In NewGraphEnvironment/fish_passage_elk_2020_reporting_cwf: Does not matter.
Methods
Workflows for the project are categorized into planning, fish passage assessments, habitat confirmation assessments and reporting. All components leveraged the R programming language and environment for statistical computing to facilitate workflow tracking and reproducibility [@rcoreteam2020languageenvironment].
source('R/packages.R')
source('R/tables.R')
# or the development version
# devtools::install_github("rstudio/bookdown")
Planning
To identify priorities for crossing structure rehabilitation, background literature, fisheries information, PSCIS, Fish Habitat Model outputs modified from @fish_habitat_model and bcfishpass [@norrisBcfishpass2020] outputs were reviewed. The Fish Habitat Model was developed by the BC Ministry of Environment to provide estimates of the amount of fish habitat potentially accessible to fish upstream of crossing locations. The model calculates the average gradient of BC Freshwater Atlas stream network lines at minimum 100m long intervals starting from the downstream end of the streamline segment and working upstream. The network lines are broken into max gradient categories with new segments created when the average gradient of the stream lines exceeds user provided gradient thresholds.
bcfishpass is comprised of sql and python based shell script libraries that "generate a simple model of aquatic habitat connectivity by identifying natural barriers to fish passage (plus hydro dams that are not feasible to remediate) and classifying all streams not upstream of these barriers as 'potentially accessible'" [@norrisBcfishpass2020]. On potentially accessible streams, bcfishpass scripts "identify known barriers and additional anthropogenic features (primarily road/railway stream crossings, i.e. culverts) that are potentially barriers. To prioritize these features for assessment or remediation," the scripts "report on how much modelled potentially accessible aquatic habitat the barriers may obstruct. The model can be refined with known fish observations. Depending on the modelling scenario, all aquatic habitat downstream of a given fish observation can be classified as 'observed accessible', overriding any downstream barriers."
Following delineation of "non-fish habitat" with the Fish Habitat Model, the average gradient of each stream segment within habitat classified as below the 20% threshold was calculated and summed using bcfishpass to quantify upstream habitat potentially available for westslope cutthrout trout and facilitate stream line symbology based on stream morphology. bcfishpass summed average gradients of stream network line segments within six categories (0 - 3%, 3 - 5%, 5 - 8%, 8 - 15%, 15 - 20% and >20%) with these outputs further amalgamated to summarize and symbolize potentially accessible upstream habitat in five categories: riffle/cascade (0 - 3%), step-pool (5 - 8%), step-pool very steep (8-15%) and extremely steep (15 - 20%) (Table \@ref(tab:tablethreshaverage)). For each crossing location, the area of lake and wetland habitat upstream, species documented upstream and an estimate of watershed area was also collated using bcfishpass [@norrisBcfishpass2020], fwapg [@norris2020fwapg] and bcfishobs [@norris2020bcfishobs] to provide an indication of the potential quantity and quality of habitat potentially gained should fish passage be restored.
#threshold and average gradient table
table_thresh_average <- tibble::tibble(`Gradient` = c('0 - 3%', '5 - 8%', '8 - 15%', '15 - 20%', '>20%'),
`Channel Type` = c('Riffle and cascade pool', 'Step pool', 'Step pool - very steep', 'Step pool - extremely steep', 'WCT Unaccessible'))
table_thresh_average %>%
knitr::kable(booktabs = T, caption = 'Stream gradient categories (threshold and average) and associated channel type.') %>%
kableExtra::column_spec(column = 1:2, width_min = '2in') %>%
kableExtra::kable_styling(c("condensed", "basic"), full_width = T, font_size = font_set)
# table_thresh_average %>%
# my_kable(caption_text = 'Stream gradient categories (threshold and average) and associated channel type.')
# Although bull trout are known to populate habitat within and above stream reaches with gradients up to 30% areas upstream of gradients estimated at >20% for more than 100m were considered non-fish habitat if no fish observations had been documented upstream.
To prepare for Phase 1 and 2 assessments in the study area, past fish passage assessment reports for the Elk River watershed group were first reviewed to identify crossing structures not yet assessed or previously ranked as priorities for rehabilitation in @irvine2016ColumbiaBasin; @vastFishPassage2013 and @grainger2011FishPassage2011. To determine which of those crossings had not yet been assessed with Phase 1 and Phase 2 assessments we cross-referenced these reports with the Phase 2 report previously completed in the study area [@masseEKConfirmation2015; @vastresourcesolutionsinc_2013FishHabitat] and reviewed outputs from PSCIS as well as the Fish Habitat Model and bcfishpass. Outputs for modelled and PSCIS crossings (barriers and potential barriers) that met the following criteria underwent a detailed review to facilitate prioritization for Phase1 - Fish Passage Assessments and Phase 2 - Habitat Confirmations.
- Confirmed fish presence upstream of the PSCIS or modelled structure.
- Stream width documented as > 2.0m in PSCIS.
- Habitat value rated as "medium" or “high” in PSCIS.
- For PSCIS crossings: linear lengths of modelled upstream habitat <20% gradient for ≥1km
- For modelled crossings crossings: linear lengths of modelled upstream habitat <20% gradient for ≥2km and no anthropogenic barriers (including modelled potential stream crossing structures) documented downstream.
- Crossings located on streams classified as 3rd order or higher.
Fish Passage Assessments
In the field, crossings prioritized for follow-up were first assessed for fish passage following the procedures outlined in “Field Assessment for Determining Fish Passage Status of Closed Bottom Structures” [@fish_passage_assessments]. Crossings surveyed included closed bottom structures (CBS), open bottom structures (OBS) and crossings considered “other” (i.e. fords). Photos were taken at surveyed crossings and when possible included images of the road, crossing inlet, crossing outlet, crossing barrel, channel downstream and channel upstream of the crossing and any other relevant features. The following information was recorded for all surveyed crossings: date of inspection, crossing reference, crew member initials, Universal Transverse Mercator (UTM) coordinates, stream name, road name and kilometer, road tenure information, crossing type, crossing subtype, culvert diameter or span for OBS, culvert length or width for OBS. A more detailed “full assessment” was completed for all closed bottom structures and included the following parameters: presence/absence of continuous culvert embedment (yes/no), average depth of embedment, whether or not the culvert bed resembled the native stream bed, presence of and percentage backwatering, fill depth, outlet drop, outlet pool depth, inlet drop, culvert slope, average downstream channel width, stream slope, presence/absence of beaver activity, presence/absence of fish at time of survey, type of valley fill, and a habitat value rating. Habitat value ratings were based on channel morphology, flow characteristics (perennial, intermittent, ephemeral), fish migration patterns, the presence/absence of deep pools, un-embedded boulders, substrate, woody debris, undercut banks, aquatic vegetation and overhanging riparian vegetation (Table \@ref(tab:tab-hab-value)). For crossings determined to be potential barriers or barriers based on the data, a culvert fix and recommended diameter/span was proposed.
tab_habvalue %>%
knitr::kable(booktabs = T, caption = 'Habitat value criteria (Fish Passage Technical Working Group, 2011).') %>%
kableExtra::column_spec(column = 1, width_min = '1.5in') %>%
kableExtra::kable_styling(c("condensed", "basic"), full_width = T, font_size = font_set)
Barrier Scoring
Fish passage potential was determined for each stream crossing identified as a closed bottom structure as per @fish_passage_assessments. The combined scores from five criteria: depth and degree to which the structure is embedded, outlet drop, stream width ratio, culvert slope, and culvert length were used to screen whether each culvert was a likely barrier to some fish species and life stages (Table \@ref(tab:tab-barrier-scoring), Table \@ref(tab:tab-barrier-result). These criteria were developed based on data obtained from various studies and reflect an estimation for the passage of a juvenile salmon or small resident rainbow trout [@clarkinNationalInventoryAssessment2005 ;@bellFisheriesHandbookEngineering1991; @thompsonAssessingFishPassage2013].
\pagebreak
tab <- as_tibble(t(tab_barrier_scoring)) %>%
mutate(V4 = names(tab_barrier_scoring)) %>%
select(V4, everything()) %>%
janitor::row_to_names(1) %>% ##turn the table sideways
mutate(Risk = case_when(Risk == 'Value' ~ ' Value',
T ~ Risk))
tab %>%
my_kable(caption_text = 'Fish Barrier Risk Assessment (MoE 2011).')
tab_barrier_result %>%
knitr::kable(booktabs = T, caption = 'Fish Barrier Scoring Results (MoE 2011).') %>%
kableExtra::column_spec(column = 1:2, width_min = '2in') %>%
kableExtra::kable_styling(c("condensed", "basic"), full_width = T, font_size = font_set)
# tab_barrier_result %>%
# my_kable(caption_text = 'Fish Barrier Scoring Results (MoE 2011).')
Cost Benefit Analysis
Cost benefit analysis were conducted for each crossing determined to be a barrier based on estimates of the costs associated with fish passage remediation and the amount of habitat (linear length and area) that would potentially be made available by remedial works (habitat gain index).
Habitat Gain Index
The habitat gain index is the quantity of modelled habitat upstream of the subject crossing and represents an estimate of habitat gained with remediation of fish passage at the crossing. For this project, a gradient threshold between accessible and non-accessible habitat was set at 20% (for a minimum length of 100m) intended to represent the maximum gradient of which westslope cutthrout trout are likely to be able to migrate upstream. For Phase 1 assessments a "gross" value of habitat quantity output from bcfishpass was used to estimate the amount of habitat upstream of each crossing less than 20% gradient before either a falls of height >5m - as recorded in @ProvincialObstaclesFish or a section of stream with an average gradient >20% for >100m. This methodology gives a best case scenario of potential habitat gain that does not consider road stream structures upstream that may be barriers to migration. To determine area of habitat potentially gained the downstream channel width from the Phase 1 assessment was multiplied by the linear amount of habitat. For Phase 2 assessments, to provide a conservative estimate of habitat to be potentially gained by fish passage restoration, the amount of habitat upstream of each crossing was measured using the measure tool within QGIS [@QGIS_software] to estimate the amount of mainstem and stream segments > 1st order upstream of the crossing before any natural migration barriers or stream crossing structures that are located upstream and confirmed or potential barriers. To determine area of habitat potentially gained for Phase 2 assessments, the average upstream channel width (from the habitat confirmation assessment) was multiplied by the linear amount of habitat.
Cost Estimates
Potential options to remediate fish passage were selected from @fish_passage_assessments and included:
- Removal (RM) - Complete removal of the structure and deactivation of the road.
- Open Bottom Structure (OBS) - Replacement of the culvert with a bridge or other open bottom structure. For this project we considered bridges as the only viable option for OBS type based on consultation with FLNR road crossing engineering experts who reported a consistent history of footing scour and eventual failure on arch culvert structures both in the Kootenay and Skeena regions.
- Streambed Simulation (SS) - Replacement of the structure with a streambed simulation design culvert. Often achieved by embedding a culvert pipe or box culvert by 40% or more. Based on consultation with FLNR engineering experts, we considered crossings on streams with a channel width of <2m and a stream gradient of <8% as candidates for replacement with streambed simulations to limit the risk of erosion of embedding substrates.
- Additional Substrate Material (EM) - Add additional substrate to the culvert and/or downstream weir to embed culvert and reduce overall velocity/turbulence. Based on @fish_passage_assessments, this option was considered only when outlet drop = 0, culvert slope <1.0% and stream width ratio < 1.0.
- Backwater (BW) - Backwatering of the structure to reduce velocity and turbulence. Based on @fish_passage_assessments, this option was considered only when outlet drop < 0.3m, culvert slope <2.0%, stream width ratio < 1.2 and stream profiling indicates it would be effective.
Cost estimates for structure replacement with bridges and embedded culverts were generated based on the channel width, slope of the culvert, depth of fill, road class and road surface type. Road details were sourced from @flnrordForestTenureRoad2020 and @flnrordDigitalRoadAtlas2020 through bcfishpass. Interviews with Phil MacDonald, Engineering Specialist FLNR - Kootenay, Steve Page, Area Engineer - FLNR - Northern Engineering Group and Matt Hawkins - MoTi - Design Supervisor for Highway Design and Survey - Nelson were utilized to helped refine estimates.
Base costs for installation of bridges on forest service roads and permit roads with surfaces specified in provincial GIS road layers as rough and loose was estimated at \$12500/linear m and assumed that the road could be closed during construction. For streams with channel widths <2m, embedded culverts were reported as an effective solution with total installation costs estimated at $25k/crossing (pers. comm. Phil MacDonald, Steve Page). For larger streams, an additional 2m was added to the replacement structure's estimated span width for each 1m of channel width >5m. For crossings with large amounts of fill, the size of replacement structure was increase by 3m for each 1m of fill >3m to account for cutslopes to the stream at a 1.5:1 ratio. To account for road type, a multiplier table was also generated to estimate incremental cost increases with costs estimated for structure replacement on paved surfaces, railways and arterial/highways costing up to 40 times more than forest service roads due to expenses associate with design/engineering requirements, traffic control and paving. The cost multiplier table (Table \@ref(tab:tab-cost-mult)) does not take into account inflation over time and should be considered very approximate with refinement recommended for future projects.
\pagebreak
# print_tab_cost_mult(caption_text = 'Cost multiplier table based on road class and surface type.')
tab_cost_rd_mult_report %>%
my_kable(caption_text = 'Cost multiplier table based on road class and surface type.')
Habitat Confirmation Assessments
Following fish passage assessments, habitat confirmations were completed in accordance with procedures outlined in the document “A Checklist for Fish Habitat Confirmation Prior to the Rehabilitation of a Stream Crossing” [@confirmation_checklist_2011]. The main objective of the field surveys was to document upstream habitat quantity and quality and to determine if any other obstructions exist above or below the crossing. Habitat value was assessed based on channel morphology, flow characteristics (perennial, intermittent, ephemeral), the presence/absence of deep pools, un-embedded boulders, substrate, woody debris, undercut banks, aquatic vegetation and overhanging riparian vegetation. Criteria used to rank habitat value was based on guidelines in @confirmation_checklist_2011 (Table \@ref(tab:tab-hab-value)).
During habitat confirmations, to standardize data collected and facilitate submission of the data to provincial databases, information was collated on "Site Cards" [@resourcesinventorycommittee2001Reconnaissance20]. Habitat characteristics recorded included channel widths, wetted widths, residual pool depths, gradients, bankfull depths, stage, temperature, conductivity, pH, cover by type, substrate and channel morphology (among others). When possible, the crew surveyed downstream of the crossing to the point where fish presence had been previously confirmed and upstream to a minimum distance of 600m. Any potential obstacles to fish passage were inventoried with photos, physical descriptions and locations recorded on site cards. Surveyed routes were recorded with time-signatures on handheld GPS units.
Fish sampling was conducted at a subset of sites when biological data was considered to add significant value to the physical habitat assessment information. When possible, electrofishing was utilized within discrete site units both upstream and downstream of the subject crossing with electrofisher settings, water quality parameters (i.e. conductivity, temperature and ph), start location, length of site and wetted widths (average of a minimum of three) recorded. For each fish captured, fork length and species was recorded, with results included within the fish data submission spreadsheet. Fish information and habitat data will be submitted to the province under scientific fish collection permit CB20-611971.
r if(html_on)knitr::asis_output("<br>")
Reporting
This pdf report and an online interactive report were generated with bookdown [@bookdown2016] from Rmarkdown [@R-rmarkdown] documents processing raw data available at the New Graph Environment Github Site . In addition to numerous spatial layers sourced through the BC Data Catalogue, data inputs for this project can be sourced here and include:
-
Populated Fish Data Submission Spreadsheet Template - V 2.0, January 20, 2020
-
Populated pscis_assessment_template_v24.xls
-
Fish Habitat Model/bcfishpass outputs.
-
Custom Excel Spreadsheet detailing Phase 2 site:
- priority level for proceeding to design for replacement
- length of survey upstream and downstream
- a conservative estimate of mainstem habitat potentially available upstream of the crossing
- fish species confirmed as present upstream of the crossing
-
GPS tracks from field surveys.
-
NewGraphEnvironment/fish_passage_elk_2020_reporting_cwf documentation built on Jan. 20, 2024, 12:05 a.m.
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Methods
Workflows for the project are categorized into planning, fish passage assessments, habitat confirmation assessments and reporting. All components leveraged the R programming language and environment for statistical computing to facilitate workflow tracking and reproducibility [@rcoreteam2020languageenvironment].
source('R/packages.R') source('R/tables.R') # or the development version # devtools::install_github("rstudio/bookdown")
Planning
To identify priorities for crossing structure rehabilitation, background literature, fisheries information, PSCIS, Fish Habitat Model outputs modified from @fish_habitat_model and bcfishpass [@norrisBcfishpass2020] outputs were reviewed. The Fish Habitat Model was developed by the BC Ministry of Environment to provide estimates of the amount of fish habitat potentially accessible to fish upstream of crossing locations. The model calculates the average gradient of BC Freshwater Atlas stream network lines at minimum 100m long intervals starting from the downstream end of the streamline segment and working upstream. The network lines are broken into max gradient categories with new segments created when the average gradient of the stream lines exceeds user provided gradient thresholds.
bcfishpass is comprised of sql and python based shell script libraries that "generate a simple model of aquatic habitat connectivity by identifying natural barriers to fish passage (plus hydro dams that are not feasible to remediate) and classifying all streams not upstream of these barriers as 'potentially accessible'" [@norrisBcfishpass2020]. On potentially accessible streams, bcfishpass scripts "identify known barriers and additional anthropogenic features (primarily road/railway stream crossings, i.e. culverts) that are potentially barriers. To prioritize these features for assessment or remediation," the scripts "report on how much modelled potentially accessible aquatic habitat the barriers may obstruct. The model can be refined with known fish observations. Depending on the modelling scenario, all aquatic habitat downstream of a given fish observation can be classified as 'observed accessible', overriding any downstream barriers."
Following delineation of "non-fish habitat" with the Fish Habitat Model, the average gradient of each stream segment within habitat classified as below the 20% threshold was calculated and summed using bcfishpass to quantify upstream habitat potentially available for westslope cutthrout trout and facilitate stream line symbology based on stream morphology. bcfishpass summed average gradients of stream network line segments within six categories (0 - 3%, 3 - 5%, 5 - 8%, 8 - 15%, 15 - 20% and >20%) with these outputs further amalgamated to summarize and symbolize potentially accessible upstream habitat in five categories: riffle/cascade (0 - 3%), step-pool (5 - 8%), step-pool very steep (8-15%) and extremely steep (15 - 20%) (Table \@ref(tab:tablethreshaverage)). For each crossing location, the area of lake and wetland habitat upstream, species documented upstream and an estimate of watershed area was also collated using bcfishpass [@norrisBcfishpass2020], fwapg [@norris2020fwapg] and bcfishobs [@norris2020bcfishobs] to provide an indication of the potential quantity and quality of habitat potentially gained should fish passage be restored.
#threshold and average gradient table table_thresh_average <- tibble::tibble(`Gradient` = c('0 - 3%', '5 - 8%', '8 - 15%', '15 - 20%', '>20%'), `Channel Type` = c('Riffle and cascade pool', 'Step pool', 'Step pool - very steep', 'Step pool - extremely steep', 'WCT Unaccessible')) table_thresh_average %>% knitr::kable(booktabs = T, caption = 'Stream gradient categories (threshold and average) and associated channel type.') %>% kableExtra::column_spec(column = 1:2, width_min = '2in') %>% kableExtra::kable_styling(c("condensed", "basic"), full_width = T, font_size = font_set) # table_thresh_average %>% # my_kable(caption_text = 'Stream gradient categories (threshold and average) and associated channel type.') # Although bull trout are known to populate habitat within and above stream reaches with gradients up to 30% areas upstream of gradients estimated at >20% for more than 100m were considered non-fish habitat if no fish observations had been documented upstream.
To prepare for Phase 1 and 2 assessments in the study area, past fish passage assessment reports for the Elk River watershed group were first reviewed to identify crossing structures not yet assessed or previously ranked as priorities for rehabilitation in @irvine2016ColumbiaBasin; @vastFishPassage2013 and @grainger2011FishPassage2011. To determine which of those crossings had not yet been assessed with Phase 1 and Phase 2 assessments we cross-referenced these reports with the Phase 2 report previously completed in the study area [@masseEKConfirmation2015; @vastresourcesolutionsinc_2013FishHabitat] and reviewed outputs from PSCIS as well as the Fish Habitat Model and bcfishpass. Outputs for modelled and PSCIS crossings (barriers and potential barriers) that met the following criteria underwent a detailed review to facilitate prioritization for Phase1 - Fish Passage Assessments and Phase 2 - Habitat Confirmations.
- Confirmed fish presence upstream of the PSCIS or modelled structure.
- Stream width documented as > 2.0m in PSCIS.
- Habitat value rated as "medium" or “high” in PSCIS.
- For PSCIS crossings: linear lengths of modelled upstream habitat <20% gradient for ≥1km
- For modelled crossings crossings: linear lengths of modelled upstream habitat <20% gradient for ≥2km and no anthropogenic barriers (including modelled potential stream crossing structures) documented downstream.
- Crossings located on streams classified as 3rd order or higher.
Fish Passage Assessments
In the field, crossings prioritized for follow-up were first assessed for fish passage following the procedures outlined in “Field Assessment for Determining Fish Passage Status of Closed Bottom Structures” [@fish_passage_assessments]. Crossings surveyed included closed bottom structures (CBS), open bottom structures (OBS) and crossings considered “other” (i.e. fords). Photos were taken at surveyed crossings and when possible included images of the road, crossing inlet, crossing outlet, crossing barrel, channel downstream and channel upstream of the crossing and any other relevant features. The following information was recorded for all surveyed crossings: date of inspection, crossing reference, crew member initials, Universal Transverse Mercator (UTM) coordinates, stream name, road name and kilometer, road tenure information, crossing type, crossing subtype, culvert diameter or span for OBS, culvert length or width for OBS. A more detailed “full assessment” was completed for all closed bottom structures and included the following parameters: presence/absence of continuous culvert embedment (yes/no), average depth of embedment, whether or not the culvert bed resembled the native stream bed, presence of and percentage backwatering, fill depth, outlet drop, outlet pool depth, inlet drop, culvert slope, average downstream channel width, stream slope, presence/absence of beaver activity, presence/absence of fish at time of survey, type of valley fill, and a habitat value rating. Habitat value ratings were based on channel morphology, flow characteristics (perennial, intermittent, ephemeral), fish migration patterns, the presence/absence of deep pools, un-embedded boulders, substrate, woody debris, undercut banks, aquatic vegetation and overhanging riparian vegetation (Table \@ref(tab:tab-hab-value)). For crossings determined to be potential barriers or barriers based on the data, a culvert fix and recommended diameter/span was proposed.
tab_habvalue %>% knitr::kable(booktabs = T, caption = 'Habitat value criteria (Fish Passage Technical Working Group, 2011).') %>% kableExtra::column_spec(column = 1, width_min = '1.5in') %>% kableExtra::kable_styling(c("condensed", "basic"), full_width = T, font_size = font_set)
Barrier Scoring
Fish passage potential was determined for each stream crossing identified as a closed bottom structure as per @fish_passage_assessments. The combined scores from five criteria: depth and degree to which the structure is embedded, outlet drop, stream width ratio, culvert slope, and culvert length were used to screen whether each culvert was a likely barrier to some fish species and life stages (Table \@ref(tab:tab-barrier-scoring), Table \@ref(tab:tab-barrier-result). These criteria were developed based on data obtained from various studies and reflect an estimation for the passage of a juvenile salmon or small resident rainbow trout [@clarkinNationalInventoryAssessment2005 ;@bellFisheriesHandbookEngineering1991; @thompsonAssessingFishPassage2013].
\pagebreak
tab <- as_tibble(t(tab_barrier_scoring)) %>% mutate(V4 = names(tab_barrier_scoring)) %>% select(V4, everything()) %>% janitor::row_to_names(1) %>% ##turn the table sideways mutate(Risk = case_when(Risk == 'Value' ~ ' Value', T ~ Risk)) tab %>% my_kable(caption_text = 'Fish Barrier Risk Assessment (MoE 2011).')
tab_barrier_result %>% knitr::kable(booktabs = T, caption = 'Fish Barrier Scoring Results (MoE 2011).') %>% kableExtra::column_spec(column = 1:2, width_min = '2in') %>% kableExtra::kable_styling(c("condensed", "basic"), full_width = T, font_size = font_set) # tab_barrier_result %>% # my_kable(caption_text = 'Fish Barrier Scoring Results (MoE 2011).')
Cost Benefit Analysis
Cost benefit analysis were conducted for each crossing determined to be a barrier based on estimates of the costs associated with fish passage remediation and the amount of habitat (linear length and area) that would potentially be made available by remedial works (habitat gain index).
Habitat Gain Index
The habitat gain index is the quantity of modelled habitat upstream of the subject crossing and represents an estimate of habitat gained with remediation of fish passage at the crossing. For this project, a gradient threshold between accessible and non-accessible habitat was set at 20% (for a minimum length of 100m) intended to represent the maximum gradient of which westslope cutthrout trout are likely to be able to migrate upstream. For Phase 1 assessments a "gross" value of habitat quantity output from bcfishpass was used to estimate the amount of habitat upstream of each crossing less than 20% gradient before either a falls of height >5m - as recorded in @ProvincialObstaclesFish or a section of stream with an average gradient >20% for >100m. This methodology gives a best case scenario of potential habitat gain that does not consider road stream structures upstream that may be barriers to migration. To determine area of habitat potentially gained the downstream channel width from the Phase 1 assessment was multiplied by the linear amount of habitat. For Phase 2 assessments, to provide a conservative estimate of habitat to be potentially gained by fish passage restoration, the amount of habitat upstream of each crossing was measured using the measure tool within QGIS [@QGIS_software] to estimate the amount of mainstem and stream segments > 1st order upstream of the crossing before any natural migration barriers or stream crossing structures that are located upstream and confirmed or potential barriers. To determine area of habitat potentially gained for Phase 2 assessments, the average upstream channel width (from the habitat confirmation assessment) was multiplied by the linear amount of habitat.
Cost Estimates
Potential options to remediate fish passage were selected from @fish_passage_assessments and included:
- Removal (RM) - Complete removal of the structure and deactivation of the road.
- Open Bottom Structure (OBS) - Replacement of the culvert with a bridge or other open bottom structure. For this project we considered bridges as the only viable option for OBS type based on consultation with FLNR road crossing engineering experts who reported a consistent history of footing scour and eventual failure on arch culvert structures both in the Kootenay and Skeena regions.
- Streambed Simulation (SS) - Replacement of the structure with a streambed simulation design culvert. Often achieved by embedding a culvert pipe or box culvert by 40% or more. Based on consultation with FLNR engineering experts, we considered crossings on streams with a channel width of <2m and a stream gradient of <8% as candidates for replacement with streambed simulations to limit the risk of erosion of embedding substrates.
- Additional Substrate Material (EM) - Add additional substrate to the culvert and/or downstream weir to embed culvert and reduce overall velocity/turbulence. Based on @fish_passage_assessments, this option was considered only when outlet drop = 0, culvert slope <1.0% and stream width ratio < 1.0.
- Backwater (BW) - Backwatering of the structure to reduce velocity and turbulence. Based on @fish_passage_assessments, this option was considered only when outlet drop < 0.3m, culvert slope <2.0%, stream width ratio < 1.2 and stream profiling indicates it would be effective.
Cost estimates for structure replacement with bridges and embedded culverts were generated based on the channel width, slope of the culvert, depth of fill, road class and road surface type. Road details were sourced from @flnrordForestTenureRoad2020 and @flnrordDigitalRoadAtlas2020 through bcfishpass. Interviews with Phil MacDonald, Engineering Specialist FLNR - Kootenay, Steve Page, Area Engineer - FLNR - Northern Engineering Group and Matt Hawkins - MoTi - Design Supervisor for Highway Design and Survey - Nelson were utilized to helped refine estimates.
Base costs for installation of bridges on forest service roads and permit roads with surfaces specified in provincial GIS road layers as rough and loose was estimated at \$12500/linear m and assumed that the road could be closed during construction. For streams with channel widths <2m, embedded culverts were reported as an effective solution with total installation costs estimated at $25k/crossing (pers. comm. Phil MacDonald, Steve Page). For larger streams, an additional 2m was added to the replacement structure's estimated span width for each 1m of channel width >5m. For crossings with large amounts of fill, the size of replacement structure was increase by 3m for each 1m of fill >3m to account for cutslopes to the stream at a 1.5:1 ratio. To account for road type, a multiplier table was also generated to estimate incremental cost increases with costs estimated for structure replacement on paved surfaces, railways and arterial/highways costing up to 40 times more than forest service roads due to expenses associate with design/engineering requirements, traffic control and paving. The cost multiplier table (Table \@ref(tab:tab-cost-mult)) does not take into account inflation over time and should be considered very approximate with refinement recommended for future projects.
\pagebreak
# print_tab_cost_mult(caption_text = 'Cost multiplier table based on road class and surface type.') tab_cost_rd_mult_report %>% my_kable(caption_text = 'Cost multiplier table based on road class and surface type.')
Habitat Confirmation Assessments
Following fish passage assessments, habitat confirmations were completed in accordance with procedures outlined in the document “A Checklist for Fish Habitat Confirmation Prior to the Rehabilitation of a Stream Crossing” [@confirmation_checklist_2011]. The main objective of the field surveys was to document upstream habitat quantity and quality and to determine if any other obstructions exist above or below the crossing. Habitat value was assessed based on channel morphology, flow characteristics (perennial, intermittent, ephemeral), the presence/absence of deep pools, un-embedded boulders, substrate, woody debris, undercut banks, aquatic vegetation and overhanging riparian vegetation. Criteria used to rank habitat value was based on guidelines in @confirmation_checklist_2011 (Table \@ref(tab:tab-hab-value)).
During habitat confirmations, to standardize data collected and facilitate submission of the data to provincial databases, information was collated on "Site Cards" [@resourcesinventorycommittee2001Reconnaissance20]. Habitat characteristics recorded included channel widths, wetted widths, residual pool depths, gradients, bankfull depths, stage, temperature, conductivity, pH, cover by type, substrate and channel morphology (among others). When possible, the crew surveyed downstream of the crossing to the point where fish presence had been previously confirmed and upstream to a minimum distance of 600m. Any potential obstacles to fish passage were inventoried with photos, physical descriptions and locations recorded on site cards. Surveyed routes were recorded with time-signatures on handheld GPS units.
Fish sampling was conducted at a subset of sites when biological data was considered to add significant value to the physical habitat assessment information. When possible, electrofishing was utilized within discrete site units both upstream and downstream of the subject crossing with electrofisher settings, water quality parameters (i.e. conductivity, temperature and ph), start location, length of site and wetted widths (average of a minimum of three) recorded. For each fish captured, fork length and species was recorded, with results included within the fish data submission spreadsheet. Fish information and habitat data will be submitted to the province under scientific fish collection permit CB20-611971.
r if(html_on)knitr::asis_output("<br>")
Reporting
This pdf report and an online interactive report were generated with bookdown [@bookdown2016] from Rmarkdown [@R-rmarkdown] documents processing raw data available at the New Graph Environment Github Site . In addition to numerous spatial layers sourced through the BC Data Catalogue, data inputs for this project can be sourced here and include:
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Populated Fish Data Submission Spreadsheet Template - V 2.0, January 20, 2020
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Populated pscis_assessment_template_v24.xls
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Fish Habitat Model/bcfishpassoutputs. -
Custom Excel Spreadsheet detailing Phase 2 site:
- priority level for proceeding to design for replacement
- length of survey upstream and downstream
- a conservative estimate of mainstem habitat potentially available upstream of the crossing
- fish species confirmed as present upstream of the crossing
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GPS tracks from field surveys.
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