PullCatch.PacFIN.RdPull catch data from the Comprehensive Fish Ticket table in PacFIN.
PullCatch.PacFIN(
pacfin_species_code,
council_code = "P",
username = getUserName("PacFIN"),
password = ask_password(),
savedir = getwd(),
addnominal = TRUE,
verbose = TRUE
)A vector of strings specifying the PacFIN species
code(s) you are interested in. This has sometimes been referred to as
"SPID" in legacy sql scripts. An example for sablefish would be
pacfin_species_code = "SABL". Lists of species codes in hierarchical order,
by
organization,
and alphabetically organized
can be found on the PacFIN website. Often you
will want to include nominal species categories. Where, nominal (i.e.,
existing in name only)
means information for a given species that is "derived" from non-species
specific information, e.g., species complexes that are split out by species
compositions like "nominal aurora rockfish" which would be ARR1. For some
functions, these nominal categories can automatically be added, see the
argument addnominal.
A vector of character strings specifying the council code
that you wish to retain data for. The default "P" means data will only be
returned for the Pacific Fisheries Management Council. Other accepted
values are "N" or "*".
Most often, this is a string containing your username for the
database of interest. You can use getUserName() if you prefer to not
enter this argument and assume the default search and/or rules for finding
your username will work. This is the default behavior if you leave
username as a missing argument, i.e., username <- getUserName(database = database). Sometimes this search will fail because of legacy rules, which
are unknown to the development team, that were used to create your
username. Please email the maintainer of this package if you need more
functionality here.
Most often, this is a string containing your password for
the database of interest. You can use the function ask_password() if you
would prefer to be prompted for your password. Please do not share this
password with anyone or push code to a repository that has your password
saved in it.
A file path to the directory where the results will be saved. The default is the current working directory. The path can be relative or absolute.
A logical, where the default, TRUE, adds nominal
PacFIN species code to pacfin_species_code. FALSE
leaves pacfin_species_code as input by the user, which will miss
catch for species such as dover sole that have more than one species
code within PacFIN, e.g., pacfin_species_code = c("DOVR", "DVR1").
Users can also input a vector to pacfin_species_code if you want to
specify the species and the nominal species code without searching for
it. This is helpful for when you are getting data for two species and
you only want nominal catch for one or if you only wanted nominal catch.
Nominal species code will be searched for using PullNominal.PacFIN() if
the input value for addnominal is TRUE.
A logical specifying if output should be written to the
screen or not. Good for testing and exploring your data but can be turned
off when output indicates information that you already know. The printing
of output to the screen does not affect any of the returned objects. The
default is to always print to the screen, i.e., verbose = TRUE.
A .RData file is saved with the object inside the file stored as
catch.pacfin. This same data frame is also returned invisibly.
There is a rockfish (URCK) category that consists of unassigned rockfish landings. The majority of the catch is prior to 2001. Currently, there is no agreed upon methodology to parsed these landing out to specific rockfish species. At present, landings in this category are not included in species-specific rockfish catch pulls.
In PacFIN there are four species code that can be associated with Pacific ocean perch. These are POP, POP1, POP2, UPOP. The POP1 is general shelf/slope rockfish and not Pacific ocean perch specific landings. These records occur only in Oregon. As of the 2017 assessment, these records should be removed from the catch file.
Values passed to pacfin_species_code are searched for in their exact form.
That is, there are no regular expression searches so mistakes such as
" POP" will not be found. In my experiences these mistakes in the species
codes are more common for PacFIN species codes that are three letters rather
than the standard four letters.
PullNominal.PacFIN() determines the nominal species codes
sql_catch() writes the sql code to pull the data
if (FALSE) { # \dontrun{
catch.pacfin <- PullCatch.PacFIN("PTRL")
# Check for confidentiality by year
# though you would also want to do this by your gear types
dplyr::group_by(catch.pacfin, LANDING_YEAR) %>%
dplyr::summarize(count = dplyr::n_distinct(VESSEL_ID)) %>%
dplyr::filter(count < 4)
# look for foreign landings
catch.pacfin <- PullCatch.PacFIN("PTRL", council_code = c("*", "N"))
# Counts of NROW() by area code(s)
dplyr::group_by(catch.pacfin, ORIG_PACFIN_CATCH_AREA_CODE) %>%
dplyr::count()
} # }