View source: R/fleet_gaspereau.R
fleet_gaspereau | R Documentation |
This is a wrapper function that facilitates extracting information for the gaspereau fleet. All of the information used to identify fleets is stored in the package's associated data files - LIC_CORE, LIC_AREAS, and LIC_GEAR_SPEC. The various wrappers can have different options (e.g. MOBILE vs FIXED, WESTERN vs EASTERN, 4XY vs 5ZJM, small mesh vs large mesh, diamond vs square mesh, etc), and depending on which options are selected, different fleets are identified, and their data is extracted.
fleet_gaspereau(
marfGear = c(41, 42, 44, 61, 70),
useLocal = NULL,
socks = FALSE,
...
)
marfGear |
default is |
useLocal |
default is
|
socks |
default is |
... |
Arguments passed on to
|
Licence Information for any fleet is accessible via the following calls. Please replace "<fleet>", with this fleet's actual fleet value identified in the NOTE, below:
Licence Type, Subtype, Gear and Species Information (if applicable)
Mar.fleets::LIC_CORE[Mar.fleets::LIC_CORE$FLEET=="<fleet>",]
Licence Areas (if applicable)
Mar.fleets::LIC_AREAS[Mar.fleets::LIC_AREAS$FLEET=="<fleet>",]
If different areas/components/units are available for this fleet, the areas associated with
each can be differentiated by the differing values of FLEET_AREA_ID
. For example, the
Redfish fleet is divided into Units 2 and 3. All of the NAFO areas associated with either of
these units these can be found in via Mar.fleets::LIC_AREAS[Mar.fleets::LIC_AREAS$FLEET=="REDFISH",]
,
but the NAFO areas associated with the Unit 2 fleet are those with FLEET_AREA_ID
== UNIT2
.
Licence Gear Specifications (if applicable)
Mar.fleets::LIC_GEAR_SPEC[Mar.fleets::LIC_GEAR_SPEC$FLEET=="<fleet>",]
If particular gear size/types are allowed, the range of sizes for each are specified by the
MIN and MAX fields. If aspects of the fleet are defined by the gear size, multiple records
may be present. For example, the SMALL mesh fleet will have different max and min values than
the LARGE MESH fleet. These records can correspond with fleet areas, but do not have to. In
this case, the gear associated with catching redfish in UNIT 2 is different than what's
allowed in UNIT 3, so the LIC_GEAR_SPEC table differentiates the gear by having different
entries in FLEET_GEARSPECS_ID
(i.e. UNIT2
vs UNIT3
). The mobile POLLOCK
fleet also has multiple categories of gear sizes, but they are not related to different areas
- the entries in FLEET_GEARSPECS_ID
are just SMALL
and LARGE
. Differing
values of Type have not been implemented, but the field exist such that gear can be filtered
by Diamond vs Square mesh.
specific returned objects can be specified by the user, but the default result is a list of objects. The list includes marfis data, isdb data, information related to the matching, and a breakdown of where the various trips and sets occurred, specifically:
params
- this is a list containing information about the extraction
user
- this contain all of the parameters sent to the function (including defaults, user-provided and hardcoded)
fleet
- this is a list object containing 3 dataframes that contain the information used to identify the fleet.
These will include licencesCore, licecesAreas, and licencesGearSpecs. Depending on how the fleet is defined, one or more of
these may be empty.
fleet
- This is a dataframe of the unique combinations of (MARFIS) LICENCE_ID, VR_NUMBER and GEAR_CODE that
was found for this fleet during the specified period
FLEET_ACTIVITY
- This is a dataframe of identifiers for all of the (MARFIS) fishing activity undertaken
by vessels of this fleet during the specified period (i.e. LICENCE_ID, PRO_SPC_INFO_ID, LOG_EFRT_STD_INFO_ID, GEAR_CODE,
MON_DOC_ID, VR_NUMBER, and several dates associated with the trip)
marf
- This is a list of 3 sets of information for the commercial catch data (i.e. marfis):
MARF_TRIPS
MARF_SETS
MARF_MATCH
This is a special dataframe containing information that can be used to link
the commercial data to the ISDB data
isdb
- This is a list of data objects from the ISDB db:
ISDB_TRIPS
These are ISDB trips that are associated with MARFIS trips from the marf$MARF_TRIPS
object above
ISDB_SETS
These are all of the ISDB sets associated with the ISDB_TRIPS (matched and unmatched)
ISDB_CATCHES
This is the data associated with the records in ISDB_TRIPS
ALL
This is the raw data from ISCATCHES for the trips found in ISDB_TRIPS
SUMMARY
This is the data from ISCATCHES for all of the trips found in ISDB_TRIPS, summarized by species. Each species
has calculated aggregate values for "EST_NUM_CAUGHT", EST_KEPT_WT", "EST_DISCARD_WT" and "EST_COMBINED_WT"
matches
This is a list item that contains all of the information used to assigne matches between MARFIS and ISDB
MATCH_SUMMARY_TRIPS
This is a simple breakdown of the various approaches used for matching, and the relative success of each.
Matches can occur using multiple approaches, so these can not be added up. This list also includes "Likely_Swapped_VR_Lic
" which
indicates how may matches seem to have the values for LICENCE_ID and VR_NUMBER reversed, and includes the count of how many rows are present
in both Multimatches
and Umatchables
MATCH_DETAILS
This is a dataframe of all of the MARFIS and ISDB trips that have been associated with each other, and whether
or not they were matched on each of the possible approaches
ISDB_UNMATCHABLES
These are the trips from MARFIS that included ISDB-type information (e.g. Observer ID, ISDB Trip name, etc), but
for which no ISDB match could be found.
ISDB_MULTIMATCHES
These are ISDB trips that were found to be match multiple MARFIS trips equally well.
location_summary
- This is a list of 1 or more dataframes that breaks down the various trips
and sets by the areas in which they occurred. NAFO locations are reported for MARFIS trips, MARFIS sets and ISDB sets
(not ISDB trips). These reported locations are shown, as are the "calculated" locations, which are based on the
reported latitudes and longitudes. No "calculated" locations are shown for MARFIS trips, as there are no coordinates for
the trip level. If a custom value for areaFile
was sent (i.e. not "NAFOSubunits_sf"), a second dataframe breaking
down the sets by the custom area will also be provided.
Hardcoded parameters for this fleet are as follows:
marfSpp
= 350
isdbSpp
= 62
fleet
= "GASP"
The following parameters are "softcoded" - any or all of the values can be provided, but other values are not allowed.
marfGear
= c(61,62)
Mike McMahon, Mike.McMahon@dfo-mpo.gc.ca
Other fleets:
fishin_CHPs()
,
fleet_bluefin()
,
fleet_cucumber()
,
fleet_flatfish()
,
fleet_hagfish()
,
fleet_halibut()
,
fleet_herring()
,
fleet_jonah()
,
fleet_redCrab()
,
fleet_redfish()
,
fleet_rockCrab()
,
fleet_scallop()
,
fleet_sculpin()
,
fleet_shrimp()
,
fleet_silverhake()
,
fleet_snowcrab()
,
fleet_surfclam()
,
fleet_swordfishTunaShark()
,
fleet_urchin()
,
fleet_whelk()
## Not run:
db <- fleet_gaspereau(useLocal = F,
year = 2018,
oracle.username = "<name>",
oracle.password="<password>",
oracle.dsn="PTRAN",
usepkg = "roracle"
)
local <- fleet_gaspereau(year = 2018,
useLocal = T,
data.dir = "c:/data_folder"
)
## End(Not run)
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