R/get_lengths.R

In andybeet/obdbs: Pulls data from the NEFSC observer database

#' Extract Length data from obdbs
#'
#'Extract a list of length for speices sampled by observers on commercial fishing boats
#'This data is extracted from oblen
#'
#' @param channel an RODBC object (see \code{\link{connect_to_database}})
#' @param species a specific species code (NESPP3) or set of codes. Either numeric or character vector. Defaults to "all" species.
#' #' Numeric codes are converted to VARCHAR2(3 BYTE) when creating the sql statement. Character codes are short character strings.
#' @param year a numeric vector containing the years to search over
#' @param sex character vector. Default = "all". options "M" (male), "F" (female), "U" (unsexed)
#'
#' @return A list is returned:
#'
#'   \item{data}{containing the result of the executed \code{$sql} statement}
#'
#'   \item{sql}{containing the sql call}
#'
#'   \item{colNames}{a vector of the table's column names}
#'
#'@section Reference:
#'Use the data dictionary (\url{http://nova.nefsc.noaa.gov/datadict/}) for field name explanations.
#'Note: species codes (nespp4) are stored in the database as VARCHAR2(4 BYTE)
#'
#' @seealso \code{\link{connect_to_database}}
#'
#' @examples
#' \dontrun{
#' # extracts info for american flounder (plaice) (124)
#' channel <- connect_to_database(server="name_of_server",uid="individuals_username")
#' get_lengths(channel, species=124, year = "all")
#' get_lengths(channel, species="124", year = 2000, sex = "M")
#'
#'}
#'
#' @export


get_lengths <- function(channel, species="all", year=1994,  sex="all"){

  if (length(year) == 1) {
    if ((year == "all") & (species == "all")) stop("Can not pull all species and all years. Too much data!!")
  }

    # create an SQL query to extract all relavent data from tables
  # list of strings to build where clause in sql statement
  whereVec <- list()

  whereVec[[1]] <-  dbutils::createStringSpecies(itemName="nespp4",species,convertToCharacter=TRUE,numChars=3)
  whereVec[[2]] <-  dbutils::createString(itemName="year",year,convertToCharacter=TRUE,numChars=4)

  # sex conversion
  if (tolower(sex) == "all") {
    sex <- c(0,1,2)
  } else if (!is.numeric(sex)) {
    sex <- gsub("M",1,sex)
    sex <- gsub("F",2,sex)
    sex <- as.numeric(gsub("U",0,sex))
  }

  whereVec[[4]] <-  paste("sex in (",toString(sex),")")

  # build where clause of SQL statement based on input above
  whereStr <- "where"
  for (item in whereVec) {
    if (is.null(item)) {next}
    if (which(item == whereVec) == length(whereVec)) {
      whereStr <- paste(whereStr,item)
      next
    }
    whereStr <- paste(whereStr,item,"and")
  }



  # eventually user will be able to pass these variables
  sqlStatement <- "select YEAR, MONTH, TRIPID,HAULNUM,NEGEAR, NESPP4, LATHBEG, LONHBEG, AREA, SEX, LENANML, NUMLEN
                    from obdbs.oblen"

  sqlStatement <- paste(sqlStatement,whereStr)

  # call database
  query <- DBI::dbGetQuery(channel,sqlStatement)

  # column names
  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'OBLEN' and owner='OBDBS';"
  colNames <- DBI::dbGetQuery(channel,sqlcolName)

  return (list(data=dplyr::as_tibble(query),sql=sqlStatement, colNames=colNames))
}