0800-appendix-198215-dale.Rmd

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output: html_document
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```{r setup-198215, 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-198215}
my_site <- 198215

```

`r fpr::fpr_appendix_title()`

## Site Location {.unnumbered}

PSCIS crossing `r as.character(my_site)` is located `r round(fpr::fpr_my_bcfishpass(col_pull = downstream_route_measure)*0.001, 1)`km
upstream from the confluence with the Kispiox River, on
`r fpr::fpr_my_pscis_info()`. The site is located on `r fpr_my_pscis_info(col_pull = road_name)` (also known as Date Creek FSR), just outside the Gitxsan village of Kispiox. This crossing is the responsibility of the Ministry of Transportation and Infrastructure (`chris_culvert_id` = 1524775). The Dale Creek watershed provides domestic water to the community of Kispiox [@rabnett_etal2003KispioxWatershed].

<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_min')`m near the crossing (Table
\@ref(tab:tab-wshd-198215)). At the time of reporting, there was no fisheries information available
for the area upstream of crossing `r as.character(my_site)` [@moe2020KnownBC; @norris2022smnorrisbcfishobs].

<br>

Two dams have been mapped as present on Dale Creek approximately 620m and 800m upstream of `r fpr_my_pscis_info(col_pull = road_name)` with `dam_id`s within `bcfishpass` of 166c070f-a324-40fb-addb-886dd23a9fc1 and 0de8a19d-eb93-4102-b124-8738f27e9e13 respectively [@canadianwildlifefederation2023CanadianAquatic; @norris2021smnorrisbcfishpass]. These GIS points may have been historical mapped in relation to drinking water diversion, storage and treatment infrastructure.    

<br>

The culverts and stream were initially assessed on September 9, 2022 and rated as moderate priority for proceeding to design for replacement, with a recommendation to conduct electrofishing to further inform prioritization. The site was revisited September 21, 2023 and electrofishing was conducted upstream and downstream of the crossing to provide insight into fish community composition and density, with results included in this report.


<br>

```{r tab-wshd-198215, 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-198215). 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 = "kisp", archive_date = "2022-09-06")`).

<br>

```{r tab-culvert-bcfp-198215, eval = T}
fpr::fpr_table_bcfp(scroll = gitbook_on) 
```

<br>

## Climate Change Risk Assessment

Preliminary climate change risk assessment data for the site is presented in Tables \@ref(tab:tab-moti-198215) - \@ref(tab:tab-moti-198215-comments).

```{r tab-moti-198215, eval = T}
fpr_table_moti() 
```

<br>

```{r tab-moti-198215-comments, eval = T}
fpr_table_moti_comments()
```

## Stream Characteristics at Crossing {.unnumbered}

At the time of the survey in 2022, 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-198215)). There were two culverts side by side, but one was not functioning and had debris blocking the outlet. There was low flow through the functioning culvert at the time of survey. The outlet drop was significant at 1.1m. 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-198215, 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')` to the confluence with the Kispiox River
`r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-198215-01) - \\@ref(fig:photo-198215-02)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-198215-d01))."))`
`r fpr_my_habitat_paragraph(loc = 'ds')` This stretch of stream was steep with one lock block step approximately 30m downstream of the culvert that was approximately 1m in height, which could block upstream migration for non adult fish species. It is thought that the lock blocks were likely originally placed in this location to backwater the site, minimize the culvert outlet drop and facilitate upstream fish passage. The habitat was rated as `r fpr::fpr_my_priority_info(loc = 'ds')` value for salmonid rearing and spawning. 


## Stream Characteristics Upstream {.unnumbered}

`r fpr_my_survey_dist(loc = 'us')` `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-198215-03) - \\@ref(fig:photo-198215-06)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-198215-d02))."))`
`r fpr_my_habitat_paragraph(loc = 'us')` Surveyors noted numerous cascades to approximately 1m in height with deep pools downstream and significant amounts of large woody debris. There were trace amount of gravels suitable for spawning. After the first 500m of the survey, it was noted that there were logs present perpendicular to the flow within the streambed at regular intervals that were potentially placed to capture substrate and provide complexity.  The stream was surveyed to the mapped location of the first mapped dam at 800m upstream of the FSR. Although the dam was not present, there appeared to be some remnants of a historic structure in the form of logs `r if(gitbook_on){knitr::asis_output("(Figure \\@ref(fig:photo-198215-05)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-198215-d03))."))`  The habitat was rated as `r fpr::fpr_my_priority_info(loc = 'us')` value as an important migration corridor containing spawning habitat suitable for coho and steelhead and having moderate rearing potential for both species.

<br>

## Fish Sampling {.unnumbered}

As per recommendations from the 2022 survey, crossing `r as.character(my_site)` was revisited on September 21, 2023 and electrofishing was conducted with results summarised in Tables \@ref(tab:tab-fish-site-198215) - \@ref(tab:tab-fish-dens-198215) and Figure
\@ref(fig:plot-fish-box-198215). A total of `r tab_fish_summary_2023 %>% filter(site_id == paste0(my_site, '_us')) %>% group_by(site_id) %>% janitor::adorn_totals() %>% filter(site_id == 'Total') %>% pull(count_fish)` fish were captured upstream, including cutthroat trout and rainbow trout, and `r tab_fish_summary_2023 %>% 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 cutthroat trout, rainbow trout, and dolly varden `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-198215-07) - \\@ref(fig:photo-198215-08)).")}else(knitr::asis_output("(Figures \\@ref(fig:photo-198215-u01))."))` 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 bridge
(`r fpr::fpr_my_pscis_info(col_pull = recommended_diameter_or_span_meters)`m
span) is recommended. The cost of the work is estimated at
\$`r format(fpr::fpr_my_cost_estimate(), big.mark = ',')` for a cost
benefit of `r fpr::fpr_my_cost_estimate(col_pull = cost_net)` linear
m/\$1000 and `r fpr::fpr_my_cost_estimate(col_pull = cost_area_net)`
m^2^/\$1000 with the relatively high costs of the work predicted primarily related to the large amount of road fill present at the site and the subsequent significant excavation required to install the large replacement structure.

<br>

## Conclusion {.unnumbered}

The BC freshwater atlas streamline indicates the stream gradient upstream of the FSR at 7.5% which coincides approximately with stream measurements.  This value barely exceeds the 7.4% cutoff used in our reporting for modelling potential steelhead rearing habitat, so we elected to include an estimate of 0.8km of upstream habitat presetn suitable for steelhead rearing to a point where mapping indicates gradients increase to 11%. Areas surveyed were rated as `r fpr::fpr_my_priority_info(sit = my_site, loc = 'us', col_pull = hab_value)` value for salmonid rearing and spawning. Although there were no dam structures located at the two mapped locations upstream of the crossing, Dale Creek watershed does provide the community of Kispiox with domestic water so it is possible there could be a dam or other diversion structure present farther upstream. Nevertheless, there were no natural or man-made barriers observed within the 800m of habitat assessed upstream of `r fpr_my_pscis_info(col_pull = road_name)` during the 2022 field surveys.

<br>


Following the 2022 survey, the site was ranked as `r fpr::fpr_my_priority_info(col_pull = priority)` priority for proceeding to design for replacement, with a recommendation to conduct electrofishing to help further inform prioritization. As also noted above, the site was revisited in September of 2023 with electrofishing conducted upstream and downstream of the crossing. Cutthroat trout and rainbow trout were captured upstream of with cuthroat, rainbow and dolly varden captured downstream. All fish over 60mm in size were tagged with PIT tags so that their movement and health can be tracked over time to help inform prioritization and effectiveness monitoring should restoration activities advance.

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

<br>

```{r tab-habitat-summary-198215}
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-198215, eval=T}
fpr_table_fish_site(dat = tab_fish_sites_sum_2023, sit = my_site)

```

<br>

```{r tab-fish-dens-198215, eval=T}
fpr_table_fish_density(dat = fish_abund_2023, sit = my_site)

```

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

```{r plot-fish-box-198215, 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(dat = fish_abund_2023, sit = my_site) 

```


<br>

```{r photo-198215-01-prep, eval=T}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = '_d1_')

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


```

```{r photo-198215-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-198215-02-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = '_d2_')

my_caption2 = paste0('Lock block step downstream of PSCIS crossing ', my_site, '.')
```

```{r photo-198215-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))

```

<br>

```{r photo-198215-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)
```

```{r photo-198215-03-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = '_u1_')

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

```{r photo-198215-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-198215-04-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = '_u2_')

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

```

```{r photo-198215-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-198215-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)
```

<br>

```{r photo-198215-05-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = '_u3_')

my_caption1 = paste0('Location of old historic dam, upstream of PSCIS crossing ', my_site, '.')
```

```{r photo-198215-05, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-198215-06-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = '_u4_')

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

```

```{r photo-198215-06, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-198215-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(my_photo1)
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(my_photo2)
```

```{r photo-198215-07-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(site = my_site, dir_photos = "data/photos/", str_to_pull = '_ct_us')

my_caption1 = paste0('Cutthroat trout captured upstream of PSCIS crossing ', my_site, '.')

```

```{r photo-198215-07, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-198215-08-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(site = my_site, dir_photos = "data/photos/", str_to_pull = '_rb_us')

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

```

```{r photo-198215-08, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

<br>

```{r photo-198215-u01, 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)
```