Level 2 of t3 process (samples standardisation).
t3_level2(
object_model_data,
object_full_trips,
maximum_lf_class = as.integer(500),
threshold_rf_minus10 = as.integer(500),
threshold_rf_plus10 = as.integer(500),
threshold_frequency_rf_minus10 = as.integer(75),
threshold_frequency_rf_plus10 = as.integer(75),
threshold_rf_total = as.integer(250),
log_file = FALSE,
log_path = NULL,
log_name = "t3_level2",
output_path = NULL,
new_directory = FALSE,
integrated_process = FALSE,
referential_template = "observe"
)Object of classes object_model_data and R6 expected.
Object of classes full_trips, list_t3 and R6 expected.
Object of type integer expected. Theorical maximum lf class that can occur (all species considered). By default 500.
Object of type integer expected. Threshold limit value for raising factor on individuals category minus 10. By default 500.
Object of type integer expected. Threshold limit value for raising factor on individuals category plus 10. By default 500.
Object of type integer expected. Threshold limit frequency value for raising factor on individuals category minus 10. By default 75.
Object of type integer expected. Threshold limit frequency value for raising factor on individuals category plus 10. By default 75.
Object of type integer expected. Threshold limit value for raising factor (all categories). By default 250.
Object of type logical expected. Initiation or not for log file creation. By default FALSE (no).
Object of type character expected. Path of the log file directory. By default NULL.
Object of type character expected. Name of the log file. By default "t3_level2".
Object of class character expected. Outputs path directory. By default NULL.
Object of class logical expected. Initiate a new outputs directory of use an existing one. By default NULL.
Object of class logical expected. Indicate if the process is integrated in another (like the one in the function "t3_process"). By default FALSE.
Object of class character expected. By default "observe". Referential template selected (for example regarding the activity_code). You can switch to "avdth".
The function return a R6 reference object named "object_full_trips" of class full_trips.
If a output_path is specified, the following output is extracted and saved in ".csv" format under the path: "global_output_path/level2/data/".
Process 2.1: sample length class conversion from ld1 (first dorsal length) to lf (fork length) (full_trips$sample_length_class_ld1_to_lf()):
process_2_1 a table (.csv) with as many rows as elementary samples raw, plus the elementary samples raw created by certain conversions from LD1 TO LF classes, and 16 columns:
full_trip_id: retained full trip id, type integer.
full_trip_name: full trip id, type integer.
trip_id: trip identification (unique topiaid from database), type character.
trip_end_date: trip end date, type character.
year_trip_end_date: year of trip end, type integer.
vessel_code: vessel code, type integer.
vessel_type_code: vessel type code, type integer.
well_id: well identification (unique topiaid from database (ps_logbook.well in Observe)), type character.
sample_id: sample identification (unique topiaid from database (ps_logbook.sample in Observe)), type character.
sub_sample_id: sub-sample identification number, type integer.
elementarysampleraw_id: elementarysampleraw identification (unique topiaid from database (ps_logbook.samplespeciesmeasure in Observe)), type character.
species_fao_code: species FAO code, type character.
sample_length_class: sample length class (cm) of measured individuals in first dorsal length (LD1), type numeric.
sample_number_measured: sample number of measured individuals in first dorsal length (LD1), type integer.
sample_length_class_lf: sample length class (cm) of measured individuals converted in curved fork length (LF), type numeric.
sample_number_measured_lf: sample number of measured individuals converted for curved fork length (LF) distribution, type numeric.
For example, for one sample (sample_number_measured=1) from the Atlantic Ocean (1), of the species YFT (Thunnus albacares), with a first dorsal length class (LD1) measured at sample_length_class=8 (cm),
the LD1 to LF conversion will create a new elementary sample row because a percentage of ratio=50 % of the number of fish in the sample will be assigned to the curved fork length class: sample_number_measured_lf=32 (cm) (sample_number_measured_lf=0.5)
and 50% of this sample will obtain a sample_number_measured_lf=34 (cm) with sample_number_measured_lf=0.5.
Process 2.2 Extrapolation of the number of individuals measured in the sample to the number of individuals counted (full_trips$sample_number_measured_extrapolation()):
process_2_2: a table (.csv) with as many rows as elementary samples raw, plus the elementary samples raw created by certain conversions from LD1 TO LF classes, and 17 columns:
full_trip_id: retained full trip id, type integer.
full_trip_name: full trip id, type integer.
trip_id: trip identification (unique topiaid from database), type character.
trip_end_date: trip end date, type character.
year_trip_end_date: year of trip end, type integer.
vessel_code: vessel code, type integer.
vessel_type_code: vessel type code, type integer.
well_id: well identification (unique topiaid from database (ps_logbook.well in Observe)), type character.
sample_id: sample identification (unique topiaid from database (ps_logbook.sample in Observe)), type character.
sub_sample_id: sub-sample identification number, type integer.
sub_sample_total_count_id: sub sample identification bis in relation with the fish total count (unique topiaid from database (ps_logbook.samplespecies in Observe)), type character.
elementarysampleraw_id: elementarysampleraw identification (unique topiaid from database (ps_logbook.samplespeciesmeasure in Observe)), type character.
species_fao_code: species FAO code, type character.
sample_length_class_lf: sample length class (cm) of measured individuals converted in curved fork length (LF), type numeric.
sample_number_measured_lf: sample number of measured individuals converted for curved fork length (LF) distribution, type numeric.
sample_total_count: total number of individuals counted for this sample, type integer.
sample_number_measured_extrapolated_lf: sample number of measured individuals (converted in LF) extrapolated to the sample number of counted individuals, type numeric.sample_number_measured_extrapolated_lf=sample_number_measured_lf x rf4.
Process 2.3 Standardization of sample length classes step (full_trips$sample_length_class_step_standardisation()):
process_2_3: a table (.csv) with as many rows as elementary samples, and 17 columns:
full_trip_id: retained full trip id, type integer.
full_trip_name: full trip id, type integer.
trip_id: trip identification (unique topiaid from database), type character.
trip_end_date: trip end date, type character.
year_trip_end_date: year of trip end, type integer.
vessel_code: vessel code, type integer.
vessel_type_code: vessel type code, type integer.
well_id: well identification (unique topiaid from database (ps_logbook.well in Observe)), type character.
sample_id: sample identification (unique topiaid from database (ps_logbook.sample in Observe)), type character.
sample_type_code: sample type type code, type integer.
sample_quality_code: sample quality code, type integer.
sub_sample_id: sub-sample identification number, type integer.
species_fao_code: species FAO code, type character.
sample_total_count: total number of individuals counted for this sample, type integer.
sample_standardised_length_class_lf: standardised sample length class (cm) in curved fork length (LF), according to the species and step associated, type numeric.
sample_number_measured_extrapolated_lf: standardised sample number of measured individuals (converted in LF and extrapolated in step 2.2, type numeric) .
Process 2.4 Distribution of weights from well scale to set scale (full_trips$well_set_weight_categories()):
process_2_4: a table (.csv) with as many rows as elementary samples, and 12 columns:
full_trip_id: retained full trip id, type integer.
full_trip_name: full trip id, type integer.
trip_id: trip identification (unique topiaid from database), type character.
trip_end_date: trip end date, type character.
year_trip_end_date: year of trip end, type integer.
vessel_code: vessel code, type integer.
vessel_type_code: vessel type code, type integer.
well_id: well identification (unique topiaid from database (ps_logbook.well in Observe)), type character.
activity_id: activity identification (unique topiaid from database (ps_logbook.activity in Observe)), type character.
weighted_weight_minus10: weighted catch weight of individuals in the less than 10 tonnes category (by well, in tonnes, considering all species), type numeric.
weighted_weight_plus10: weighted catch weight of individuals in the over 10 kg category (by well, in tonnes, considering all species), type numeric.
weighted_weight: weighted catch weight (WW) of individuals (less and more 10kg categories, by well, in tonnes, considering all species), which represents the weight of a set in a well, type numeric.
Process 2.5 Creation of object standardised sample (full_trips$standardised_sample_creation()):
process_2_5: a table (.csv) with as many rows as standardized samples, and 12 columns:
full_trip_id: retained full trip id, type integer.
full_trip_name: full trip id, type integer.
trip_id: trip identification (unique topiaid from database), type character.
trip_end_date: trip end date, type character.
year_trip_end_date: year of trip end, type integer.
vessel_code: vessel code, type integer.
vessel_type_code: vessel type code, type integer.
well_id: well identification (unique topiaid from database (ps_logbook.well in Observe)), type character.
sample_id: sample identification (unique topiaid from database (ps_logbook.sample in Observe)), type character.
species_fao_code: species FAO code, type character.
sample_standardised_length_class_lf: standardized sample length class in curved fork length (LF) (cm), type numeric.
sample_number_measured_extrapolated_lf: standardized sample number of measured individuals (converted in LF and extrapolated to all counted individuals), type numeric.
Process 2.6 Creation of object standardised sample set (full_trips$standardised_sample_set_creation()):
process_2_6: a table (.csv) with as many rows as , and 15 columns:
full_trip_id: retained full trip id, type integer.
full_trip_name: full trip id, type integer.
trip_id: trip identification (unique topiaid from database), type character.
trip_end_date: trip end date, type character.
year_trip_end_date: year of trip end, type integer.
vessel_code: vessel code, type integer.
vessel_type_code: vessel type code, type integer.
well_id: well identification (unique topiaid from database (ps_logbook.well in Observe)), type character.
sample_id: sample identification (unique topiaid from database (ps_logbook.sample in Observe)), type character.
species_fao_code: species FAO code, type character.
sample_standardised_length_class_lf: standardized sample length class in curved fork length (LF) (cm), type numeric.
sample_number_weighted: sample number of measured individuals weighted by set weight, after conversion in LF and extrapolation to all counted individuals, type numeric.sample_number_weighted = sample_number_measured_extrapolated_lf * PWW.
sample_weight_unit: weight (kg) of one individual,
calculated using length weight relationships as in Referential LWR table: sample_weight_unit = parameter_a * sample_standardised_length_class_lf ^ parameter_b),
type numeric.
sample_weight: weight (kg) of all measured individuals weighted by set weight, after conversion in LF and extrapolation to all counted individuals, type numeric.sample_weight = sample_weight_unit * sample_number_weighted.
sample_category: sample category ("-10kg" or "+10kg"), according to sample_weight_unit value, type character.
Process 2.7 Raised factors determination to check relevance of the object standardized sample set (full_trips$raised_factors_determination()):
process_2_7: a table (.csv) with as many rows as , and 13 columns:
full_trip_id: retained full trip id, type integer.
full_trip_name: full trip id, type integer.
trip_id: trip identification (unique topiaid from database), type character.
trip_end_date: trip end date, type character.
year_trip_end_date: year of trip end, type integer.
vessel_code: vessel code, type integer.
vessel_type_code: vessel type code, type integer.
well_id: well identification (unique topiaid from database (ps_logbook.well in Observe)), type character.
activity_id: activity identification (unique topiaid from database (ps_logbook.activity in Observe)), type character.
weighted_samples_minus10: weight of sampled individuals (tonnes), for weight category (\(\leq\) 10kg, type numeric.
weighted_samples_plus10: weight of sampled individuals (tonnes), for weight category > 10kg, type numeric.
weighted_samples_total: weight of sampled individuals (tonnes), for all weight categories (\(\leq\) 10kg and > 10kg), type numeric.
rf_validation: raising factor status, type integer.
rf_validation_label: raising factor status label, type character.
Process 2.8 Application of raised factors calculated in process 2.7 on standardised sample set (full_trips$raised_standardised_sample_set()):
process_2_8: a table (.csv) with as many rows as , and 14 columns:
full_trip_id: retained full trip id, type integer.
full_trip_name: full trip id, type integer.
trip_id: trip identification (unique topiaid from database), type character.
trip_end_date: trip end date, type character.
year_trip_end_date: year of trip end, type integer.
vessel_code: vessel code, type integer.
vessel_type_code: vessel type code, type integer.
well_id: well identification (unique topiaid from database (ps_logbook.well in Observe)), type character.
activity_id: activity identification (unique topiaid from database (ps_logbook.activity in Observe)), type character.
sample_id: sample identification (unique topiaid from database (ps_logbook.sample in Observe)), type character.
species_fao_code: species FAO code, type character.
sample_standardised_length_class_lf: standardized sample length class in curved fork length (LF), (cm), type numeric.
sample_number_weighted_set: sample number weighted by set, type numeric. sample_number_weighted_set = sample_number_weighted * rf, where :
rf: is one of the raising factors calculated in the process 2.7,
according to sample weight category (\(\leq\) 10kg and > 10kg).
sample_number_weighted: is the sample number of measured individuals weighted by set weight, after conversion in LF and extrapolation to all counted individuals,
calculated in the process 2.6.
sample_weight_set: sample weight by set (tonnes), type numeric.sample_weight_set = sample_weight_unit/1000 * sample_number_weighted_set