0800-appendix-197662.Rmd

```{r setup-197662, 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-197662}
my_site <- 197662

```

`r appendix_title()`

## Site Location {-}

PSCIS crossing `r as.character(my_site)` is located on `r my_pscis_info() %>% pull(stream_name)` on `r my_overview_info() %>% pull(road_name)` approximately 30km east of Houston, BC with the highway located approximately 1km 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.

```{r eval=F}
##idon't think we need this here but...
#During 2020 surveys, PSCIS culvert 197669 was documented on `r my_pscis_info() %>% pull(stream_name)`, 1.2km upstream of the FSR.

```

<br>

## Background {-}


`r my_pscis_info() %>% pull(stream_name)` drains one of the largest tributary watersheds in the upper Bulkley River.  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 1660 to 680m at PSCIS crossing `r as.character(my_site)`. Upstream of the highway, `r my_pscis_info() %>% pull(stream_name)` is known to contain coho, chinook, steelhead, rainbow trout, longnose dace and longnose sucker [@data_fish_obs]. Steelhead, coho and chinook spawning has been noted in the downstream reaches of the stream with historical escapements ranging from 0-100 spawners in the reach adjacent to the Bulkley River confluence [@gottesfeld_etal2002ConservingSkeena; @hancock_etal1983CatalogueSalmon].  @gottesfeld_etal2002ConservingSkeena note that in some years during  low  flow  conditions, Richfield is partially dewatered and impassable to fish. A bridge (modelled crossing 1805593) is located under the railway approximately 830m downstream of the crossing which is reported by @wilson_rabnett2007FishPassage to constrict the channel.  Although numerous modelled crossings are located upstream of the highway an impassable waterfall is located approximately 2km upstream of the highway (pers. comm. Jonathan Van Barneveld, Forester - FLNR).


<br>

In the summer of 1998,  the Nadina Community Futures Development Corporation (NCFDC) contracted the British Columbia Conservation Foundation to carry out a detailed Level 1 Fish, Fish Habitat and Riparian Assessment in the first two reaches of `r my_pscis_info() %>% pull(stream_name)` as well as several other large Upper Bulkley River tributary streams and the Upper Bulkley mainstem.  The area surveyed extended to approximately 2km upstream of the culvert where an 18m high waterfall is located [@ncfdc1998MidBulkleyDetailed]. Building on these assessments and detailed fish sampling, @ncfdc1998MidBulkleyDetailed developed restoration prescriptions for the lower reaches of the watershed based on the following assessment of impacts associated with landuse in the watershed:

 * loss of riparian forest and soil compaction in areas used for agriculture, the powerline corridor, transportation corridors and at housing developments within the floodplain.
 * loss of the shrub/herb layer and soil compaction from cattle grazing where overstory still present.
 * removal of large woody debris which controls lateral channel movement and plant community distribution on the floodplain.
 * loss of connectivity during low flow periods due to a lack of flow and outlet drop at the highway culverts.
 * poor LWD function, channelization, high summer water temperatures, extensive eroding banks and associated sediment load, and the consistently high compaction and embeddedness of substrate.

<br>
 
Overall, @ncfdc1998MidBulkleyDetailed report that, in an unimpacted state, the first reach of `r my_pscis_info() %>% pull(stream_name)` (including the 2.5km upstream of the culvert) is a critical and productive area for spawning and rearing particularly for coho and steelhead.  They also note that the area may be an important area for chinook salmon summer rearing and summer/fall spawning habitat as it contains larger substrate, greater foraging opportunities, greater channel complexity and cooler temperatures than present in the adjacent Bulkley mainstem.  The proximity of the reach to the mainstem provides easy access to overwintering habitat, mainstem rearing areas for older juvenile salmonids and options for refuge during high flow events.  Detailed prescriptions for restorative measures that address noted impacts (including the construction of riffle structures to backwater the culverts) are documented in @ncfdc1998MidBulkleyDetailed.

<br>

Overwintering studies using minnowtrapping were conducted downstream of the highway culvert between 2006 and 2009 with coho, rainbow trout/steelhead and northern pikeminnow captured.  Results are summarized in @donas_newman2007BulkleyRiver, @donas_newman2008BulkleyRiver and @donas_newman2010BulkleyRiver.

<br>
 
A water temperature monitoring station has been operational on Richfield Creek just upstream of the highway since November 2014. Results in  @westcott2020UpperBulkley, indicate that from 2017 - 2019, mean weekly maximum temperatures in Richfield Creek were 3-5$^\circ$C cooler than temperatures recorded at stations located on the Upper Bulkley River mainstem. @westcott2020UpperBulkley also reports that a continuous water level and temperature monitoring station is proposed on the stream.

<br>


Although in 2007, @wilson_rabnett2007FishPassage reported that fish passage at `r as.character(my_site)` was not hindered by the culverts at that time the site was rated as a priority for follow up following background review and a Phase 1 assessment in 2020 indicating that the crossing was not passable according to provincial metrics and due to the presence of significant quantities of upstream habitat suitable for salmonid rearing and spawning. 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 considered a barrier to upstream fish passage. 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 an outlet drop of `r my_pscis_info() %>% pull(outlet_drop_meters)`m (Table \@ref(tab:tab-culvert-197662)). Water temperature was `r my_habitat_info() %>% filter(rowname == 'temperature c') %>% pull(us)`$^\circ$C, pH was `r my_habitat_info() %>% filter(rowname == 'p h') %>% pull(us)` and conductivity was `r my_habitat_info() %>% filter(rowname == 'conductivity m s cm') %>% pull(us)`uS/cm.  


<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 `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-197662-01) - \\@ref(fig:photo-197662-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-197662-d01))"))`. Overall, 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-197662)). 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. There were unembedded gravels and cobbles suitable for spawning present throughout.

<br>

Immediately downstream of the culverts for approximately 80m, channel structure was simplified with no pools present and a lack of large woody debris. This is likely the result of armouring of the banks and the high flow velocities out of the crossing structure pipes. Further downstream, the channel flows through a residential area with some deep pools and glides to over 1m deep. Riparian vegetation is comprised of a narrow band of mature cottonwood forest with some areas adjacent to houses lacking trees altogether. There was evidence of large woody debris removal from the channel (chainsaw cut logs in the stream) and some stream corners were armoured with rock, concrete and old vehicles. Although some degradation of habitat was apparent, the area downstream of the crossing was rated as `r my_priority_info(loc = 'ds') %>%  pull(hab_value)` high value for salmonid rearing and spawning.  

<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-197662-03) - \\@ref(fig:photo-197662-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-197662-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-197662)). 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. Within the area surveyed, riparian areas adjacent to both banks were used as rangeland with several cattle access points on the stream and evidence of understory shrub degradation from cattle grazing. There was a debris jam (up to 1m high in places) located just upstream of the highway.  Overall, the stream had high habitat complexity including numerous pools up to 2m deep and frequent glide sections to 1m deep throughout. There were also extensive areas of gravel suitable for spawning for resident and anadromous species. Robert Hatch Creek enters the main channel approximately 400m upstream of the culvert and adjacent to Richfield Creek was comprised of beaver influenced wetland type habitat. Habitat value in the areas surveyed was rated as `r my_priority_info(loc = 'us') %>% pull(hab_value)` for resident, fluvial and anadromous salmonid rearing and spawning. 

<br>


## Fish Sampling {-}

Minnowtrapping was conducted with three traps set overnight upstream as well as downstream of the crossing.  A total of `r tab_fish_summary %>% filter(site_id == paste0(my_site, '_ds') & species_code == 'CO') %>% pull(count_fish)` coho and `r tab_fish_summary %>% filter(site_id == paste0(my_site, '_ds') & species_code == 'RB') %>% pull(count_fish)` rainbow trout were captured downstream.  Only rainbow trout (`r tab_fish_summary %>% filter(site_id == paste0(my_site, '_us') & species_code == 'RB') %>% pull(count_fish)` fish) were captured upstream (Table \@ref(tab:tab-fish-dens-197662) and `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-197662-05) - \\@ref(fig:photo-197662-06))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-197662-d03))"))`.

<br>


Table \@ref(tab:tab-culvert-bcfp-197662) `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)`  before an impassable falls.  Habitat in the area surveyed upstream of the crossing was rated as `r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value)` value for resident, fluvial and anadromous salmonid rearing/spawning. The results of temperature monitoring in Richfield Creek and the Upper Bulkley River mainstem by @westcott2020UpperBulkley indicate that Rcihfield Creek (and other major tributaries to the upper Bulkley River) may have great importance for providing fish refuge from high temperatures during the hottest and driest months of the year as well as for moderation of temperatures downstream in the Upper Bulkley River. Although the ability of minnowtrapping to detect presence/absence is low when compared to other sampling techniques, the lack of coho salmon captured upstream is consistent with sampling conducted by @ncfdc1998MidBulkleyDetailed and adds to the weight of evidence that the culvert is preventing upstream spawner migration.

<br>

The crossing at the highway presents a barrier not only to some fry and juvenile salmonids due to the small outlet drop and high flow velocities within the pipes but also to adult salmon migrating upstream to spawn during low flows due to shallow water depths in the pipes. Future electrofishing surveys upstream and downstream of the crossing are recommended to provide presence/absence as well as density data for chinook salmon, coho salmon and other species. `r my_overview_info() %>% pull(road_name)` is the responsibility of the Ministry of Transportation and Infrastructure and was ranked as a `r my_priority_info() %>% pull(priority)` priority for proceeding to design for replacement. Restoration of riparian forests, cattle exclusion, bank stabilization and habitat complexing as per @ncfdc1998MidBulkleyDetailed could be considered alongside fish passage restoration activities and an assessment of the passability of the debris jam just upstream of the crossing is recommended when fish passage restoration works at the highway are initiated.

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

<br>

```{r tab-culvert-197662, eval = T}
print_tab_summary()

```


<br>

```{r tab-habitat-summary-197662}
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-197662, eval = T}
print_tab_summary_bcfp()
```



<br>

```{r tab-fish-dens-197662, eval=T}
my_caption <- paste0('Fish captured in minnowtraps set overnight upstream and downstream of PSCIS crossing ', my_site, '.')

tab_fish_mt() %>% 
  my_kable(caption_text = my_caption)
```

<br>


```{r photo-197662-01-prep, eval=T}
my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')

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

```

```{r photo-197662-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))
```

<br>

```{r photo-197662-02-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_d2_')

my_caption2 = paste0('Typical habitat downstream of PSCIS crossing ', my_site, '.')
```

```{r photo-197662-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))

```

<br>

```{r photo-197662-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-197662-03-prep}
my_photo1 = pull_photo_by_str(str_to_pull = '_u1_')

my_caption1 = paste0('Gravel and cobble substrate upstream of PSCIS crossing ', my_site, '.')

```

```{r photo-197662-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))

```

<br>

```{r photo-197662-04-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_u2_')

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

```

```{r photo-197662-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))
```

```{r photo-197662-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))
```

<br>


```{r photo-197662-05-prep}
my_photo1 = pull_photo_by_str(str_to_pull = '_df1_')

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

```

```{r photo-197662-05, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))

```

<br>

```{r photo-197662-06-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_uf1_')

my_caption2 = paste0('Rainbow trout captured upstream of PSCIS crossing ', my_site, '.')

```

```{r photo-197662-06, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))
```

```{r photo-197662-d03, 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))
```