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 <- 123794

r appendix_title()

Site Location {-}

PSCIS crossing r as.character(my_site) is located on r my_pscis_info() %>% pull(stream_name) at km 19.3 of the r my_overview_info() %>% pull(road_name). The site is accessed via Moricetown Road through Witset approximately 40km north of Smithers. The culvert is located approximately 670m upstream from the confluence with a major tributary to Blunt Creek. Blunt Creek flows east into Harold Price Creek which in turn flows into the Suskwa River. The Suskwa River enters the Bulkley River near Hazleton BC. r my_overview_info() %>% pull(road_name) is the responsibility of the FLNR - Skeena Stikine 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. Watershed area upstream of the crossing is estimated at r round(my_bcfishpass() %>% pull(watershed_upstr_ha)/100,1)km^2^ ranging from a maximum elevation of 1260m to 1070m at PSCIS crossing r as.character(my_site). Upstream of the r my_overview_info() %>% pull(road_name), r my_fish_sp() have been previously recorded as present [@data_fish_obs]. @data_fish_obs also indicates that salmon (unidentified species) have been recorded in an adjacent tributary with cutthrout recorded nearby within multiple streams connecting to the greater stream network just downstream of the subject tributary. PSCIS crossing 123785 has been ranked as a barrier and is located on the tributary that the subject stream drains into. It is located approximately 250m north-east on a spur road (R09533) accessed at km 18.3 of the Blunt Creek FSR.

PSCIS stream crossing r as.character(my_site) was ranked as a high priority for follow up by @irvine2018AnalysisPriority because there was salmon noted nearby, due to the presence of a small lake upstream, and because PSCIS data indicated a larger channel containing habitat rated as high value. Although on a smaller stream, the crossing's location on a forest service road was considered advantageous as these sites are often eligible for funding through forestry supported funds such as the Land Based Investment Fund if restoration of fish passage is warranted. 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 acoording 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-123794)). 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 r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-123794-01) - \\@ref(fig:photo-123794-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-123794-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-123794)). 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. Within the area surveyed, the stream had good flow volume and frequent patches of gravel suitable for spawning for coho and resident salmonids. The habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value.

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-123794-03) - \\@ref(fig:photo-123794-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-123794-d02))")). 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-123794)). 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. The channel was noted as having good complexity and abundant gravels suitably sized for both coho and resident salmonid spawning. Some small woody debris/large woody debris steps (30-50cm in height) were present intermittently starting approximately 400m above the culvert. A fish (~120mm) was observed 500m upstream of the culvert. A 4m high falls was noted at the top end of the site and represents an impassable barrier to upstream migration. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) for salmonid spawning and rearing.

Table \@ref(tab:tab-culvert-bcfp-123794) r text_ref_tab_summary_bcfp()

Structure Remediation and Cost Estimate {-}

Replacement of PSCIS crossing r as.character(my_site) with a embedded culvert (streambed simulation - r my_pscis_info() %>% pull(recommended_diameter_or_span_meters)m span) is recommended in the long term. 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 {-}

There is r my_priority_info() %>% pull(upstream_habitat_length_km)km of habitat upstream of crossing r as.character(my_site) with habitat value rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing and spawning. r my_overview_info() %>% pull(road_name) is the responsibility of FLNR - Skeena Stikine District. The crossing was ranked as a r my_priority_info() %>% pull(priority) priority for proceeding to design for replacement. Future fish sampling is recommended upstream and downstream of the crossing to scope for anadromous species and evaluate potential impacts of the culvert on fish densities. Although the upstream channel appears to split into three channels just upstream of the crossing, it is also recommended that PSCIS crossing 123785 (located on the spur road R09533 accessed from km 18.3 of the Blunt Creek FSR) be scoped as a habitat confirmation candidate at the same time that other fish passage assessment work is conducted in the area.

print_tab_summary()

r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")

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

print_tab_summary_bcfp()

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('Cascade 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))