VermontTerrestrialPassageTool.jl

Compute and summarize connectivity around road culverts in Vermont. This package was built under an assumption that spatial data will have projections with units of meters. All input data should be in the same projection to guarantee functionality. You will need Julia 1.5 or higher to use this package.

Installation

julia> using Pkg; Pkg.add(PackageSpec(url = "https://github.com/csp-inc/VermontTerrestrialPassageTool.jl"))

Quickstart Guide

This package provides one user-facing function, compute_all_culverts(). It has one parameter (argument) that specifies the file path for an INI file that contains run options.

The INI file

The INI file should have an entry for each of the following:

• culvert_shapefile_path - The file path for the shapefile containing culverts. This shapefile must contain only single part point geometries (e.g. Point, and not MultiPoint geometry types).
• culvert_id_field - The field the culverts shapefile that contains unique IDs for each structure
• culvert_ids_path - The file path to a one-column CSV file (with no column names/headers) with entries specifying the IDs of the culverts for which the analysis should be run (e.g. unique IDs corresponding to the values in culvert_id_field in the culverts shapefile.
• landcover_path - The file path to the landcover raster to be used for generating resistance surfaces and masking source strength surfaces
• reclass_table_path - The file path to a reclass table to be used in Omniscape.jl for converting landcover into resistance. See reclass_table in the Omniscape.jl docs under Arguments for more info.
• source_strength_path - The file path to the source strength raster to be used for generating a source strength surface. This layer will be resampled and if needed, reprojected, to match the projection and resolution of the landcover dataset.
• mask_values - A list of values corresponding to the landcover data set to use for masking source strength. e.g., [1 2] specifies that any source strength pixel where the corresponding land cover pixel is not equal to 1 or 2 will be set to 0.
• os_radius_pixels - This argument is passed as the radius argument to Omniscape.jl. See radius in the Omniscape.jl docs under Arguments for more info.
• os_source_threshold - This argument is passed as the source_threshold argument to Omniscape.jl. See source_threshold in the Omniscape.jl docs under Arguments for more info.
• os_block_size - This argument is passed as the block_size argument to Omniscape.jl. See block_size in the Omniscape.jl docs under Arguments for more info.
• solver - The Circuitscape solver to use. See solver in the Omniscape.jl docs under Arguments for more info.
• summary_radius_pixels - The radius in pixels to use for summarizing connectivity around culverts. For example, summary_radius_pixels of 100 will result in summaries being reported for current within 100 pixels of the structure.
• output_folder - The file path specifying the path for a new folder where outputs should be written. Inside this folder will be a file called results.summary.csv containing summaries for current flow around each culvert. compute_all_culverts() will also create a new folder inside of output_folder for each culvert and save current maps there.

Note that all file paths should be relative to the working directory of your Julia session.

Example

Example INI file:

[Culvert Options]
culvert_id_field = TNC_Join_I
culvert_shapefile_path = ../data/source/culverts/vt_culverts_bridges_statefed_3ft_AI091720_vt_utm.shp
culvert_ids_path = test_culvert_ids.csv

[Raster inputs]
landcover_path = ../data/source/LandLandcov_BaseLC2016/LandLandcov_BaseLC2016.tif
source_strength_path = ../data/source/marten/MartenOccVT30.tif

[Omniscape options]
os_radius_pixels = 200
os_source_threshold = 0.85
os_block_size = 31
reclass_table_path = reclass_table.txt

[Run options]
mask_values = [1]
summary_radius_pixels = 100

[Output options]
output_folder = output/testrun

Using the package

Once you have installed this package and have an INI file created, to use this package simply run:

julia> using VermontTerrestrialPassageTool
julia> compute_all_culverts("<file path to your INI file>")

Replace <file path to your INI file> with the file path to your INI file.