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 <- 124500
r appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is located approximately 5km south of Telkwa adjacent to the W Diamond Ramch on r my_pscis_info() %>% pull(stream_name) and r my_overview_info() %>% pull(road_name). The culvert is located approximately 1.7km 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 an upstream watershed area of approximately r round(my_bcfishpass() %>% pull(watershed_upstr_ha)/100,1)km^2^. The elevation of the watershed ranges from a maximum of 1350m to 530m at PSCIS crossing r as.character(my_site). Upstream of r my_overview_info() %>% pull(road_name), r my_fish_sp() have been previously recorded as present and coho, steelhead, rainbow trout and burbot have been observed below the crossing [@data_fish_obs]. A backwatered and passable rail stream crossing consisting of three round culverts (PSCIS 197666) is located under the railway approximately 1.2km downstream. There is one major tributary to r my_pscis_info() %>% pull(stream_name) that intersects the mainstem of the creek approximately 1.7km upstream of r my_overview_info() %>% pull(road_name). There are several stream crossing structures documented on this tributary with the first of which located 4.7km upstream of r my_overview_info() %>% pull(road_name). The adjacent landowner anecdotally reported a drop in numbers of fry/parr in stream over last 20 years and also mentioned that - at some points in
time in the past - there were large numbers of adult lamprey present within the downstream railway crossing. At the time of the survey a staff gauge was present just upstream of crossing r as.character(my_site) on r my_overview_info() %>% pull(road_name).
PSCIS stream crossing r as.character(my_site) was ranked as a high priority for follow up by @irvine2018AnalysisPriority. The site was assessed by @smith2018AssessingBarriers in 2017 with maintenance to clear the inlet of debris recommended and replacement of the crossing assessed as a low priority.
Following the 2020 assessment, planning began to replace crossing r as.character(my_site) with preliminary designs commissioned
from the Canadian Wildlife Federation in collaboration with the MoTI. To assess the severity of impacts of the culvert on fisheries values in the stream and inform baseline monitoring before a potential replacement, the site was electrofished in the summer of 2023 to provide insight into fish community composition and density. Results from 2023 have been incorperated into an updated version of this report.
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-124500)). 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. There was a beaver grate on the inlet of the culvert.
##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 beginning at the culvert location with a short survey conducted adjacent to the downstream railway r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124500-01) - \\@ref(fig:photo-124500-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-124500-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-124500)). 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 channel flowed through an agricultural field with minimal riparian buffer present. The habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value with gravels present suitable for resident, fluvial and anadromous salmonid spawning throughout. At the railway culverts located 1.3km downstream of r my_overview_info() %>% pull(road_name), the habitat transitioned to wetland type habitat with low velocities likely influenced by beaver (Table \@ref(tab:tab-culvert-197666)). The landowners of the adjacent property noted that they had seen large numbers of lamprey in the railway culverts in the past and that they suspected negative impacts on the lamprey from dredging by CN Rail.
Stream Characteristics Upstream {-}
The stream was surveyed immediately upstream of crossing r as.character(my_site) for approximately 200m, then an adjacent road was walked to access the stream r my_priority_info(loc = 'us') %>% pull(survey_length_m)m upstream of the crossing within an area comprised of swamp r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124500-03) - \\@ref(fig:photo-124500-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-124500-d02))")). Within the area immediately upstream of r my_overview_info() %>% pull(road_name), the stream had multiple braided channels flowing within beaver influenced wetland areas. The area surveyed had a total cover amount 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-124500)). 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. At the top end of the site, the beaver ponds had wetted widths of approximately 12-14m wide and estimated depths of 1m. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) for salmonid rearing with habitat noted as suitable for coho and cuthrout rearing.
Table \@ref(tab:tab-culvert-bcfp-124500) r text_ref_tab_summary_bcfp()
Fish Sampling {-}
As noted above, to assess the severity of impacts of the culvert on fisheries values in the stream and inform baseline monitoring,
the site was revisited on September 15, 2023 with electrofishing conducted upstream and downstream of the crossing.
Results are summarized in Tables \@ref(tab:tab-fish-site-124500) - \@ref(tab:tab-fish-dens-124500) and Figure \@ref(fig:plot-fish-box-124500).
A total of r tab_fish_summary_2023 %>% filter(site_id == paste0(my_site, '_us')) %>% group_by(site_id) %>% janitor::adorn_totals() %>% filter(site_id == 'Total') %>% pull(count_fish) fish were captured upstream, including coho, longnose dace and suckers.
Downstream, r tab_fish_summary_2023 %>% filter(site_id == paste0(my_site, '_ds')) %>% group_by(site_id) %>% janitor::adorn_totals() %>% filter(site_id == 'Total') %>% pull(count_fish) fish were captured including coho, rainbow trout, longnose dace, suckers and lamprey r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124500-05) - \\@ref(fig:photo-124500-06)).")}else(knitr::asis_output("(Figures \\@ref(fig:photo-124500-d03)).")) All coho and rainbow
captured with a fork length greater than 60mm were tagged with Passive Integrated Transponders (PIT tags) with data stored here.
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 and major tributary habitat upstream of crossing r as.character(my_site) on r my_overview_info() %>% pull(road_name) is r my_priority_info() %>% pull(upstream_habitat_length_km)km. Habitat in the areas surveyed was rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing with habitat noted as particularly suitable for coho and cutthroat. the crossing is likely passable to upstream
migrating adult salmonids during moderate flows as no outlet drop was present and because low gradient habitat was
not expected to result in overly high flow velocities. During low flow periods, water depths in the culverts may be an impediment to upstream passage for large adult fish but this is unconfirmed. r my_overview_info() %>% pull(road_name) is the responsibility of the Ministry of Transportation and Infrastructure and the crossing was ranked as a r my_priority_info() %>% pull(priority) priority for proceeding to design for replacement.
Although classified as a "barrier" according to the provincial metric, the presence of coho fry and parr upstream of r my_overview_info() %>% pull(road_name) in areas surveyed with electrofishing in 2023 demonstrated that some or all life stages of coho were able to ascend above the crossing in 2022 and/or 2023. Although,
this indicates that PSCIS crossing r as.character(my_site) was not blocking upstream migration for these species during the
years preceding the sampling event, it may still be hindering connectivity at some times of year and for some species and life stages
of fish present in the watershed including lamprey.
r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")
print_tab_summary()
r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")
print_tab_summary(dat = pscis_all, site = 197666, site_photo_id = 2020083101)
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()
fpr::fpr_table_fish_site(dat = tab_fish_sites_sum_2023, sit = my_site)
fpr::fpr_table_fish_density(dat = fish_abund_2023, sit = my_site)
r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")
my_caption <- paste0('Densites of fish (fish/100m2) captured upstream and downstream of PSCIS crossing ', my_site, '.')
fpr::fpr_plot_fish_box(dat = fish_abund_2023, sit = 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, ' below the railway culverts.')
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))
my_photo1 = fpr::fpr_photo_pull_by_str(site = my_site, dir_photos = "data/2023/photos/", str_to_pull = 'fish1')
my_caption1 = paste0('Coho captured upstream of crossing ', my_site, '.')
knitr::include_graphics(my_photo1)
my_photo2 = fpr::fpr_photo_pull_by_str(site = my_site, dir_photos = "data/2023/photos/", str_to_pull = 'fish2')
my_caption2 = paste0('Coho captured upstream of crossing ', my_site, '.')
knitr::include_graphics(my_photo2)
my_caption <- paste0('Left: ', my_caption1, ' Right: ', my_caption2)
knitr::include_graphics(my_photo1)
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(my_photo2)
NewGraphEnvironment/fish_passage_bulkley_2020_reporting documentation built on July 9, 2024, 4:10 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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 <- 124500
r appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is located approximately 5km south of Telkwa adjacent to the W Diamond Ramch on r my_pscis_info() %>% pull(stream_name) and r my_overview_info() %>% pull(road_name). The culvert is located approximately 1.7km 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 an upstream watershed area of approximately r round(my_bcfishpass() %>% pull(watershed_upstr_ha)/100,1)km^2^. The elevation of the watershed ranges from a maximum of 1350m to 530m at PSCIS crossing r as.character(my_site). Upstream of r my_overview_info() %>% pull(road_name), r my_fish_sp() have been previously recorded as present and coho, steelhead, rainbow trout and burbot have been observed below the crossing [@data_fish_obs]. A backwatered and passable rail stream crossing consisting of three round culverts (PSCIS 197666) is located under the railway approximately 1.2km downstream. There is one major tributary to r my_pscis_info() %>% pull(stream_name) that intersects the mainstem of the creek approximately 1.7km upstream of r my_overview_info() %>% pull(road_name). There are several stream crossing structures documented on this tributary with the first of which located 4.7km upstream of r my_overview_info() %>% pull(road_name). The adjacent landowner anecdotally reported a drop in numbers of fry/parr in stream over last 20 years and also mentioned that - at some points in
time in the past - there were large numbers of adult lamprey present within the downstream railway crossing. At the time of the survey a staff gauge was present just upstream of crossing r as.character(my_site) on r my_overview_info() %>% pull(road_name).
PSCIS stream crossing r as.character(my_site) was ranked as a high priority for follow up by @irvine2018AnalysisPriority. The site was assessed by @smith2018AssessingBarriers in 2017 with maintenance to clear the inlet of debris recommended and replacement of the crossing assessed as a low priority.
Following the 2020 assessment, planning began to replace crossing r as.character(my_site) with preliminary designs commissioned
from the Canadian Wildlife Federation in collaboration with the MoTI. To assess the severity of impacts of the culvert on fisheries values in the stream and inform baseline monitoring before a potential replacement, the site was electrofished in the summer of 2023 to provide insight into fish community composition and density. Results from 2023 have been incorperated into an updated version of this report.
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-124500)). 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. There was a beaver grate on the inlet of the culvert.
##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 beginning at the culvert location with a short survey conducted adjacent to the downstream railway r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124500-01) - \\@ref(fig:photo-124500-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-124500-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-124500)). 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 channel flowed through an agricultural field with minimal riparian buffer present. The habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value with gravels present suitable for resident, fluvial and anadromous salmonid spawning throughout. At the railway culverts located 1.3km downstream of r my_overview_info() %>% pull(road_name), the habitat transitioned to wetland type habitat with low velocities likely influenced by beaver (Table \@ref(tab:tab-culvert-197666)). The landowners of the adjacent property noted that they had seen large numbers of lamprey in the railway culverts in the past and that they suspected negative impacts on the lamprey from dredging by CN Rail.
Stream Characteristics Upstream {-}
The stream was surveyed immediately upstream of crossing r as.character(my_site) for approximately 200m, then an adjacent road was walked to access the stream r my_priority_info(loc = 'us') %>% pull(survey_length_m)m upstream of the crossing within an area comprised of swamp r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124500-03) - \\@ref(fig:photo-124500-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-124500-d02))")). Within the area immediately upstream of r my_overview_info() %>% pull(road_name), the stream had multiple braided channels flowing within beaver influenced wetland areas. The area surveyed had a total cover amount 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-124500)). 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. At the top end of the site, the beaver ponds had wetted widths of approximately 12-14m wide and estimated depths of 1m. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) for salmonid rearing with habitat noted as suitable for coho and cuthrout rearing.
Table \@ref(tab:tab-culvert-bcfp-124500) r text_ref_tab_summary_bcfp()
Fish Sampling {-}
As noted above, to assess the severity of impacts of the culvert on fisheries values in the stream and inform baseline monitoring, the site was revisited on September 15, 2023 with electrofishing conducted upstream and downstream of the crossing. Results are summarized in Tables \@ref(tab:tab-fish-site-124500) - \@ref(tab:tab-fish-dens-124500) and Figure \@ref(fig:plot-fish-box-124500).
A total of r tab_fish_summary_2023 %>% filter(site_id == paste0(my_site, '_us')) %>% group_by(site_id) %>% janitor::adorn_totals() %>% filter(site_id == 'Total') %>% pull(count_fish) fish were captured upstream, including coho, longnose dace and suckers.
Downstream, r tab_fish_summary_2023 %>% filter(site_id == paste0(my_site, '_ds')) %>% group_by(site_id) %>% janitor::adorn_totals() %>% filter(site_id == 'Total') %>% pull(count_fish) fish were captured including coho, rainbow trout, longnose dace, suckers and lamprey r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124500-05) - \\@ref(fig:photo-124500-06)).")}else(knitr::asis_output("(Figures \\@ref(fig:photo-124500-d03)).")) All coho and rainbow
captured with a fork length greater than 60mm were tagged with Passive Integrated Transponders (PIT tags) with data stored here.
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 and major tributary habitat upstream of crossing r as.character(my_site) on r my_overview_info() %>% pull(road_name) is r my_priority_info() %>% pull(upstream_habitat_length_km)km. Habitat in the areas surveyed was rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing with habitat noted as particularly suitable for coho and cutthroat. the crossing is likely passable to upstream
migrating adult salmonids during moderate flows as no outlet drop was present and because low gradient habitat was
not expected to result in overly high flow velocities. During low flow periods, water depths in the culverts may be an impediment to upstream passage for large adult fish but this is unconfirmed. r my_overview_info() %>% pull(road_name) is the responsibility of the Ministry of Transportation and Infrastructure and the crossing was ranked as a r my_priority_info() %>% pull(priority) priority for proceeding to design for replacement.
Although classified as a "barrier" according to the provincial metric, the presence of coho fry and parr upstream of r my_overview_info() %>% pull(road_name) in areas surveyed with electrofishing in 2023 demonstrated that some or all life stages of coho were able to ascend above the crossing in 2022 and/or 2023. Although,
this indicates that PSCIS crossing r as.character(my_site) was not blocking upstream migration for these species during the
years preceding the sampling event, it may still be hindering connectivity at some times of year and for some species and life stages
of fish present in the watershed including lamprey.
r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")
print_tab_summary()
r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")
print_tab_summary(dat = pscis_all, site = 197666, site_photo_id = 2020083101)
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()
fpr::fpr_table_fish_site(dat = tab_fish_sites_sum_2023, sit = my_site)
fpr::fpr_table_fish_density(dat = fish_abund_2023, sit = my_site)
r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")
my_caption <- paste0('Densites of fish (fish/100m2) captured upstream and downstream of PSCIS crossing ', my_site, '.') fpr::fpr_plot_fish_box(dat = fish_abund_2023, sit = 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, ' below the railway culverts.')
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))
my_photo1 = fpr::fpr_photo_pull_by_str(site = my_site, dir_photos = "data/2023/photos/", str_to_pull = 'fish1') my_caption1 = paste0('Coho captured upstream of crossing ', my_site, '.')
knitr::include_graphics(my_photo1)
my_photo2 = fpr::fpr_photo_pull_by_str(site = my_site, dir_photos = "data/2023/photos/", str_to_pull = 'fish2') my_caption2 = paste0('Coho captured upstream of crossing ', my_site, '.')
knitr::include_graphics(my_photo2)
my_caption <- paste0('Left: ', my_caption1, ' Right: ', my_caption2) knitr::include_graphics(my_photo1) knitr::include_graphics("fig/pixel.png") knitr::include_graphics(my_photo2)
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