0800-appendix-198220-tea.Rmd

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output: html_document
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```{r setup-198220, 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-198220}
my_site <- 198220
my_site2 <- 8300012
my_site3 <- 8300917
```

`r fpr::fpr_appendix_title()`

## Site Location {.unnumbered}

PSCIS crossing `r as.character(my_site)` (MoTi `chris_hwy_structure_road_id` 4092) is located on `r fpr::fpr_my_pscis_info()`, approximately 4.5km north of the village of Kitwanga, on `r fpr_my_pscis_info(col_pull = road_name)` approximately `r round(fpr::fpr_my_bcfishpass(col_pull = downstream_route_measure)*0.001, 1)`km
upstream from the confluence with the Kitwanga River. PSCIS crossing 198200 on Moore Road (MoTi `chris_culvert_id` of 1528424) located approximately 200m upstream from the highway was also assessed and PSCIS crossing 198201 (MoTi `chris_culvert_id`s of 1528425 and 1528426) on Moore Road and a tributary to Tea Creek were also assessed.  All crossings are the responsibility of the Ministry of Transportation and Infrastructure. Several other road stream crossings are modelled upstream however none are modelled as located on the mainstem of Tea Creek until approximately 4.5km upstream of Moore Road.

<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 near the crossing (Table
\@ref(tab:tab-wshd-198220)). Upstream of crossing `r as.character(my_site)`, `r fpr::fpr_my_fish_sp()` have previously
been recorded [@moe2020KnownBC; @norris2022smnorrisbcfishobs]. Steelhead use of the system upstream of the highway was confirmed by a local landowner who reported historic spawning in the tributary to Tea Creek that flows into the stream just below Moore Road and PSCIS crossing 198200.

<br>

```{r tab-wshd-198220, 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>

In 1997, in partnership with Fisheries and Oceans Canada, the Ministry of Environment, Lands and Parks, Habitat Conservation Trust Fund, and non-governmental organizations (Gitanyow Fisheries Authorities and the Steelhead Society of BC), the Ministry of Transportation conducted fish passage remediation activities on Tea Creek at both Highway 37 as well as on Moore Road.  At the highway, backwater weir structures, comprised of notched pre-cast concrete lock block designed to reduce the outlet drop were installed below crossing `r as.character(my_site)`. At the Moore Road crossing, previously perched culverts were replaced with a bottomless pipe arch [@sweeting].

<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 due to the large size of the stream, with many species confirmed upstream. A summary of habitat modelling outputs is presented
in Table \@ref(tab:tab-culvert-bcfp-198220). 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-198220, eval = T}
fpr::fpr_table_bcfp(scroll = gitbook_on) 
```

<br>

## Climate Change Risk Assessment

Preliminary climate change risk assessment data is presented in Tables \@ref(tab:tab-moti-198220) - \@ref(tab:tab-moti-198220-comments).

```{r tab-moti-198220, eval = T}
fpr_table_moti()
```

<br>

```{r tab-moti-198220-comments, eval = T}
fpr_table_moti_comments()
```

## 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) %>% stringr::str_to_lower()` to upstream fish passage according to the provincial protocol
[@moe2011Fieldassessment] (Table \@ref(tab:tab-culvert-198220)). There was low flow through the culvert at the time of survey. Water temperature was
`r fpr::fpr_my_habitat_info(loc = "us", col_pull = 'temperature_c')`$^\circ$C, pH was `r fpr::fpr_my_habitat_info(loc = "us", col_pull = 'p_h')` and
conductivity was `r fpr::fpr_my_habitat_info(loc = "us", col_pull = 'conductivity_m_s_cm')`uS/cm.

<br>

PSCIS culvert 198200 culvert located on Moore Road approximately 220m upstream from the highway had a natural streambed and was ranked as
passable to all species and life stages at the time of survey (Table \@ref(tab:tab-culvert-8300012)).  Although this crossing was incorrectly recorded as a closed bottom structure in 2022, the crossing was more likely an open bottomed pipe arch as noted in @sweeting.   

<br>

PSCIS crossing 198201 located on Moore Road approximately 350m east of crossing 198200 was assessed and ranked as passable at the time of survey (Table \@ref(tab:tab-culvert-8300917)). There were two culverts side by side, with both embedded and non backwatered within a channel noted as 2.1m wide. Fish (up to 20cm in length) were observed within the culverts. 

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

```{r tab-culvert-198220, eval = T}
fpr::fpr_table_cv_summary_memo()

```

<br>

```{r tab-culvert-8300012, eval = T}
fpr::fpr_table_cv_summary_memo(dat = pscis_phase1, site = my_site2, site_photo_id = my_site2, col_filter = my_crossing_reference)
```

<br>

```{r tab-culvert-8300917, eval = T}
fpr::fpr_table_cv_summary_memo(dat = pscis_phase1, site = my_site3, site_photo_id = my_site3, col_filter = my_crossing_reference)
```

```{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')`
`r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-198220-01) - \\@ref(fig:photo-198220-02)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-198220-d01))."))`
`r fpr_my_habitat_paragraph(loc = 'ds')`  There was boulder cover and gravels throughout the survey but very few pools. 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-198220-03) - \\@ref(fig:photo-198220-06)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-198220-d02))."))`
`r fpr_my_habitat_paragraph(loc = 'us')` Only a few areas contained gravels suitable for spawning. The channel was wide throughout with a lot of woody debris. There were large amounts of undercut banks that provided cover, but very few deep pools. Some steep eroding banks were seen in a few locations on the survey. Juvenile fish were spotted, in the culvert on Moore Road. Overall, 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>

## 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)` 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. `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. Electrofishing upstream and
downstream of the culvert is recommended to provide insight into fish density and migration patterns.

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

<br>

```{r tab-habitat-summary-198220}
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 photo-198220-01-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-198220-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-198220-02-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(str_to_pull = '_d2_')

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

```{r photo-198220-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))

```

<br>

```{r photo-198220-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-198220-03-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-198220-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-198220-04-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-198220-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-198220-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-198220-05-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-198220-05, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-198220-06-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-198220-06, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-198220-d04, 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)
```