t3_level3: T3 process level 3
In OB7-IRD/t3: Tropical Tuna Treatment

t3_level3

R Documentation

T3 process level 3

Description

Level 3 of t3 process (modelislation).

Usage

t3_level3(
  inputs_level3,
  inputs_level3_path = NULL,
  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,
  log_file = FALSE,
  log_path = NULL,
  log_name = "t3_level3",
  output_path = NULL,
  output_format = "eu",
  new_directory = FALSE,
  integrated_process = FALSE
)

Arguments

`inputs_level3`	Object of type `data.frame` expected. Inputs of levels 3 (see function path to level 3).
`inputs_level3_path`	Object of type `character` expected. Path to the folder containing yearly data output of the level 1 and 2 (output of the function the path to level 3). If provide, replace the inputs_level3 object.
`periode_reference_level3`	Object of type `integer` expected. Year(s) period of reference for modelling estimation.
`target_year`	Object of type `integer` expected. Year of interest for the model estimation and prediction.Default value is current year -1.
`period_duration`	Object of type `integer` expected. number of years use for the modelling. The default value is 5
`distance_maximum`	Object of type `integer` expected. Maximum distance between all sets of a sampled well. By default 5.
`number_sets_maximum`	Object of type `integer` expected. Maximum number of sets allowed in mixture. By default 5.
`set_weight_minimum`	Object of type `integer` expected. Minimum set size considered. Remove smallest set for which sample could not be representative. By default 6 t.
`minimum_set_frequency`	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.
`vessel_id_ignored`	Object of type `integer` expected. Specify list of vessel(s) id(s) to be ignored in the model estimation and prediction .By default NULL.
`num.trees`	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.
`mtry`	Object of type `integer` expected. Number of variables randomly sampled as candidates at each split. The default value is 2.
`min.node.size`	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.
`seed_number`	Object of type `integer` expected. Set the initial seed for the modelling. The default value is 7.
`small_fish_only`	Object of type `logical` expected. Whether the model estimate proportion for small fish only (< 10 kg).
`plot_sample`	`logical`. Whether the sample figure is computed. Default value = F
`avdth_patch_coord`	parameter waiting for coordinate conversion patch from avdth database
`ci`	Object of type `logical` expected. Logical indicating whether confidence interval is computed. The default value is FALSE as it is a time consuming step.
`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 `numeric` expected. The number of bootstrap samples desired for the ci computation. The default value is 10.
`plot_predict`	Object of type `logical` expected. Logical indicating whether maps of catch at size have to be done.
`log_file`	Object of type `logical` expected. Initiation or not for log file creation. By default FALSE (no).
`log_path`	Object of type `character` expected. Path of the log file directory. By default NULL.
`log_name`	Object of type `character` expected. Name of the log file. By default "t3_level2".
`output_path`	Object of class `character` expected. Outputs path directory. By default NULL.
`output_format`	Object of class `character` expected. By default "eu". Select outputs format regarding European format (eu) or United States format (us).
`new_directory`	Object of class `logical` expected. Initiate a new outputs directory of use an existing one. By default NULL.
`integrated_process`	Object of class `logical` expected. Indicate if the process is integrated in another (like the one in the function "t3_process"). By default FALSE.