0800-appendix-197640.Rmd

```{r setup-197640, eval = F}
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')


```



```{r  load-data-197640}
my_site <- 197640

```

`r appendix_title()`

## Site Location {-}

PSCIS crossing `r as.character(my_site)` is located on a `r my_pscis_info() %>% pull(stream_name)` on `r my_overview_info() %>% pull(road_name)` approximately 18km south of Houston and immediately south of the Carrier FSR turn-off.  The crossing consisted of two culverts (`moti_chris_culvert_id:` 1756173 and 1756168) 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 B.C. Ministry of Transportation and Infrastructure (MoTI).

<br>

## 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, has an upstream watershed area of approximately `r round(my_bcfishpass() %>% pull(watershed_upstr_ha)/100,1)`km^2^ that contains an estimated `r my_bcfishpass() %>% pull(total_wetland_ha)`ha of wetland. The elevation of the watershed ranges from a maximum of 1460m to 820m at the crossing. Upstream of `r my_overview_info() %>% pull(road_name)`, `r my_fish_sp()` have been previously recorded as present while downstream, chinook, coho and pink salmon are known to spawn in Buck Creek [@data_fish_obs; @wilson_rabnett2007FishPassage; @ncfdc1998MidBulkleyDetailed]. Pink salmon have been noted as spawning in the first reach of Buck Creek, with coho spawners noted to Reach 3, and chinook spawners to Reach 5 where the subject tributary enters the mainstem [@ncfdc1998MidBulkleyDetailed].  @dfo1991FishHabitat reports that Buck Creek supports a small chinook population ranging from 12-100 spawners. 

<br>

Three water temperature sensors have been deployed on the Buck Creek mainstem since 2016 [@westcott2020UpperBulkley]. The closest water sensor to the subject stream is near the 9km mark of Buck Flats Road.  The sensor has been gathering water temperature data at 1hour intervals since 2017 with data available through the Skeena Salmon Data Centre [here](https://data.skeenasalmon.info/dataset/upper-bulkley-water-temperature-monitoring-data) [@dfo/flnro2019WaterTemperature]. 

<br>

Upstream of crossing `r as.character(my_site)` on `r my_pscis_info() %>% pull(stream_name)`, multiple tributaries containing contain numerous modelled road stream crossings enter the mainstem, however, these tributaries are not expected to contain much valuable habitat due to the small size and low elevation of their contributing watersheds.  

<br>

PSCIS stream crossing `r as.character(my_site)` was ranked as a high priority for follow up following 2020 Phase 1 - fish passage assessments that targeted all major streams in the Buck Creek watershed. Crossing `r as.character(my_site)` was located on the stream with the highest value habitat potentially blocked to anadromous species by a road-stream crossing structure in the watershed. Therefore, a habitat confirmation was conducted in 2020 with results in this memo. 

<br>
 
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. Crossing `r as.character(my_site)` was revisited in the 
summer of 2023 to conduct baseline fish sampling but at the time of the survey the stream adjacent to the crossing was primarily dry so sampling was not conducted.

<br>

A map of the watershed is provided in map attachment [`r my_bcfishpass() %>% pull(dbm_mof_50k_grid)`](`r my_mapsheet()`).

<br>

## Stream Characteristics at Crossing {-}

At the time of the 2020 survey, both culverts were un-embedded, non-backwatered and ranked as a barrier to upstream fish passage according to the provincial protocol [@fish_passage_assessments]. The pipes were `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-197640)). 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.


<br>

As previously noted, during the 2023 reassessment the crossing was primarily dry with only a very small outlet pool (Figure \@ref(fig:summary-197640-2023)). Both culverts were un-embedded, non-backwatered and had 0.6m outlet drops. Complete 
reassessment data from the 2023 fish passage assessment will be submitted to the PSCIS database and is available [here](https://github.com/NewGraphEnvironment/fish_passage_skeena_2023_reporting/blob/main/data/backup/pscis_all.csv).

<br>

```{r eval=F}
##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 Buck Creek `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-197640-01) - \\@ref(fig:photo-197640-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-197640-d1))"))`. 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-197640)). 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. A fish (130mm) was observed in the culvert outlet pool and a substance suspected to be didymo was noted on the substrate.  The habitat was rated as `r my_priority_info(loc = 'ds') %>%  pull(hab_value)` value as it was considered an important migration corridor with habitat of moderate rearing potential for fry and juvenile salmonids. 

<br>

## 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 `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-197640-03) - \\@ref(fig:photo-197640-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-197640-d2))"))`. 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-197640)). 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. Rare pockets of gravel suitable for spawning resident, fluvial and anadromous salmonids were noted. The stream appeared to be aggraded with side bars common.  One salmonid (110mm - unidentified species) was observed just upstream of `r my_overview_info() %>% pull(road_name)`. The habitat was rated as r my_priority_info(loc = 'us') %>% pull(hab_value)` value for fry and juvenile salmonid rearing. 

<br>

Approximately 4km upstream on an east-forking tributary is PSCIS crossing 197647, located on Carrier FSR (Table \@ref(tab:tab-culvert-197647)). This culvert was also assessed during the 2020 survey but the stream was dry and did not provide any viable fish habitat, although there are numerous fish sample sites, conducted in the early 2000's, located just downstream [@moeStreamInventorySample].

<br>

Table \@ref(tab:tab-culvert-bcfp-197640) `r text_ref_tab_summary_bcfp()` 

<br>

## 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.

<br>

As of March 2024, replacement of PSCIS crossing `r as.character(my_site)` is currently in the planning process, lead by the Ministry of Transportation and Infrastructure.

<br>

## Conclusion {-}

A conservative estimate of mainstem 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 to the top end of a 71ha wetland where rainbow trout have been recorded. Habitat in the areas surveyed upstream of the culvert were rated as `r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value)` value for salmonid rearing with areas of wetland habitat likely suitable for rainbow trout, coho and steelhead rearing. `r my_overview_info() %>% pull(road_name)` is the responsibility of the Ministry of Transportation and Infrastructure adn the crossing was ranked as a `r my_priority_info() %>% pull(priority)` priority for proceeding to design for replacement. 

<br>

Following the 2020 habitat confirmation assessment and the initial release of this report, planning began to replace crossing `r as.character(my_site)` with preliminary designs commissioned by the Canadian Wildlife Federation in collaboration with the MoTI. Although baseline fish sampling could not be completed in 2023 due to low water conditions, the crossing 
was still considered a high priority for replacement due to relatively lower costs of replacement (when compared to paved major roads), significant amounts of potential habitat upstream, its proximity to the high value Buck Creek and because of the severity of migration barrier presented by the large culvert outlet drops.


<br>

```{r tab-culvert-197640, eval = T}
print_tab_summary()

```


`r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")`

<br>

```{r tab-culvert-197647, eval = T}
print_tab_summary(dat = pscis_all, 
                  site = 197647, 
                  site_photo_id = 1804986
                  )

```

<br>

```{r summary-197640-2023-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(site = my_site, dir_photos = "data/2023/photos/", str_to_pull = 'crossing_all')

my_caption1 = paste0('Photos of PSCIS crossing ', my_site, ' taken in September 2023. From top left clockwise: Road/Site Card, Barrel, Outlet, Downstream, Upstream, Inlet.')

```

```{r summary-197640-2023, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo1)

```

<br>

```{r tab-habitat-summary-197640}
tab_hab_summary %>% 
  filter(Site  == my_site) %>% 
  # select(-Site) %>% 
  my_kable(caption_text = paste0('Summary of habitat details for PSCIS crossing ', my_site, '.')) 

```

<br>

```{r tab-culvert-bcfp-197640, eval = T}
print_tab_summary_bcfp()
```

<br>

```{r photo-197640-01-prep, eval=T}
my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')

my_caption1 = paste0('Habitat downstream of PSCIS crossing ', my_site, '.')

```

```{r photo-197640-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))
```

<br>

```{r photo-197640-02-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_d2_')

my_caption2 = paste0('Habitat downstream of crossing ', my_site, ' at the confluence with Buck Creek.')
```

```{r photo-197640-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))

```

<br>

```{r photo-197640-d01, fig.cap = my_caption, fig.show="hold", out.width= c("49.5%","1%","49.5%"), eval=identical(gitbook_on, FALSE)}

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))
```


```{r photo-197640-03-prep}
my_photo1 = pull_photo_by_str(str_to_pull = '_u1_')

my_caption1 = paste0('Habitat upstream of PSCIS crossing ', my_site, '.')
```

```{r photo-197640-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))

```

<br>

```{r photo-197640-04-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_u2_')

my_caption2 = paste0('Habitat upstream of PSCIS crossing ', my_site, '.')

```

```{r photo-197640-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))
```

```{r photo-197640-d02, fig.cap = my_caption, fig.show="hold", out.width= c("49.5%","1%","49.5%"), eval=identical(gitbook_on, FALSE)}

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))
```