In FlowWest/cvpiaHabitat: Estimate Spawning and Rearing Habitat

knitr::opts_chunk$set(echo = TRUE, message=FALSE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
library(tidyverse)
library(readxl)
library(cvpiaHabitat)

Future Data Improvements

[Future data improvement bullets]

Instream Spawning and Rearing Habiat

Data Source: Holton 1985

Instream spawning and rearing habitat for Fall Run Chinook Salmon [and Steelhead?] in the Bear River is based on data from California Department of Water Resources and Thomas R. Payne & Associates instream flow evaluations for the relicensing of Oroville facilities. [These evaluations developed relationships between flow and suitable spawning and rearing habitat for 23.25 miles of the Bear River between the Fish Barrier Dam and Honcut Creek, consisting of two river segments. The DWR FERC instream spawning and rearing habitat data] was provided by Mark Gard from the U.S. Fish and Wildlife Service in a spreadsheet (see '~/cvpiaHabitat/data-raw/mark_gard_data/IFIMWUA.xlsx').Mark Gard instructed us to use A1:D5 of the 'BearR' tab within his 'IFIMWUA.xlsx'.

Modeling for spawning and juvenile rearing.

Units are in square feet per 1000 feet.

# bear <- read_excel('data-raw/mark_gard_data/IFIMWUA.xlsx', 
#                             range = "A1:D5", sheet = 'BearR')
# 
# bear_river_instream <- bear %>% 
# select(flow_cfs = Flow, FR_spawn_wua = Spawning, FR_juv_wua = `Juv Rearing`) %>% 
# mutate(watershed = 'Bear River')
#  
# bear_river_instream
# devtools::use_data(bear_river_instream, overwrite = TRUE)

Spawning WUA

[description]

Spawning WUA Plot

The following plot shows the weighted usable spawning area in square feet per thousand feet of river for Fall Run Chinook Salmon. These area per length rates are multiplied by the total spawning reach length mapped by the SIT.

``` {r,echo=FALSE} bear_river_instream %>% filter(!is.na(FR_spawn_wua)) %>% ggplot(aes(x = flow_cfs , y = FR_spawn_wua)) + geom_line(color= '#7570b3') + labs(x = 'Flow (cfs)', y = 'WUA (sqft/1000ft)') + theme_minimal()

### Rearing WUA
The juvenile instream rearing habitat weighted usable areas for Fall Run Chinook Salmon in the Bear River provided by Mark Gard (see '~/cvpiaHabitat/data-raw/mark_gard_data/IFIMWUA.xlsx'). 

#### Rearing WUA Plot

The following plot shows the weighted usable rearing area in square feet per thousand feet of river for Fall Run Chinook Salmon juvenile. These rates are multiplied by the total rearing reach length mapped by the SIT. 
``` {r,echo=FALSE}
bear_river_instream %>% 
  gather(Lifestage, wua, -flow_cfs, -watershed)  %>% 
  filter(!is.na(wua), Lifestage != 'FR_spawn_wua') %>%
  mutate(Lifestage = ifelse(Lifestage == 'FR_juv_wua', 'Juvenile')) %>% 
  ggplot(aes(x = flow_cfs , y = wua, color = Lifestage)) +
  geom_line(color = '#7570b3') +
  labs(x = 'Flow (cfs)', y = 'WUA (sqft/1000ft)') +
  theme_minimal()

FlowWest/cvpiaHabitat documentation built on Oct. 27, 2020, 2:09 p.m.