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 improvements bullets]

Instream Spawning and Rearing Habiat

Data Source: CDFW 1979 and FWS 2014

Instream spawning and rearing habitat for Fall Run Chinook Salmon in the Cottonwood Creek is based on data from [data source description]. 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 A2:B8 for spawning, and A10:C40 for rearing of the 'Cottonwood' tab within his 'IFIMWUA.xlsx'.

Units are in square feet and study length is 10.76 miles.

# mi <- 10.76
# cotton_spawn <- read_excel('data-raw/mark_gard_data/IFIMWUA.xlsx', 
#                            range = "A2:B8", sheet = 'Cottonwood') %>% 
#   mutate(FR_spawn_wua = Spawning/mi/5.28) %>% 
#   select(flow_cfs = Flow, FR_spawn_wua)
# 
# cotton_rear <- read_excel('data-raw/mark_gard_data/IFIMWUA.xlsx', 
#                           range = "A10:C40", sheet = 'Cottonwood') %>% 
#   mutate(FR_fry_wua = `Fry Rearing`/mi/5.28, FR_juv_wua = `Juv Rearing`/mi/5.28) %>% 
#   select(flow_cfs = Flow, FR_fry_wua, FR_juv_wua)
# 
# cottonwood_creek_instream <- cotton_spawn %>% 
#   full_join(cotton_rear) %>% 
#   arrange(flow_cfs) %>% 
#   mutate(watershed = 'Cottonwood Creek')
# 
# cottonwood_creek_instream
# devtools::use_data(cottonwood_creek_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} cottonwood_creek_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 fry and juvenile instream rearing habitat weighted usable areas for Fall Run Chinook Salmon in the Cottonwood River are 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 fry and juvenile. These rates are multiplied by the total rearing reach length mapped by the SIT. 
``` {r,echo=FALSE}
cottonwood_creek_instream %>% 
  gather(Lifestage, wua, -flow_cfs, -watershed)  %>% 
  filter(!is.na(wua), Lifestage != 'FR_spawn_wua') %>%
  mutate(Lifestage = ifelse(Lifestage == 'FR_fry_wua', 'Fry', 'Juvenile')) %>% 
  ggplot(aes(x = flow_cfs , y = wua, color = Lifestage)) +
  geom_line() +
  labs(x = 'Flow (cfs)', y = 'WUA (sqft/1000ft)') + 
  theme_minimal() + 
  scale_color_manual(values = c('#d95f02','#7570b3'))

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