In NewGraphEnvironment/fish_passage_elk_2021_reporting: Does not matter.
knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
source('R/packages.R')
source('R/functions.R')
source('R/tables.R')
my_site <- 197844
r fpr_appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is located on a r my_pscis_info() %>% pull(stream_name) on the r my_overview_info() %>% pull(road_name). The site is located approximately 11km west of the junction with the Wigwam FSR at a point approximately 30k south of Morrissey. r my_overview_info() %>% pull(road_name)(forest file ID 5466) is ultimately the responsibility of Ministry of Forests, Lands, Natural Resource Operations and Rural Development - Rocky Mountain Forest District. Although unconfirmed, Canfor may have a road use permit for this section of FSR.
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 fpr_wshd_par()km^2^. The elevation of the east facing watershed ranges from a maximum of r fpr_wshd_par(col = 'elev_max')m to r fpr_wshd_par(col = 'elev_site')m at the crossing (Table \@ref(tab:tab-wshd-197844)). Upstream of r my_overview_info() %>% pull(road_name), no fish have previously been recorded [@moe2020KnownBC]. Downstream, Bighorn Creek supports westslope cutthroat trout, bull trout and mountain whitefish [@moe2020KnownBC]. Bighorn Creek has been noted as contributing significantly to habitat suitable for bull trout spawning in the Wigwam River system with spawning been noted just upstream of the confluence with the Wigwam River. The Wigwam River has been characterized as the most important spawning system in the East Kootenay region, supporting some of the largest westslope cutthrout trout in the Kootenay Region and is located ~11.5km downstream of the subject culvert [@strong_k_d_2015McNeilSubstrate; @cope_morris2001WigwamRiver]. @strong_k_d_2015McNeilSubstrate report that substrate core samples have been taken within Bighorn Creek at an index site ~700m upstream of the confluence with the Wigwam River between 2003 - 2008 and again in 2015 with an objective of analyzing stream substrate material/sediment levels to produce trend data valuable in monitoring suitability of stream reaches identified as critical for bull trout spawning.
fpr_tab_wshd_sum(site_id = my_site) %>%
my_kable(caption_text = paste0('Summary of derived upstream watershed statistics for PSCIS crossing ', my_site, '.'),
footnote_text = 'Elev P60 = Elevation at which 60% of the watershed area is above')
PSCIS crossing r as.character(my_site) was surveyed with a phase 1 assessment opportunistically during field assessments in the area and was prioritized for follow up with a habitat confirmation as it was considered the crossing with the highest potential for remediation located within the Bighorn Creek watershed area. The site was noted as having a significantly sized outlet drop and good flow with a location very close to the mainstem of Bighorn Creek which contains confirmed spawning habitat for westslope cutthrout trout. Table \@ref(tab:tab-culvert-bcfp-197787) r text_ref_tab_summary_bcfp(). Additionally, 0.6km of habitat <8% gradient was modelled as located upstream. A map of the watershed is provided in map attachment r my_bcfishpass() %>% pull(dbm_mof_50k_grid).
r if(identical(gitbook_on, FALSE)){knitr::asis_output("\\pagebreak")}
print_tab_summary_bcfp()
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 [@moe2011Fieldassessment]. The pipe was 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 an outlet drop of r my_pscis_info() %>% pull(outlet_drop_meters)m (Table \@ref(tab:tab-culvert-197844)). Water temperature was r my_habitat_info(sit = my_site) %>% filter(rowname == 'temperature c') %>% pull(us)$^\circ$C, pH was r my_habitat_info(sit = my_site) %>% filter(rowname == 'p h') %>% pull(us) and conductivity was r my_habitat_info(sit = my_site) %>% 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 to the confluence with Bighorn Creek r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-197844-01) - \\@ref(fig:photo-197844-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-197844-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-197844)). The average channel width was r my_habitat_info3(loc = 'ds', row = 'avg channel 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 stream was noted as going subsurface at ~40m downstream of the road then rewatering at ~80m downstream. There was evidence of high velocity/volume flows with a general lack of complexity. The habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value for salmonid rearing and spawning due to dewatering, as well as a lack of deep pool and undercut bank cover.
Stream Characteristics Upstream {-}
The stream was surveyed 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 1.1m high rock that likely presents a barrier to upstream fish passage r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-197844-03) - \\@ref(fig:photo-197844-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-197844-d02))")). A ford (PSCIS 197801) was located on a spur road located upstream approximately 220m upstream of the FSR. 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-197844)). 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. Occasional pools suitable for juvenile westslope cutthroat trout overwintering and frequent pockets of gravel present suitable for spawning were noted throughout. The fairly steep system had good flow with intermittent small woody debris drops between 0.5 and 1m in height. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) with moderate potential for juvenile salmonid rearing.
Structure Remediation and Cost Estimate {-}
Should restoration/maintenance activities proceed at the site, 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 {-}
There was r my_priority_info() %>% pull(upstream_habitat_length_km)km of steep but viable juvenile rearing habitat surveyed upstream of crossing r as.character(my_site) before a 1.1m high rock drop considered to likely represent the upstream limit of fish migration. Habitat in the area surveyed was rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing with frequent pockets of gravel suitable for spawning. Although Canfor may have a road use permit for this section of FSR, r my_overview_info() %>% pull(road_name) is detailed as the responsibility of Ministry of Forests, Lands, Natural Resource Operations and Rural Development - Rocky Mountain Forest District [@flnrordForestTenureRoad2020]. Crossing r as.character(my_site) was ranked as a r my_priority_info() %>% pull(priority) priority for proceeding to design for replacement.
r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")
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, '.'))
my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')
my_caption1 = paste0('Habitat downstream of 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('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_elk_2021_reporting documentation built on June 23, 2022, 8:21 p.m.
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knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE) source('R/packages.R') source('R/functions.R') source('R/tables.R')
my_site <- 197844
r fpr_appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is located on a r my_pscis_info() %>% pull(stream_name) on the r my_overview_info() %>% pull(road_name). The site is located approximately 11km west of the junction with the Wigwam FSR at a point approximately 30k south of Morrissey. r my_overview_info() %>% pull(road_name)(forest file ID 5466) is ultimately the responsibility of Ministry of Forests, Lands, Natural Resource Operations and Rural Development - Rocky Mountain Forest District. Although unconfirmed, Canfor may have a road use permit for this section of FSR.
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 fpr_wshd_par()km^2^. The elevation of the east facing watershed ranges from a maximum of r fpr_wshd_par(col = 'elev_max')m to r fpr_wshd_par(col = 'elev_site')m at the crossing (Table \@ref(tab:tab-wshd-197844)). Upstream of r my_overview_info() %>% pull(road_name), no fish have previously been recorded [@moe2020KnownBC]. Downstream, Bighorn Creek supports westslope cutthroat trout, bull trout and mountain whitefish [@moe2020KnownBC]. Bighorn Creek has been noted as contributing significantly to habitat suitable for bull trout spawning in the Wigwam River system with spawning been noted just upstream of the confluence with the Wigwam River. The Wigwam River has been characterized as the most important spawning system in the East Kootenay region, supporting some of the largest westslope cutthrout trout in the Kootenay Region and is located ~11.5km downstream of the subject culvert [@strong_k_d_2015McNeilSubstrate; @cope_morris2001WigwamRiver]. @strong_k_d_2015McNeilSubstrate report that substrate core samples have been taken within Bighorn Creek at an index site ~700m upstream of the confluence with the Wigwam River between 2003 - 2008 and again in 2015 with an objective of analyzing stream substrate material/sediment levels to produce trend data valuable in monitoring suitability of stream reaches identified as critical for bull trout spawning.
fpr_tab_wshd_sum(site_id = my_site) %>% my_kable(caption_text = paste0('Summary of derived upstream watershed statistics for PSCIS crossing ', my_site, '.'), footnote_text = 'Elev P60 = Elevation at which 60% of the watershed area is above')
PSCIS crossing r as.character(my_site) was surveyed with a phase 1 assessment opportunistically during field assessments in the area and was prioritized for follow up with a habitat confirmation as it was considered the crossing with the highest potential for remediation located within the Bighorn Creek watershed area. The site was noted as having a significantly sized outlet drop and good flow with a location very close to the mainstem of Bighorn Creek which contains confirmed spawning habitat for westslope cutthrout trout. Table \@ref(tab:tab-culvert-bcfp-197787) r text_ref_tab_summary_bcfp(). Additionally, 0.6km of habitat <8% gradient was modelled as located upstream. A map of the watershed is provided in map attachment r my_bcfishpass() %>% pull(dbm_mof_50k_grid).
r if(identical(gitbook_on, FALSE)){knitr::asis_output("\\pagebreak")}
print_tab_summary_bcfp()
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 [@moe2011Fieldassessment]. The pipe was 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 an outlet drop of r my_pscis_info() %>% pull(outlet_drop_meters)m (Table \@ref(tab:tab-culvert-197844)). Water temperature was r my_habitat_info(sit = my_site) %>% filter(rowname == 'temperature c') %>% pull(us)$^\circ$C, pH was r my_habitat_info(sit = my_site) %>% filter(rowname == 'p h') %>% pull(us) and conductivity was r my_habitat_info(sit = my_site) %>% 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 to the confluence with Bighorn Creek r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-197844-01) - \\@ref(fig:photo-197844-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-197844-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-197844)). The average channel width was r my_habitat_info3(loc = 'ds', row = 'avg channel 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 stream was noted as going subsurface at ~40m downstream of the road then rewatering at ~80m downstream. There was evidence of high velocity/volume flows with a general lack of complexity. The habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value for salmonid rearing and spawning due to dewatering, as well as a lack of deep pool and undercut bank cover.
Stream Characteristics Upstream {-}
The stream was surveyed 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 1.1m high rock that likely presents a barrier to upstream fish passage r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-197844-03) - \\@ref(fig:photo-197844-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-197844-d02))")). A ford (PSCIS 197801) was located on a spur road located upstream approximately 220m upstream of the FSR. 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-197844)). 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. Occasional pools suitable for juvenile westslope cutthroat trout overwintering and frequent pockets of gravel present suitable for spawning were noted throughout. The fairly steep system had good flow with intermittent small woody debris drops between 0.5 and 1m in height. Habitat value was rated as r my_priority_info(loc = 'us') %>% pull(hab_value) with moderate potential for juvenile salmonid rearing.
Structure Remediation and Cost Estimate {-}
Should restoration/maintenance activities proceed at the site, 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 {-}
There was r my_priority_info() %>% pull(upstream_habitat_length_km)km of steep but viable juvenile rearing habitat surveyed upstream of crossing r as.character(my_site) before a 1.1m high rock drop considered to likely represent the upstream limit of fish migration. Habitat in the area surveyed was rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing with frequent pockets of gravel suitable for spawning. Although Canfor may have a road use permit for this section of FSR, r my_overview_info() %>% pull(road_name) is detailed as the responsibility of Ministry of Forests, Lands, Natural Resource Operations and Rural Development - Rocky Mountain Forest District [@flnrordForestTenureRoad2020]. Crossing r as.character(my_site) was ranked as a r my_priority_info() %>% pull(priority) priority for proceeding to design for replacement.
r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")
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, '.'))
my_photo1 = pull_photo_by_str(str_to_pull = '_d1_') my_caption1 = paste0('Habitat downstream of 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('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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