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 <- 62505
r fpr_appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is located on a r my_pscis_info() %>% pull(stream_name) 2.5km west of Fernie on r my_overview_info() %>% pull(road_name). The crossing is located within the Mount Fernie Provincial Park Boundary and approximately 75m upstream from the confluence with Lizard Creek and the responsibility of the Ministry of Environment and Climate Change Strategy. The area is a popular recreational destination for hikers and mountain bikers.
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 south-west 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-62505)). Upstream of r my_overview_info() %>% pull(road_name), no fish have previously been recorded [@moe2020KnownBC]. Downstream, Lizard Creek supports westslope cutthroat trout, bull trout, mountain whitefish, brook trout, longnose sucker and longnose dace [@data_fish_obs]. @elkriveralliance2020ElkRiver conducted redd surveys in Lizard Creek in 2019 along with Morrissey Creek, Coal Creek and Forsyth Creek. A total of 55 redds were observed within a 2.4km section of Lizard Creek comprising the largest densities of redds of the four tributaries surveyed (22.9 redds/km).
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 prioritized for assessment due to it's location within provincial park boundaries and the associated positive implications for restoration potential. Although assessed as a low priority for follow up in planning for 2020 field work [@irvine2021UpperElk], during 2020 field surveys the site was noted as having a significant sized outlet drop, good flow during the dryest part of the year and a location directly adjacent to Lizard Creek which contains confirmed spawning habitat for westslope cutthrout trout. Table \@ref(tab:tab-bcfp-62505) presents preliminary fish passage modelling data for crossing 62505 with linear length of habitat <8% upstream estimated at 0.4km and an additional 0.5km of habitat modeled between 8 - 15%. 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-62505)). 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 Lizard Creek r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-62505-01) - \\@ref(fig:photo-62505-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-62505-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-62505)). 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. No barriers were noted downstream and there were gravels suitable for spawning westslope cutthroat trout throughout. The habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value for resident salmonid rearing due to a lack of water.
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 ~60m above PSCIS culvert 197863 r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-62505-03) - \\@ref(fig:photo-62505-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-62505-d02))")). Immediately above culvert 197863 the stream became very steep with gradients exceeding 20%. 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-62505)). 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 habitat rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing upstream of crossing r as.character(my_site) and below crossing 197863 (where gradients increased to >20%). r my_overview_info() %>% pull(road_name), at the crossing location, is located within the Mount Fernie Provincial Park Boundary and is the responsibility of the Ministry of Environment and Climate Change Strategy. As the culvert is located approximately 75m upstream from the confluence with Lizard Creek where westslope cutthrout trout spawning is known to occur, remediation of fish passage at the site could reduce the risk that the culvert prevents passage by spawning strays and progeny potentially migrating from areas of the tributary downstream of the culvert as well as from the mainstem of Lizard Creek. 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('Confluence with Lizard Creek located ~70m 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 <- 62505
r fpr_appendix_title()
Site Location {-}
PSCIS crossing r as.character(my_site) is located on a r my_pscis_info() %>% pull(stream_name) 2.5km west of Fernie on r my_overview_info() %>% pull(road_name). The crossing is located within the Mount Fernie Provincial Park Boundary and approximately 75m upstream from the confluence with Lizard Creek and the responsibility of the Ministry of Environment and Climate Change Strategy. The area is a popular recreational destination for hikers and mountain bikers.
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 south-west 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-62505)). Upstream of r my_overview_info() %>% pull(road_name), no fish have previously been recorded [@moe2020KnownBC]. Downstream, Lizard Creek supports westslope cutthroat trout, bull trout, mountain whitefish, brook trout, longnose sucker and longnose dace [@data_fish_obs]. @elkriveralliance2020ElkRiver conducted redd surveys in Lizard Creek in 2019 along with Morrissey Creek, Coal Creek and Forsyth Creek. A total of 55 redds were observed within a 2.4km section of Lizard Creek comprising the largest densities of redds of the four tributaries surveyed (22.9 redds/km).
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 prioritized for assessment due to it's location within provincial park boundaries and the associated positive implications for restoration potential. Although assessed as a low priority for follow up in planning for 2020 field work [@irvine2021UpperElk], during 2020 field surveys the site was noted as having a significant sized outlet drop, good flow during the dryest part of the year and a location directly adjacent to Lizard Creek which contains confirmed spawning habitat for westslope cutthrout trout. Table \@ref(tab:tab-bcfp-62505) presents preliminary fish passage modelling data for crossing 62505 with linear length of habitat <8% upstream estimated at 0.4km and an additional 0.5km of habitat modeled between 8 - 15%. 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-62505)). 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 Lizard Creek r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-62505-01) - \\@ref(fig:photo-62505-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-62505-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-62505)). 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. No barriers were noted downstream and there were gravels suitable for spawning westslope cutthroat trout throughout. The habitat was rated as r my_priority_info(loc = 'ds') %>% pull(hab_value) value for resident salmonid rearing due to a lack of water.
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 ~60m above PSCIS culvert 197863 r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-62505-03) - \\@ref(fig:photo-62505-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-62505-d02))")). Immediately above culvert 197863 the stream became very steep with gradients exceeding 20%. 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-62505)). 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 habitat rated as r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value) value for salmonid rearing upstream of crossing r as.character(my_site) and below crossing 197863 (where gradients increased to >20%). r my_overview_info() %>% pull(road_name), at the crossing location, is located within the Mount Fernie Provincial Park Boundary and is the responsibility of the Ministry of Environment and Climate Change Strategy. As the culvert is located approximately 75m upstream from the confluence with Lizard Creek where westslope cutthrout trout spawning is known to occur, remediation of fish passage at the site could reduce the risk that the culvert prevents passage by spawning strays and progeny potentially migrating from areas of the tributary downstream of the culvert as well as from the mainstem of Lizard Creek. 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('Confluence with Lizard Creek located ~70m 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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