In NewGraphEnvironment/fish_passage_bulkley_2020_reporting: Does not matter.

knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
source('R/packages.R')
source('R/functions.R')
source('R/functions-phase2.R')
source('R/tables-phase2.R')
source('R/tables.R')
source('R/extract-fish.R')
source('R/functions-fish.R')

my_site <- 123445
my_site2 <- 123446
my_site3 <- 123463

# mbcfp1 <- my_bcfishpass(site = my_site)
# mbcfp2 <- my_bcfishpass(site = my_site2)

##see species downstream
# my_fish_sp(col_to_pull = quo(observedspp_dnstr))

r appendix_title2()

Site Location {-}

PSCIS crossing r as.character(my_site) is located on r my_pscis_info() %>% pull(stream_name) on r my_overview_info() %>% pull(road_name) approximately 2km south of Telkwa, BC. The highway is located approximately r my_priority_info(loc = 'ds') %>% pull(survey_length_m)m upstream from the confluence with the Bulkley River. PSCIS crossing r as.character(my_site2) is located on r my_overview_info(site = my_site2) %>% pull(road_name) approximately r my_priority_info(loc = 'us') %>% pull(survey_length_m)m upstream of r my_overview_info() %>% pull(road_name). Both crossings are the responsibility of the Ministry of Transportation and Infrastructure.

Background {-}

At crossing r as.character(my_site), r my_pscis_info() %>% pull(stream_name) is a r my_bcfishpass() %>% pull(stream_order) %>% english::ordinal() order stream with a watershed area upstream of the crossing of approximately r round(my_bcfishpass() %>% pull(watershed_upstr_ha)/100,1)km^2^. The elevation of the watershed ranges from 1000m to 520m at the highway. Numerous fish species have been documented upstream of both crossings including r my_fish_sp() [@data_fish_obs].

Tyhee Lake is located approximatley 800m upstream of crossing r as.character(my_site2). Tyhee Lake has a surface area of 3.18km^2^, a mean depth of 11.1m, a maximum depth of 22.2m and a mean water retention time estimated at 5 years [@reavie_etal2000Paleolimnologicalanalyses]. @reavie_etal2000Paleolimnologicalanalyses report that Tyhee Lake was a naturally productive system that has experienced moderate eutrophication over time due to adjacent land use. In response to concerns expressed by the Tyhee Lake Protection Society, a management plan was drafted for the lake in 1999 with the objective of slowing down or eliminating eutrophication [@rysavy_etal1999TyheeLake]. Fish passage issues at the highway have also been highlighted by the protection society in the past [@hatlevik1992LetterCommunications]. Cutthrout trout have been observed unsuccessfully attempting to ascend into the culvert at the highway (pers comm Mike Ridsdale, Environmental Assessment Coordinator - Office of the Wet'suwet'en). Tyhee Lake has been stocked with rainbow trout since 1955, with stocking events occuring annual since 1990 [@bcministryofenvironment2021FishInventories].

There are five tributaries that flow into the lake from the east and north with all systems containing crossings previously inventoried as barriers or potential barriers.

# Tyhee Lake is one of two lakes in the province known to contain giant pygmy whitefish. Although ranked by COSEWIC as not at risk [@sereda_etal2017COSEWICassessment], and not listed as at risk on the B.C. Conservation Data Centre website [@b_c_conservationdatacentre2021BCSpecies], this species is noted as threatened (red-listed) in @cannings_ptolemy1998RareFreshwater due to limited distribution and eutrophication.

PSCIS stream crossings r as.character(my_site) and r as.character(my_site2) were rated high priorities for follow up by @wilson_rabnett2007FishPassage and @irvine2018AnalysisPriority due to significant quantities of lake habitat upstream and historical records of steelhead and salmon upstream. A map of the watershed is provided in mapsheet attachment r my_bcfishpass() %>% pull(dbm_mof_50k_grid).

Stream Characteristics at Crossings `r as.character(my_site)` and `r as.character(my_site2)` {-}

At the time of the survey, crossing r as.character(my_site) on r my_overview_info() %>% pull(road_name) was un-embedded, non-backwatered and a barrier to upstream fish passage. Downcutting of the downstream area was apparent and due likely to high flow velocities through the pipes during elevated flow events. The pipes were r my_pscis_info() %>% pull(diameter_or_span_meters)m in diameter with lengths of r my_pscis_info() %>% pull(length_or_width_meters)m, a culvert slope of r my_pscis_info() %>% pull(culvert_slope_percent)%, a stream width ratio of r my_pscis_info() %>% pull(stream_width_ratio) and an outlet drop of r my_pscis_info() %>% pull(outlet_drop_meters)m (Table \@ref(tab:tab-culvert-123445)). Water temperature was r my_habitat_info3(row = 'temperature c')$^\circ$C, pH was r my_habitat_info3(row = 'p h') and conductivity was r my_habitat_info3(row = 'conductivity m s cm')uS/cm.

Crossing r as.character(my_site2) on r my_overview_info(site = my_site2) %>% pull(road_name) was un-embedded, 10% backwatered and classified as a barrier to upstream fish passage. The pipe was r my_pscis_info(site = my_site2) %>% pull(diameter_or_span_meters)m in diameter with a length of r my_pscis_info(site = my_site2) %>% pull(length_or_width_meters)m, a culvert slope of r my_pscis_info(site = my_site2) %>% pull(culvert_slope_percent)%, a stream width ratio of r my_pscis_info(site = my_site2) %>% pull(stream_width_ratio) and an outlet drop of r my_pscis_info(site = my_site2) %>% pull(outlet_drop_meters)m (Table \@ref(tab:tab-culvert-123446)).

##this is useful to get some comments for the report
hab_site %>% filter(site == my_site2 & location == 'us') %>% pull(comments)
my_priority <-  my_priority_info()

# north road assessment file here https://a100.gov.bc.ca/pub/acat/public/viewReport.do?reportId=18959

Stream Characteristics Downstream of `r as.character(my_site)` {-}

The stream was surveyed downstream from the culvert for r my_priority_info(loc = 'ds') %>% pull(survey_length_m)m to the confluence with the Bulkley River r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-123445-01) - \\@ref(fig:photo-123445-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-123445-d01))")). Flows were very low at the time of the survey and the stream channel went subsurface near the Bulkley River floodplain. Overall, total cover amount was rated as r my_habitat_info2(loc = 'ds') %>% filter(rowname == 'total cover') %>% pull(v) with r my_habitat_info2(loc = 'ds') %>% filter(v == 'dominant') %>% pull(rowname) dominant. Cover was also present as r my_habitat_info2(loc = 'ds') %>% filter(v == 'sub-dominant') %>% pull(rowname) %>% knitr::combine_words() (Table \@ref(tab:tab-habitat-summary-123445)). The average channel width was r my_habitat_info3(loc = 'ds', row = 'avg channel width m')m, the average wetted width was r my_habitat_info3(loc = 'ds', row = 'avg wetted width m')m and the average gradient was r my_habitat_info3(loc = 'ds', row = 'average gradient percent')%. The dominant substrate was r my_habitat_info3(loc = 'ds', row = "bed material dominant") with r my_habitat_info3(loc = 'ds', row = "bed material subdominant") subdominant. Some gravels suitable for spawning were observed and unidentified fry/juvenile fish (3 @ 50mm, and 1 @ 90mm) were observed. Habitat value was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) as it was considered an important migration corridor with moderate value habitat for fry/juvenile salmonid rearing.

Stream Characteristics Upstream of `r as.character(my_site)` and downstream of `r as.character(my_site2)`{-}

The stream was surveyed from r as.character(my_site) for r my_priority_info(loc = 'us') %>% pull(survey_length_m)m to r as.character(my_site2)``r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-123445-03) - \\@ref(fig:photo-123445-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-123445-d02))")). Within the area surveyed, total cover amount was rated as r my_habitat_info2(sit = my_site, loc = 'us') %>% filter(rowname == 'total cover') %>% pull(v) with r my_habitat_info2(sit = my_site, loc = 'us') %>% filter(v == 'dominant') %>% pull(rowname) dominant. Cover was also present as r my_habitat_info2(sit = my_site, loc = 'us') %>% filter(v == 'sub-dominant') %>% pull(rowname) %>% knitr::combine_words() (Table \@ref(tab:tab-habitat-summary-123445)). The average channel width was r my_habitat_info3(sit = my_site, loc = 'us', row = 'avg channel width m')m, the average wetted width was r my_habitat_info3(sit = my_site, loc = 'us', row = 'avg wetted width m')m and the average gradient was r my_habitat_info3(sit = my_site, loc = 'us', row = 'average gradient percent')%. Water within the narrow channel was noted as often stagnant with aquatic vegetation present throughout. Some riparian disturbance by adjacent livestock was also noted. Although, habitat value was considered of low value for rearing and spawning it was rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) overall as it was considered an important migration corridor providing access to the lake.

Stream Characteristics Upstream of `r as.character(my_site2)`{-}

r my_pscis_info() %>% pull(stream_name) was surveyed upstream from r as.character(my_site2) for r my_priority_info(sit = my_site2, loc = 'us') %>% pull(survey_length_m)m with the survey discontinued due to difficult survey conditions within the wetland type habitat and the presence of fenced private land r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-123445-05) - \\@ref(fig:photo-123445-06))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-123445-d03))")). Within the area surveyed, total cover amount was rated as r my_habitat_info2(sit = my_site2, loc = 'us') %>% filter(rowname == 'total cover') %>% pull(v) with r my_habitat_info2(sit = my_site2, loc = 'us') %>% filter(v == 'dominant') %>% pull(rowname) dominant. Cover was also present as r my_habitat_info2(sit = my_site2, loc = 'us') %>% filter(v == 'sub-dominant') %>% pull(rowname) %>% knitr::combine_words() (Table \@ref(tab:tab-habitat-summary-123445)). The average channel width was r my_habitat_info3(sit = my_site2, loc = 'us', row = 'avg channel width m')m, the average wetted width was r my_habitat_info3(sit = my_site2, loc = 'us', row = 'avg wetted width m')m and the average gradient was r my_habitat_info3(sit = my_site2, loc = 'us', row = 'average gradient percent')%. Beaver activity was prevalent in the area surveyed and there was a large agricultural field located on the right bank of the stream. Habitat value was rated as r my_priority_info(sit = my_site2, loc = 'us') %>% pull(hab_value) as it was considered an important migration corridor providing access to the lake.

Crossing 123463 is located on Victor Creek and Tyhee Lake Road. Victor Creek flows into the east side of Tyhee Lake approximately 1.7km upstream from the mouth. At the time of the survey, the round culvert appeared to have been recently replaced. The structure was un-embedded, non-backwatered and considered a barrier to upstream fish passage according to the provincial protocol. The pipe was r my_pscis_info(dat = pscis_all, site = my_site3) %>% pull(diameter_or_span_meters)m in diameter with a length of r my_pscis_info(dat = pscis_all, site = my_site3) %>% pull(length_or_width_meters)m, a culvert slope of r my_pscis_info(dat = pscis_all, site = my_site3) %>% pull(culvert_slope_percent)%, a stream width ratio of r my_pscis_info() %>% pull(stream_width_ratio) and an outlet drop of r my_pscis_info(dat = pscis_all, site = my_site3) %>% pull(outlet_drop_meters)m (Table \@ref(tab:tab-culvert-123463)).

Table \@ref(tab:tab-culvert-bcfp-123445) r text_ref_tab_summary_bcfp() Table \@ref(tab:tab-culvert-bcfp-123446) r text_ref_tab_summary_bcfp(site = my_site2)

Structure Remediation and Cost Estimate {-}

Structure replacement with bridges for r as.character(my_site) (r my_pscis_info() %>% pull(recommended_diameter_or_span_meters)m span) and r as.character(my_site2) (r my_pscis_info(site = my_site2) %>% pull(recommended_diameter_or_span_meters)m span) could be considered to provide access to the habitat located upstream. An estimate of cost for replacement of r as.character(my_site) is \$r format(my_cost_estimate() %>% pull(cost_est_1000s) * 1000, big.mark = ',') and \$r format(my_cost_estimate(site = my_site2) %>% pull(cost_est_1000s) * 1000, big.mark = ',') for r as.character(my_site2).

Conclusion {-}

As Tyhee Lake is located upstream of both crossings surveyed with steelhead and mulitple salmon species historically recorded upstream of the highway, the restoration of fish passage at r as.character(my_site) was rated as a r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) priority for proceeding to design for replacement. Although classified as a barrier to upstream fish passage according to the provincial protocol, crossing r as.character(my_site2) appeared likely passable for resident, fluvial and anadromous adult salmonids migrating to Tyhee Lake if passage to above the highway was facilitated. Crossing r as.character(my_site2) was ranked as a r my_priority_info() %>% pull(priority) priority for proceeding to design for replacement. Adjacent land use has been documented as negatively impacting fish habitat values in the watershed and the multiple strategies to quantify and reduce those impacts noted in @rysavy_etal1999TyheeLake should be considered alongside restorative works addressing fish passage in the watershed.

print_tab_summary()