0800-appendix-8530-sandstone.Rmd

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```{r setup-8530, eval = F}
knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
source('scripts/packages.R')
source('scripts/tables.R')

```

```{r  load-data-8530}
my_site <- 8530

```

`r fpr::fpr_appendix_title()`

## Site Location {.unnumbered}

PSCIS crossing `r as.character(my_site)` is located on
`r fpr::fpr_my_pscis_info()` approximately 35km west of the town of
Smithers, on `r fpr_my_pscis_info(col_pull = road_name)`. This crossing is located approximately 650m upstream from the confluence with the Zymoetz River.  This crossing 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 a
watershed area upstream of the crossing 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 at the crossing (Table
\@ref(tab:tab-wshd-8530)). Upstream of crossing
`r as.character(my_site)`, dolly varden, rainbow trout, and cutthroat trout have previously
been recorded [@moe2020KnownBC; @norris2022smnorrisbcfishobs]. The mainstem of Sandstone Creek is 9.8km in length and is fed by 13 tributaries. Sandstone Lake is located approximately 4km
upstream of crossing `r as.character(my_site)`, and has an area of 67ha.
According to historical records, dolly varden and cutthroat trout have
been known to reside in Sandstone Lake.

<br>

```{r tab-wshd-8530, eval = T}
fpr::fpr_table_wshd_sum(site_id = my_site) %>% 
  select(-'Elev Min') %>% 
  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>

@tritonenvironmentalconsultantsltd.1998 conducted a reconnaissance
level fish and fish habitat inventory on Sandstone Creek. In 1996, they conducted fish sampling at two sites located downstream of crossing `r as.character(my_site)` and caught cutthroat trout.
In 1997, Rainbow trout were caught by electrofishing upstream of Sandstone Lake and cutthroat trout
were caught by electrofishing in a tributary located approximately 800m upstream of
crossing `r as.character(my_site)`. At that time, Sandstone Creek was generally a low gradient stream with areas of moderate confinement. Upstream of Sandstone Lake, the stream flows for approximately 2.5km through an area of fisheries sensitive wetlands before draining a small unnamed lake.

<br>

PSCIS stream crossing `r as.character(my_site)` was ranked as a high
priority for follow up by the Society for Ecosystem Restoration in
Northern BC because of significant amounts of habitat modelled upstream
of the crossing. @viveiros2011 assessed crossing
`r as.character(my_site)` in 2010. At the time of survey, it was
recommended that the material in the pipe be embedded to reduce
water velocity. A summary of habitat modelling outputs is presented in
Table \@ref(tab:tab-culvert-bcfp-8530). 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")`).

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

<br>

```{r tab-culvert-bcfp-8530, eval = T}
fpr::fpr_table_bcfp(scroll = gitbook_on) 
```

<br>

```{r lidar-sandstone, fig.cap = 'Lidar generated digital elevation model of Sandstone Creek at McDonell FSR (using elevation data from 2018).',eval=T}
knitr::include_graphics("fig/lidar_sandstone.png")
```

<br>

## Stream Characteristics at Crossing {.unnumbered}

At the time of the survey, 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)` to upstream fish
passage according to the provincial protocol [@moe2011Fieldassessment]
(Table \@ref(tab:tab-culvert-8530)). Water temperature was
`r fpr::fpr_my_habitat_info(col_pull = 'temperature_c')`$^\circ$C, pH
was `r fpr::fpr_my_habitat_info(col_pull = 'p_h')` and conductivity was
`r fpr::fpr_my_habitat_info(col_pull = 'conductivity_m_s_cm')`uS/cm.

<br>

```{r tab-culvert-8530, 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 == 'us') %>% pull(comments)
hab_site %>% filter(site == my_site & location == 'ds') %>% pull(comments)
#fpr::fpr_my_priority_info()

```

## Stream Characteristics Downstream {.unnumbered}

`r fpr::fpr_my_survey_dist(loc = 'ds')`
`r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-8530-01) - \\@ref(fig:photo-8530-02)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-8530-d01))."))`
`r fpr_my_habitat_paragraph(loc = 'ds')` There was good flow at the time
of survey. Riparian vegetation was healthy, providing plenty of shade
and cover. There were small packets of gravel suitable for spawning.
Large woody debris jams and cascades were present that
could act as a natural barrier to fish passage. However, during periods of high
flow there's a good chance that strong fish can traverse these barriers. Plenty of pools
were available for fish rearing. There was abundant functional  woody debris
and boulders present that added complexity to the stream habitat. The stream was confined in a bed rock canyon, with overhanging vegetation
and shrubs dominating the riparian zone. 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-8530-03) - \\@ref(fig:photo-8530-06)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-8530-d02))."))`
`r fpr_my_habitat_paragraph(loc = 'us')` There was abundant cover from
woody debris, overhanging veg and undercut banks at the time of survey.
The channel was wide throughout with graveled areas suitable for
spawning. There was trace amounts of deep pools suitable for
rearing. A couple smaller cascades (\<1m in height) were present that
may block the upstream migration of smaller fish. The habitat was rated as
`r fpr::fpr_my_priority_info(loc = 'us')` value as an important
migration corridor containing suitable spawning habitat and having
moderate rearing potential.

<br>

## Fish Sampling {.unnumbered}

Electrofishing was conducted with results summarised in Tables
\@ref(tab:tab-fish-site-8530) - \@ref(tab:tab-fish-dens-8530) and Figure
\@ref(fig:plot-fish-box-8530). Dolly varden and cutthroat trout were caught both downstream and upstream of the culvert, while rainbow trout were only caught upstream `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-8530-07) - \\@ref(fig:photo-8530-08)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-8530-u01))."))` There was some uncertainty as to whether some fish were hybrids of rainbowe and ctthrout.  Fish over 60mm in length were tagged with passive integrated transponders with tag ID and asssociated data located [here](https://github.com/NewGraphEnvironment/fish_passage_skeena_2022_reporting/raw/main/data/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.

<br>

## Conclusion {.unnumbered}

There was
`r fpr::fpr_my_priority_info(col_pull= upstream_habitat_length_km)`km of
habitat modelled upstream of crossing `r as.character(my_site)` modelled as potential steelhead rearing habitat with
areas surveyed rated as
`r fpr::fpr_my_priority_info(sit = my_site, loc = 'us', col_pull = hab_value)`
value for salmonid rearing and spawning. Additionally, Sandstone Lake upstream provides habitat and flow moderating values to the sytem.  Crossing
`r as.character(my_site)` was ranked as a
`r fpr::fpr_my_priority_info(col_pull = priority)` priority for
proceeding to design for replacement. Sandstone Creek is a large system
with habitat suitable for numerous species including cutthroat and dolly
varden. Although habitat has modeled as suitable for steelhead and coho, presence of anadromous species was not confirmed through sampling. Nevertheless, replacement the crossing with a bridge
would eliminate the outlet drop and reduce flow
velocities at the road crossing.

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

<br>

```{r tab-habitat-summary-8530}
tab_hab_summary %>% 
  filter(Site  == my_site) %>% 
  fpr::fpr_kable(caption_text = paste0('Summary of habitat details for PSCIS crossing ', my_site, '.'),
                 scroll = F) 

```

<br>

```{r tab-fish-site-8530, eval=T}
fpr_table_fish_site()

```

<br>

```{r tab-fish-dens-8530, eval=T}
fpr_table_fish_density()

```

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

```{r plot-fish-box-8530, fig.cap= my_caption, eval=T}
my_caption <- paste0('Densites of fish (fish/100m2) captured upstream of PSCIS crossing ', my_site, '.')

fpr_plot_fish_box() 

```

<br>

```{r photo-8530-01-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-8530-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-8530-02-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = '_d2_')

my_caption2 = paste0('Large woody debris jam downstream of PSCIS crossing ', my_site, '.')
```

```{r photo-8530-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))

```

<br>

```{r photo-8530-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-8530-03-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-8530-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-8530-04-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = '_u2_')

my_caption2 = paste0('Area with suitable spawning gravels, upstream of PSCIS crossing ', my_site, '.')

```

```{r photo-8530-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-8530-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)
```

```{r photo-8530-05-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = '_u3_')

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

```{r photo-8530-05, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-8530-06-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-8530-06, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-8530-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)
```

<br>

```{r photo-8530-07-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(str_to_pull = '_ef1_')

my_caption1 = paste0('Dolly Varden captured upstream of PSCIS crossing ', my_site, '.')
```

```{r photo-8530-07, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-8530-08-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = '_ef2_')

my_caption2 = paste0('Cutthroat trout captured downstream of PSCIS crossing ', my_site, '.')

```

```{r photo-8530-08, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-8530-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)
```