ├── erosa_priority.tif
│ │ ├── priority_datatable.csv
│ │ └── vestita_priority.tif
│ ├── sdm_outputs
│ │ ├── californica_sdm.rda
│ │ ├── californica_sdm.tif
│ │ ├── eriocarpa_sdm.rda
│ │ ├── eriocarpa_sdm.tif
│ │ ├── erosa_sdm.rda
│ │ ├── erosa_sdm.tif
│ │ ├── max_suitable_sdm.tif
│ │ ├── vestita_sdm.rda
│ │ └── vestita_sdm.tif
│ └── site_accessibility_outputs
│ ├── access_index_final.tif
│ ├── canopy_rescaled.tif
│ ├── ownership_rescaled.tif
│ ├── roads_rescaled.tif
│ ├── slope_rescaled.tif
│ └── trails_rescaled.tif
└── raw_data
└── trails_and_roads
└── 2023_Regional_Trails_and_Roads_lines
├── 2023_Regional_Trails_and_Roads_lines.shp
└── ...
README.md
GENERAL INFORMATION
- Project Title: Identifying Priority Survey Sites for Early-Season Milkweed Conservation
- Author Information
- Anna Ramji
- Institution: University of California, Santa Barbara
- Email: anna@ramji.org
- ORCID iD: https://orcid.org/0009-0006-7576-7793
- Amanda Herbst
- Institution: University of California, Santa Barbara
- Email: amandaeherbst@gmail.com
- ORCID iD: https://orcid.org/0000-0002-0478-5947
- Sam Muir
- Institution: University of California, Santa Barbara
- Email: shmuir1@gmail.com
- ORCID iD: https://orcid.org/0000-0001-9868-7186
- Melissa Widas
- Institution: University of California, Santa Barbara
- Email: mel.widas@gmail.com
- ORCID iD: https://orcid.org/0009-0002-9045-2969
- Principal Investigator Contact Information
- Name: Dr. Sarah Cusser
- Institution: Santa Barbara Botanic Garden
- Address: 1212 Mission Canyon Rd, Santa Barbara, CA 93105
- Email: scusser@sbbotanicgarden.org
- ORCID iD: https://orcid.org/0000-0002-0100-026X
- Anna Ramji
Data collection timeframe: All publicly accessible data was downloaded between 2024-01-10 and 2024-03-22.
Disclaimer:
Many data products and outputs archived from this project contain or relate to sensitive data concerning locations of habitat for a federally endangered species. Our team was given permission to share this data by the U.S. Forest Service under the condition that a disclaimer is included: “Plant and seed collection on Forest Service land is not permissible without a plant collection permit from the Los Padres National Forest”.
Data and File Overview:
Data Sources
Raw data source details are formatted using the following template:
Raw data source title
Brief description:
How it was accessed:
Use: [name of file(s) in our archive it contributes to]
Units (when relevant):
Citation:
Licenses:
***
Bioclimatic Data
Brief description: Historical climate data – 19 bioclimatic variables to represent annual trends, seasonality, extreme/limiting environmental factors based on monthly temperature and rainfall data (.tif)
How it was accessed: wallace::envs_worldclim(), which utilizes raster::getData()
Use:
clean_data/bioclim/wallace_bioclim.tif
clean_data/sdm_env_stack/
outputs/priority_sites_outputs/
outputs/sdm_outputs/
Units: Spatial Reference: WGS 1984 (EPSG 4326)
Citation: Fick, S.E. and R.J. Hijmans. (2017). WorldClim 2: new 1 km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37 (12): 4302-4315.
https://www.worldclim.org/data/worldclim21.html
Licenses: The data are freely available for academic use and other non-commercial use. Redistribution or commercial use is not allowed without prior permission. Using the data to create maps for publishing of academic research articles is allowed.
***
California Multi-Source Land Ownership:
Brief description: Classification of land ownership, excluding lands under private ownership, in California(.shp)
How it was accessed: Downloaded the “California Land Ownership” feature layer from California State Geoportal as a shapefile
Use:
clean_data/lpnf_land_ownership/lpnf_land_ownership.shp
outputs/priority_sites_outputs/
outputs/site_accessibility_outputs/access_index_final.tif
outputs/site_accessibility_outputs/ownership_rescaled.tif
Units: Spatial Reference: WGS 1984 Pseudo-Mercator (EPSG 3857)
Citation:
California Department of Forestry and Fire Protection; California State Geoportal, hosted on CAL FIRE Portal (via gis.data.ca.gov)
https://gis.data.ca.gov/datasets/CALFIRE-Forestry::california-land-ownership/about
Licenses:
The State of California and the Department of Forestry and Fire Protection make no representations or warranties regarding the accuracy of data or maps. Neither the State nor the Department shall be liable under any circumstances for any direct, special, incidental, or consequential damages with respect to any claim by any user or third party on account of, or arising from, the use of data or maps.
For more information about this product, date or terms of use, contact calfire.egis@fire.ca.gov.
***
Canopy Cover:
Brief description: Horizontal cover fraction occupied by tree canopies (.tif)
How it was accessed: Downloaded from the California Forest Observatory website, selected “Canopy Cover” from available datasets to download. If counties need to be selected please select Kern County, Monterey County, San Luis Obispo County, and Ventura County
Use:
clean_data/canopy_cover/canopy_cover_cleaned.tif
clean_data/sdm_env_stack
outputs/priority_sites_outputs/
outputs/sdm_outputs
outputs/site_accessibility/access_index_final.tif
outputs/site_accessibility/canopy_rescaled.tif
Units: Spatial Reference: WGS 1984 Pseudo-Mercator (EPSG 3857)
Citation: California Forest Observatory. (2020). A Statewide Tree-Level Forest Monitoring System. Salo Sciences, Inc. San Francisco, CA. https://forestobservatory.com
Licenses: For more information regarding licensing please visit: https://forestobservatory.com/legal.html
***
Digital Elevation Model (DEM):
Brief description: Topographic surface of the earth and flattened water surfaces (.tif). Seven tiles were downloaded to cover the extent of the Los Padres National Forest (LPNF).
Tiles:
n35w119_20190919
n35w120_20190924
n35w121_20190924
n36w120_20190919
n36w121_20190919
n36w122_20210301
n37w122_20201207
How it was accessed: USGS’s The National Map (TNM) download interface; searched for California, USA; selected Elevation Products (3DEP) 1 arc-second DEM; downloaded as GeoTIFF.
Use:
clean_data/dem/
clean_data/sdm_env_stack/
outputs/priority_sites_outputs/
outputs/sdm_outputs/
outputs/site_accessibility_outputs/access_index_final.tif
outputs/site_accessibility_outputs/slope_rescaled.tif
Units: Spatial Reference: NAD 1983 (EPSG 4269)
Citation: U.S. Geological Survey, 2019, 2020, 2021, USGS 3D Elevation Program Digital Elevation Model https://apps.nationalmap.gov/downloader/ , courtesy of the U.S. Geological Survey.
Licenses: Data from The National Map is free and in the public domain. There are no restrictions on downloaded data; however, we request that the following statement be used when citing, copying, or reprinting data: “Data available from U.S. Geological Survey, National Geospatial Program.”
***
Los Padres National Forest (LPNF) Boundary:
Brief description: Boundary of the northern and southern regions of Los Padres National Forest in California filtered from the Forest Service Administrative Boundaries (.shp)
How it was accessed: USDA Download National Datasets interface; Scroll to Administrative Forest Boundaries and Select ESRI Geodatabase; downloaded as GeoDatabase
Use:
clean_data/lpnf_boundary/
outputs/priority_sites_outputs/
outputs/sdm_outputs/
outputs/site_accessibility_outputs/
Units: esriMeters, Spatial Reference: WGS 1984 Web Mercator Auxiliary Sphere (EPSG 3857)
Citation: United States Department of Agriculture Forest Service, Administrative Forest Boundaries. (2024); https://data.fs.usda.gov/geodata/edw/datasets.php
Licenses: The USDA Forest Service makes no warranty, expressed or implied, including the warranties of merchantability and fitness for a particular purpose, nor assumes any legal liability or responsibility for the accuracy, reliability, completeness or utility of these geospatial data, or for the improper or incorrect use of these geospatial data. These geospatial data and related maps or graphics are not legal documents and are not intended to be used as such. The data and maps may not be used to determine title, ownership, legal descriptions or boundaries, legal jurisdiction, or restrictions that may be in place on either public or private land. Natural hazards may or may not be depicted on the data and maps, and land users should exercise due caution. The data are dynamic and may change over time. The user is responsible to verify the limitations of the geospatial data and to use the data accordingly.
***
Santa Barbara Botanic Garden Polygon Data:
Brief description: Polygons indicating the shape of the outer border of observed milkweed plots in the Los Padres National Forest during field surveys in the summer of 2023. Includes information on milkweed species, presence/absence, location and number of plants
How it was accessed: Shared directly by the Santa Barbara Botanic Garden as a shapefile.
Use:
clean_data/milkweed_data/sdm_milkweed_points/ clean_data/milkweed_data/survey_location_centroids/all_species_points.shp
outputs/priority_sites_outputs/
outputs/sdm_outputs/
Units: Spatial Reference: WGS 1984 Pseudo-Mercator (EPSG 3857)
Citation: Santa Barbara Botanic Garden, shared January 2024
Licenses: This data was privately shared with the MilkweedMod capstone team and is part of the Santa Barbara Botanic Garden’s long-term milkweed restoration project. The capstone team was given permission to share this data by the U.S. Forest Service under the condition that the following disclaimer is included: “Plant and seed collection on Forest Service land is not permissible without a plant collection permit from the Los Padres National Forest”.
***
Trails & Roads Data — Los Padres Forest Watch:
Brief description: Trails and road geometries, along with names and open/closed status, within the southern section of the Los Padres National Forest as of June 2023
How it was accessed: Downloaded from ArcGIS online with an ArcGIS Pro account as a shapefile
Use:
clean_data/site_accessibility/roads_distance_raster.tif
clean_data/site_accessibility/trails_distance_raster.tif
clean_data/trails_and_roads/forest_watch/forest_open_roads_south.shp
clean_datatrails_and_roads/forest_watch/forest_open_trails_south.shp
clean_data/trails_and_roads/forest_watch/forest_roads_south.shp
clean_data/trails_and_roads/forest_watch/forest_trails_south.shp
outputs/priority_sites_outputs/
outputs/site_accessibility_outputs/access_index_final.tif
outputs/site_accessibility_outputs/roads_rescaled.tif
outputs/site_accessibility_outputs/trails_rescaled.tif
Units: esriMeters, Spatial Reference: WGS 1984 Pseudo-Mercator (EPSG 3857)
Citation: ForestWatchGIS, 2023 Regional Trails and Roads, Los Padres Forest Watch via ArcGIS
Licenses: No license information was provided. For more information regarding licensing please visit this page.
***
Trails & Roads Data — USGS:
Brief description: National Transportation Data (NTD) California Shapefile, courtesy of the U.S. Geological Survey – trails and different types of roads in California (.shp), used data from within the northern region of the LPNF
How it was accessed: Downloaded from the National Transportation Dataset via the USGS ScienceBase Catalog.
Use:
clean_data/site_accessibility/roads_distance_raster.tif
clean_data/site_accessibility/trails_distance_raster.tif
outputs/priority_sites_outputs/
outputs/site_accessibility_outputs/access_index_final.tif
outputs/site_accessibility_outputs/roads_rescaled.tif
outputs/site_accessibility_outputs/trails_rescaled.tif
Units: esriMeters, Spatial Reference: NAD 1983 (EPSG 4269)
Citation: Courtesy of the U.S. Geological Survey, 2024, USGS National Transportation Dataset (NTD) for California
https://www.sciencebase.gov/catalog/item/5f6345ee82ce38aaa238c9df
Licenses: Data from The National Map is free and in the public domain. There are no restrictions on downloaded data; however, we request that the following statement be used when citing, copying, or reprinting data: “Data available from U.S. Geological Survey, National Geospatial Program.”
***
The following sections follow the folder and file description format as outlined below:
folder_name
Folder details:
Units:
Notebooks:
Methodology:
***
clean_data
bioclim
Folder details: This folder contains one file, a raster brick of the 19 layers of bioclimatic data spanning our project’s area of interest: the Los Padres National Forest (LPNF) in California, USA.
Units:
- Coordinate Reference System (CRS): EPSG 4326
- Resolution: 0.008333333 x 0.008333333 degrees per pixel
- Extent: [-149.999999999967, -89.9999999999667, 29.9999999999967, 59.9999999999967] (xmin, xmax, ymin, ymax)
- Origin: (3.373657e-11, -3.311129e-12)
Notebook: The code used to generate these intermediate data products can be found at data_cleaning/bioclim/bioclim.R
Methodology: Used wallace::envs_worldclim(), selected all 19 bioclimatic layers at 30 arcsec resolution and then selected the two centers of the tiles that cover the northern and southern regions of the LPNF. The final step was to use terra::mosaic() to mosaic the tiles together.
File-specific information:
wallace_bioclim.tif– raster of bioclim data spanning area of interest (northern and southern regions of LPNF)
canopy_cover
Folder details: This folder contains one file, a raster of canopy cover data spanning the LPNF. Canopy cover is defined as the horizontal cover fraction occupied by tree canopies.
Units: The file in this folder has the same units as the wallace_bioclim.tif file, as that raster is used to set the CRS, extent, and resolution of the template raster. The template raster was used to crop the data layers used to create the survey site accessibility index.
Notebook: The code used to generate these intermediate data products can be found at data_cleaning/canopy_cover/canopy_cover.qmd
Methodology: Used terra::mosaic() to mosaic the kern_county, los_angeles_county, monterey_county, san_luis_obispo_county, santa_barbara_county, and ventura_county tiles together, then used the wallace_bioclim.tif file within terra::project() to set the resolution and CRS of raster. Cropped to the polygon of the LPNF boundary.
File-specific information:
canopy_cover_cleaned.tif– raster of canopy cover data, cropped to the LPNF boundary
dem
Folder details: This folder contains the intermediate data products from processing the digital elevation model (DEM) data. This data was used to calculate the slope, aspect, eastness, and northness, which are then used in the species distribution modeling (SDM) for our project. The slope is also used in the development of the survey site accessibility index.
Units: All files in this notebook are in the following units (all products are eventually resampled and masked to meet the standard output units described later in this document)
- Coordinate Reference System: NAD83 EPSG 4269
- Resolution: 0.0002777778 x 0.0002777778
- Extent: [-122.001666666583, -117.998333329528, 33.9983333328179, 37.001666668943] (xmin, xmax, ymin, ymax)
- Origin: (1.134929e-07, -3.211905e-08)
- Raster values in degrees
Notebooks: The code used to generate these intermediate data products can be found at
milkweed-mod/data_cleaning/dem_cleaning.qmd and milkweed-mod/data_cleaning/solar_rad/solar_radiation.qmd
Methodology: The DEM data was created by using terra::mosaic() to mosaic 7 USGS tiles together. Slope (lpnf_slope.tif) and aspect (lpnf_aspect.tif) were calculated from the DEM (lpnf_dem) using terra::terrain(), specifying the unit as “degrees”. The slope and aspect were then used to calculate eastness and northness using the following equations:
eastness = sin(aspect * pi/180) * sin(slope * pi/180)
northness = cos(aspect * pi/180) * sin(slope * pi/180)
Eastness and northness were then used as proxies for solar radiation in species distribution modeling. They were considered in this model because according to the SBBG survey team, A. californica seemed to prefer steep, south-facing slopes. The CRS, resolution, and extent were transformed to fit the standard detailed in the notebooks in the sdm_env_stack folder.
File-specific information:
eastness.tif– raster file containing the eastness index, cropped to the LPNF boundary, with 1 indicating a sheer vertical surface facing completely East, and -1 indicating a sheer vertical surface facing completely Westlpnf_aspect.tif– raster file containing the aspect, or direction of the slope, cropped to the LPNF boundarylpnf_dem.tif– raster file containing the digital elevation model (DEM) cropped to the LPNF boundarylpnf_slope.tif– raster file containing the slope (in degrees), cropped to the LPNF boundarynorthness.tif– raster file containing the eastness index, cropped to the LPNF boundary, with 1 indicating a sheer vertical surface facing completely North, and -1 indicating a sheer vertical surface facing completely South
lpnf_boundary
lpnf_boundary
Folder details: This folder contains the shapefile for the boundary of the Los Padres National Forest (LPNF)
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate this intermediate data product can be found at milkweed-mod/data_cleaning/boundary/lpnf_boundary.qmd
File-specific information:
lpnf_boundary.shp– file containing the full boundary of the LPNF as a multipolygon
lpnf_boundary_buffered
Folder details: This folder contains the shapefile for the northern and southern regions of the LPNF boundary with a buffer of 1,000 meters applied.
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate this intermediate data product can be found at milkweed-mod/data_cleaning/boundary/lpnf_boundary.qmd
File-specific information:
lpnf_boundary_buffered.shp– file containing the full buffered boundary of the LPNF as a multipolygon
lpnf_boundary_north
Folder details: This folder contains the shapefile for the northern region of the boundary of the LPNF.
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate these intermediate data products can be found at milkweed-mod/data_cleaning/boundary/lpnf_boundary.qmd
File-specific information:
lpnf_boundary_north.shp– file containing the northern region of the boundary of the LPNF as a multipolygon
lpnf_boundary_north_buffered
Folder details: This folder contains the shapefile for the northern region of the LPNF boundary with a buffer of 1,000 meters applied.
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate this intermediate data product can be found at milkweed-mod/data_cleaning/boundary/lpnf_boundary.qmd
File-specific information:
lpnf_boundary_north_buffered.shp– file containing the buffered northern region of the boundary of the LPNF as a multipolygon
lpnf_boundary_south
Folder details: This folder contains the shapefile for the southern region of the LPNF boundary.
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate these intermediate data products can be found at milkweed-mod/data_cleaning/boundary/lpnf_boundary.qmd
File-specific information:
lpnf_boundary_south.shp– file containing the southern region of the boundary of the LPNF as a multipolygon
lpnf_boundary_south_buffered
Folder details: This folder contains the shapefile for the southern region of the LPNF boundary with a buffer of 1,000 meters applied.
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate this intermediate data product can be found at milkweed-mod/data_cleaning/boundary/lpnf_boundary.qmd
File-specific information:
lpnf_boundary_south_buffered.shp– file containing the buffered southern region of the boundary of the LPNF as a multipolygon
lpnf_land_ownership
Folder details: This folder contains the shapefile for the land ownership status cropped to the LPNF boundary
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate this intermediate data product can be found at milkweed-mod/data_cleaning/land_ownership/land_ownership.qmd
Methodology: Cropped the land ownership shapefile to the LPNF.
File-specific information:
lpnf_land_ownership.shp– shapefile containing information on land ownership classification within the LPNF (both the northern and southern regions)
milkweed_data
sdm_milkweed_points
Folder details: This folder contains the output of transforming the milkweed survey polygons to points – filtered for polygons marked as presence data (not absence) – stored as .csv files.
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate these intermediate data products can be found at data_cleaning/milkweed_polygon/points_clean_export.R
Methodology: To convert the milkweed presence data from polygons to points, we used sf::st_cast() to convert the multipolygons to “multipoint” data types, then to “point” data types. We then used sf::st_coordinates() to extract the latitude and longitude from each point and saved these point locations in a data frame, renaming the latitude and longitude columns appropriately and adding the column “occ_ID” (short for occurrence ID) with the row numbers as values to serve as an additional indexing column in preparation for use in MaxEnt. This process was performed for each of the four species of early-season milkweed modeled in our project. This method essentially saves each outer convex point on the polygon outline as a point. This was performed to maximize the data points for the SDM, and was appropriate because the border of the polygon represents the farthest extent at which a particular species was identified in the survey, meaning that the area is the full range of where that species was observed at that survey location.
File-specific information:
californica_points.csv– file containing columns: (longitude, latitude, species_name, occID), which contain information on location, species name, and an additional row ID column used indismo::maxent()calculations, with species_name filtered to Asclepias californica.eriocarpa_points.csv– file containing the same information as thecalifornica_points.csvfile, filtered to Asclepias eriocarpa.erosa_points.csv– file containing the same information as thecalifornica_points.csvfile, filtered to Asclepias erosa.vestita_points.csv– file containing the same information as thecalifornica_points.csvfile, filtered to Asclepias vestita.
survey_location_centroids
Folder details: This folder contains the centroids of each milkweed survey polygon.
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate these intermediate data products can be found at data_cleaning/milkweed_polygon/milkweed_subsets_points.qmd
Methodology: Created using sf::st_centroid() in R, selecting presence data only (NA values for the milkweed_p (milkweed presence) column were not included.
File-specific information:
all_species_points.shp– shapefile with centroids of each milkweed survey polygon, filtered to “presence” data only
sdm_env_stack
Folder details: This folder contains the raster stacks of environmental layers used in the species distribution models.
Units:
- Coordinate Reference System: EPSG 4326
- Resolution: 0.008333333 x 0.008333333 degrees per pixel
- Extent: [-122.01324133097, -117.479907997637, 33.679743833477, 36.9214105001436] (xmin, xmax, ymin, ymax)
- Origin: (0.003425336, -0.003589500)
Notebooks: The code used to generate this intermediate data product can be found at
data_cleaning/combine_layers/crop_stack.R
Methodology: Rasters of bioclim, northness, and eastness are resampled to the canopy cover raster, and then all layers are combined into a single raster stack.
File-specific information:
env_stack.tif– raster brick of bioclim, canopy cover, northness, and eastness
site_accessibility
Folder details: This folder contains the template raster used in the development of the survey site accessibility index, as well as two rasters that contain the distance from the centroid of each raster cell to the nearest road or trail, respectively.
Units: These .tifs follow approximately the same units as the output from the species distribution model – the resolution is slightly rounded (one rather than many 3s in the 0.0083 resolution) for processing. The rest of our products made using the template_raster.tif have these same units:
- Coordinate Reference System: EPSG 4326
- Resolution: 0.0083 x 0.0083 degrees per pixel
- Extent: [-122.0, -117.5014, 33.6, 36.9034] (xmin, xmax, ymin, ymax)
- Origin: (0.0017, 0.0016)
Notebooks: The code used to generate these intermediate data products can be found at the following notebooks:
data_cleaning/accessibility_template/template_raster.qmd
data_cleaning/trails_and_roads/trails_and_roads.qmd
site_accessibility/distance_calculations.qmd
Methodology: More information on how the distance from roads and trails was calculated can be found in site_accessibility/distance_calculations.qmd. The template raster was created using data_cleaning/accessibility_template/template_raster.qmd.
File-specific information:
roads_distance_raster.tif– raster in which cell values equal the distance to the nearest road in the northern and southern regions of the LPNF, in meterstemplate_raster.tif– template raster used for distance calculations, reprojecting and preparing other survey site accessibility layers (canopy cover, land ownership, slope) for zonal calculations (multiplication of rasters)trails_distance_raster.tif– raster in which cell values equal the distance to the nearest trail in the northern and southern regions of the LPNF, in meters
trails_and_roads
Folder details: This folder contains the intermediate products for calculating the distance from trails and roads contained in the previous folder: clean_data/site_accessibility.
Units: Coordinate Reference System: EPSG 4326
Notebooks: The code used to generate these intermediate data products can be found at data_cleaning/trails_and_roads/trails_and_roads.qmd
Methodology: Columns were renamed to follow the same lower_snake_case naming convention, and columns of relevance were selected for the distance from roads and trails calculations performed as part of the development of the survey site accessibility index.
File-specific information:
forest_open_roads_south.shp– shapefile containing all roads in the Los Padres Forest Watch trails and roads dataset for the southern region of the LPNF, filtered to the status “OPEN”forest_open_trails_south.shp– shapefile containing all trails in the Los Padres Forest Watch trails and roads dataset for the southern region of the LPNF, filtered to the status “OPEN”forest_roads_south.shp– shapefile containing all roads in the Los Padres Forest Watch trails and roads dataset for the southern region of the LPNFforest_trails_south.shp– shapefile containing all trails in the Los Padres Forest Watch trails and roads dataset for the southern region of the LPNF
***
outputs
All raster (.tif) outputs have the following units:
- Coordinate Reference System: EPSG 4326
- Resolution: 0.0083 x 0.0083 degrees per pixel
- Extent: [-122.0, -117.5014, 33.6, 36.9034] (xmin, xmax, ymin, ymax)
- Origin: (0.0017, 0.0016)
priority_sites_outputs
Folder details: This folder contains the output raster files (.tif) of multiplying the final survey site accessibility index raster (access_index_final.tif) by the raster outputs resulting from the species distribution modeling (files in the sdm_outputs folder). There is one raster for each of the four species, as well as a “combined” or “maximum” priority raster, which is the product of the accessibility index and the max_suitable_sdm.tif file described in the next section.
Notebooks: The code used to generate these outputs can be found at priority_sites/priority_sites.qmd
Methodology: Species-specific SDM output rasters were multiplied by the survey site accessibility index, then rescaled from 0 to 1 using the rescale_raster.R function that our team developed, and saved the rescaled outputs as rasters.
File-specific information:
californica_priority.tif– raster in which each cell is assigned a survey site priority score, following the methodology described earlier, specifically using the A. californica SDM output (californica_sdm.tif)eriocarpa_priority.tif– raster in which each cell is assigned a survey site priority score, following the methodology described earlier, specifically using the A. eriocarpa SDM output (eriocarpa_sdm.tif)erosa_priority.tif– raster in which each cell is assigned a survey site priority score, following the methodology described earlier, specifically using the A. erosa SDM output (erosa_sdm.tif)priority_datatable.csv– file that contains the following columns and associated data:- Longitude: numeric, with range [-118.71735, -121.90455]
- Latitude: numeric, with range [34.39265, 36.40125]
- A. californica Priority: integer with range [0,1]
- A. eriocarpa Priority: integer with range [0,1]
- A. erosa Priority: integer with range [0,1]
- A. vestita Priority: integer with range [0,1]
- Accessibility Score: integer with range [0,1]
- Survey Status: indicates “not visited” or “visited” depending on whether or not the location has been visited by the survey team previously
vestita_priority.tif– raster in which each cell is assigned a survey site priority score, following the methodology described earlier, specifically using the A. vestita SDM output (vestita_sdm.tif)
sdm_outputs
Folder details: This folder contains raster files (.tif) and R data files (.rda) for each of the four species of early-season milkweed that inhabit the LPNF (A. californica, A. eriocarpa, A. erosa, and A. vestita). It also contains a raster of the maximum suitability found in each raster cell across all species.
Notebooks: The code used to generate these model outputs can be found at the following notebooks:
maxent/max_suitability_sdm.qmd
Methodology: MaxEnt model outputs generated using milkweed species occurrence data and environmental raster stack.
File-specific information:
californica_sdm.rda– ENMeval model object generated using A. californica occurrence pointscalifornica_sdm.tif– model output raster generated using A. californica occurrence points- Layer name is set to the selected model run for that species (from
californica_sdm.rda)
- Layer name is set to the selected model run for that species (from
eriocarpa_sdm.rda– ENMeval model object generated using A. eriocarpa occurrence pointseriocarpa_sdm.tif– model output raster generated using A. eriocarpa occurrence points- Layer name is set to the selected model run for that species (from
eriocarpa_sdm.rda)
- Layer name is set to the selected model run for that species (from
erosa_sdm.rda– ENMeval model object generated using A. erosa occurrence pointserosa_sdm.tif– model output raster generated using A. erosa occurrence points- Layer name is set to the selected model run for that species (from
erosa_sdm.rda)
- Layer name is set to the selected model run for that species (from
max_suitable_sdm.tif– raster populated with the maximum suitability value at each raster cell in the LPNF based on predicted suitability of all four milkweed speciesvestita_sdm.rda– ENMeval model object generated using A. vestita occurrence pointsvestita_sdm.tif– model output raster generated using A. vestita occurrence points- Layer name is set to the selected model run for that species (from
vestita_sdm.rda)
- Layer name is set to the selected model run for that species (from
site_accessibility_outputs
Folder details: This folder contains the outputs of the survey site accessibility index created for this project, including the rescaled rasters of each layer: canopy cover, land ownership, distance to roads, slope, and distance to trails. It also contains the combined (multiplicative raster operation) accessibility raster, in which each cell value is associated with the relative level of physical accessibility to the centroid of that raster cell in the LPNF.
Notebooks: The code used to generate these outputs can be found at
site_accessibility/rescale_all_layers.qmd and
site_accessibility/create_accessibility_index.qmd
Methodology: The survey site index was calculated by multiplying individually rescaled rasters of selected variables that contribute to the physical accessibility of a site, including canopy cover (as a proxy for vegetation density), distance from trails and roads (methodology described in clean_data/site_accessibility/), land ownership status (cells set to 0 if privately owned land and 1 if public land), and slope (calculated from the DEM, methodology described in (clean_data/dem). These layers were individually rescaled from 0 to 1 (with the exception of land ownership status), with 1 indicating the highest level of accessibility, and 0 indicating the lowest or least accessible locations in the Los Padres National Forest (LPNF). The layers were then combined using multiplication, and rescaled once again from 0 to 1, with 1 representing the maximum relative physical accessibility and 0 representing the minimum relative physical accessibility.
File-specific information:
access_index_final.tif– raster file containing the final rescaled survey site accessibility indexcanopy_rescaled.tif– raster file containing one layer of canopy cover in the LPNF rescaled to a scale of 0 to 1 based on the original values in the raster, then all values subtracted from 1 so that a value of 0 indicates a maximum canopy cover and therefore low survey site accessibility (and 1 indicates no canopy cover and therefore high survey site accessibility)ownership_rescaled.tif– raster file containing one layer of land ownership in the LPNF where 0 indicates private land and 1 indicates public land.roads_rescaled.tif– raster file containing one layer (“distance”) of the calculated distance from roads in the Los Padres National Forest rescaled to a scale of 0 to 1 based on the original values in the raster, then all values subtracted from 1 so that a value of 0 indicates a maximum distance from a road and therefore low survey site accessibility (and 1 indicates a location that is extremely close to a road and therefore high survey site accessibility)slope_rescaled.tif– raster file containing one layer (“lpnf_slope”) of slope in the LPNF rescaled to a scale of 0 to 1 based on the original values in the raster, then all values subtracted from 1 so that a value of 0 indicates a maximum (steep) slope and therefore low survey site accessibility (and 1 indicates low slope (flat) and therefore high survey site accessibility)trails_rescaled.tif– raster file containing one layer (“distance”) of canopy cover in the LPNF rescaled to a scale of 0 to 1 based on the original values in the raster, then all values subtracted from 1 so that a value of 0 indicates a maximum canopy cover and therefore low survey site accessibility (and 1 indicates a location that is extremely close to a trail and therefore higher survey site accessibility)
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raw_data
trails_and_roads
2023_Regional_Trails_and_Roads_lines
Folder details: This folder contains the raw data created by the Los Padres Forest Watch, downloaded from ArcGIS Online with an ArcGIS Pro account.
Units: esriMeters, Coordinate Reference System: WGS 84 / Pseudo-Mercator EPSG 3857
Methodology: Raw data [see “Trails & Roads Data – Los Padres Forest Watch” in the Data Sources section].
File-specific information:
2023_Regional_Trails_and_Roads_lines.shp– missing data values code: “NA”
Coding environment specs
Session Info can be found here:
https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/session_info.txt
Our team collected data from publicly available data sources between 2024-01-10 and 2024-03-22. More details on these sources can be found in our README.md. All data cleaning, processing, and development of modeling and indices for our project have been recorded in notebooks and repositories in our team's GitHub organization, which is also linked as "Related Works" to this archival. We developed a species distribution model to predict habitat suitability for four species of early-season milkweed (Asclepias californica, Asclepias eriocarpa, Asclepias erosa, and Asclepias vestita) in the southern region of the Los Padres National Forest (LPNF), using publicly available environmental data, along with milkweed survey data collected in 2023 by the Santa Barbara Botanic Garden (SBBG). We also created a novel survey site accessibility index to assess how physically accessible locations in the LPNF are for the SBBG team. Since the forest has a vast extent (1.75 million acres) and the garden's survey team has limited resources, we used the data in this archive to identify high-priority locations for the team to visit in upcoming field surveys by determining locations that were both highly suitable for each species of milkweed and relatively physically accessible for the SBBG team.