Purpose: derive metrics of fragmentation and connectivity for reporting units

8.0.1 Load spatial data

Load spatial datasets and view barrier point locations (dams, roads, and waterfalls) in relation to reporting unit watersheds.

Code
# basin
basin <- vect("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Data/Spatial/Basin Delineation/BasinDelineation/MajorBasins_Watersheds.shp") 
basin <- subset(basin, basin$site %in% c("SnakeHeadwaters"))

# reporting unit watersheds
watersheds <- vect("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Watershed Delineation/RepUnits_Watersheds.shp")

# waterfalls
# falls <- terra::vect("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/SARP Waterfalls/Archive_Falls_Mar082024.gdb")
# falls <- project(falls, crs(basin))
# falls <- crop(falls, basin)
# writeVector(falls, "/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/SARP Waterfalls/SARP_Waterfalls_SnakeHeadwaters.shp")
falls <- vect("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/SARP Waterfalls/SARP_Waterfalls_SnakeHeadwaters.shp")
falls$BarrierType <- "Waterfall"

# barriers
barriers <- read_csv("/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/aquatic_barrier_ranks_Jan2025/aquatic_barrier_ranks.csv") %>% filter(Removed == "no", Passability %in% c("Complete barrier", "Partial passability", "Seasonably passable - non salmonid", "Seasonably passable - salmonid"), HasNetwork == "yes")
barriers <- vect(barriers, geom = c("lon", "lat"), crs = "+proj=longlat +datum=WGS84")
barriers <- project(barriers, crs(basin))

# combine falls and barriers
barriers_comb <- union(falls, barriers)
barriers_comb$BarrierType <- recode(barriers_comb$BarrierType, "Assessed road-related barrier" = "Road")

# map it
mapview(st_as_sf(watersheds)) + mapview(st_as_sf(barriers_comb), zcol = "BarrierType")

8.0.2 Fragmentation

Derive metric of habitat fragmentation as the number of barriers per square kilometer of watershed area.

Code
cell_counts <- terra::extract(watersheds, barriers_comb)
point_counts <- cell_counts %>% group_by(site) %>% summarise(numbarr = n()) %>% rename(repunit = site)

sitetib <- tibble(repunit = watersheds$site, areasqkm = watersheds$aresqkm) %>% left_join(point_counts) %>% replace_na(list(numbarr = 0)) %>% mutate(barrier_dens = numbarr/areasqkm)

8.0.3 Connectivity

Define binary variable describing connectivity between downstream extent of reporting unit and mainstem Snake River: 1 = connected and 0 = disconnected. Connectivity may be interrupted by barriers (as mapped above; e.g., waterfalls, culverts, or diversion dams) or by low flow/intermittent reaches (based on field observations/expert opinion…e.g., Spread, Ditch, etc.). Note: all streams in the Gros Ventre River and Spread Creek basins have connectivity = 0 because the lower Gros Vente River (between Hwy 191 and Spring Gulch Road) and lower Spread Creek () is intermittent during typical

Code
sitetib$connectivity <- c(1,1,1,1,1,1,0,1,1,1,1,0,1,1,0,0,1,1,1,0,1,0,1,0,1,1,0,1,1,0,1,0,0,1,1,1,1,1,1,1,1,0,1,1,1,1,0,1,1,1,1,1)
sitetib$connect_type <- c(NA,NA,NA,NA,NA,NA,"low flow",NA,NA,NA,NA,"low flow",NA,NA,"low flow","waterfall",NA,NA,NA,"low flow",NA,"waterfall",NA,"low flow",NA,NA,"low flow",NA,NA,"low flow",NA,"culvert","diversion dam",NA,NA,NA,NA,NA,NA,NA,NA,"waterfall",NA,NA,NA,NA,"culvert",NA,NA,NA,NA,NA)

8.0.4 Final data

Code
write_csv(sitetib, "/Users/jeffbaldock/Library/CloudStorage/GoogleDrive-jbaldock@uwyo.edu/Shared drives/wyo-coop-baldock/UWyoming/Snake River Cutthroat/Analyses/Snake River GSI Quarto/Landscape Covariates/Barriers/RepUnits_BarrierSummary.csv")

sitetib %>% kable()
repunit areasqkm numbarr barrier_dens connectivity connect_type
bailey_NA 41.5714362 0 0.0000000 1 NA
blackrock_lower 124.9215920 3 0.0240151 1 NA
blackrock_upper 80.6862046 2 0.0247874 1 NA
blacktail_NA 61.1445506 0 0.0000000 1 NA
blindbull_NA 36.3517449 3 0.0825270 1 NA
boulder_NA 53.6999801 0 0.0000000 1 NA
box_NA 29.1414701 0 0.0000000 0 low flow
cabin_NA 23.5100427 0 0.0000000 1 NA
clear_NA 16.6041016 0 0.0000000 1 NA
cliff_NA 158.3813174 9 0.0568249 1 NA
cody_bluecrane 18.5117071 0 0.0000000 1 NA
cottonwood_grosventre 89.1780292 2 0.0224270 0 low flow
cottonwood_nps 187.1527021 14 0.0748052 1 NA
cowboycabin_NA 6.6392953 0 0.0000000 1 NA
crystal_lower 185.1148874 0 0.0000000 0 low flow
crystal_upper 155.6115004 0 0.0000000 0 waterfall
deadman_greys 42.6069634 6 0.1408221 1 NA
deadmansbar_NA 11.7612083 0 0.0000000 1 NA
dell_NA 118.1568591 1 0.0084633 1 NA
ditch_NA 67.6914863 1 0.0147729 0 low flow
dog_NA 31.0904837 1 0.0321642 1 NA
fall_coburn 116.5315084 1 0.0085814 0 waterfall
fish_NA 233.3741441 7 0.0299948 1 NA
fish_grosventre 587.8758585 8 0.0136083 0 low flow
flat_NA 173.3686411 0 0.0000000 1 NA
fordspring_NA 0.3712985 0 0.0000000 1 NA
goosewing_NA 40.3960756 0 0.0000000 0 low flow
granite_lower 220.3826608 3 0.0136127 1 NA
granite_upper 131.1747886 3 0.0228702 1 NA
grosventre_lower 1589.6465468 28 0.0176140 0 low flow
hoback_upper 114.0778330 4 0.0350638 1 NA
horse_NA 63.2035547 2 0.0316438 0 culvert
lava_NA 65.3337290 0 0.0000000 0 diversion dam
leidy_NA 10.7360331 0 0.0000000 1 NA
littlegreys_steer 179.3457294 3 0.0167275 1 NA
lowerbarbc_NA 6.3968311 0 0.0000000 1 NA
mosquito_NA 61.6412867 4 0.0648916 1 NA
northbuffalofork_NA 211.7277107 8 0.0377844 1 NA
pacific_NA 415.0574929 8 0.0192744 1 NA
rock_NA 11.9857990 0 0.0000000 1 NA
shoal_NA 82.6496949 1 0.0120993 1 NA
slate_NA 97.2568238 1 0.0102821 0 waterfall
snakeriversidechannel_NA 18.8103796 0 0.0000000 1 NA
spread_southfork 98.9032021 1 0.0101109 1 NA
spread_uppermainstem 202.6088599 5 0.0246781 1 NA
spreadnf_flagstaff 62.1057535 3 0.0483047 1 NA
spring_nps 4.0130319 0 0.0000000 0 culvert
spring_tss 24.8578294 0 0.0000000 1 NA
threechannel_NA 32.3647548 0 0.0000000 1 NA
upperbarbc_NA 5.7370505 0 0.0000000 1 NA
white_NA 32.6721618 2 0.0612142 1 NA
willow_NA 185.7033361 2 0.0107699 1 NA