0800-appendix-8525-trib-to-coal.Rmd

---
output: html_document
editor_options: 
  chunk_output_type: console
  markdown: 
    wrap: 72
---

```{r setup-8525, eval = F}
knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
source('scripts/packages.R')
source('scripts/tables.R')
source('scripts/moti_climate.R')
source('scripts/functions.R')
```

```{r  load-data-8525}
my_site <- 8525
my_site2 <- 8529

```

`r fpr::fpr_appendix_title()`

## Site Location {.unnumbered}

PSCIS crossing `r as.character(my_site)` on a `r fpr::fpr_my_pscis_info()` is located on `r fpr_my_pscis_info(col_pull = road_name)` 
approximately 7.5km west of the downstream end of McDonnell Lake. The road at the crossing location is the responsibility of the Ministry of Forests.

<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^. The
elevation of the watershed 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-8525)).  The stream flows in a 
south-west direction into Coal Creek approximately `r round(fpr::fpr_my_bcfishpass(col_pull = downstream_route_measure)*0.001, 1)`km 
downstream of `r fpr_my_pscis_info(col_pull = road_name)`.

<br>

The crossing was originally assessed with a fish passage assessment by @viveiros2011FishPassage in 2010.  The site
was re-assessed in 2022 and ranked as a moderate priority for follow up
in @irvine_wintersheidt2023SkeenaWatershed due to relatively low mapped gradients, the crossing's proximity to Coal Creek, 
and relatively good flow volumes. Upstream of the crossing, `r fpr::fpr_my_fish_sp()` have been documented in the past 
[@norris2024smnorrisbcfishobs; @moe2024KnownBC]. In 2022, minnow traps were set at crossing `r as.character(my_site)` to 
scope for coho presence with only dolly varden captured. Revisited in 2023, surveyors conducted a habitat confirmation 
assessment and electrofishing with results included in this memo. 

<br>

```{r tab-wshd-8525, 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>

A summary of habitat modelling outputs is presented in Table
\@ref(tab:tab-culvert-bcfp-8525). 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-8525, eval = T}
fpr::fpr_table_bcfp(scroll = gitbook_on) 
```


```{r tab-moti-8525, eval = FALSE}
## Climate Change Risk Assessment

# Preliminary climate change risk assessment data for the site is presented in Table \@ref(tab:tab-moti-8525).
fpr_table_moti()
```

## 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-8525)). There was a small blockage at the inlet and a 0.5m outlet drop. 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-8525, 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}

`r fpr_my_survey_dist(loc = 'ds')`. The stream was noted to have intermittent dewatering, but good flow relative to
other streams in the area given it was a very dry year. Water was noted as relatively turbid
`r if(gitbook_on){knitr::asis_output("(Figure \\@ref(fig:photo-8525-01)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-8525-d01))."))` There were few deep pools and abundant small gravels present throughout the area surveyed.
`r fpr_my_habitat_paragraph(loc = 'ds')` The habitat was rated as `r fpr::fpr_my_priority_info(loc = 'ds') %>% stringr::str_to_lower()` 
value for salmonid rearing and spawning. 

<br>

## Stream Characteristics Upstream {.unnumbered}

`r fpr_my_survey_dist(loc = 'us')`  `r if(gitbook_on){knitr::asis_output("(Figure \\@ref(fig:photo-8525-02)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-8525-d01))."))` `r fpr_my_habitat_paragraph(loc = 'us')` 
There were isolated pools every 30 to 50m that were up to 55cm in depth, and abundant gravel throughout. The habitat was 
wetland in character dominated by fern, alder and mature spruce. The habitat was rated as `r fpr::fpr_my_priority_info(loc = 'us') %>% stringr::str_to_lower()` for salmonid rearing and spawning.

<br>

Approximately 1.7km upstream of crossing `r as.character(my_site)`, PSCIS crossing `r as.character(my_site2)` was previously documented as a wooden box culvert.  This site was reassessed in 2023 and the habitat adjacent to the structure
assessed.  The wooden box culvert had recently been replaced with a bridge. The stream was surveyed upstream from crossing `r as.character(my_site2)` for approximately 100m and was noted as having good flow for a small system on a dry year. `r fpr_my_habitat_paragraph(loc = 'us2')` `r if(gitbook_on){knitr::asis_output("(Figure \\@ref(fig:photo-8529-01) - \\@ref(fig:photo-8529-02)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-8529-d01))."))` `r fpr_my_habitat_paragraph(loc = 'us2')` The habitat was rated as `r fpr::fpr_my_priority_info(loc = 'us2') %>% stringr::str_to_lower()` value for salmonid rearing and spawning. 

<br>


## Fish Sampling {.unnumbered}

As noted, in 2022, minnow traps were set at `r as.character(my_site)` to scope for coho presence.  Dolly varden were captured both above and below the crossing, with fish sampling data [here](https://github.com/NewGraphEnvironment/fish_passage_skeena_2022_reporting/blob/main/data/habitat_confirmations.xls)

<br>

During the 2023 survey, electrofishing was conducted at three sites above and three sites below crossing `r as.character(my_site)`,  with results summarised in Tables \@ref(tab:tab-fish-site-8525) - \@ref(tab:tab-fish-dens-8525) and Figure
\@ref(fig:plot-fish-box-8525). A total of `r tab_fish_summary %>% dplyr::filter(site_id == paste0(my_site, '_us')) %>% group_by(site_id) %>% janitor::adorn_totals() %>% dplyr::filter(site_id == 'Total') %>% pull(count_fish)` dolly varden were captured upstream, and `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)` fish were captured downstream, including dolly varden and rainbow trout `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-8525-03) - \\@ref(fig:photo-8525-04)).")}else(knitr::asis_output("(Figures \\@ref(fig:photo-8525-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}

Should restoration/maintenance activities proceed, replacement of PSCIS
crossing `r as.character(my_site)` with a streambed simulation (embedded culvert) recommended
(`r fpr::fpr_my_pscis_info(col_pull = recommended_diameter_or_span_meters)`m
span). Although preliminary - a rough cost of the work is estimated at
\$`r format(fpr::fpr_my_cost_estimate(), big.mark = ',')`.

<br>

## Conclusion {.unnumbered}

There was `r fpr::fpr_my_priority_info(col_pull= upstream_habitat_length_km)`km of steelhead rearing habitat modelled upstream of crossing
`r as.character(my_site)`. Electrofishing surveys in 2023 captured dolly varden upstream of the FSR and rainbow trout and dolly varden downstream. 
Although no coho were captured during assessments in 2022 or 2023, these species may have populated
the system in the past as it is connected to Coal Creek ~800m downstream, where historic presence of coho has been confirmed [@norris2024smnorrisbcfishobs; ; @moe2024KnownBC]. Electrofishing results from the site indicate the stream is a productive for dolly varden providing
flows suitable for rearing and spawning.  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.


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

<br>

```{r tab-habitat-summary-8525}
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-8525, eval=T}
fpr_table_fish_site()

```

<br>

```{r tab-fish-dens-8525, eval=T}
fpr_table_fish_density()

```

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

```{r plot-fish-box-8525, 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-8525-01-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-8525-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo1)
```

<br>

```{r photo-8525-02-prep, eval=T}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = 'us_typical_2')

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


```

```{r photo-8525-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo2)
```

```{r photo-8525-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-8529-01-prep, eval=T}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = 'us2_typical_2')

my_caption1 = paste0('Typical habitat upstream of PSCIS crossing ', my_site2, '.')


```

```{r photo-8529-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo1)
```

<br>

```{r photo-8529-02-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = '_us2_pool')

my_caption2 = paste0('Typical pool habitat at PSCIS crossing ', my_site2, '.')
```

```{r photo-8529-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo2)
```

```{r photo-8529-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-8525-03-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = 'fish1')

my_caption1 = paste0('Rainbow trout captured downstream of crossing ', my_site, '.')
```

```{r photo-8525-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo1)
```

<br>

```{r photo-8525-04-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = 'fish2')

my_caption2 = paste0('Dolly varden captured upstream of crossing ', my_site, '.')

```

```{r photo-8525-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
knitr::include_graphics(my_photo2)
```

```{r photo-8525-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)
```