0800-appendix-8478-trib-to-mcdonell.Rmd

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output: html_document
editor_options: 
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```{r setup-8478, eval = F}
knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
source('scripts/packages.R')
source('scripts/tables.R')
source('scripts/functions.R')
```

```{r  load-data-8478}
my_site <- 8478

```

`r fpr::fpr_appendix_title()`

## Site Location {.unnumbered}

PSCIS crossing `r as.character(my_site)` is a located on a `r fpr::fpr_my_pscis_info()` within the Zymoetz River watershed. 
The culvert is located on the `r fpr_my_pscis_info(col_pull = road_name)` at a point `r round(fpr::fpr_my_bcfishpass(col_pull = downstream_route_measure)*0.001, 1)`km upstream of where the stream flows north-west into the western end of McDonell Lake. 
The Forest Tenure Layer indicates that BC Timber Sales is responsible for the road at the crossing location.

<br>

## Background {.unnumbered}

At crossing `r as.character(my_site)`, `r fpr::fpr_my_pscis_info()` is a
`r fpr::fpr_my_bcfishpass() %>% english::ordinal()` order stream with an
upstream watershed area of approximately
`r fpr::fpr_my_wshd()`km^2^. This stream drains a steep cold water system, where the elevation ranges from
a maximum of `r fpr::fpr_my_wshd(col = 'elev_max')`m to
`r fpr::fpr_my_wshd(col = 'elev_site')`m near the crossing (Table
\@ref(tab:tab-wshd-8478)).

<br>

The crossing was previously assessed with a fish passage assessment by @viveiros2011FishPassage in 2010, with fish sampling 
and replacement with a streambed simulation recommneded. Approximately 1.5km downstream of crossing `r as.character(my_site)`
there is a documented sockeye spawning location in the FISS database, and upstream of the FSR `r fpr::fpr_my_fish_sp()` 
have been documented in the past [@norris2024smnorrisbcfishobs; @moe2024KnownBC]. Revisited in 2023, surveyors conducted 
a habitat confirmation assessment and electrofishing with results included in this memo.  

<br>


```{r tab-wshd-8478, eval = T}
fpr::fpr_table_wshd_sum(site_id = my_site) %>% 
  fpr::fpr_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',
           scroll = F)

```

<br>

Habitat modelling outputs form `bcfishpass` indicated only 400m of habitat accessible to steelhead or coho (stream gradients <20% and 15%) and no habitat of high intrinsic potential for either species (gradients <8.5% for steelhead and <5.5% for coho).  Outputs are presented in Table
\@ref(tab:tab-culvert-bcfp-8478). A map of the watershed is provided in
map attachment
[`r fpr::fpr_my_bcfishpass(col_pull = dbm_mof_50k_grid)`](`r fpr::fpr_my_mapsheet(wshd = "zymo", archive_date = "2022-09-06")`).

<br>

```{r tab-culvert-bcfp-8478, eval = T}
fpr::fpr_table_bcfp(scroll = gitbook_on) 
```

<br>


## Stream Characteristics at Crossing `r as.character(my_site)` {.unnumbered}

At the time of the survey in 2023, PSCIS crossing `r as.character(my_site)` was
un-embedded, non-backwatered and ranked as a
`r fpr::fpr_my_pscis_info(col_pull = barrier_result) %>% stringr::str_to_lower()` to upstream fish passage according to the provincial protocol
[@moe2011Fieldassessment] (Table \@ref(tab:tab-culvert-8478)). The culvert was slightly undersized for the size of the stream with an outlet drop measured at 0.2m high. Water temperature was `r fpr::fpr_my_habitat_info(loc = "ds", col_pull = 'temperature_c')`$^\circ$C,
pH was `r fpr::fpr_my_habitat_info(loc = "ds", col_pull = 'p_h')` and
conductivity was `r fpr::fpr_my_habitat_info(loc = "ds", col_pull = 'conductivity_m_s_cm')`uS/cm.

`r if(identical(gitbook_on, FALSE)){knitr::asis_output("\\pagebreak")}`

<br>

```{r tab-culvert-8478, eval = T}
fpr::fpr_table_cv_summary_memo()

```


```{r eval=F}
##this is useful to get some comments for the report
hab_site %>% filter(site == my_site & location == 'ds') %>% pull(comments)
hab_site %>% filter(site == my_site & location == 'us') %>% pull(comments)

```

## Stream Characteristics Downstream {.unnumbered}

<!-- 8478_ds says abundant gravels but the ef sites say limited gravels so not too sure what to go with here -->
`r fpr_my_survey_dist(loc = 'ds')`. `r fpr_my_habitat_paragraph(loc = 'ds')` The stream was noted as having good flow and containing pockets of gravel suitable for spawning `r if(gitbook_on){knitr::asis_output("(Figure \\@ref(fig:photo-8478-01)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-8478-d01))."))` Deep pools were infrequent and the morphology was step-pool cobble. The habitat was rated as `r fpr::fpr_my_priority_info(loc = 'ds') %>% stringr::str_to_lower()` value suitable for salmonid rearing and spawning. 

<br>

## Stream Characteristics Upstream {.unnumbered}

`r fpr_my_survey_dist(loc = 'us')` to a point where gradients increased to 20% `r if(gitbook_on){knitr::asis_output("(Figure \\@ref(fig:photo-8478-02)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-8478-d01))."))` `r fpr_my_habitat_paragraph(loc = 'us')` There was good flow volume in the area surveyed and step-pool cascades (<1m high) created by large woody debris present throughout and pockets of gravel present suitable for spawning. The habitat was rated as `r fpr::fpr_my_priority_info(loc = 'us') %>% stringr::str_to_lower()` value with moderate rearing potential for dolly varden.

<br>


## Fish Sampling {.unnumbered}

Electrofishing was conducted at three sites below and one site above the FSR with results summarised in Tables \@ref(tab:tab-fish-site-8478) - \@ref(tab:tab-fish-dens-8478) and Figure
\@ref(fig:plot-fish-box-8478). A total of `r tab_fish_summary %>% filter(site_id == paste0(my_site, '_ds')) %>% group_by(site_id) %>% janitor::adorn_totals() %>% filter(site_id == 'Total') %>% pull(count_fish)` dolly varden were captured downstream, and `r tab_fish_summary %>% filter(site_id == paste0(my_site, '_us')) %>% group_by(site_id) %>% janitor::adorn_totals() %>% filter(site_id == 'Total') %>% pull(count_fish)` dolly varden were captured upstream. Multiple fish captured had deteriorating purple gill plates and unusual round black spots `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-8478-03) - \\@ref(fig:photo-8478-04)).")}else(knitr::asis_output("(Figures \\@ref(fig:photo-8478-d02))."))` All fish captured with a fork length greater than 60mm were tagged with Passive Integrated Transponders (PIT tags) with data stored [here](`r paste0(params$repo_url, "blob/main/data/2023/habitat_confirmations.xls")`).


<br>

## Structure Remediation and Cost Estimate {.unnumbered}

Although replacement of PSCIS crossing `r as.character(my_site)` with a streambed simulation may be feasible and a potentially more economical option, replacement with a bridge (`r fpr::fpr_my_pscis_info(col_pull = recommended_diameter_or_span_meters)`m span) is roughly estimated to cost \$`r format(fpr::fpr_my_cost_estimate(), big.mark = ',')`. Deactivation of the `r fpr_my_pscis_info(col_pull = road_name)` beyond the culvert and removal of the crossing could also be explored as a cost-effective option.


<br>

## Conclusion {.unnumbered}

PSCIS crossing `r as.character(my_site)` is located on a steeper, colder water stream providing medium value habitat for dolly varden in the areas surveyed. Habitat modelling and ground measurements of gradient upstream of the `r fpr_my_pscis_info(col_pull = road_name)` were slightly above the selected threshold for high intrinsic potential for steelhead rearing (>8.5%) with averaged values at 10%.  As these relatively steep gradients drain a relatively high elevation watershed it may be most suitable for dolly varden. The site was rated as a `r fpr::fpr_my_priority_info(col_pull = priority) %>% stringr::str_to_lower()` 
priority for replacement containing `r fpr::fpr_my_priority_info() %>% stringr::str_to_lower()` value for salmonid rearing and spawning. As noted earlier, multiple fish captured had deteriorating purple gill plates and unusual round black spots potentially indicating some sort of natural or anthropogenic contaminants draining into the watershed. 


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

<br>

```{r tab-habitat-summary-8478}
tab_hab_summary %>% 
  filter(Site  == my_site) %>% 
  # select(-Site) %>% 
  fpr::fpr_kable(caption_text = paste0('Summary of habitat details for PSCIS crossing ', my_site, '.'),
                 scroll = F) 

```

<br>

```{r tab-fish-site-8478, eval=T}
fpr_table_fish_site()

```

<br>

```{r tab-fish-dens-8478, eval=T}
fpr_table_fish_density()

```

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

```{r plot-fish-box-8478, fig.cap= my_caption, eval=T}
my_caption <- paste0('Densites of fish (fish/100m2) captured upstream and downstream of PSCIS crossing ', my_site, '.')

fpr_plot_fish_box() 

```

<br>

```{r photo-8478-01-prep, eval=T}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = 'ds_typical_1_')

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


```

```{r photo-8478-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo1)
```

<br>

```{r photo-8478-02-prep, eval=T}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = 'us_typical_1')

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


```

```{r photo-8478-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo2)
```

```{r photo-8478-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(my_photo1)
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(my_photo2)
```

<br>

```{r photo-8478-03-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = 'fish1')

my_caption1 = paste0('Dolly varden with deteriorating purple gill plates and unusual black spots captured downstream of crossing ', my_site, '.')
```

```{r photo-8478-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo1)
```

<br>

```{r photo-8478-04-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = 'f1_gills_')

my_caption2 = paste0('Dolly varden with deteriorating purple gill plates and unusual black spots captured upstream of crossing ', my_site, '.')

```

```{r photo-8478-04, fig.cap=my_caption2, out.width=photo_width}
knitr::include_graphics(my_photo2)


```

```{r photo-8478-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(my_photo1)
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(my_photo2)
```