t3_process | R Documentation |
Run the t3 process, with the possibility to run all the process or stop.
t3_process(
process = "all",
data_source = "t3_db",
db_con,
log_file = FALSE,
log_path = NULL,
output_path = NULL,
output_format = "eu",
new_directory = TRUE,
periode_reference,
countries,
oceans,
sample_type,
trips_selected = NULL,
species_rf1 = as.integer(c(1, 2, 3, 4, 9, 11)),
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
)
process |
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. |
data_source |
Object of class character expected. Identification of data source. By default "t3_db" but you can switch to "avdth_db". |
db_con |
Database connection R object expected. Mandatory argument for data source "t3_db", "avdth_db" and "sql_query". |
log_file |
Object of class logical expected. Initiation or not for log file creation. By default FALSE (no). |
log_path |
Object of class character expected. Path of the log file directory. By default NULL. |
output_path |
Object of class |
output_format |
Object of class |
new_directory |
Object of class |
periode_reference |
Object of class integer expected. Year(s) of the reference period coded on 4 digits. By default NULL. |
countries |
Object of class character expected. ISO code on 3 letters related to one or more countries. By default NULL. |
oceans |
Object of class integer expected. Ocean(s) related to data coded on 1 digit. By default NULL. |
sample_type |
(integer) Sample type identification (landing, observer, ...). By default NULL. |
trips_selected |
Object of class character expected. Additional parameter only used with data source "t3_db". Use trip(s) identification(s) for selected trip(s) kept in the query (by periode of reference and countries). By default NULL. |
species_rf1 |
Object of type |
rf1_lowest_limit |
Object of type |
rf1_highest_limit |
Object of type |
sunrise_schema |
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. |
sunset_schema |
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. |
maximum_lf_class |
Object of type |
threshold_rf_minus10 |
Object of type |
threshold_rf_plus10 |
Object of type |
threshold_frequency_rf_minus10 |
Object of type |
threshold_frequency_rf_plus10 |
Object of type |
threshold_rf_total |
Object of type |
periode_reference_level3 |
Object of type |
target_year |
Object of type |
period_duration |
Object of type |
distance_maximum |
Object of type |
number_sets_maximum |
Object of type |
set_weight_minimum |
Object of type |
minimum_set_frequency |
Object of type |
vessel_id_ignored |
Object of type |
num.trees |
Object of type |
mtry |
Object of type |
min.node.size |
Object of type |
seed_number |
Object of type |
small_fish_only |
Object of type |
plot_sample |
|
avdth_patch_coord |
parameter waiting for coordinate conversion patch from avdth database |
ci |
Object of type |
ci_type |
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. |
Nboot |
Object of type |
plot_predict |
Object of type |
For the argument "process", you can choose between 5 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
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