0800-appendix-124487.Rmd

```{r setup-124487, 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-124487}
my_site <- 124487

```

`r appendix_title()`

## Site Location {-}

PSCIS crossing `r as.character(my_site)` is on `r my_pscis_info() %>% pull(stream_name)` and `r my_overview_info() %>% pull(road_name)` approximately 18km  south of New Hazelton, BC. The crossing is 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 Ministry of Transportation and Infrastructure.


<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 with a watershed area upstream of the crossing of approximately `r round(my_bcfishpass() %>% pull(watershed_upstr_ha)/100,1)`km^2^. The elevation of the watershed ranges from a maximum of 2300m to 330m at the highway. Upstream, rainbow trout and dolly varden have been recorded [@data_fish_obs]. A large railway trestle bridge is located over the stream approximately 500m upstream of the highway.  


<br>

PSCIS stream crossing `r as.character(my_site)` was ranked as a high priority for follow up by @irvine2018AnalysisPriority due to the large quantity of habitat modelled upstream and selected for assessment in 2020 following consultation with Alecia Fernando from the Gitksan Watershed Authority.  @wilson_rabnett2007FishPassage assessed the site and reported it as not a priority restoration site due to "the limited amount of high value habitat upstream of Highway 16". A map of the watershed is provided in map attachment [`r my_bcfishpass() %>% pull(dbm_mof_50k_grid)`](`r my_mapsheet()`).


## Stream Characteristics at Crossing {-}

At the time of the survey, the two culverts under Highway 16 were un-embedded, non-backwatered and ranked as a barrier to upstream fish passage [@fish_passage_assessments]. The culvert is located under an estimated 40m of highway fill.  The pipes were `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 outlet drops of `r my_pscis_info() %>% pull(outlet_drop_meters)`m (Table \@ref(tab:tab-culvert-124487)). 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. Survey conditions were difficult at the time of assessment as stream flows were high due to recent rain events.


<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 the Bulkley River `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124487-01) - \\@ref(fig:photo-124487-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-124487-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-124487)). 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. The cascade-boulder habitat was rated as `r my_priority_info(loc = 'ds') %>%  pull(hab_value)` value as it was considered an important migration corridor with `r my_priority_info(loc = 'ds') %>% pull(hab_value)` value habitat for salmonid rearing and spawning.  During the survey, an approximately 40cm long salomonid was observed attempting to ascend from the outlet pool into the culvert outlet.


<br>

## Stream Characteristics Upstream {-}

The stream was surveyed upstream from `r as.character(my_site)` for `r my_priority_info(loc = 'us') %>% pull(survey_length_m)`m `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-124487-03) - \\@ref(fig:photo-124487-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-124487-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-124487)). 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. There were pockets of gravel suitable for spawning for resident and anadromous species with minimal pool habitat observed. Habitat value was rated as `r my_priority_info(loc = 'us') %>% pull(hab_value)` as an important migration corridor with limited spawning habitat and moderate rearing potential for coho, dolly varden, cutthrout rearing and spawning. 

<br>


Table \@ref(tab:tab-culvert-bcfp-124487) `r text_ref_tab_summary_bcfp()` 

<br>

## Structure Remediation and Cost Estimate {-}

Structure replacement with a bridge (`r my_pscis_info() %>% pull(recommended_diameter_or_span_meters)`m span) is recommended to provide access to the habitat located upstream of PSCIS crossing `r as.character(my_site)`. 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>


## Conclusion {-}

There is an estimated `r my_priority_info() %>% pull(upstream_habitat_length_km)`km of mainstem habitat upstream of crossing `r as.character(my_site)`.  Habitat in the areas surveyed upstream of the crossing was rated as `r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value)` value for salmonid rearing/spawning. The crossing represents a complete barrier to upstream migration for fish in the Bulkley River watershed regardless of species or life stage. `r my_overview_info() %>% pull(road_name)` is the responsibility of the Ministry of Transportation and Infrastructure.  The crossing was ranked as a `r my_priority_info() %>% pull(priority)` priority for proceeding to design for replacement. 

<!-- this is a bit strange but the pages.js will not build beyond this so we leave for now -->
<!-- `r if(gitbook_on){knitr::asis_output("<br>")} else knitr::asis_output("\\pagebreak")` -->

<br>

```{r tab-culvert-124487, eval = T}
print_tab_summary()

```


<br>

```{r tab-habitat-summary-124487}
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-124487, eval = T}
print_tab_summary_bcfp()
```



<br>


```{r photo-124487-01-prep, eval=T}
my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')

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

```

```{r photo-124487-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))
```

<br>

```{r photo-124487-02-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_d2_')

my_caption2 = paste0('Typical habitat downstream of crossing ', my_site, ' below the railway bridge and adjacent to the Bulkley River mainstem.')
```

```{r photo-124487-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))

```

<br>

```{r photo-124487-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-124487-03-prep}
my_photo1 = pull_photo_by_str(str_to_pull = '_u1_')

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

```

```{r photo-124487-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))

```

<br>

```{r photo-124487-04-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_u2_')

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

```

```{r photo-124487-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))
```

```{r photo-124487-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))
```