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 <- 123795
r appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is located on r my_pscis_info() %>% pull(stream_name) at km 18.9 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), the r my_pscis_info() %>% pull(stream_name) is a r my_bcfishpass() %>% pull(stream_order) %>% english::ordinal() order stream. The elevation of the watershed ranges from a maximum of 1260m to 1070m at the crossing. Upstream of the r my_overview_info() %>% pull(road_name), r my_fish_sp() have been previously recorded as present [@data_fish_obs] with dolly varden recorded as present in the adjacent connected stream. We suspect the salmon noted were likely coho due to the smaller size of the watershed.
PSCIS stream crossing r as.character(my_site) was ranked as a high priority for follow up by @irvine2018AnalysisPriority because there was salmon noted upstream and because PSCIS data indicated a larger channel containing habitat rated as high value. Although on a generally smaller stream, the crossing's location on a forest service road was considered advantageous for funding eligibility through forestry supported programs such as the Land Based Investment Fund. 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-123795)). 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)
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-123795-01) - \\@ref(fig:photo-123795-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-123795-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-123795)). 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 was noted as having somewhat low complexity, with occasional deep pools and primarily glide habitat. Abundant gravels were noted as present but with only occasional patches unembedded. 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 to the location of a ford (PSCIS123796).r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-123795-03) - \\@ref(fig:photo-123795-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-123795-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-123795)). 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. Deep glide habitat was noted as prevalent in the area surveyed. Gradients leveled out at top end of site, with primarily shrub and wetland riparian area present. Very occasional pockets of gravel suitable for resident and adfluvial salmonid spawning were noted. 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-123795) r text_ref_tab_summary_bcfp()
Structure Remediation and Cost Estimate {-}
Replacement of PSCIS crossing r as.character(my_site) with an embedded culvert (streambed simulation - r my_pscis_info() %>% pull(recommended_diameter_or_span_meters)m diameter) 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 {-}
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. Habitat in the areas surveyed was 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 fo the road to clarify salmon species presence and assess densities of fish present.
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")
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))
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 <- 123795
r appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is located on r my_pscis_info() %>% pull(stream_name) at km 18.9 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), the r my_pscis_info() %>% pull(stream_name) is a r my_bcfishpass() %>% pull(stream_order) %>% english::ordinal() order stream. The elevation of the watershed ranges from a maximum of 1260m to 1070m at the crossing. Upstream of the r my_overview_info() %>% pull(road_name), r my_fish_sp() have been previously recorded as present [@data_fish_obs] with dolly varden recorded as present in the adjacent connected stream. We suspect the salmon noted were likely coho due to the smaller size of the watershed.
PSCIS stream crossing r as.character(my_site) was ranked as a high priority for follow up by @irvine2018AnalysisPriority because there was salmon noted upstream and because PSCIS data indicated a larger channel containing habitat rated as high value. Although on a generally smaller stream, the crossing's location on a forest service road was considered advantageous for funding eligibility through forestry supported programs such as the Land Based Investment Fund. 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-123795)). 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)
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-123795-01) - \\@ref(fig:photo-123795-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-123795-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-123795)). 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 was noted as having somewhat low complexity, with occasional deep pools and primarily glide habitat. Abundant gravels were noted as present but with only occasional patches unembedded. 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 to the location of a ford (PSCIS123796).r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-123795-03) - \\@ref(fig:photo-123795-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-123795-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-123795)). 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. Deep glide habitat was noted as prevalent in the area surveyed. Gradients leveled out at top end of site, with primarily shrub and wetland riparian area present. Very occasional pockets of gravel suitable for resident and adfluvial salmonid spawning were noted. 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-123795) r text_ref_tab_summary_bcfp()
Structure Remediation and Cost Estimate {-}
Replacement of PSCIS crossing r as.character(my_site) with an embedded culvert (streambed simulation - r my_pscis_info() %>% pull(recommended_diameter_or_span_meters)m diameter) 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 {-}
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. Habitat in the areas surveyed was 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 fo the road to clarify salmon species presence and assess densities of fish present.
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")
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))
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