#' Read from table fiskar.stodvar or fjolst::stodvar
#'
#' @param year Years to include
#' @param month Months to include
#' @param cruise.id Cruises to include
#' @param gear.id Gear to include
#' @param rect Statistical rectangle to include
#' @param id Station id (synis.id) to include
#' @param col.names Column names to return
#' @param oracle Boolean, if TRUE (default) obtains data from database,
#' otherwise from the binary data in fjolst.
#'
#' @return A dataframe
#' @export
#'
read_stations <- function(year = NULL,
month = NULL,
cruise.id = NULL,
gear.id = NULL,
rect = NULL,
id = NULL,
col.names,
oracle = TRUE) {
d <- fjolst::lesa.stodvar(ar = year, man = month, leidangur = cruise.id,
veidarfaeri = gear.id,
reitur = rect,
synis.id = id,
col.names = col.names,
oracle = oracle) %>%
dplyr::tbl_df() %>%
dplyr::rename_(.dots=setNames(names(.),dictionary$eng[match(names(.),dictionary$ice)]))
return(d)
}
#' Title
#'
#' @param id station id
#' @param species species id
#' @param col.names column names to return
#' @param sex include sex
#' @param mat include maturity
#' @param length specify length
#' @param corrected xx
#' @param oracle xx
#'
#' @return A dataframe
#' @export
#'
read_lengths <- function(id, species, col.names = c("id","length","n"),
sex = NULL, mat = NULL, length = NULL,
corrected = F, oracle = TRUE) {
d <- fjolst::lesa.lengdir(id, teg = species,
kyn = sex,
kynthroski = mat,
lengd = length,
leidrett = corrected,
col.names = c("synis.id", "tegund", "lengd", "fjoldi"),
oracle = oracle) %>%
dplyr::tbl_df() %>%
dplyr::rename_(.dots=setNames(names(.),dictionary$eng[match(names(.),dictionary$ice)]))
return(d)
}
#' Title
#'
#' @param id xxx
#' @param species xxx
#' @param weight xxx
#' @param corrected xxx
#' @param oracle xxx
#'
#' @return A dataframe
#' @export
#'
read_subsampling <- function(id, species, weight = FALSE,
corrected = FALSE,
oracle = TRUE) {
d <- fjolst::lesa.numer(id, teg = species,
vigt = weight,
col.names =c("synis.id", "tegund", "fj.maelt", "fj.talid"),
leidrett = corrected,
oracle = oracle) %>%
dplyr::tbl_df() %>%
dplyr::rename_(.dots=setNames(names(.),dictionary$eng[match(names(.),dictionary$ice)])) %>%
dplyr::mutate(r = 1 + n.counted/n.measured) %>%
dplyr::select(-n.counted, -n.measured)
return(d)
}
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