Run the t3 process, with the possibility to run all the process or stop.
t3_process(
process = "all",
data_source = "observe_database",
database_connection,
log_file = FALSE,
log_path = NULL,
output_path = NULL,
output_format = "eu",
referential_template = "observe",
new_directory = TRUE,
years_period,
flag_codes,
ocean_codes,
vessel_type_codes,
species_fate_codes,
sample_type_codes,
trip_ids = NULL,
species_fao_codes_rf1 = as.integer(c(1, 2, 3, 4, 9, 11)),
species_fate_codes_rf1 = as.integer(c(6, 11)),
vessel_type_codes_rf1 = as.integer(c(4, 5, 6)),
rf1_lowest_limit = 0.8,
rf1_highest_limit = 1.2,
sunrise_schema = "sunrise",
sunset_schema = "sunset",
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),
periode_reference_level3 = NULL,
target_year,
period_duration,
distance_maximum = as.integer(5),
number_sets_maximum = as.integer(5),
set_weight_minimum = as.integer(6),
minimum_set_frequency = 0.1,
vessel_id_ignored = NULL,
num.trees = 1000L,
mtry = 2L,
min.node.size = 5,
seed_number = 7L,
small_fish_only = FALSE,
plot_sample = FALSE,
avdth_patch_coord = FALSE,
ci = FALSE,
ci_type = "all",
Nboot = 50,
plot_predict = FALSE
)Object of class character expected. Specify here if you want to run the whole process or just a part of it. By default "all". Check detail section below for more information.
Object of class character expected. By default "observe_database". Identification of data source. You can to "avdth_database".
Database connection R object expected. By default NULL. Mandatory argument for data source "observe_database" and "avdth_database".
Object of class logical expected. Initiation or not for log file creation. By default FALSE (no).
Object of class character expected. Path of the log file directory. By default NULL.
Object of class character expected. Outputs path directory. By default NULL.
Object of class character expected. By default "eu". Select outputs format regarding European format (eu) or United States format (us).
Object of class character expected. By default "observe". Referential template selected (for example regarding the activity_code). You can switch to "avdth".
Object of class logical expected. Initiate a new outputs directory of use an existing one. By default NULL.
Object 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".
Object of class character expected. By default NULL. Country(ies) code related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
Object 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".
Object of class integer expected. By default NULL. Vessel type(s) related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
Object of class integer expected. By default NULL. Specie fate(s) related to data extraction. Necessary argument for data source "observe_database" and "avdth_database".
Object of class integer expected. By default NULL. Sample type identification.
Object 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".
Object of type character expected. By default YFT, SKJ, BET, ALB, MIX and LOT. Specie(s) FAO code(s) used for the RF1 process.
Object of type integer expected. By default 6 ("Retained, presumably destined for the cannery"). Specie(s) fate code(s) used for the RF1 process.
Object of type integer expected. By default 4, 5 and 6. Vessel type(s).
Object of type numeric expected. Verification value for the lowest limit of the RF1. By default 0.8.
Object of type numeric expected. Verification value for the highest limit of the RF1. By default 1.2.
Object of class character expected. Sunrise caracteristic. By default "sunrise" (top edge of the sun appears on the horizon). See function fishing_time() for more details.
Object of class character expected. Sunset caracteristic. By default "sunset" (sun disappears below the horizon, evening civil twilight starts). See function fishing_time() for more details.
Object of type integer expected. Theorical maximum lf class that can occur (all species considerated). By default 500.
Object of type integer expected. Threshold limite value for raising factor on individuals category minus 10. By default 500.
Object of type integer expected. Threshold limite value for raising factor on individuals category plus 10. By default 500.
Object of type integer expected. Threshold limite frequency value for raising factor on individuals category minus 10. By default 75.
Object of type integer expected. Threshold limite frequency value for raising factor on individuals category plus 10. By default 75.
Object of type integer expected. Threshold limite value for raising factor (all categories). By default 250.
Object of type integer expected. Year(s) period of reference for modelling estimation.
Object of type integer expected. Year of interest for the model estimation and prediction.Default value is current year -1.
Object of type integer expected. number of years use for the modelling. The default value is 5
Object of type integer expected. Maximum distance between all sets of a sampled well. By default 5.
Object of type integer expected. Maximum number of sets allowed in mixture. By default 5.
Object of type integer expected. Minimum set size considered. Remove smallest set for which sample could not be representative. By default 6 t.
Object of type numeric expected. Minimum threshold proportion of set in awell to be used for model training in the process. By default 0.1.
Object of type integer expected. Specify list of vessel(s) id(s) to be ignored in the model estimation and prediction .By default NULL.
Object of type integer expected. Number of trees to grow. This should not be set to too small a number, to ensure that every input row gets predicted at least a few times. The default value is 1000.
Object of type integer expected. Number of variables randomly sampled as candidates at each split. The default value is 2.
Object of type numeric expected. Minimum size of terminal nodes. Setting this number larger causes smaller trees to be grown (and thus take less time).The default value is 5.
Object of type integer expected. Set the initial seed for the modelling. The default value is 7.
Object of type logical expected. Whether the model estimate proportion for small fish only (< 10 kg).
logical. Whether the sample figure is computed. Default value = F
parameter waiting for coordinate conversion patch from avdth database
Object of type logical expected. Logical indicating whether confidence interval is computed. The default value is FALSE as it is a time consuming step.
Type of confidence interval to compute. The default value is "all". Other options are "set" for ci on each set, "t1" for ci on nominal catch by species, "t1-fmod" for ci on nominal catch by species and fishing mode "t2" and "t2-fmod" for ci by 1 degree square and month. A vector of several ci option can be provided. ci_type are computed only if the ci parameter is TRUE.
Object of type numeric expected. The number of bootstrap samples desired for the ci computation. The default value is 10.
Object of type logical expected. Logical indicating whether maps of catch at size have to be done.
For the argument "process", you can choose between 4 modalities (descending size classification):
all: argument by default, you launch all the process
level1: you launch data model initialisation and the process level 1
level2: you launch data model initialisation and the process level 2
until_level2: you launch data model initialisation, the process level 1 and 2