CCIRA Fish distribution and abundance model

Coordinated by the Pacific Salmon Foundation in support of salmon restoration work by Heiltsuk, Kitasoo Xai’xais, Nuxalk, and Wuikinuxv Nations, these scripts adapt fish distribution / abundance models developed for the Haida Gwaii by Gowgaia (2009) to the CCIRA study area using current tools, methods and data.

Data prep

1. Determine BC Freshwater Atlas watershed groups present within the study area: ATNA,BELA,KHTZ,KITL,KLIN,KTSU,LDEN,LRDO,NASC,NECL,NIEL,OWIK

2. Reference Pacific Salmon Explorer known spawning streams to BC Freshwater Atlas stream network and load to bcfishpass, discarding modelled natural barriers downstream of known habitat

3. Perform basic QA checks of observations and barriers present in study area from all sources

4. Download NuSEDS Conservation_Unit_System_Sites.csv (linking NuSEDS to FWA streams), discarding all columns other than pop_id and fwa_watershed_cde and saving as data/nuseds_sites.csv

Model method

1. Generate three bcfishpass access models using these natural barrier assumptions:

   • Salmon (CH/CM/CO/PK/SK): falls >5m, subsurface flow, 15% gradient for >= 100m
   • Steelhead (ST): falls >5m, subsurface flow, 20% gradient for >= 100m
   • Resident (CT/DV/RB): falls >5m, subsurface flow, 25% gradient for >= 100m

2. Extend the bcfishpass accessibility model with the Gowgaia stream classifications:

   Anadromous (CH/CM/CO/PK/SK)

   • KNOWN fish presence: stream downstream of known observation(s) for given species
   • INFERRED fish presence: stream upstream of known observations and downstream of known/modelled barriers
   • POTENTIAL anadromous fish presence: unsurveyed streams from stream mouth to first known/modelled barrier

   Resident (CT/DV/RB)

   • KNOWN fish presence: stream downstream of known observation(s) for given species
   • INFERRED fish presence: stream upstream of known observations and downstream of known/modelled barriers
   • POTENTIAL resident fish presence: unsurveyed streams from stream mouth to first known/modelled barrier and below the elevation of the highest observation of the species in the study area
   • POTENTIAL_BARRIER_DNSTR all stream upstream of known/modelled barriers, not downstream of observations, and below the elevation of the highest observation of the species in the study area

   Elevation maximums:

   • CT: 1508m
   • DV: 1005m
   • RB: 1831m

3. Extend the above fish accessibility model with an adaptation of the Gowgaia abundance classification:

   Anadromous

   For all KNOWN,INFERRED,POTENTIAL streams, classify as follows:

   • FEW_SALMON: magnitude < 5
   • SOME_SALMON: magnitude >= 5, < 40
   • MANY_SALMON: magnitude >= 40
   • MOST_SALMON: where a stream is noted as a top ten producer (as documented below)

   Top 10 producer streams in the CCIRA study area were derived from the New Salmon Escapement Database System (NuSEDS) using the MAX_ESTIMATE field (removing zeros) for each POP_ID for the period 1954-2021 (as per Central Coast escapement estimate guidance in English et al. 2016). The geometric mean of MAX_ESTIMATE for each POP_ID was then ranked from high to low by seven salmon species/populations (Chinook, Coho, Pink even, Pink odd, Chum, Sockeye lake, Sockeye river). NuSEDS data for steelhead over this period was too sparse to define data-driven estimates of abundance to override stream magnitude-based estimates of steelhead population abundance.

   Resident

   For streams modelled as inaccessible to salmon:

   • RESIDENT_FISH_ONLY: streams with no known/modelled barrier to resident fish downstream
   • RESIDENT_FISH_ONLY_BARRIER_DNSTR: streams with known/modelled barrier to resident fish downstream

   Output dataset includes the column upstream_area_ha to enable further adjustments to this classification. Note that upstream_area_ha includes all watersheds upstream of a stream with a given watershed code, but does not include the area of the watershed(s) having the equivalent watershed code as the stream.

Setup

Install the following tools (for the August 2023 deliverable, the noted versions were used:

• fwapg : [v0.5.1]
• bcfishobs : [v0.1.3]
• bcfishpass : [v0.1.dev5]

Note: Scripts will require minor adjustments if re-running with the latest bcfishpass models.

Run scripts

1. Build the bcfishpass database using the CCIRA parameters and generate these access models for the above noted watershed groups (see instructions in bcfishpass):

   • salmon
   • resident
   • steelhead

2. Process NuSEDS, apply the Gowgaia model and generate deliverables:

    ./ccira.sh
   

Model output is dumped to /outputs/ccira.gpkg.zip Streams with abundance upgraded to MOST_SALMON based on NuSEDs productivity ranking (and their original, magnitude based abundance values) are noted in upgraded_streams.csv

Data definitions

Note that the salmon species codes used by bcfishpass and PSF/NuSEDs (and in these outputs) do not quite match.
BC fish observations and bcfishpass models do not distinguish between even/odd Pink or lake/river Sockeye.

species	BC/bcfishpass	PSF/NuSEDS
Chinook	CH	CN
Chum	CM	CM
Coho	CO	CO
Pink (even)	PK	PKE
Pink (odd)	PK	PKO
Sockeye (lake)	SK	SEL
Sockeye (river)	SK	SEL

fish_distribution_model

Column	Type	Description
ccira_id	integer	ccira model output unique identifier
segmented_stream_id	text	bcfishpass unique stream segment id
linear_feature_id	bigint	FWA stream segment identifier
blue_line_key	integer	Uniquely identifies a single flow line such that a main channel and a secondary channel with the same watershed code would have different blue line keys (the Fraser River and all side channels have different blue line keys).
edge_type	integer	A 4 digit numeric code used by the Freshwater Atlas to identify the various types of water network linear features. eg. 1050.
downstream_route_measure	double precision	The distance, in meters, along the route from the mouth of the route to the feature. This distance is measured from the mouth of the containing route to the downstream end of the feature.
upstream_route_measure	double precision	The distance, in meters, along the route from the mouth of the route to upstream end of the feature. This distance is measured from the mouth of the containing route to the upstream end of the feature.
gnis_name	character varying(80)	The BCGNIS (BC Geographical Names Information System) name associated with the GNIS feature id (an English name was used where available, otherwise another language was selected).
wscode	text	Abbreviated version of source FWA watershed code
localcode	text	Abbreviated version of source local watershed code
stream_order	integer	The calculated modified Strahler order.
stream_magnitude	integer	The calculated magnitude.
watershed_group_code	text	The watershed group code associated with the stream.
upstream_area_ha	double precision	Area upstream of the stream(s) with the given local watershed code. NOTE - does not include the area of the watershed(s) in which the streams lie.
barriers_ch_cm_co_pk_sk_dnstr	text	Natural barriers to salmon downstream
barriers_dams_dnstr	text	CABD dams noted as barriers downstream
barriers_ct_dv_rb_dnstr	text	Natural barriers to cutthroat, dolly varden, rainbow downstream
obsrvtn_species_codes_upstr	text	Species codes of known observations upstream (for species of interest only, within the same watershed group as stream)
species_codes_dnstr	text	Species codes of known observations downstream (for species of interest only, within the same watershed group as stream)
model_ch	text	Fish distribution model for Chinoook (see above for method and codes)
model_cm	text	Fish distribution model for Chum (see above for method and codes)
model_co	text	Fish distribution model for Coho (see above for method and codes)
model_pk	text	Fish distribution model for Pink (see above for method and codes)
model_sk	text	Fish distribution model for Sockeye (see above for method and codes)
model_st	text	Fish distribution model for Steelhead (see above for method and codes)
model_ct	text	Fish distribution model for Cutthroat Trout (see above for method and codes)
model_dv	text	Fish distribution model for Dolly Varden Char (see above for method and codes)
model_rb	text	Fish distribution model for Rainbow Trout (see above for method and codes)
nuseds_top10_cm	boolean	Identifies if stream is one of top 10 producers for study area for CM
nuseds_top10_cn	boolean	Identifies if stream is one of top 10 producers for study area for CN
nuseds_top10_co	boolean	Identifies if stream is one of top 10 producers for study area for CO
nuseds_top10_pke	boolean	Identifies if stream is one of top 10 producers for study area for PKE
nuseds_top10_pko	boolean	Identifies if stream is one of top 10 producers for study area for PKO
nuseds_top10_sel	boolean	Identifies if stream is one of top 10 producers for study area for SEL
nuseds_top10_ser	boolean	Identifies if stream is one of top 10 producers for study area for SER
abundance	text	Abundance/fishyness index - based on distribution model, magnitude, escapement
geom	geometry(LineStringZM,3005)	Stream segment geometry

barriers_salmon/barriers_steelhead/barriers_resident

Natural barriers to noted species.

Column	Type	Description
barriers__id	text	unique identifier
barrier_type	text	Natural barrier type (falls, gradient barrier, etc)
barrier_name	text	Name of barrier, where applicable
linear_feature_id	integer	See FWA documentation
blue_line_key	integer	See FWA documentation
watershed_key	integer	See FWA documentation
downstream_route_measure	double precision	See FWA documentation
wscode	ltree	Abbreviated version of source FWA watershed code
localcode	ltree	Abbreviated version of source local watershed code
watershed_group_code	character varying(4)	See FWA documentation
total_network_km	double precision	Total length of stream upstream of barrier, useful for barrier QA
geom	geometry(Point,3005)	Geometry

dams

All dams in study area, taken from Canadian Aquatic Barrier Database (CABD), as documented here

Column	Type	Description
dam_id	text	Source CABD unique identifier
barrier_status	text	Derived from CABD passability_status_code
dam_name	text	CABD dam_name_en
dam_height	text	CABD dam_height_m
dam_owner	text	CABD owner
dam_use	text	CABD dam_use
dam_operating_status	text	CABD operating_status
linear_feature_id	integer	See FWA documentation
blue_line_key	integer	See FWA documentation
watershed_key	integer	See FWA documentation
downstream_route_measure	double precision	See FWA documentation
wscode	text	See FWA documentation
localcode	text	See FWA documentation
watershed_group_code	text	See FWA documentation
gnis_name	text	See FWA documentation
stream_order	integer	See FWA documentation
stream_magnitude	integer	See FWA documentation
geom	geometry(Point,3005)	Geometry

observations

From Known Fish Observations via bcfishobs

Column	Type	Description
fish_observation_point_id	integer	DataBC provided unique ID (does not remain constant over time)
fish_obsrvtn_event_id	bigint	bcfishpass internal unique id
linear_feature_id	bigint	See FWA documentation
blue_line_key	integer	See FWA documentation
wscode_ltree	ltree	Abbreviated version of source FWA watershed code
localcode_ltree	ltree	Abbreviated version of source FWA watershed code
downstream_route_measure	double precision	See FWA documentation
watershed_group_code	character varying(4)	See FWA documentation
species_code	text	See observation documentation
observation_date	date	See observation documentation
activity_code	character varying(100)	See observation documentation
activity	character varying(300)	See observation documentation
life_stage_code	character varying(100)	See observation documentation
life_stage	character varying(300)	See observation documentation
acat_report_url	character varying(254)	See observation documentation
geom	geometry(PointZM,3005)	Geometry