R/read.bird.r

In jasonelaw/BESdata: Retrieve BES data from internal databases.

#'Read point count data from Watershed database
#'
#'Reads point count data and survey information from BES watershed database
#'@param ... query parameters in \code{tag = value} form
#'@param start an object of class Date; the earliest survey start date to retrieve
#'@param end an object of class Date; the latest survey start date to retrieve
#'@param server Alternate server for the WATERSHED database - for access to production or test instances.
#'@examples
#'\dontrun{
#'#Get some data
#'d <- read.bird(start = as.Date('2017-01-01'))
#'}
#'@describeIn read.bird Read point count data
#'@export
read.bird <- function (..., start = NULL, end = NULL, server = NULL){
  on.exit(dbDisconnect(con))

   kView <- "V_RPT_AVIAN_POINT_COUNT_SPECIES_DATA"
  where <- constructWhereStatement(..., start = start, end = end,
                                   date.field = "survey_start")
  query <- constructQuery(kView, where, unrestricted = TRUE)
  con <- dbConnect("WATERSHED", server = server)
  ret <- dbGetQuery(con, query)
  ret <- formatDataFrame(
    ret,
    date = c("survey_start"),
    drop = c("avian_project_id", "avian_species_id", "avian_time_bracket_id",
             "avian_detection_type_id", "avian_detection_code_id", "is_flock_id", "is_juvenile_id"),
    bool = c("is_flock_name", "is_juvenile_name"), true.value = "Yes")
  return(ret)
}

#'@describeIn read.bird Read point count survey information
#'@export
read.bird.survey <- function (..., start = NULL, end = NULL, server = NULL,
                              date.field = "survey_start"){
  on.exit(dbDisconnect(con))
  kView <- "V_RPT_AVIAN_POINT_COUNT_SURVEY"
  where <- constructWhereStatement(..., start = start, end = end,
                                   date.field = "survey_start")
  query <- constructQuery(kView, where, unrestricted = TRUE)
  con <- dbConnect("WATERSHED", server = server)
  ret <- dbGetQuery(con, query)
  ret <- formatDataFrame(
    ret,
    date = c("survey_start", "survey_end"),
    numeric = "sound_meter_decibals",
    drop = c("avian_project_id", "avian_beaufort_scale_id", "avian_noise_scale_id", "avian_observer_id", "cloud_cover_id", "drizzle_id", "wind_category_id")
  )
  return(ret)
}