Create R6 reference object class object_model_data
trips_object_creation()Creation of an R6 reference object class trips which contains one or more R6 reference object class trip.
object_model_data$trips_object_creation(
data_source = "observe_database",
database_connection = NULL,
years_period = NULL,
flag_codes = NULL,
ocean_codes = NULL,
vessel_type_codes = NULL,
trip_ids = NULL,
data_path = NULL,
envir = NULL
)data_sourceObject of class character expected. By default "observe_database". Identification of data source. You can switch between "observe_database", "avdth_database", "csv_file" (with separator ";" and decimal ","), "rdata_file" or "envir" (for an object in the R environment).
database_connectionDatabase connection, list of one or more R object(s) expected. By default NULL. Mandatory argument for data source "observe_database" ("PqConnection" R object), corresponding to the second element of the object returned by `furdeb::postgresql_dbconnection()`. Or mandatory argument for data source"avdth_database" ("JDBCConnection" R object) corresponding to the second element of the object returned by `furdeb::access_dbconnection()`. For data source "observe_database", a list of "PqConnection" R objects can be specified to query data from different observe databases. For example, a list of two database connection arguments for "observe_main" and "observe_acquisition" can be specified to simultaneously import and process recent data from acquisition database, which has not yet been imported into the main database, and older data from the main database.
years_periodObject of class integer expected. By default NULL. Year(s) of the reference time period coded on 4 digits. Mandatory for data source "observe_database" and "avdth_database".
flag_codesObject of class character expected. By default NULL. Three letters country(ies) ISO 3 code(s) related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
ocean_codesObject of class integer expected. By default NULL. Ocean(s) related to data coded on 1 digit. Necessary argument for data source "observe_database" and "avdth_database".
vessel_type_codesObject of class integer expected. By default NULL. Vessel type(s) related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
trip_idsObject of class character expected. By default NULL. Additional parameter only used with data source "observe_database". Use trip(s) identification(s) for selected trip(s) kept in the query. This argument overrides all others arguments like "years_period", "flag_codes" or "ocean_codes".
data_pathObject of class character expected. By default NULL. Path of the data csv/RData file.
envirObject of class character expected. By default the first environment where data are found will be used. Specify an environment to look in for data source "envir".
activities_object_creation()Creation of a R6 reference object of class activities which contain one or more R6 reference object of class activity, including related elementarycatch(es).
object_model_data$activities_object_creation(
data_source = "observe_database",
database_connection = NULL,
weight_categories_avdth_ref = NULL,
years_period = NULL,
flag_codes = NULL,
ocean_codes = NULL,
vessel_type_codes = NULL,
species_fate_codes = NULL,
trip_ids = NULL,
data_path = NULL,
envir = NULL
)data_sourceObject of class character expected. By default "observe_database". Identification of data source. You can switch between "observe_database", "avdth_database", "csv_file" (with separator ";" and decimal ","), "rdata_file" or "envir" (for an object in the R environment).
database_connectionDatabase connection, list of one or more R object(s) expected. By default NULL. Mandatory argument for data source "observe_database" ("PqConnection" R object), corresponding to the second element of the object returned by `furdeb::postgresql_dbconnection()`. Or mandatory argument for data source"avdth_database" ("JDBCConnection" R object) corresponding to the second element of the object returned by `furdeb::access_dbconnection()`. For data source "observe_database", a list of "PqConnection" R objects can be specified to query data from different observe databases. For example, a list of two database connection arguments for "observe_main" and "observe_acquisition" can be specified to simultaneously import and process recent data from acquisition database, which has not yet been imported into the main database, and older data from the main database.
weight_categories_avdth_refObject of type data.frame or tbl_df expected.
Reference table defining the logbook weight categories with the following columns:
avdth_weight_category_code: Logbook weight category code from avdth database, type character.
species_fao_code: species FAO code, type character.
weight_category_min: lower limit of the weight category (kg), type numeric.
weight_category_max: upper limit of the weight category (kg), type numeric.
Mandatory for data_source = "avdth_database".
By default the referential table data("weight_categories_avdth_ref", package="t3") is considered (weight_categories_avdth_ref).
years_periodObject of class integer expected. By default NULL. Year(s) of the reference time period coded on 4 digits. Mandatory for data source "observe_database" and "avdth_database".
flag_codesObject of class character expected. By default NULL. Country(ies) code related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
ocean_codesObject of class integer expected. By default NULL. Ocean(s) related to data coded on 1 digit. Necessary argument for data source "observe_database" and "avdth_database".
vessel_type_codesObject of class integer expected. By default NULL. Vessel type(s) related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
species_fate_codesObject of class integer expected. By default NULL. Specie fate(s) related to elementarycatch(es) data extraction. Necessary argument for data source "observe_database" and "avdth_database".
trip_idsObject of class character expected. By default NULL. Additional parameter only used with data source "observe_database". Use trip(s) identification(s) for selected trip(s) kept in the query. This argument overrides all others arguments like "years_period", "country" or "ocean".
data_pathObject of class character expected. By default NULL. Path of the data csv/RData file.
envirObject of class character expected. By default the first environment where data are found will be used. Specify an environment to look in for data source "envir".
elementarylandings_object_creation()Creation of a R6 reference object class elementarylandings which contain one or more R6 reference object class elementarylanding
object_model_data$elementarylandings_object_creation(
data_source = "observe_database",
database_connection = NULL,
years_period = NULL,
flag_codes = NULL,
ocean_codes = NULL,
vessel_type_codes = NULL,
trip_ids = NULL,
data_path = NULL,
envir = NULL
)data_sourceObject of class character expected. By default "observe_database". Identification of data source. You can switch between "observe_database", "avdth_database", "csv_file" (with separator ";" and decimal ","), "rdata_file" or "envir" (for an object in the R environment).
database_connectionDatabase connection, list of one or more R object(s) expected. By default NULL. Mandatory argument for data source "observe_database" ("PqConnection" R object), corresponding to the second element of the object returned by `furdeb::postgresql_dbconnection()`. Or mandatory argument for data source"avdth_database" ("JDBCConnection" R object) corresponding to the second element of the object returned by `furdeb::access_dbconnection()`. For data source "observe_database", a list of "PqConnection" R objects can be specified to query data from different observe databases. For example, a list of two database connection arguments for "observe_main" and "observe_acquisition" can be specified to simultaneously import and process recent data from acquisition database, which has not yet been imported into the main database, and older data from the main database.
years_periodObject of class integer expected. By default NULL. Year(s) of the reference time period coded on 4 digits. Mandatory for data source "observe_database" and "avdth_database".
flag_codesObject of class character expected. By default NULL. Country(ies) code related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
ocean_codesObject of class integer expected. By default NULL. Ocean(s) related to data coded on 1 digit. Necessary argument for data source "observe_database" and "avdth_database".
vessel_type_codesObject of class integer expected. By default NULL. Vessel type(s) related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
trip_idsObject of class character expected. By default NULL. Additional parameter only used with data source "observe_database". Use trip(s) identification(s) for selected trip(s) kept in the query. This argument overrides all others arguments like "years_period", "country" or "ocean".
data_pathObject of class character expected. By default NULL. Path of the data csv/RData file.
envirObject of class character expected. By default the first environment where data are found will be used. Specify an environment to look in for data source "envir".
wells_object_creation()Creation of a R6 reference object class wells which contain one or more R6 reference object class well, wellset, samples and elementarywellplan.
object_model_data$wells_object_creation(
data_source = "observe_database",
database_connection = NULL,
years_period = NULL,
flag_codes = NULL,
ocean_codes = NULL,
vessel_type_codes = NULL,
sample_type_codes = NULL,
trip_ids = NULL,
data_path_sample = NULL,
data_path_wellplan = NULL,
envir = NULL
)data_sourceObject of class character expected. By default "observe_database". Identification of data source. You can switch between "observe_database", "avdth_database", "csv_file" (with separator ";" and decimal ","), "rdata_file" or "envir" (for an object in the R environment).
database_connectionDatabase connection, list of one or more R object(s) expected. By default NULL. Mandatory argument for data source "observe_database" ("PqConnection" R object), corresponding to the second element of the object returned by `furdeb::postgresql_dbconnection()`. Or mandatory argument for data source"avdth_database" ("JDBCConnection" R object) corresponding to the second element of the object returned by `furdeb::access_dbconnection()`. For data source "observe_database", a list of "PqConnection" R objects can be specified to query data from different observe databases. For example, a list of two database connection arguments for "observe_main" and "observe_acquisition" can be specified to simultaneously import and process recent data from acquisition database, which has not yet been imported into the main database, and older data from the main database.
years_periodObject of class integer expected. By default NULL. Year(s) of the reference time period coded on 4 digits. Mandatory for data source "observe_database" and "avdth_database".
flag_codesObject of class character expected. By default NULL. Country(ies) code related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
ocean_codesObject of class integer expected. By default NULL. Ocean(s) related to data coded on 1 digit. Necessary argument for data source "observe_database" and "avdth_database".
vessel_type_codesObject of class integer expected. By default NULL. Vessel type(s) related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
sample_type_codesObject of class integer expected. By default NULL. Sample type identification.
trip_idsObject of class character expected. By default NULL. Additional parameter only used with data source "observe_database". Use trip(s) identification(s) for selected trip(s) kept in the query. This argument overrides all others arguments like "years_period", "country" or "ocean".
data_path_sampleObject of class character expected. By default NULL. Path of the data sql/csv file for samples.
data_path_wellplanObject of class character expected. By default NULL. Path of the data sql/csv file for well plans.
envirObject of class character expected. By default NULL. Specify an environment to look in for data source "envir".
setdurationrefs_data()Creation of a data frame object with parameters of set duration algorithms.
object_model_data$setdurationrefs_data(
data_source = "csv_file",
data_path = NULL,
envir = NULL
)data_sourceObject of class character expected. Identification of data source. By default "csv_file" (with separator character ";" and decimal ","). Identification of data source. You can switch to "rdata_file" or "envir" (for an object in the R environment).
data_pathObject of class character expected. By default NULL. Mandatory argument for data source "csv_file", "rdata_file" or "envir". Path of the data file.
envirObject of class character expected. By default NULL. Specify an environment to look in for data source "envir".
lengthsteps_data()Creation of a data frame object with length ratio between ld1 and lf class.
object_model_data$lengthsteps_data(
data_source = "csv_file",
data_path = NULL,
envir = NULL
)data_sourceObject of class character expected. By default "csv_file" (with separator character ";" and decimal ","). Identification of data source. You can switch to "rdata_file" or "envir" (for an object in the R environment).
data_pathObject of class character expected. By default NULL. Mandatory argument for data source "csv_file", "rdata_file" or "envir". Path of the data file.
envirObject of class character expected. By default NULL. Specify an environment to look in for data source "envir".
samplesets_data()Creation of a data frame object with weighted weight of each set sampled.
object_model_data$samplesets_data(
data_source = "observe_database",
database_connection = NULL,
years_period = NULL,
flag_codes = NULL,
ocean_codes = NULL,
vessel_type_codes = NULL,
trip_ids = NULL,
data_path = NULL,
envir = NULL
)data_sourceObject of class character expected. By default "observe_database". Identification of data source. You can switch between "observe_database", "avdth_database", "csv_file" (with separator ";" and decimal ","), "rdata_file" or "envir" (for an object in the R environment).
database_connectionDatabase connection, list of one or more R object(s) expected. By default NULL. Mandatory argument for data source "observe_database" ("PqConnection" R object), corresponding to the second element of the object returned by `furdeb::postgresql_dbconnection()`. Or mandatory argument for data source"avdth_database" ("JDBCConnection" R object) corresponding to the second element of the object returned by `furdeb::access_dbconnection()`. For data source "observe_database", a list of "PqConnection" R objects can be specified to query data from different observe databases. For example, a list of two database connection arguments for "observe_main" and "observe_acquisition" can be specified to simultaneously import and process recent data from acquisition database, which has not yet been imported into the main database, and older data from the main database.
years_periodObject of class integer expected. By default NULL. Year(s) of the reference time period coded on 4 digits. Mandatory for data source "observe_database" and "avdth_database".
flag_codesObject of class character expected. By default NULL. Country(ies) code related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
ocean_codesObject of class integer expected. By default NULL. Ocean(s) related to data coded on 1 digit. Necessary argument for data source "observe_database" and "avdth_database".
vessel_type_codesObject of class integer expected. By default NULL. Vessel type(s) related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
trip_idsObject of class character expected. By default NULL. Additional parameter only used with data source "observe_database". Use trip(s) identification(s) for selected trip(s) kept in the query. This argument overrides all others arguments like "years_period", "country" or "ocean".
data_pathObject of class character expected. By default NULL. Path of the data csv/RData file.
envirObject of class character expected. By default the first environment where data are found will be used. Specify an environment to look in for data source "envir".
lengthweightrelationships_data()Creation of a data frame object with parameters for length weight relationship.
object_model_data$lengthweightrelationships_data(
data_source = "observe_database",
database_connection = NULL,
data_path = NULL,
envir = NULL
)data_sourceObject of class character expected. By default "observe_database". Identification of data source. You can switch to "csv_file" (with separator character ";" and decimal ","), "rdata_file" or "envir" (for an object in the R environment).
database_connectionDatabase connection R object expected. By default NULL. Mandatory argument for data source "observe_database".
data_pathObject of class character expected. By default NULL. Path of the data file.
envirObject of class character expected. By default NULL. Specify an environment to look in for data source "envir".
activitycoderefs_data()Creation of reference table with the activity codes to be taken into account for the allocation of sea and/or fishing time, and/or searching time and/or set duration..
object_model_data$activitycoderefs_data(
data_source = "csv_file",
data_path = NULL,
envir = NULL
)data_sourceObject of class character expected. Identification of data source. By default "csv_file" (with separator character ";" and decimal ","). Identification of data source. You can switch to "rdata_file" or "envir" (for an object in the R environment).
data_pathObject of class character expected. By default NULL. Mandatory argument for data source "csv_file", "rdata_file" or "envir". Path of the data file.
envirObject of class character expected. By default NULL. Specify an environment to look in for data source "envir".