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 <- 124487
r appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is on r my_pscis_info() %>% pull(stream_name) and r my_overview_info() %>% pull(road_name) approximately 18km south of New Hazelton, BC. The crossing is located approximately r my_priority_info(loc = 'ds') %>% pull(survey_length_m)m upstream from the confluence with the Bulkley River. r my_overview_info() %>% pull(road_name) is 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 a maximum of 2300m to 330m at the highway. Upstream, rainbow trout and dolly varden have been recorded [@data_fish_obs]. A large railway trestle bridge is located over the stream approximately 500m upstream of the highway.
PSCIS stream crossing r as.character(my_site) was ranked as a high priority for follow up by @irvine2018AnalysisPriority due to the large quantity of habitat modelled upstream and selected for assessment in 2020 following consultation with Alecia Fernando from the Gitksan Watershed Authority. @wilson_rabnett2007FishPassage assessed the site and reported it as not a priority restoration site due to "the limited amount of high value habitat upstream of Highway 16". 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 two culverts under Highway 16 were un-embedded, non-backwatered and ranked as a barrier to upstream fish passage [@fish_passage_assessments]. The culvert is located under an estimated 40m of highway fill. 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 outlet drops of r my_pscis_info() %>% pull(outlet_drop_meters)m (Table \@ref(tab:tab-culvert-124487)). 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. Survey conditions were difficult at the time of assessment as stream flows were high due to recent rain events.
##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 the Bulkley River r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124487-01) - \\@ref(fig:photo-124487-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-124487-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-124487)). 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. The cascade-boulder habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value as it was considered an important migration corridor with r my_priority_info(loc = 'ds') %>% pull(hab_value) value habitat for salmonid rearing and spawning. During the survey, an approximately 40cm long salomonid was observed attempting to ascend from the outlet pool into the culvert outlet.
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-124487-03) - \\@ref(fig:photo-124487-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-124487-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-124487)). 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. There were pockets of gravel suitable for spawning for resident and anadromous species with minimal pool habitat observed. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) as an important migration corridor with limited spawning habitat and moderate rearing potential for coho, dolly varden, cutthrout rearing and spawning.
Table \@ref(tab:tab-culvert-bcfp-124487) r text_ref_tab_summary_bcfp()
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 an estimated r my_priority_info() %>% pull(upstream_habitat_length_km)km of mainstem habitat upstream of crossing r as.character(my_site). Habitat in the areas surveyed upstream of the crossing was rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing/spawning. The crossing represents a complete barrier to upstream migration for fish in the Bulkley River watershed regardless of species or life stage. r my_overview_info() %>% pull(road_name) is the responsibility of the Ministry of Transportation and Infrastructure. The crossing 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, '.'))
print_tab_summary_bcfp()
my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')
my_caption1 = paste0('Outlets 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('Typical habitat downstream of crossing ', my_site, ' below the railway bridge and adjacent to the Bulkley River mainstem.')
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))
NewGraphEnvironment/fish_passage_bulkley_2020_reporting documentation built on July 9, 2024, 4:10 a.m.
R Package Documentation
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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 <- 124487
r appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is on r my_pscis_info() %>% pull(stream_name) and r my_overview_info() %>% pull(road_name) approximately 18km south of New Hazelton, BC. The crossing is located approximately r my_priority_info(loc = 'ds') %>% pull(survey_length_m)m upstream from the confluence with the Bulkley River. r my_overview_info() %>% pull(road_name) is 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 a maximum of 2300m to 330m at the highway. Upstream, rainbow trout and dolly varden have been recorded [@data_fish_obs]. A large railway trestle bridge is located over the stream approximately 500m upstream of the highway.
PSCIS stream crossing r as.character(my_site) was ranked as a high priority for follow up by @irvine2018AnalysisPriority due to the large quantity of habitat modelled upstream and selected for assessment in 2020 following consultation with Alecia Fernando from the Gitksan Watershed Authority. @wilson_rabnett2007FishPassage assessed the site and reported it as not a priority restoration site due to "the limited amount of high value habitat upstream of Highway 16". 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 two culverts under Highway 16 were un-embedded, non-backwatered and ranked as a barrier to upstream fish passage [@fish_passage_assessments]. The culvert is located under an estimated 40m of highway fill. 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 outlet drops of r my_pscis_info() %>% pull(outlet_drop_meters)m (Table \@ref(tab:tab-culvert-124487)). 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. Survey conditions were difficult at the time of assessment as stream flows were high due to recent rain events.
##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 the Bulkley River r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124487-01) - \\@ref(fig:photo-124487-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-124487-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-124487)). 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. The cascade-boulder habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value as it was considered an important migration corridor with r my_priority_info(loc = 'ds') %>% pull(hab_value) value habitat for salmonid rearing and spawning. During the survey, an approximately 40cm long salomonid was observed attempting to ascend from the outlet pool into the culvert outlet.
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-124487-03) - \\@ref(fig:photo-124487-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-124487-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-124487)). 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. There were pockets of gravel suitable for spawning for resident and anadromous species with minimal pool habitat observed. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) as an important migration corridor with limited spawning habitat and moderate rearing potential for coho, dolly varden, cutthrout rearing and spawning.
Table \@ref(tab:tab-culvert-bcfp-124487) r text_ref_tab_summary_bcfp()
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 an estimated r my_priority_info() %>% pull(upstream_habitat_length_km)km of mainstem habitat upstream of crossing r as.character(my_site). Habitat in the areas surveyed upstream of the crossing was rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing/spawning. The crossing represents a complete barrier to upstream migration for fish in the Bulkley River watershed regardless of species or life stage. r my_overview_info() %>% pull(road_name) is the responsibility of the Ministry of Transportation and Infrastructure. The crossing 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, '.'))
print_tab_summary_bcfp()
my_photo1 = pull_photo_by_str(str_to_pull = '_d1_') my_caption1 = paste0('Outlets 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('Typical habitat downstream of crossing ', my_site, ' below the railway bridge and adjacent to the Bulkley River mainstem.')
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))
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