KevinSee / STADEM

Estimate escapment across a dam
https://kevinsee.github.io/STADEM/
Other
1 stars 6 forks source link

Improve PIT tag query at dams #24

Open KevinSee opened 6 months ago

KevinSee commented 6 months ago

Based on a suggestion from @tbuehrens, the queryPITtagObs function could be expanded to include more sites (currently only works for Lower Granite). It might be improved by focusing on adult PIT tag detections only, which would involve changing some code from pitall_obs_de to pitadult_obs_de. Here's Thomas's suggested function:

get_unique_adult_dam_observations<-function(years, 
                                            species, #Chinook, Steelhead, Coho, Sockeye
                                            run, #1= spring, 2=summer, 3=fall, 4=winter 5=unknown, Null=all
                                            rear, #W or H or Null = all
                                            dam #B2A = BON
                                            ){
  spp_code = tibble(spp_nm = c('Chinook', 'Coho', 'Steelhead', 'Sockeye'),
                  spp_code = 1:4)  %>%
  filter(spp_nm %in% species) %>%
  pull(spp_code)

  results<-tibble()
  baseurl<-"https://www.cbr.washington.edu/dart/cs/php/rpt/pitall_obs_de.php?sc=1&queryName=pitadult_obs_de&outputFormat=csv&year="
  for(y in years){
    for(s in spp_code){
      fullurl=paste0(baseurl,y,"&proj=",dam,"&species=",s,"&run=",run,"&rear_type=",rear,"&span=no&startdate=1%2F1&enddate=12%2F31&syear=",y,"&eyear=",y,"&reltype=alpha&relloc=251&summary=no")
    dat<-readr::read_csv(fullurl)%>%
      filter(!is.na(`Tag ID`))
    results <- bind_rows(results, dat)
    }
  }
  return(results)
}