Summer Townet Fish Data

Information on the Summer Townet Survey is available on the California Department of Fish and Wildlife website: https://wildlife.ca.gov/Conservation/Delta/Townet-Survey

All sampling stations

Complete sampling effort summary

Final sampling sites with custom regions

Save final datasets

## Annual, no regions:

STN_annual_values <- STN_combined_derived %>%
  group_by(Year, Method, CommonName) %>%
  summarise(Biomass=mean(Biomass),
            Catch_per_tow=mean(Count)) %>%
  group_by(Year, Method, CommonName) %>%
  summarise(Biomass=mean(Biomass),
            Catch_per_tow=mean(Catch_per_tow))


STN_annual_values_CPUE <- STN_annual_values %>%
  filter(Method=="STN net") %>%
  subset(select=c(Year,CommonName,Catch_per_tow)) %>%
  pivot_wider(names_from=CommonName,
              values_from=Catch_per_tow,
              names_prefix="STN_fish_catch_per_tow_") %>%
  mutate(STN_fish_catch_per_tow_Estuarine_pelagic_forage_fishes=
           (STN_fish_catch_per_tow_AmericanShad +
               STN_fish_catch_per_tow_ThreadfinShad +
               STN_fish_catch_per_tow_DeltaSmelt +
               STN_fish_catch_per_tow_LongfinSmelt +
               STN_fish_catch_per_tow_StripedBass_age0),
         STN_fish_catch_per_tow_Marine_pelagic_forage_fishes=
           (STN_fish_catch_per_tow_NorthernAnchovy +
               STN_fish_catch_per_tow_PacificHerring))


STN_annual_values_biomass <- STN_annual_values %>%
  filter(Method=="STN net") %>%
  subset(select=c(Year,CommonName,Biomass)) %>%
  pivot_wider(names_from=CommonName,
              values_from=Biomass,
              names_prefix="STN_fish_biomass_") %>%
  mutate(STN_fish_biomass_Estuarine_pelagic_forage_fishes=
           (STN_fish_biomass_AmericanShad +
               STN_fish_biomass_ThreadfinShad +
               STN_fish_biomass_DeltaSmelt +
               STN_fish_biomass_LongfinSmelt +
               STN_fish_biomass_StripedBass_age0),
         STN_fish_biomass_Marine_pelagic_forage_fishes=
           (STN_fish_biomass_NorthernAnchovy +
               STN_fish_biomass_PacificHerring))


STN_annual_values_final <- full_join(STN_annual_values_CPUE,
                                     STN_annual_values_biomass)


write.csv(STN_annual_values_final, row.names=FALSE,
          file=file.path("data/annual_averages/fish_STN_noregions.csv"))

## Annual, with regions:

STN_annual_regional_values <- STN_combined_derived %>%
  group_by(Year, Region, Method, CommonName) %>%
  summarise(Biomass=mean(Biomass),
            Catch_per_tow=mean(Count)) %>%
  group_by(Year, Method, CommonName, Region) %>%
  summarise(Biomass=mean(Biomass),
            Catch_per_tow=mean(Catch_per_tow))


STN_annual_regional_values_CPUE <- STN_annual_regional_values %>%
  filter(Method=="STN net") %>%
  subset(select=c(Year,CommonName,Catch_per_tow, Region)) %>%
  pivot_wider(names_from=CommonName,
              values_from=Catch_per_tow,
              names_prefix="STN_fish_catch_per_tow_") %>%
  mutate(STN_fish_catch_per_tow_Estuarine_pelagic_forage_fishes=
           (STN_fish_catch_per_tow_AmericanShad +
               STN_fish_catch_per_tow_ThreadfinShad +
               STN_fish_catch_per_tow_DeltaSmelt +
               STN_fish_catch_per_tow_LongfinSmelt +
               STN_fish_catch_per_tow_StripedBass_age0),
         STN_fish_catch_per_tow_Marine_pelagic_forage_fishes=
           (STN_fish_catch_per_tow_NorthernAnchovy +
               STN_fish_catch_per_tow_PacificHerring))


STN_annual_regional_values_biomass <- STN_annual_regional_values %>%
  filter(Method=="STN net") %>%
  subset(select=c(Year,CommonName,Biomass, Region)) %>%
  pivot_wider(names_from=CommonName,
              values_from=Biomass,
              names_prefix="STN_fish_biomass_") %>%
  mutate(STN_fish_biomass_Estuarine_pelagic_forage_fishes=
           (STN_fish_biomass_AmericanShad +
               STN_fish_biomass_ThreadfinShad +
               STN_fish_biomass_DeltaSmelt +
               STN_fish_biomass_LongfinSmelt +
               STN_fish_biomass_StripedBass_age0),
         STN_fish_biomass_Marine_pelagic_forage_fishes=
           (STN_fish_biomass_NorthernAnchovy +
               STN_fish_biomass_PacificHerring))


STN_annual_regional_values_final <- full_join(STN_annual_regional_values_CPUE,
                                              STN_annual_regional_values_biomass)


write.csv(STN_annual_regional_values_final, row.names=FALSE,
          file=file.path("data/annual_averages/fish_STN_regions.csv"))

Lastly, export out station list to data/stations folder

## Use STN_combined_derived so the stations saved here match those used in the annual 
## and annual regional datasets saved above.
STN_combined_derived %>%
  dplyr::select(Station, Latitude, Longitude) %>%
  dplyr::distinct() %>%
  dplyr::arrange(Station) %>%
  dplyr::mutate(Survey="Summer Townet") %>%
  write.csv(row.names=FALSE,
            file=file.path("data/stations/stations_fish_STN_annual.csv"))