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 <- 58159
my_site2 <- 58158

r appendix_title()

Site Location {-}

PSCIS crossing r as.character(my_site) is located on r my_pscis_info() %>% pull(stream_name) on the r my_overview_info() %>% pull(road_name) accessed from Highway 16 immediately south of Telkwa, BC. The r my_overview_info() %>% pull(road_name) is a private road owned by the Woodmere Nursery. At the time of field surveys it was used to access a newly constructed agricultural facility and by nursery operations to access a waste storage/burn pile area.

##idon't think we need this here but...
#During 2020 surveys, PSCIS culvert 197669 was documented on `r my_pscis_info() %>% pull(stream_name)`, 1.2km upstream of the FSR.

Background {-}

r my_pscis_info() %>% pull(stream_name) drains McDowell Lake (35ha), Dorsay Lake (4ha) and one other unnamed lake (9ha) flowing from McDowell Lake in a south then west direction for approximately 9km to the confluence with the Bulkley River. 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 a maximum of 1000 to 520m at PSCIS crossing r as.character(my_site). r my_pscis_info() %>% pull(stream_name) is known to contain coho and rainbow trout upstream of the subject culvert [@data_fish_obs]. There are numerous stream crossing structures located on r my_pscis_info() %>% pull(stream_name) upstream of r as.character(my_site) including crossings on Highway 16, an unnamed road 300m upstream of the highway, Woodmere Road and others.

PSCIS stream crossings r as.character(my_site) and r as.character(my_site2) were rated as high priorities for follow up by both @irvine2018AnalysisPriority and @smith2018AssessingBarriers due to significant quantities of upstream habitat suitable for salmonid rearing. 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 was un-embedded, non-backwatered and considered a barrier to upstream fish passage. The pipe was r my_pscis_info() %>% pull(diameter_or_span_meters)m in diameter with a pipe 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-58159)). Water temperature was r my_habitat_info() %>% filter(rowname == 'temperature c') %>% pull(us)$^\circ$C, pH was r my_habitat_info() %>% filter(rowname == 'p h') %>% pull(us) and conductivity was r my_habitat_info() %>% filter(rowname == 'conductivity m s cm') %>% pull(us)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-58159-01) - \\@ref(fig:photo-58159-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-58159-d01))")). 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-58159)). 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. Habitat 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 {-}

The stream was surveyed upstream from r as.character(my_site) for r my_priority_info(loc = 'us') %>% pull(survey_length_m)m r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-58159-03) - \\@ref(fig:photo-58159-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-58159-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-58159)). 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')%. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) for salmonid rearing and spawning.

PSCIS culvert r as.character(my_site2) was documented on r my_pscis_info() %>% pull(stream_name), 500m upstream on Highway 16. At the time of the survey the culvert had been newly replaced with a baffled structure embedded with a natural cobble and gravel substrates. Although ranked as a barrier to upstream fish passage using the provincial metric the crossing is likely not a barrier during most flows for adult anadromous salmon and fluvial salmonids migrating upstream from the Bulkley River. The pipe was r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(diameter_or_span_meters)m in diameter with a pipe length of r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(length_or_width_meters)m, a culvert slope of r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(culvert_slope_percent)%, a stream width ratio of r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(stream_width_ratio) and an outlet drop of r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(outlet_drop_meters)m (Table \@ref(tab:tab-culvert-58158)).

PSCIS crossing 123544, located on an unnamed road approximately 300m upstream of Highway 16 has been documented as a barrier in the PSCIS system. The culvert is documented as 30m long, with a 1m diameter, a slope of 3.5% and an outlet drop of 0.3m. The culvert is noted as not embedded and not backwatered.

Table \@ref(tab:tab-culvert-bcfp-58159) r text_ref_tab_summary_bcfp()

Fish Sampling {-}

To assess potential impacts of the culvert on fisheries values in the stream, electrofishing was conducted upstream and downstream of the crossing. A total of r tab_fish_summary %>% filter(site_id == paste0(my_site, '_ds') & species_code == 'CO') %>% pull(count_fish) coho were captured downstream with r tab_fish_summary %>% filter(site_id == paste0(my_site, '_us') & species_code == 'CO') %>% pull(count_fish) coho captured upstream. Although there is only moderate confidence in their identification, r tab_fish_summary %>% filter(site_id == paste0(my_site, '_ds') & species_code == 'CH') %>% pull(count_fish) fish captured were identified as chinook. With the exception of one coho, only rainbow trout (r tab_fish_summary %>% filter(site_id == paste0(my_site, '_us') & species_code == 'RB') %>% pull(count_fish) fish) were captured upstream. Sampling results are summarized in Tables \@ref(tab:tab-fish-site-58159) - \@ref(tab:tab-fish-dens-58159) and Figure \@ref(fig:plot-fish-box-58159).

Structure Remediation and Cost Estimate {-}

Structure replacement with a bridge (r my_pscis_info() %>% pull(recommended_diameter_or_span_meters)m span) is recommended to provide access to the habitat located upstream of PSCIS crossing r as.character(my_site). 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) to PSCIS crossing 123544 located on an unnamed road approximately 300m upstream of Highway 16. Habitat in this area was rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing/spawning. r my_overview_info() %>% pull(road_name) is on private land owned by the Woodmere Nursury. The crossing was ranked as a r my_priority_info() %>% pull(priority) priority for proceeding to design for replacement. Although remediation of fish passage at r as.character(my_site) is considered beneficial, detailed habitat confirmation assessments of upstream culverts (PSCIS 123544) could be pursued to scope for additional potential habitat gains possible within the same system.

print_tab_summary()

print_tab_summary(site = my_site2, dat = pscis_reassessments, site_photo_id = my_site2)

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_caption <- paste0('Electrofishing sites for PSCIS crossing ', my_site, '.')

tab_fish_site() %>% 
  my_kable(caption_text = my_caption)

my_caption <- paste0('Fish densities (fish/100m2) for PSCIS crossing ', my_site, '.')

tab_fish_dens() %>% 
  my_kable(caption_text = my_caption)

my_caption <- paste0('Densities of fish captured (fish/100m2) during electrofishing upstream and downstream of PSCIS crossing ', my_site, '.')

plot_fish_box()

my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')

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

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

my_photo2 = pull_photo_by_str(str_to_pull = '_df1_')

my_caption2 = paste0('Chinook captured downstream of PSCIS crossing ', my_site, '.')

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

##we could put 2 photos in on box but it is lots of extra work with the crossreferences. pdfs suck anyway.  Don't get too custom with it!!!

# my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')
# my_caption1 = paste0('Typical habitat downstream of PSCIS crossing ', my_site, '.')
# 
# my_photo2 = pull_photo_by_str(str_to_pull = '_u1_')
# my_caption2 = paste0('Typical habitat upstream of PSCIS crossing ', my_site, '.')

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('Typical habitat upstream of PSCIS crossing ', my_site, '.')

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

my_photo2 = pull_photo_by_str(str_to_pull = '_uf1_')

my_caption2 = paste0('Coho captured 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))