bcfishpass

bcfishpass is a collection of scripts to create and maintain an aquatic connectivity / fish passage database for British Columbia to:

• track known barriers to fish passage (eg dams, waterfalls)
• work with BC Provincial Stream Crossing Information System (PSCIS) crossings and barriers
• model potential barriers to fish passage (stream gradient, road/rail stream crossings)
• model passability/accessibility of streams based on barriers and species swimming ability
• model streams with potential for spawning and rearing activity (for select species)
• prioritize assessment and remediation of barriers based on modelled accessibility and habitat potential

Also provided are tools for mapping features in the database:

• basic web viewer
• comprehensive QGIS layer file

General Methodology

bcfishpass is an update and extension of the BC Fish Passage Technical Working Group (FPTWG) Fish Passage modelling - the basic logic for evaluating connectivity is much the same as in previous versions.

Using the BC Freshwater Atlas as the mapping base:

1. Collect known 'natural' barriers to fish passage (waterfalls, subsurface flow, etc) and reference to the stream network
2. Model stream gradient barriers (where a stream slope is steeper than a given percentage for >=100m)
3. Using Known Fish Observations referenced to streams, remove natural barriers from 1 and 2 that are downstream of known observation(s)
4. Using gradient barriers above the threshold of the target species swimming ability, combine all resulting natural barriers and retain only those with no barriers downstream. All stream downstream of these barriers is termed 'potentially accessible' to the target species (ie, ignoring other barriers such as insufficent flow, temperature, etc a migratory fish of the given swimming ability could potentially access all these streams if no anthropogenic barrers are present)
5. Collect anthropogenic barriers, both known (dams, PSCIS barriers) and potential (mapped road/railway FWA stream intersections, ie culverts)
6. Prioritize anthropogenic barriers for assessment or remediation by reporting on how much potentially accessible stream is upstream of each barrier (and downstream of other anthropogenic barriers)

To improve prioritization of barriers for assessment and remediation, bcfishpass also includes basic 'intrinsic potential' habitat modelling for select species of interest (Bull Trout, Chinook, Chum, Coho, Pink, Sockeye, Steelhead, Westslope Cuthroat Trout). Intrinsic habitat potential (spawning and rearing) is based on:

1. Stream gradient
2. Stream discharge or stream channel width (as per data availability and user preference)
3. Various species-specific connectivitiy criteria (eg. sockeye spawn must be connected to rearing lakes)

Streams meeting the criteria for a given species are classified as spawning or rearing habitat, and the amount of potential spawning/rearing habitat disconnected by barriers is summarized.

General requirements

• bash
• GDAL (tested with v3.6.2)
• a PostgreSQL / PostGIS database (tested with v14/v3.3.2)
• Python (tested with v3.11.0)
• bcdata (v0.7.6)
• fwapg (v0.3.1)
• bcfishobs (v0.1.0)

Installation / Setup

bcfishpass is a collection of shell/sql/Python scripts - no installation is required. To download and use the latest:

git clone https://github.com/smnorris/bcfishpass.git
cd bcfishpass

Presuming PostgreSQL/PostGIS are already installed, the easiest way to install dependencies is likely via conda. A environment.yml is provided to set up the processing environment. Edit the environment variables in this file as required (to match your database connection parameters) and then create/activate the environment:

conda env create -f environment.yml
conda activate bcfishpass

Note that cdo is required for processing NetCDF discharge files, but this tool is not included in the conda environment. Install cdo separately (either from source or via homebrew).

If the database you are working with does not already exist, create it and create the required schema:

psql -c "CREATE DATABASE bcfishpass" postgres
psql -c "CREATE SCHEMA bcfishpass" bcfishpass

Once the database is created, load requirements fwapg and bcfishobs as per instructions in the respective projects.

Usage

Once you have fwapg and bcfishobs loaded to your database, bcfishpass processing is controlled by the Makefile.

To run:

make

It is possible to build individual components of the model separately (if their dependencies are met, see the Makefile). Refer to the various README files in the folders within the model folder for more info.

Credits

These tools are made possible by the work and funding of the following groups:

• BC Fish Passage Technical Working Group (FPTWG)
• Canadian Wildlife Federation (CWF)
• Pacific Salmon Foundation (PSF)
• New Graph Environment
• Hillcrest Geographics

With additional funding from:

• BC Fish and Wildlife Compensation Program (FWCP)
• Society for Ecosystem Restoration in Northern British Columbia (SERNBC)
• BC Salmon Restoration and Innovation Fund (BCSRIF)
• Canada Nature Fund for Aquatic Species at Risk (CNFASAR)