0800-appendix-198048-cesford.Rmd

---
output: html_document
editor_options: 
  chunk_output_type: inline
---

```{r setup-198048, eval = F}
knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
source('scripts/packages.R')
source('scripts/tables.R')



```



```{r  load-data-198048}
my_site <- 198048
my_site2 <- 198049
my_site3 <- 198090

```

`r fpr::fpr_appendix_title(site2 = my_site2)`

## Site Location {-}

PSCIS crossing `r as.character(my_site)` and `r as.character(my_site2)` are located on `r fpr::fpr_my_pscis_info()` near Topley, BC. PSCIS crossing `r as.character(my_site)` is located on `r fpr_my_pscis_info(col_pull = road_name)` and `r as.character(my_site2)` is located on `r fpr_my_pscis_info(site = my_site2, col_pull = road_name)`.  Crossing `r as.character(my_site)` was located `r round(fpr::fpr_my_bcfishpass(col_pull = downstream_route_measure)*0.001, 1)`km upstream from the confluence with the Bulkley River and `r as.character(my_site2)` was located `r round(fpr::fpr_my_bcfishpass(site = my_site2, col_pull = downstream_route_measure)*0.001, 1)`km upstream of the confluence. Crossings `r as.character(my_site)` and `r as.character(my_site2)` are the responsibility of the Ministry of Transportation and Infrastructure. PSCIS crossing `r as.character(my_site3)` makes reference to a potential crossing location under the `r fpr::fpr_my_pscis_info(site = my_site3, col_pull = road_name)`. The survey team was not able to locate a crossing in the field which coincides with personal communications with the adjacent landowner (Figure \@ref(fig:fig-channel-198048)). 



## Background {-}


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_min')`m near the crossing (Table \@ref(tab:tab-wshd-198048)). Upstream of crossing `r as.character(my_site)`, rainbow trout have previously been recorded [@moe2020KnownBC; @norris2020bcfishobs]. 

<br>


```{r fig-channel-198048, fig.cap= 'Location of potential location of crossing 198090 which was not present in the field.',  eval = T}
grid::grid.raster(jpeg::readJPEG("fig/cesford.JPG"))
```


<br>

```{r tab-wshd-198048, 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>

PSCIS stream crossing `r as.character(my_site)` was ranked as a priority for follow up by @irvine2021BulkleyRiver because of the relatively large size of the stream and the potential for large amounts of habitat gains through fish passage remediation (Table \@ref(tab:tab-culvert-bcfp-198048).  Although @wilson_rabnett2007FishPassage recommended establishing a downstream weir and excavating adequate outfall drop pools to facilitate fish passage at crossing `r as.character(my_site)`, they ranked the site as a moderate priority for remediation due to dewatering below Highway 16. @smith2018AssessingBarriers assessed the site in 2017 and noted that a comparison of photos taken in 2006 and 2017 indicates that a significant amount of gravel has been deposited in the channel below the culvert outlets. 

<br>

Upon review of aerial imagery, it appears that a large portion of the historical paths of Cesford Creek are located with the floodplain of the Bulkley River with extensive impacts apparent due to land clearing and the installation of the railway. The railway in this section of the upper Bulkley River bisects numerous historical meanders blocking access to extensive areas of likely very high value low velocity salmon rearing habitat. In addition there also appears to be ditching within these lands used for agriculture that although unconfirmed, may function to lower the water table in the floodplain, reducing productivity exacerbating seasonal dewatering. 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()`).  


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

<br>


```{r tab-culvert-bcfp-198048, eval = T}
fpr::fpr_table_bcfp(scroll = gitbook_on) 
```

<br>


## Stream Characteristics at Crossing {-}

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()` barrier to upstream fish passage according to the provincial protocol [@moe2011Fieldassessment](Table \@ref(tab:tab-culvert-198048)). 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-198048, eval = T}
fpr::fpr_table_cv_summary_memo()

```

<br>

```{r tab-culvert-198048-site2, eval = T}
fpr::fpr_table_cv_summary_memo(site = my_site2, site_photo_id = my_site2)

```

<br>

```{r tab-culvert-198048-site3, eval = T}
fpr::fpr_table_cv_summary_memo(site = my_site3, site_photo_id = my_site3)

```


```{r eval=F}
##this is useful to get some comments for the report
hab_site %>% filter(site == my_site2 & location == 'us') %>% pull(comments)
my_priority <-  my_priority_info()

```

## Stream Characteristics Downstream {-}

The stream was surveyed downstream from crossing 198048 at Highway 16 for `r fpr::fpr_my_priority_info(loc = 'ds', col_pull = 'length_surveyed')`m to the mainstem of the Bulkley River `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-198048-01) - \\@ref(fig:photo-198048-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-198048-d01))"))`. Total cover amount was rated as `r fpr::fpr_my_habitat_cover(loc = 'ds', cover_type = 'total cover')` with  `r fpr::fpr_my_habitat_cover(loc = 'ds', cover_type = 'dominant')` dominant. Cover was also present as `r fpr::fpr_my_habitat_cover(loc = 'ds', cover_type = 'sub-dominant')` (Table \@ref(tab:tab-habitat-summary-198048)). The average channel width was `r fpr::fpr_my_habitat_info(loc = 'ds', col_pull = 'avg_channel_width_m')`m, the average wetted width was `r fpr::fpr_my_habitat_info(loc = 'ds', col_pull = 'avg_wetted_width_m')`m and the average gradient was `r fpr::fpr_my_habitat_info(loc = 'ds', col_pull = 'average_gradient_percent')`%. The dominant substrate was `r fpr::fpr_my_habitat_info(loc = 'ds', col_pull = "bed_material_dominant")` with `r fpr::fpr_my_habitat_info(loc = 'ds', col_pull = "bed_material_subdominant")` subdominant.  The habitat was rated as `r fpr::fpr_my_priority_info(loc = 'ds')` value for salmonid rearing and spawning. 

<br>

## Stream Characteristics Upstream of `r as.character(my_site)` and downstream of `r as.character(my_site2)`{-}


The stream was surveyed immediately upstream from `r as.character(my_site)` for approximately `r fpr::fpr_my_priority_info(col_pull = 'length_surveyed')`m `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-198048-03) - \\@ref(fig:photo-198048-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-198048-d02))"))`. Within the area surveyed, total cover amount was rated as `r fpr::fpr_my_habitat_cover(loc = 'us', cover_type = 'total_cover')` with  `r fpr::fpr_my_habitat_cover(loc = 'us', cover_type = 'dominant')` dominant. Cover was also present as `r fpr::fpr_my_habitat_cover(loc = 'us',cover_type = 'sub-dominant')` (Table \@ref(tab:tab-habitat-summary-198048)). The average channel width was `r fpr::fpr_my_habitat_info(loc = 'us', col_pull = 'avg_channel_width_m')`m, the average wetted width was `r fpr::fpr_my_habitat_info(loc = 'us', col_pull = 'avg_wetted_width_m')`m and the average gradient was `r fpr::fpr_my_habitat_info(loc = 'us', col_pull = 'average_gradient_percent')`%.  The dominant substrate was `r fpr::fpr_my_habitat_info(loc = 'us', col_pull = "bed_material_dominant")` with `r fpr::fpr_my_habitat_info(loc = 'us', col_pull = "bed_material_subdominant")` subdominant. Habitat value was rated as `r fpr::fpr_my_priority_info()` value for resident salmonid rearing and spawning. 

## Stream Characteristics Upstream of `r as.character(my_site)` {-}
`r fpr_my_survey_dist(sit = my_site2, loc = 'us')`
`r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-198048-05) - \\@ref(fig:photo-198048-06)).")}else(knitr::asis_output("(Figure \\@ref(fig:photo-198048-d03))."))`
`r fpr_my_habitat_paragraph(sit = my_site2)`
The stream had good flow and moderate complexity due to mature cottonwood riparian and frequent large woody debris. Occasional pool and frequent gravel sections were also noted.
Habitat value was rated as `r fpr::fpr_my_priority_info(sit = my_site2, loc = 'us')` as the surveyed area was considered an important migration corridor containing suitable spawning habitat and having moderate rearing potential.

<br>

Cesford Creek was also surveyed approximately 950m upstream from 198049 for a distance of approximately 500m.

`r fpr_my_habitat_paragraph(sit = my_site2, loc = 'us2')`
Habitat value was rated as `r fpr::fpr_my_priority_info(sit = my_site2, loc = 'us2')` with moderate value habitat for salmonid rearing and occasional pockets of gravel suitable for salmonid spawning.

## Structure Remediation and Cost Estimate {-}

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>

Should restoration/maintenance activities proceed, replacement of PSCIS crossing `r as.character(my_site2)` with a bridge (`r fpr::fpr_my_pscis_info(site = my_site2, 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(site = my_site2), big.mark = ',')` for a cost benefit of `r fpr::fpr_my_cost_estimate(site = my_site2, col_pull = cost_net)` linear m/\$1000 and `r fpr::fpr_my_cost_estimate(site = my_site2, col_pull = cost_area_net)` m^2^/\$1000. Relocation of the driveway accessing the private land from the other side of the stream and removal of the crossing could also be considered. 

<br>

For PSCIS crossing `r as.character(my_site3)` it is recommended some sort of fish passable structure be installed under the railway to reconnect Cesford Creek with the Bulkley River.  The cost of the work is roughly estimated at \$`r format(fpr::fpr_my_cost_estimate(site = my_site2), big.mark = ',')`.


## Conclusion {-}

Management of connectivity within Cesford Creek would be most appropriately managed on the watershed level beginning with re-connection of the stream under the railway in the vicinity of the location of PSCIS `r as.character(my_site3)`. Without re-connection at the railway, the stream cannot provide habitat for species other than the rainbow trout documented as resident.  A large portion of the historical paths of Cesford Creek are located with the floodplain of the Bulkley River with extensive impacts apparent due to land clearing and the installation of the railway which bisects numerous historical upper Bulkley River meanders. In addition there also appears to be ditching within these lands used for agriculture that although unconfirmed, may function to lower the water table in the floodplain.  It is recommended that a plan be developed in conjunction with CN Rail, adjacent landowners, First Nations regulators and local stewardship groups to reconnect the channel at the railway, exclude cattle from the riparian area, implement stream restoration actions and explore possibilities related to progressive beaver management in the watershed.

<br>

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)` rated as `r fpr::fpr_my_priority_info(sit = my_site, loc = 'us', col_pull = hab_value)` value for salmonid rearing and spawning. 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. 

<br>

There was `r fpr::fpr_my_priority_info(sit = my_site2, col_pull= upstream_habitat_length_km)`km of habitat modelled upstream of crossing `r as.character(my_site2)` rated as `r fpr::fpr_my_priority_info(sit = my_site2, loc = 'us', col_pull = hab_value)` value for salmonid rearing and spawning. Crossing `r as.character(my_site2)` was ranked as a `r fpr::fpr_my_priority_info(sit = my_site2, col_pull = priority)` priority for proceeding to design for replacement. 

<br>

There was `r as.character(my_site2)` is `r fpr::fpr_my_priority_info(sit = my_site2, col_pull= upstream_habitat_length_km)`km of habitat upstream of crossing rated as `r fpr::fpr_my_priority_info(sit = my_site2, loc = 'us', col_pull = hab_value)` value for salmonid rearing and spawning. Crossing `r as.character(my_site2)` was ranked as a `r fpr::fpr_my_priority_info(sit = my_site2, col_pull = priority)` priority for proceeding to design for replacement. 

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

<br>

```{r tab-habitat-summary-198048}
tab_hab_summary %>% 
  filter(Site  == my_site |
           Site == my_site2) %>% 
  # select(-Site) %>% 
  fpr::fpr_kable(caption_text = paste0('Summary of habitat details for PSCIS crossing ', my_site, ' and ', my_site2, '.'),
                 scroll = F) 

```

<br>



```{r photo-198048-01-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, '.')


# fpr::fpr_photo_flip(site_id = 1802488, str_to_pull = '6257')

```

```{r photo-198048-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```

<br>

```{r photo-198048-02-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-198048-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))

```

<br>

```{r photo-198048-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-198048-03-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-198048-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```



<br>

```{r photo-198048-04-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-198048-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-198048-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-198048-05-prep}
my_photo1 = fpr::fpr_photo_pull_by_str(site = my_site2, str_to_pull = '_u1_')

my_caption1 = paste0('Habitat upstream of PSCIS crossing ', my_site2, '.')
```

```{r photo-198048-05, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo1))
```



<br>

```{r photo-198048-06-prep}
my_photo2 = fpr::fpr_photo_pull_by_str(site = my_site2, str_to_pull = '_u2_')

my_caption2 = paste0('Habitat upstream of PSCIS crossing ', my_site2, '.')

```

```{r photo-198048-06, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(jpeg::readJPEG(my_photo2))
```

```{r photo-198048-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)
```