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)
library(scales)

Future Data Improvements

[Future data improvement bullets]

Instream Spawning and Rearing Habiat

Data Source:
[???--combo of mokelunme and calaveras]

There is no habitat modeling, using mokelumne and calaveras

Instream spawning and rearing habitat for Fall Run Chinook Salmon in the Cosumnes River 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').

# # cosumnes -----
# region <- cvpiaHabitat::modeling_exist %>%
#   filter(Region == 'South Delta') %>%
#   select(Watershed, Region, FR_fry, FR_juv)
# 
# flows <- seq(100, 1000, by = 100)
# 
# # spawn
# cal_st_spwn <- approx(calaveras_river_instream$flow_cfs, 
#                       calaveras_river_instream$ST_spawn_wua, 
#                       rule = 2, xout = flows)$y
# 
# mok_fr_spwn <- approx(mokelumne_river_instream$flow_cfs, 
#                       mokelumne_river_instream$FR_spawn_wua, 
#                       rule = 2, xout = flows)$y
# 
# cos_spwn <- (cal_st_spwn + mok_fr_spwn) / 2
# 
# # fry
# cal_st_fry <- approx(calaveras_river_instream$flow_cfs, 
#                       calaveras_river_instream$ST_fry_wua, 
#                       rule = 2, xout = flows)$y
# 
# mok_fr_fry <- approx(mokelumne_river_instream$flow_cfs, 
#                       mokelumne_river_instream$FR_fry_wua, 
#                       rule = 2, xout = flows)$y
# 
# cos_fry <- (cal_st_fry + mok_fr_fry) / 2
# 
# # juv
# cal_st_juv <- approx(calaveras_river_instream$flow_cfs, 
#                       calaveras_river_instream$ST_juv_wua, 
#                       rule = 2, xout = flows)$y
# 
# mok_fr_juv <- approx(mokelumne_river_instream$flow_cfs, 
#                       mokelumne_river_instream$FR_juv_wua, 
#                       rule = 2, xout = flows)$y
# 
# cos_juv <- (cal_st_juv + mok_fr_juv) / 2
# 
# 
# 
# cosumnes_river_instream <- tibble(flow_cfs = flows, FR_spawn_wua = cos_spwn, 
#                                   FR_fry_wua = cos_fry, FR_juv_wua = cos_juv,
#                                   watershed = 'Cosumnes River')
# 
# cosumnes_river_instream
# devtools::use_data(cosumnes_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} cosumnes_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 fry and juvenile instream rearing habitat weighted usable areas for Fall Run Chinook Salmon in the Consumnes 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}
cosumnes_river_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.