2 Background

knitr::opts_chunk$set(fig.path = "fig/background/", dev = "png")

2.1 Project Location

The study area spans from Burns Lake to Valemount, British Columbia, and includes the Nechako River, Lower Chilako River, François Lake, Morkhill River and Upper Fraser River watershed groups.

# grab the latest version when updates happen
# fs::file_copy(
#   path = "~/Projects/gis/restoration_bc_2024/exports/maps/fishpassage_2024_sern_summary.jpeg",
#   new_path = "fig/fishpassage_2024_sern_summary.jpeg",
#   overwrite = TRUE
# )
knitr::include_graphics("fig/fishpassage_2024_fraser.png")

Figure 2.1: Overview map of the Fraser Region study areas

# ## Dakelh
# 
# The Dakelh (Carrier) people are indigenous to north-central British Columbia, with a deep connection to the region's waterways. Their name, Dakelh, translates to "people who travel by water," reflecting their reliance on rivers such as the Lhtakoh (Fraser), Nechakoh (Nechako), and Nak'alkoh (Stuart) for transportation, trade, and sustenance [@hudson2010Dakelhcarrier]. 
# 
# <br>
# 
# The Dakelh were key participants in the Grease Trails, trading inland goods for coastal eulachon oil [@hudson2010Dakelhcarrier]. Their Athabaskan language, Dakelh, has declined due to colonial policies, but revitalization efforts are ongoing. Organizations like the [Yinka Dene Language Institute](https://www.ydli.org/) work to document and promote Dakelh through education, literacy programs, and linguistic research [@yinkadenelanguageinstitute2025]. The Lheidli T'enneh First Nation and local school districts have also developed language programs to preserve and teach Dakelh (@Ourlanguage2025).
# 
# <br>
# 
# The Dakelh people traditionally organize their lands into Keyohs, family-run territories passed down through generations. Each Keyoh is overseen by a Keyohwhudachun (Keyoh Holder), who manages land use and stewardship [@Keyohhuwunline2025]. Despite historical disruptions, Keyohs remain central to Dakelh identity and land management practices.
# 
# 
# ### Lheidli T’enneh
# 
# The Lheidli T'enneh First Nations are a Dakelh sub-group whose traditional territory encompasses the Nechakoh (Nechako) River, Lhtakoh (Fraser) River, and Morkill River, and spans from west of Lheidli (Prince George) to Valemount. "Lheidli" translates to "The People from the Confluence of the River," referring to the meeting of the Nechako ("Nee Incha Koh" – "river with strong undercurrents") and Fraser ("Ltha Koh" – "Big Mouth River") rivers in what is now Prince George, British Columbia [@Ourstory2025]. 
# 
# <br>
# 
# Located within the traditional territory of the Lheidli T’enneh is Chun T’oh Whudujut (Ancient Forest), a Provincial Park and Protected Area 120km east of Prince George. The park has thousand-year-old western red cedars and a rich biodiversity of plants, mosses, lichens and fungi which can be explored through the trail network. Historically, Lheidli people would visit the stands from summer fishing camps along the upper Fraser River as well as gather medicinal plants, some of which were thought to be extinct. However, the park was not always a protected area and was initially slated for logging until a UNBC graduate student studying lichen biodiversity identified the ancient stands of western red cedars. Recognizing their ecological and cultural significance, trails were developed to highlight the cedars and advocate for their protection. Through partnerships with local hiking groups, UNBC, Lheidli T’enneh, and the Provincial Government, the Ancient Forest biodiversity assessment project has contributed to conservation efforts and tourism-based economic development in the Prince George area [@Chuntohwhudujutancientforest2025].
# 
# <br>
# 
# ### Carrier Sekani
# 
# The Carrier Sekani Tribal Council unifies six nations west of Lheidli (Prince George) whose traditional territories include the Lhtakoh (Fraser), Nechakoh (Nechako), Tsalakoh (Chilako), Endako, and Nadleh (Nautley) Rivers [@CSTCCSFNs]. The Carrier Sekani Tribal Council includes:
# 
#   - Ts’il Kaz Koh First Nation - located near Burns Lake 
#   - Nadleh Whut’en First Nation - located near Fraser Lake 
#   - Saik’uz First Nation - located near Vanderhoof
#   - Stellat’en First Nation - located near Fraser Lake
#   - Takla Nation - located near Takla Lake
#   - Wet’suwet’en First Nation - located west of Burns Lake
# 
# <br>
# 
# ### Nazko
# 
# Nazko, meaning "river flowing from the south," is a Dakelh sub-group located 120 km west of Quesnel along the Nazko River. Originally known for its strong ranching history, the community expanded into forestry in the 1980s, establishing Nazko Logging, a successful enterprise that created jobs and supported economic growth [@adams_stokes2025Historynazko].
# 
# <br>
# 
# ## Simpcw
# 
# Simpcw, which translates to "People of the Rivers", is one of the 17 campfires (bands) that make up the Secwepemc, or Shuwap Nation. Their traditional territory stretches from north of McBride, south to Barrier, and east to Mt.Robson Provincial Park, and includes the North Thompson River and the Upper Fraser River [@UsSimpcw]. 
# 
# <br>

2.2 Lhtakoh

Known as the Lhtakoh, meaning “rivers within one another” to the Dakelh (Carrier) people, the Fraser River stretches nearly 1,400 kilometers from the Rocky Mountains of Mount Robson Provincial Park to the Strait of Georgia near Vancouver. As the largest salmon-producing river on Canada’s west coast (Bradford and Taylor 2023; “Dakleh Placenames” n.d.), it plays a crucial economic role in supporting forestry, agriculture, and hydroelectric power generation. Additionally, the Fraser River is vital for fisheries, especially for salmon populations, which are essential to both the local ecosystem and indigenous communities.

The Upper Fraser River is commonly defined as the section of the mainstem north of Quesnel, flowing through the Cariboo and Fraser Plateau regions. Major tributaries include the Nechako, Quesnel, and McGregor rivers (D. P. Shaw and Tuominen, n.d.). This vast expanse supports many indigenous groups who utilize the land for cultural, spiritual, and economic practices.

The Upper Fraser River, an 8th order stream, drains an area of 232,134km² upstream of the McGregor River confluence. The seasonal hydrograph has a single broad peak in early summer due to snow and glacial melt from surrounding mountain ranges (Figure 2.2). The mean annual discharge at station 08KA005 in McBride, located roughly 200km southeast of Prince George, is 200.4m³/s

# get date range for figure caption
# flow_raw <- tidyhydat::hy_daily_flows("08KA005")
# print(start_year <- flow_raw$Date %>% min() %>% lubridate::year())
# print(end_year <- flow_raw$Date %>% max() %>% lubridate::year())

plot1 <- fasstr::plot_longterm_monthly_stats(
  station_number = "08KA005",
  ignore_missing = TRUE,
  add_year = 2023
)

print(plot1$`Long-term_Monthly_Statistics`)

Figure 2.2: Hydrograph for the Fraser River At McBride (Station #08KA005 - Lat 53.30172 Lon -120.14092). Available mean daily discharge data from 1953 to 2023.

2.3 Nechakoh

# nechako
fwapgr::fwa_watershed_at_measure(356362759)
# endako
fwapgr::fwa_watershed_at_measure(356361442) %>% mutate(area_km2 = round(area_ha/100, 1)) %>% mutate(area_km2 = ifelse(area_km2 >= 1000, format(area_km2, big.mark = ",", scientific = FALSE), area_km2)) %>% pull(area_km2)
# chilako
fwapgr::fwa_watershed_at_measure(356363121) %>% mutate(area_km2 = round(area_ha/100, 1)) %>% mutate(area_km2 = ifelse(area_km2 >= 1000, format(area_km2, big.mark = ",", scientific = FALSE), area_km2)) %>% pull(area_km2)

The Nechako River is an 8th order stream that drains an area of 47,269km². Beginning at the Nechako Plateau, it flows north toward Fort Fraser, then east to its confluence with the Fraser River in Prince George. The Nechako River has three main tributaries: the Stuart River, the Endako River, and the Chilako River. It has a mean annual discharge of 278.5m³/s at station 08JC002, located near Isle Pierre, approximately 25km downstream of the Stuart River confluence. Upstream at station 08JC001 in Vanderhoof, the mean annual discharge is 141.3m³/s. Flow at Isle Pierre is strongly influenced by inflows from the Stuart River, resulting in higher peak levels and average discharge (Figure 2.3). In contrast, the hydrograph at Vanderhoof shows lower peak levels and mean flows, with peaks occurring in June and August (Figure 2.4).

The Nechako River, meaning “Blackwater people’s river”, is home to the Cheslatta Carrier Nation who are part of the Dakelh people. Traditionally, they lived off the land near Tsetl’adak Bunk’ut “Peak Rock Lake” (Cheslatta Lake), however, in 1952, the construction of the Kenney Dam by the Aluminum Company of Canada (now Rio Tinto Alcan) and the subsequent flooding of the Nechako Reservoir forced the Cheslatta Carrier people to abandon their ancestral lands (“The History of the Cheslatta Carrier Nation” n.d.; “Dakleh Placenames” n.d.). This relocation was done with little notice or compensation, causing significant disruptions to their community, culture, and way of life. Despite these challenges, the Cheslatta Carrier Nation has worked to preserve their cultural heritage and advocate for their rights and land restoration.

# get date range for figure caption
# flow_raw <- tidyhydat::hy_daily_flows("08JC002")
# print(start_year <- flow_raw$Date %>% min() %>% lubridate::year())
# print(end_year <- flow_raw$Date %>% max() %>% lubridate::year())

plot1 <- fasstr::plot_longterm_monthly_stats(
  station_number = "08JC002",
  ignore_missing = TRUE,
  add_year = 2023
)

print(plot1$`Long-term_Monthly_Statistics`)

Figure 2.3: Hydrograph for the Nechako River at Isle Pierre, below the confluence of the Stuart River (Station #08JC002). Available mean daily discharge data from 1950 to 2023.

# get date range for figure caption
# flow_raw <- tidyhydat::hy_daily_flows("08JC001")
# print(start_year <- flow_raw$Date %>% min() %>% lubridate::year())
# print(end_year <- flow_raw$Date %>% max() %>% lubridate::year())

plot1 <- fasstr::plot_longterm_monthly_stats(
  station_number = "08JC001",
  ignore_missing = TRUE,
  add_year = 2023
)

print(plot1$`Long-term_Monthly_Statistics`)

Figure 2.4: Hydrograph for the Nechako River at Vanderhoof (Station #08JC001). Available mean daily discharge data from 1915 to 2023.

2.4 Endako River

The Endako River is a 6th order stream that flows southeast from Burns Lake to Fraser Lake, draining an area of 5,970km². One hydrometric station (08JB004) was located in Endako but was only active during 1951. The mean annual discharge for that year was 12.7m³/s, with the hydrograph peaking in May–June.

2.5 Tsalakoh

The Chilako River, known as Tsalakoh by the Dakelh people, translates to “beaver paw river”. It is a 6th order stream that flows north from the Nechako Plateau to its confluence with the Nechako River, draining an area of 3,634km². One hydrometric station (08JC005) is located approximately 10km upstream of the confluence with the Nechako River; however, it was only active from 1960 to 1974. During this period, the mean annual discharge was 13.3m³/s, with peak flows typically occurring in May–June (Figure 2.5).

# get date range for figure caption
# flow_raw <- tidyhydat::hy_daily_flows("08JC005")
# print(start_year <- flow_raw$Date %>% min() %>% lubridate::year())
# print(end_year <- flow_raw$Date %>% max() %>% lubridate::year())

plot1 <- fasstr::plot_longterm_monthly_stats(
  station_number = "08JC005",
  ignore_missing = TRUE,
  add_year = 2023
)

print(plot1$`Long-term_Monthly_Statistics`)

Figure 2.5: Hydrograph for the Chilako River Near Prince George (Station #08JC005 - Lat 53.808891 Lon -122.988892). Available mean daily discharge data from 1960 to 1974.

2.6 Fisheries

The Fraser River watershed is the largest salmon-producing river system in British Columbia and one of the most significant on the Pacific Coast. It provides critical habitat for anadromous salmonids, resident freshwater species, and other aquatic organisms. The river supports indigenous, commercial, and recreational fisheries, with Pacific salmon (Oncorhynchus spp.) playing a key ecological and economic role.

The 2019 Big Bar landslide created a significant barrier to salmon migration in the Fraser River, further stressing already vulnerable populations. Extensive mitigation efforts, including rock removal and the construction of a fishway, have helped improve passage, with an estimated 2.9 million salmon successfully navigating the site in 2022. The Upper Fraser Fisheries Conservation Alliance (UFFCA) has played a key role in supporting emergency response and recovery planning, working with federal and provincial agencies to ensure First Nations’ interests and traditional knowledge are incorporated into long-term recovery strategies. This includes ongoing monitoring, habitat restoration, and collaborative management to mitigate future risks to Fraser salmon populations (“Upper Fraser Fisheries Conservation Alliance,” n.d.).

2.6.1 Lhtakoh

The Fraser River mainstem serves as the primary migration corridor for all anadromous fish species returning to spawn in its tributaries. Historically, the Fraser supported some of the largest sockeye and chinook salmon runs in North America. However, climate change, habitat degradation, and fisheries pressures have led to declining salmon populations in recent decades.

Upper Fraser sockeye populations have been in decline for several decades, likely due to reduced flows and altered water temperatures, affecting migration and spawning success (Levy and Nicklin 2018). The Early Stuart and Late Stuart sockeye are now classified as “Endangered” by COSEWIC (COSEWIC 2017). Under the Wild Salmon Policy, several Upper Fraser sockeye conservation units have been classified as “red-zoned” (Levy and Nicklin 2018).

In 2005, Nesbit, Thibeault, and Borgstrom (2005) outlined key fisheries areas in the upper Fraser River watershed as the McLennan River, Swift Creek, and the upper mainstem of the Fraser River near Valemount and Tête Jaune Cache. These systems are known to support chinook salmon, with documented spawning in both Swift Creek and the McLennan River. At the time of reporting by Nesbit, Thibeault, and Borgstrom (2005), two Wildlife Habitat Areas (WHA 3155 and WHA 6012) were designated in the Tête Jaune Cache area based on high fisheries values. WHA 3155 encompassed the confluence of the McLennan and Fraser Rivers and was recognized as the largest chinook spawning area in the upper Fraser system. WHA 6012 protected an adjacent side channel further downstream, which was identified as important juvenile rearing and refuge habitat during high flow events. Although both WHAs have since been removed, their prior designation underscores the ecological importance of the area.

Swift Creek is the site of ongoing conservation hatchery efforts by the Spruce City Wildlife Association (SCWA), which has operated a volunteer-run hatchery since 1987. Following upgrades in 2020, it is now considered the most technologically advanced hatchery in the province. Focused on restoring upper Fraser River chinook, which are listed as “Endangered” by COSEWIC (COSEWIC 2019), SCWA releases thousands of chinook fry into Swift Creek each spring as part of broader recovery initiatives targeting key spawning systems in the region (Spruce City Wildlife Association 2023).

Three sub-watersheds within the upper Fraser River basin are designated as Fisheries Sensitive Watersheds (FSWs) due to the presence of sensitive fish species, including chinook salmon and bull trout. The Goat River and Milk River watersheds have held FSW status since 2013 (FLNRORD 2004b), and the Walker Creek watershed has been designated since 2004 (FLNRORD 2004a).

The importance of salmon in the upper Fraser is strongly reflected in Valemount’s community identity, education, and ecotourism initiatives. Public engagement with the salmon run is encouraged through accessible viewing areas at George Hicks Regional Park on Swift Creek, the Fraser River at Tête Jaune Cache, and along the McLennan River—locations that serve both as local gathering points and platforms for increasing awareness of salmon life cycles and watershed stewardship (Tourism Valemount n.d.).

2.6.2 Nechakoh

The Nechako River, a tributary of the Fraser River, supports Chinook salmon populations and serves as a migration corridor for sockeye salmon that spawn in the Stuart and Nadina/Francois Basins. Since the construction of the Kenney Dam in the 1950s, flows in the Nechako River have been regulated by Rio Tinto Alcan for hydroelectric power generation at the Kemano Generating Station on the Pacific Coast. In response to concerns over impacts on Nechako Chinook and Upper Fraser sockeye, flow management practices have been implemented. Since 1987, the Nechako Fisheries Conservation Program (NFCP) has operated an annual monitoring program, focussed on Nechako Chinook and migratory sockeye salmon designed to monitor the effectiveness of conservation measures specified in the 1987 Settlement Agreement between Canada, British Columbia, and Alcan (Levy and Nicklin 2018).

The Nechako River also supports a genetically distinct and endangered population of white sturgeon with low natural recruitment. To address this decline, the Nechako White Sturgeon Recovery Initiative (NWSRI) was established, implementing conservation measures such as the Nechako White Sturgeon Conservation Centre. The facility focuses on conservation aquaculture to maintain genetic diversity and support population recovery. Since 2006, the NWSRI has been releasing tagged juvenile sturgeon annually into the Nechako River to aid in species restoration (“Nechako White Sturgeon Recovery Initiative | Home” n.d.).

Indigenous fisheries organizations, including individual First Nations, the Carrier Sekani Tribal Council, and the Upper Fraser Fisheries Conservation Alliance (UFFCA), are actively involved in fisheries management in the Nechako watershed. These organizations work to support conservation while ensuring the sustainability of Indigenous fisheries, which have cultural and subsistence importance (“Upper Fraser Fisheries Conservation Alliance,” n.d.).

2.6.3 François Lake

François Lake is one of the largest natural lakes in BC and supports landlocked Kokanee (O. nerka), as well as migratory sockeye salmon that access the lake via the Stellako River. François Lake is a key rearing area for juvenile salmon before migrating to the Fraser River.

2.6.4 Morkill River

The Morkill River, a tributary to the upper Fraser, supports populations of bull trout, mountain whitefish, and rainbow trout. While salmon presence in the system is limited, the Morkill provides cold water inputs to the Fraser River, which may offer thermal refuge for migrating salmonids during warm summer months.

2.6.5 Salmon Stock Assessment Data

Fisheries and Oceans Canada stock assessment data was accessed via the NuSEDS-New Salmon Escapement Database System through the Open Government Portal with results presented in Table 2.1 (Fisheries and Oceans Canada n.d.). A brief memo on the data extraction process is available here.

library("ckanr")

# set up the connection to the data portal
ckanr_setup(url = "https://open.canada.ca/data/en")

nuseds <- rgovcan::govcan_search(keywords = c("Fraser NuSEDS"), records = 150, format_results = TRUE) |>  
  pull(resources) %>% 
  bind_rows()

# Load the most recent Nuseds - currently 20250103 (update july 2025 - looks like that file vanished and now we need nuseds_all_20250513.csv )
url <- "https://api-proxy.edh.azure.cloud.dfo-mpo.gc.ca/catalogue/records/c48669a3-045b-400d-b730-48aafe8c5ee6/attachments/All%20Areas%20NuSEDS_20250513.csv"
# burn directly without bringing into memory
ckanr::ckan_fetch(url, store = "disk", path = "data/inputs_raw/nuseds_all_20250513.csv") 

# ignore the huge file
usethis::use_git_ignore("data/inputs_raw/nuseds_all_20250513.csv")

#read it in
all_area_nuseds <- readr::read_csv('data/inputs_raw/nuseds_all_20250513.csv')


# Big study area so lets filter using the stream names from `form_pscis` (which is the 2024 and 2024 form pscis combined)
stream_names <- form_pscis |> 
  dplyr::pull(stream_name) |> 
  stringr::str_trim() |> 
  # Must be upper case to match those in Nuseds
  stringr::str_to_upper() |> 
  unique()

# we also need to add in these waterbodies that we didn't explicilty sample but are that heavy hitters in the project area
major_streams <- "NECHAKO|CHILAKO|ENDAKO|FRANÇOIS LAKE|FRASER RIVER|MORKILL RIVER"

# Combine into one regex pattern
stream_names_regex <- c(stream_names, major_streams) |> 
  stringr::str_c(collapse = "|")

# Filter Nuseds to just include streams we visited
study_area_streams <- all_area_nuseds |> 
  dplyr::filter(stringr::str_detect(WATERBODY, stream_names_regex)) |> 
  # We have some duplicate streams so remove streams with SHORE in the name which are in the Sushwap area
  dplyr::filter(!stringr::str_detect(WATERBODY, "SHORE")) |> 
  janitor::clean_names() |> 
  dplyr::arrange(waterbody)

check_names <- study_area_streams |> 
  dplyr::distinct(waterbody)

## Burn to csv. Updated name so it's clear this contains only the study area streams.
study_area_streams |> 
  readr::write_csv('data/inputs_raw/study_area_NuSEDS.csv')

Table 2.1: Fisheries and Oceans Canada stock assessment data for select watershed groups in the Fraser watershed. Data can be filtered to specific waterbodies, columns can be dragged to reorder and filtered/reordered table can be exported to csv/excel. NOTE: To view all columns in the table - please click on one of the sort arrows within column headers before scrolling to the right.

2.6.6 Fish Species

Summary of historical fish observations in the Upper Fraser River, Nechako River, Lower Chilako River, and François Lake watershed groups (Table 2.2) (MoE 2024).

A review of available fisheries data, for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups, stratified by different habitat characteristics can provide insight into which habitats may provide the highest intrinsic value for fish species based on the number of fish captured in those habitats in past assessment work (Figures 2.6 - 2.7 - 2.8). It should be noted however that it should not be assumed that all habitat types have been sampled in a non-biased fashion or that particular sites selected do not have a disproportionate influence on the overall dataset composition (ie. fish salvage sites are often located adjacent to construction sites which are more commonly located near lower gradient stream reaches).

fiss_species_table <- readr::read_csv('data/inputs_extracted/fiss_species_table.csv')

fiss_species_table %>% 
  fpr::fpr_kable(caption_text = 'Fish species recorded in the Upper Fraser River, Nechako River, Lower Chilako River, and François Lake watershed groups.', 
                 footnote_text = 'COSEWIC abbreviations : 
                 SC - Special concern 
                 DD - Data deficient
                 NAR - Not at risk
                 E - Endangered
                 T - Threatened
                 
                 BC List definitions : 
                 Yellow - Species that is apparently secure 
                 Blue - Species that is of special concern
                 Exotic - Species that have been moved beyond their natural range as a result of human activity
                 ',
                 scroll = gitbook_on)

Table 2.2: Fish species recorded in the Upper Fraser River, Nechako River, Lower Chilako River, and François Lake watershed groups.

Scientific Name	Species Name	Species Code	BC List	COSEWIC	SARA	Francois Lake	Lower Chilako	Nechako	Upper Fraser
Acipenser transmontanus	White Sturgeon	WSG	No Status	E/T (Nov 2012)	1-E	Yes	Yes	Yes	–
Carassius auratus	Goldfish	GC	Exotic	–	–	–	Yes	–	–
Catostomus bondi	Northern Mountain Sucker	MSU	Blue	T (Dec 2022)	–	–	Yes	–	–
Catostomus catostomus	Longnose Sucker	LSU	Yellow	–	–	Yes	Yes	Yes	Yes
Catostomus columbianus	Bridgelip Sucker	BSU	Yellow	–	–	Yes	–	Yes	–
Catostomus commersonii	White Sucker	WSU	Yellow	–	–	Yes	Yes	Yes	–
Catostomus macrocheilus	Largescale Sucker	CSU	Yellow	–	–	Yes	Yes	Yes	–
Chrosomus neogaeus	Finescale Dace	FDC	Yellow	–	–	Yes	–	–	–
Coregonus clupeaformis	Lake Whitefish	LW	Yellow	–	–	Yes	Yes	Yes	–
Cottus asper	Prickly Sculpin	CAS	Yellow	–	–	Yes	Yes	Yes	–
Cottus cognatus	Slimy Sculpin	CCG	Yellow	–	–	Yes	Yes	Yes	Yes
Cottus ricei	Spoonhead Sculpin	CRI	Yellow	NAR (May 1989)	–	Yes	–	–	Yes
Couesius plumbeus	Lake Chub	LKC	Yellow	DD	–	Yes	Yes	Yes	Yes
Cyprinus carpio	Carp	CP	Exotic	–	–	Yes	–	–	–
Hybognathus hankinsoni	Brassy Minnow	BMC	No Status	–	–	Yes	Yes	Yes	–
Lota lota	Burbot	BB	Yellow	–	–	Yes	Yes	Yes	Yes
Micropterus salmoides	Largemouth Bass	LMB	Exotic	–	–	–	–	Yes	–
Mylocheilus caurinus	Peamouth Chub	PCC	Yellow	–	–	Yes	Yes	Yes	–
Oncorhynchus clarkii	Cutthroat Trout	CT	No Status	–	–	Yes	–	–	–
Oncorhynchus gorbuscha	Pink Salmon	PK	Not Reviewed	–	–	–	Yes	–	–
Oncorhynchus kisutch	Coho Salmon	CO	Not Reviewed	–	–	Yes	Yes	Yes	–
Oncorhynchus mykiss	Rainbow Trout	RB	Yellow	–	–	Yes	Yes	Yes	Yes
Oncorhynchus nerka	Kokanee	KO	Not Reviewed	–	–	Yes	Yes	Yes	Yes
Oncorhynchus nerka	Sockeye Salmon	SK	Not Reviewed	–	–	Yes	Yes	Yes	Yes
Oncorhynchus tshawytscha	Chinook Salmon	CH	Not Reviewed	E/T/SC/DD/NAR (Nov 2020)	–	Yes	Yes	Yes	Yes
Prosopium coulterii	Pygmy Whitefish	PW	Yellow	NAR (Nov 2016)	–	–	Yes	Yes	Yes
Prosopium williamsoni	Mountain Whitefish	MW	Yellow	–	–	Yes	Yes	Yes	Yes
Ptychocheilus oregonensis	Northern Pikeminnow	NSC	Yellow	–	–	Yes	Yes	Yes	–
Rhinichthys cataractae	Longnose Dace	LNC	Yellow	–	–	Yes	Yes	Yes	Yes
Rhinichthys falcatus	Leopard Dace	LDC	Yellow	NAR (May 1990)	–	Yes	Yes	Yes	–
Richardsonius balteatus	Redside Shiner	RSC	Yellow	–	–	Yes	Yes	Yes	–
Salvelinus confluentus	Anadromous Bull Trout	ABT	Blue	SC (Nov 2012)	–	–	–	Yes	–
Salvelinus confluentus pop. 26	Bull Trout	BT	Blue	NAR (Nov 2012)	–	Yes	Yes	Yes	Yes
Salvelinus fontinalis	Brook Trout	EB	Exotic	–	–	Yes	Yes	Yes	Yes
Salvelinus malma	Dolly Varden	DV	Yellow	–	–	Yes	Yes	Yes	Yes
Salvelinus namaycush	Lake Trout	LT	Yellow	–	–	Yes	Yes	Yes	Yes
–	All Salmon	AO	–	–	–	–	Yes	–	–
–	Char, General	SLV	–	–	–	–	–	–	Yes
–	Chub (General)	CBC	–	–	–	Yes	Yes	Yes	–
–	Dace (General)	DC	–	–	–	Yes	Yes	Yes	–
–	Minnow (General)	C	–	–	–	Yes	Yes	Yes	–
–	Northern Pearl Dace	PDC	–	–	–	Yes	–	–	–
–	Salmon (General)	SA	–	–	–	–	Yes	–	Yes
–	Sculpin (General)	CC	–	–	–	Yes	Yes	Yes	Yes
–	Sucker (General)	SU	–	–	–	Yes	Yes	Yes	Yes
–	Whitefish (General)	WF	–	–	–	Yes	Yes	Yes	Yes
* COSEWIC abbreviations : SC - Special concern DD - Data deficient NAR - Not at risk E - Endangered T - Threatened BC List definitions : Yellow - Species that is apparently secure Blue - Species that is of special concern Exotic - Species that have been moved beyond their natural range as a result of human activity

# Remove the 1 steelhead observation from these csvs because is it likely a mistake
fiss_sum_grad <- readr::read_csv(file =  'data/inputs_extracted/fiss_sum_grad.csv') |> 
  dplyr::filter(species_code != "ST")

fiss_sum_width <- readr::read_csv(file = 'data/inputs_extracted/fiss_sum_width.csv')|> 
  dplyr::filter(species_code != "ST")

fiss_sum_wshed <- readr::read_csv(file = 'data/inputs_extracted/fiss_sum_wshed.csv') |> 
  dplyr::filter(species_code != "ST")

my_caption <- 'Summary of historic fish observations vs. stream gradient category for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups.'
fiss_sum_grad %>% 
  dplyr::select(-gradient_id) |> 
  fpr::fpr_kable(caption_text = my_caption,
                 scroll = gitbook_on)

Table 2.3: Summary of historic fish observations vs. stream gradient category for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups.

species_code	Gradient	Count	total_spp	Percent
BT	0 - 3 %	174	318	55
BT	03 - 5 %	49	318	15
BT	05 - 8 %	36	318	11
BT	08 - 15 %	45	318	14
BT	15 - 22 %	9	318	3
BT	22+ %	5	318	2
CH	0 - 3 %	1185	1267	94
CH	03 - 5 %	47	1267	4
CH	05 - 8 %	17	1267	1
CH	08 - 15 %	10	1267	1
CH	15 - 22 %	2	1267	0
CH	22+ %	6	1267	0
CO	0 - 3 %	12	18	67
CO	03 - 5 %	2	18	11
CO	08 - 15 %	2	18	11
CO	22+ %	2	18	11
CT	0 - 3 %	2	2	100
DV	0 - 3 %	239	342	70
DV	03 - 5 %	49	342	14
DV	05 - 8 %	26	342	8
DV	08 - 15 %	25	342	7
DV	15 - 22 %	3	342	1
PK	0 - 3 %	4	4	100
RB	0 - 3 %	3950	4810	82
RB	03 - 5 %	408	4810	8
RB	05 - 8 %	303	4810	6
RB	08 - 15 %	125	4810	3
RB	15 - 22 %	19	4810	0
RB	22+ %	5	4810	0
SK	0 - 3 %	71	73	97
SK	05 - 8 %	2	73	3

## bar graph
plot_grad <- fiss_sum_grad |>
  dplyr::filter(gradient_id != 99) |>
  ggplot2::ggplot(ggplot2::aes(x = Gradient, y = Percent)) +
  ggplot2::geom_bar(stat = "identity") +
  ggplot2::facet_wrap(~species_code, ncol = 2) +
  ggplot2::theme_bw(base_size = 11) +
  ggplot2::labs(x = "Average Stream Gradient", y = "Occurrences (%)")

plot_grad

Figure 2.6: Summary of historic fish observations vs. stream gradient category for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups.

my_caption <- 'Summary of historic fish observations vs. channel width category for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups.'
fiss_sum_width |>
  dplyr::select(-width_id) |>
  fpr::fpr_kable(caption_text = my_caption,
                 scroll = gitbook_on)

Table 2.4: Summary of historic fish observations vs. channel width category for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups.

species_code	Width	Count	total_spp	Percent
BT	0 - 2m	8	318	3
BT	02 - 04m	54	318	17
BT	04 - 06m	29	318	9
BT	06 - 10m	82	318	26
BT	10 - 15m	32	318	10
BT	15m+	93	318	29
BT	–	20	318	6
CH	0 - 2m	10	1267	1
CH	02 - 04m	26	1267	2
CH	04 - 06m	19	1267	1
CH	06 - 10m	105	1267	8
CH	10 - 15m	97	1267	8
CH	15m+	983	1267	78
CH	–	27	1267	2
CO	02 - 04m	2	18	11
CO	04 - 06m	6	18	33
CO	10 - 15m	2	18	11
CO	15m+	8	18	44
CT	06 - 10m	2	2	100
DV	0 - 2m	67	342	20
DV	02 - 04m	65	342	19
DV	04 - 06m	33	342	10
DV	06 - 10m	41	342	12
DV	10 - 15m	20	342	6
DV	15m+	97	342	28
DV	–	19	342	6
PK	15m+	2	4	50
PK	–	2	4	50
RB	0 - 2m	610	4810	13
RB	02 - 04m	1265	4810	26
RB	04 - 06m	470	4810	10
RB	06 - 10m	732	4810	15
RB	10 - 15m	316	4810	7
RB	15m+	480	4810	10
RB	–	937	4810	19
SK	10 - 15m	6	73	8
SK	15m+	65	73	89
SK	–	2	73	3

## bar graph
plot_width <- fiss_sum_width |>
  dplyr::filter(!is.na(width_id)) |>
  ggplot2::ggplot(ggplot2::aes(x = Width, y = Percent)) +
  ggplot2::geom_bar(stat = "identity") +
  ggplot2::facet_wrap(~species_code, ncol = 2) +
  ggplot2::theme_bw(base_size = 11) +
  ggplot2::labs(x = "Channel Width", y = "Occurrences (%)")

plot_width

Figure 2.7: Summary of historic fish observations vs. channel width category for the Parsnip River watershed group.

my_caption <- 'Summary of historic fish observations vs. watershed size category for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups.'
fiss_sum_wshed |>
  fpr::fpr_kable(caption_text = my_caption,
                 scroll = gitbook_on)

Table 2.5: Summary of historic fish observations vs. watershed size category for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups.

species_code	Watershed	count_wshd	total_spp	Percent
BT	0 - 25km2	155	318	49
BT	25 - 50km2	48	318	15
BT	50 - 75km2	18	318	6
BT	75 - 100km2	8	318	3
BT	100km2+	89	318	28
CH	0 - 25km2	79	1267	6
CH	25 - 50km2	56	1267	4
CH	50 - 75km2	59	1267	5
CH	75 - 100km2	42	1267	3
CH	100km2+	1031	1267	81
CO	0 - 25km2	4	18	22
CO	100km2+	14	18	78
CT	25 - 50km2	2	2	100
DV	0 - 25km2	185	342	54
DV	25 - 50km2	27	342	8
DV	50 - 75km2	19	342	6
DV	75 - 100km2	14	342	4
DV	100km2+	97	342	28
PK	0 - 25km2	1	4	25
PK	100km2+	3	4	75
RB	0 - 25km2	2912	4810	61
RB	25 - 50km2	439	4810	9
RB	50 - 75km2	226	4810	5
RB	75 - 100km2	383	4810	8
RB	100km2+	850	4810	18
SK	0 - 25km2	2	73	3
SK	100km2+	71	73	97

plot_wshed <- fiss_sum_wshed |>
  ggplot2::ggplot(ggplot2::aes(x = Watershed, y = Percent)) +
  ggplot2::geom_bar(stat = "identity") +
  ggplot2::facet_wrap(~species_code, ncol = 2) +
  ggplot2::theme_bw(base_size = 11) +
  ggplot2::labs(x = "Watershed Area", y = "Occurrences (%)") +
  ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))

plot_wshed

Figure 2.8: Summary of historic fish observations vs. watershed size category for the Nechako River, Lower Chilako River, François Lake, Morkill River and Upper Fraser River watershed groups.