DOI: 10.5061/dryad.2rbnzs7x4
title: Identifying priority survey sites for early-season milkweed conservation

description: 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.
description: 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
 (<em>Asclepias californica</em>,<em> Asclepias
 eriocarpa</em>, <em>Asclepias erosa</em>, and
 <em>Asclepias vestita</em>) 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.
description: # Identifying Priority Survey Sites for Early-Season Milkweed Conservation
 [https://doi.org/10.5061/dryad.2rbnzs7x4](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](https://bren.ucsb.edu/projects/identifying-priority-survey-sites-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** 1. **Project Title:** **Identifying Priority Survey Sites for Early-Season Milkweed Conservation**  2. **Author Information** 1. **Anna Ramji** 1. Institution: University of California, Santa Barbara 2. Email: [anna@ramji.org](mailto:anna@ramji.org)   3. ORCID iD: [https://orcid.org/0009-0006-7576-7793](https://orcid.org/0009-0006-7576-7793)  2. **Amanda Herbst** 1. Institution: University of California, Santa Barbara 2. Email: [amandaeherbst@gmail.com](mailto:amandaeherbst@gmail.com)  3. ORCID iD: [https://orcid.org/0000-0002-0478-5947](https://orcid.org/0000-0002-0478-5947) 3. **Sam Muir** 1. Institution: University of California, Santa Barbara 2. Email: [shmuir1@gmail.com](mailto:shmuir1@gmail.com)   3. ORCID iD: [https://orcid.org/0000-0001-9868-7186](https://orcid.org/0000-0001-9868-7186)    4. **Melissa Widas** 1. Institution: University of California, Santa Barbara 2. Email: [mel.widas@gmail.com](mailto:mel.widas@gmail.com)  3. ORCID iD: [https://orcid.org/0009-0002-9045-2969](https://orcid.org/0009-0002-9045-2969) 5. **Principal Investigator Contact Information**  1. Name: Dr. Sarah Cusser 2. Institution: Santa Barbara Botanic Garden 3. Address: 1212 Mission Canyon Rd, Santa Barbara, CA 93105 4. Email: [scusser@sbbotanicgarden.org](mailto:scusser@sbbotanicgarden.org) 5. ORCID iD: [https://orcid.org/0000-0002-0100-026X](https://orcid.org/0000-0002-0100-026X) ***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](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](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](mailto: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](https://forestobservatory.com) **Licenses**: For more information regarding licensing please visit: [https://forestobservatory.com/legal.html](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;](https://apps.nationalmap.gov/downloader/) 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/](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](https://data.fs.usda.gov/geodata/edw/datasets.php?dsetCategory=boundaries); 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](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](https://services9.arcgis.com/olCAyDMW794Lg7Au/arcgis/rest/services/2023_Regional_Trails_and_Roads/FeatureServer)  **Licenses**: No license information was provided. For more information regarding licensing please visit [this](https://services9.arcgis.com/olCAyDMW794Lg7Au/arcgis/rest/services/2023_Regional_Trails_and_Roads/FeatureServer/info/itemInfo?f=pjson) page.  \*** #### Trails & Roads Data — USGS: **Brief description**: National Transportation Data (NTD) [California Shapefile](https://www.sciencebase.gov/catalog/item/5f6345ee82ce38aaa238c9df), 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](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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/data_cleaning/dem/dem_cleaning.qmd) and [milkweed-mod/data_cleaning/solar_rad/solar_radiation.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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 West * `lpnf_aspect.tif` – raster file containing the aspect, or direction of the slope, cropped to the LPNF boundary * `lpnf_dem.tif` – raster file containing the digital elevation model (DEM) cropped to the LPNF boundary * `lpnf_slope.tif` – raster file containing the slope (in degrees), cropped to the LPNF boundary * `northness.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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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 in `dismo::maxent()` calculations, with species_name filtered to *Asclepias californica*.  * `eriocarpa_points.csv` – file containing the same information as the `californica_points.csv` file, filtered to *Asclepias eriocarpa*.  * `erosa_points.csv` – file containing the same information as the `californica_points.csv` file, filtered to *Asclepias erosa*.  * `vestita_points.csv` – file containing the same information as the `californica_points.csv` file, 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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/data_cleaning/accessibility_template/template_raster.qmd)  [data_cleaning/trails_and_roads/trails_and_roads.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/data_cleaning/trails_and_roads/trails_and_roads.qmd) [site_accessibility/distance_calculations.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/site_accessibility/distance_calculations.qmd). The template raster was created using [data_cleaning/accessibility_template/template_raster.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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 meters * `template_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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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 LPNF  * `forest_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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/R/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/A_californica_sdm.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/maxent/A_californica_sdm.qmd)  [maxent/A_eriocarpa_sdm.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/maxent/A_eriocarpa_sdm.qmd) [maxent/A_erosa_sdm.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/maxent/A_erosa_sdm.qmd) [maxent/A_vestita_sdm.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/maxent/A_vestita_sdm.qmd) [maxent/max_suitability_sdm.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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 points * `californica_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`) * `eriocarpa_sdm.rda`– ENMeval model object generated using *A. eriocarpa* occurrence points  * `eriocarpa_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`) * `erosa_sdm.rda` – ENMeval model object generated using *A. erosa* occurrence points  * `erosa_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`) * `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 species * `vestita_sdm.rda` – ENMeval model object generated using *A. vestita* occurrence points  * `vestita_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`) ### `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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/site_accessibility/rescale_all_layers.qmd) and  [site_accessibility/create_accessibility_index.qmd](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/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 index  * `canopy_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) \*** ## `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](https://github.com/MEDS-SBBG-milkweed/milkweed-mod/blob/main/session_info.txt)