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 <- 3139
bcfp <- my_bcfishpass()

r appendix_title()

Site Location {-}

PSCIS crossing r as.character(my_site) is located on a r my_pscis_info() %>% pull(stream_name) at km 31 of r my_overview_info() %>% pull(road_name). r my_overview_info() %>% pull(road_name) can be accessed from Summit Lake Rd East which meets Highway 16 approximately 11km east of Houston. The culvert is located approximately 490m upstream from the confluence with McQuarrie Creek. r my_overview_info() %>% pull(road_name) is the responsibility of FLNR - Nadina Forest District.

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^, containing an estimated r my_bcfishpass() %>% pull(total_wetland_ha)ha of wetland and r my_bcfishpass() %>% pull(total_lakereservoir_ha)ha of lake. The elevation of the watershed ranges from a maximum of 1200m to 935m at the crossing. Upstream of r my_overview_info() %>% pull(road_name), no fish have previously been recorded [@data_fish_obs].

Downstream in McQuarrie Creek, r my_fish_sp(df = bcfishpass_all, sit = 3143) have been recorded as present. Although @data_fish_obs note steelhead in McQuarrie Creek near the confluence with the subject stream (with source reference noted as "personal communications"), @ncfdc1998MidBulkleyDetailed recorded a 4-5 m impassable falls (significant overhanging section, lack of plunge pool) in the canyon downstream (UTM 9.662200.6045550). This falls was not recorded in provincial databases at the time of planning and reporting.

Beginning in 2016, the BC Ministry of Forests, Land, Natural Resource Operations and Rural Development (FLNRORD), Land and Water Section established a continuous discharge monitoring station on McQuarrie Creek just upstream of the highway [@westcott2020UpperBulkley]. Additionally, three water temperature sensors have been deployed in the watershed. One is located in McQuarrie Creek just above Highway 16, another is in McQuarrie Creek above North Road and one is in McQuarrie Lake [@westcott2020UpperBulkley]. Sensors in McQuarrie Creek have been gathering water temperature data at 1hour intervals since 2016 and the sensor in McQuarrie Lake is gathering maximum temperature information from 1m below the surface since July 2018. Data from the two McQuarrie Creek temperature monitoring stations is available through the Skeena Salmon Data Centre [@dfo/flnro2019WaterTemperaturea; @dfo/flnro2019WaterTemperatureb].

The McQuarrie Creek watershed has been selected as a focus watershed for Environmental Stewardship Initiative (ESI) research including critical flow monitoring, benthic invertebrate sampling, water quality monitoring and fisheries assessments (pers. comm Don Morgan, Ministry of Environment and Climate Change Strategy).

PSCIS stream crossing r as.character(my_site) was ranked as a high priority for follow up in @irvine2018AnalysisPriority. It was also selected for follow up with habitat confirmation because McQuarrie Creek was noted as an important rearing area for steelhead by @tredger1982UpperBulkley, because the stream is lake headed (which can stabilize system flows), as steelhead were noted near the confluence, and due to engagement activities with Wet'suwet'en, FLNRO, and Ministry of Environment and Climate Change Strategy representatives that indicated that there could be potential benefits in fish passage remediation/monitoring activities in ESI target watersheds.

Of note, an erronous input into the provincial database for PSCIS crossing 3138 indicated that the oval culvert structure located on McQuarrie Creek just upstream of the confluence with the subject stream was an open bottomed structure and fully passable. The error was discovered during review of PSCIS photos as part of the background review for drafting of this report. @ncfdc1998MidBulkleyDetailed noted that this culvert was a barrier to upstream fish passage at low flows, was undersized and was causing fill slope erosion at the road crossing. A map of the watershed is provided in map attachment r my_bcfishpass() %>% pull(dbm_mof_50k_grid).

Stream Characteristics at Crossing {-}

At the time of the survey, the culvert under r my_overview_info() %>% pull(road_name) was un-embedded, non-backwatered and ranked as a barrier to upstream fish passage according to the provincial protocol [@fish_passage_assessments]. The pipe was r my_pscis_info() %>% pull(diameter_or_span_meters)m in diameter with a length 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-3139)). 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.

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

Stream Characteristics Downstream {-}

The stream was surveyed downstream from the culvert for r my_priority_info(loc = 'ds') %>% pull(survey_length_m)m to the confluence with Buck Creek r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-3139-01) - \\@ref(fig:photo-3139-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-3139-d01))")). 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-3139)). 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. There were occasional pockets of gravels suitable for resident salmonids. The habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value for resident salmonid rearing.

Stream Characteristics Upstream {-}

The stream was surveyed immediately upstream from r as.character(my_site) for approximately r my_priority_info(loc = 'us') %>% pull(survey_length_m)m r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-3139-03) - \\@ref(fig:photo-3139-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-3139-d2))")). Within the area surveyed, total cover amount was rated as r my_habitat_info2(loc = 'us') %>% filter(rowname == 'total cover') %>% pull(v) with r my_habitat_info2(loc = 'us') %>% filter(v == 'dominant') %>% pull(rowname) dominant. Cover was also present as r my_habitat_info2(loc = 'us') %>% filter(v == 'sub-dominant') %>% pull(rowname) %>% knitr::combine_words() (Table \@ref(tab:tab-habitat-summary-3139)). The average channel width was r my_habitat_info3(loc = 'us', row = 'avg channel width m')m, the average wetted width was r my_habitat_info3(loc = 'us', row = 'avg wetted width m')m and the average gradient was r my_habitat_info3(loc = 'us', row = 'average gradient percent')%. The dominant substrate was r my_habitat_info3(loc = 'us', row = "bed material dominant") with r my_habitat_info3(loc = 'us', row = "bed material subdominant") subdominant. Extensive areas of gravels suitable for spawning resident salmonids were present and fry were observed throughout the surveyed area. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) value resident salmonid rearing and spawning.

Structure Remediation and Cost Estimate {-}

Replacement of PSCIS crossing r as.character(my_site) with a bridge (r my_pscis_info() %>% pull(recommended_diameter_or_span_meters)m span) is recommended. The cost of the work is estimated at \$r format(my_cost_estimate() %>% pull(cost_est_1000s) * 1000, big.mark = ',') for a cost benefit of r as.character(my_cost_estimate() %>% pull(cost_net)) linear m/\$1000 and r as.character(my_cost_estimate() %>% pull(cost_area_net))m^2^/\$1000.

Conclusion {-}

A conservative estimate of mainstem habitat upstream of crossing r as.character(my_site) is r my_priority_info() %>% pull(upstream_habitat_length_km)km to the top end of a 71ha wetland where rainbow trout have been recorded. Habitat in the areas surveyed upstream of the culvert were rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing and spawning with extensive areas of wetland and lake habitat located upstream. As there is a 4-5 m impassable falls downstream in McQuarrie Creek, remediation of fish passage at the crossing would benefit resident fish species in the watershed and not anadromous fish populations migrating from the Bulkley River mainstem. r my_overview_info() %>% pull(road_name) is the responsibility of the Ministry of Transportation and Infrastructure. Crossing r as.character(my_site) was ranked as a r my_priority_info() %>% pull(priority) priority for proceeding to design for replacement.

print_tab_summary()

tab_hab_summary %>% 
  filter(Site  == my_site) %>% 
  # select(-Site) %>% 
  my_kable(caption_text = paste0('Summary of habitat details for PSCIS crossing ', my_site, '.'))

my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')

my_caption1 = paste0('Habitat downstream of PSCIS crossing ', my_site, '.')

grid::grid.raster(get_img(photo = my_photo1))

my_photo2 = pull_photo_by_str(str_to_pull = '_d2_')

my_caption2 = paste0('Habitat downstream of crossing ', my_site, '.')

grid::grid.raster(get_img(photo = my_photo2))

my_caption <- paste0('Left: ', my_caption1, ' Right: ', my_caption2)

knitr::include_graphics(get_img_path(photo = my_photo1))
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(get_img_path(photo = my_photo2))

my_photo1 = pull_photo_by_str(str_to_pull = '_u1_')

my_caption1 = paste0('Habitat upstream of PSCIS crossing ', my_site, '.')

grid::grid.raster(get_img(photo = my_photo1))

my_photo2 = pull_photo_by_str(str_to_pull = '_u2_')

my_caption2 = paste0('Habitat upstream of PSCIS crossing ', my_site, '.')

grid::grid.raster(get_img(photo = my_photo2))

my_caption <- paste0('Left: ', my_caption1, ' Right: ', my_caption2)

knitr::include_graphics(get_img_path(photo = my_photo1))
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(get_img_path(photo = my_photo2))