In NewGraphEnvironment/fish_passage_elk_2021_reporting: Does not matter.

Results and Discussion

r if(gitbook_on)knitr::asis_output("Results are summarized in Figure \\@ref(fig:map-interactive) with additional details provided in sections below.")

##make colors for the priorities
pal <- 
   colorFactor(palette = c("red", "yellow", "grey", "black"), 
               levels = c("high", "moderate", "low", "no fix"))

pal_phase1 <- 
   colorFactor(palette = c("red", "yellow", "grey", "black"), 
               levels = c("high", "moderate", "low", NA))

tab_map_phase2 <- tab_map %>% filter(source %like% 'phase2')
#https://stackoverflow.com/questions/61026700/bring-a-group-of-markers-to-front-in-leaflet
# marker_options <- markerOptions(  
#   zIndexOffset = 1000)
tracks <- sf::read_sf("./data/habitat_confirmation_tracks.gpx", layer = "tracks")
wshds <- sf::read_sf('data/fishpass_mapping/fishpass_mapping.gpkg', layer = 'hab_wshds')
  # filter(!pscis_crossing_id %in% c(62423, 62426, 50181, 50159)) ##these ones are not correct - fix later

wshd_study_areas <- sf::read_sf('data/fishpass_mapping/fishpass_mapping.gpkg', layer = 'wshd_study_areas')
  # st_transform(crs = 4326)
photo_metadata <- readr::read_csv(file = 'data/photo_metadata.csv')


map <- leaflet(height=500, width=780) %>%
  # leaflet() %>% 
  addTiles()  %>% 
  # leafem::addMouseCoordinates(proj4 = 26911) %>% ##can't seem to get it to render utms yet
  # addProviderTiles(providers$"Esri.DeLorme") %>% 
  addProviderTiles("Esri.WorldTopoMap", group = "Topo") %>%
  addProviderTiles("Esri.WorldImagery", group = "ESRI Aerial") %>% 
  addPolygons(data = wshds, color = "#0859C6", weight = 1, smoothFactor = 0.5,
    opacity = 1.0, fillOpacity = 0.25,
    fillColor = "#00DBFF", label = wshds$stream_crossing_id, group = "Phase 2") %>%
  addPolygons(data = wshd_study_areas %>% filter(watershed_group_code == 'BULK'), color = "#F29A6E", weight = 1, smoothFactor = 0.5,
    opacity = 1.0, fillOpacity = 0,
    fillColor = "#F29A6E", label = 'Bulkley River') %>%
  addPolygons(data = wshd_study_areas %>% filter(watershed_group_code == 'MORR'), color = "#C39D50", weight = 1, smoothFactor = 0.5,
    opacity = 1.0, fillOpacity = 0,
    fillColor = "#C39D50", label = 'Morice River') %>%
  # addPolylines(data=drake::readd(fish_habitat_model_lines),  opacity=1, color = '#6498d2',
  #              fillOpacity = 0.75, weight=2) %>% 
  # addPolylines(data=forest_tenure_road_lines,  opacity=1, color = '#ff7f00',
  #              fillOpacity = 0.75, weight=2) %>%
    addLegend(
    position = "topright",
    colors = c("red", "yellow", "grey", "black"),
    labels = c("High", "Moderate", "Low", 'No fix'), opacity = 1,
    title = "Fish Passage Priorities",
  ) %>%
    addCircleMarkers(
    data=tab_plan_sf,
    label = tab_plan_sf$Comments,
    labelOptions = labelOptions(noHide = F, textOnly = F),
    popup = leafpop::popupTable(x = tab_plan_sf %>% st_drop_geometry(),
                                feature.id = F,
                                row.numbers = F),
    radius = 9,
    fillColor = ~pal_phase1(tab_plan_sf$Priority),
    color= "#ffffff",
    stroke = TRUE,
    fillOpacity = 1.0,
    weight = 2,
    opacity = 1.0,
    group = "Planning") %>% 

    addCircleMarkers(data=tab_map %>% filter(source %like% 'phase1' | source %like% 'pscis_reassessments'),
    label = tab_map %>% filter(source %like% 'phase1' | source %like% 'pscis_reassessments') %>% pull(pscis_crossing_id),               
    # label = tab_map$pscis_crossing_id,
    labelOptions = labelOptions(noHide = F, textOnly = TRUE),
    popup = leafpop::popupTable(x = select((tab_map %>% st_set_geometry(NULL) %>% filter(source %like% 'phase1' | source %like% 'pscis_reassessments')),
                                           Site = pscis_crossing_id, Priority = priority_phase1, Stream = stream_name, Road = road_name, `Habitat value`= habitat_value, `Barrier Result` = barrier_result, `Culvert data` = data_link, `Culvert photos` = photo_link),
                                feature.id = F,
                                row.numbers = F),
    radius = 9,
    fillColor = ~pal_phase1(priority_phase1),
    color= "#ffffff",
    stroke = TRUE,
    fillOpacity = 1.0,
    weight = 2,
    opacity = 1.0,
    group = "Phase 1"
    ) %>% 
    addPolylines(data=tracks,  
                 opacity=0.75, color = '#e216c4',
               fillOpacity = 0.75, weight=5, group = "Phase 2") %>%
  addAwesomeMarkers(
    lng = photo_metadata$gpslongitude,lat = photo_metadata$gpslatitude,
                    popup = leafpop::popupImage(photo_metadata$url, src = "remote"),
                    clusterOptions = markerClusterOptions(),
                    group = "Phase 2") %>%
    addCircleMarkers(
    data=tab_hab_map,
    label = tab_hab_map$pscis_crossing_id,
    labelOptions = labelOptions(noHide = T, textOnly = TRUE),
    popup = leafpop::popupTable(x = select((tab_hab_map %>% st_set_geometry(NULL)),
                                           Site = pscis_crossing_id, Priority = priority, Stream = stream_name, Road = road_name, `Habitat (m)`= upstream_habitat_length_m, Comments = comments, `Culvert data` = data_link, `Culvert photos` = photo_link, `Model data` = model_link),
                                feature.id = F,
                                row.numbers = F),
    radius = 9,
    fillColor = ~pal(priority),
    color= "#ffffff",
    stroke = TRUE,
    fillOpacity = 1.0,
    weight = 2,
    opacity = 1.0,
    group = "Phase 2"
    ) %>%
  #     # addScaleBar(position = 'bottomleft', options = scaleBarOptions(imperial = FALSE)) %>% 
  addLayersControl(
    baseGroups = c(
      "Esri.DeLorme",
      "ESRI Aerial"),
    overlayGroups = c("Planning", "Phase 1", "Phase 2"),
    options = layersControlOptions(collapsed = F)) %>%
  leaflet.extras::addFullscreenControl() %>% 
  addMiniMap(tiles = providers$"Esri.NatGeoWorldMap",
             zoomLevelOffset = -6, width = 100, height = 100)

map %>% 
  hideGroup(c("Planning","Phase 1"))

r if(gitbook_on){knitr::asis_output(" ")} else knitr::asis_output(" ")

Tables \@ref(tab:tab-overview) - \@ref(fig:plot-fish-all)

r if(gitbook_on){knitr::asis_output(" ")} else knitr::asis_output("\\pagebreak")

model_url <- '<iframe src="https://www.mapsmadeeasy.com/maps/public_3D/9ee5bee50be8436abbeb1dc83f4235cb" scrolling="no" title="Maps Made Easy" width="100%" height="500" frameBorder ="0"></iframe>'

knitr::asis_output(model_url)

my_photo = 'fig/pixel.png'

my_caption = paste0('Interactive 3D model of habitat immediately upstream and downstream of PSCIS crossing ', my_site, '.')

knitr::include_graphics(my_photo, dpi = NA)

my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')

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

grid::grid.raster(get_img(photo = my_photo1))

# eval=gitbook_on

my_photo2 = pull_photo_by_str(str_to_pull = '_f1_')

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

grid::grid.raster(get_img(photo = my_photo2))

# eval=identical(gitbook_on, FALSE)

my_caption <- paste0('Left: ', my_caption1, ' Right: ', my_caption2)

knitr::include_graphics(get_img_path(photo = my_photo1))
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(get_img_path(photo = my_photo2))