Gadget likelihood components — gadget_likelihood

Structures representing a component of a GADGET likelihood file.

gadget_likelihood_component(type, weight = 0, name = type,
    likelihoodfile = 'likelihood', ...)

Arguments

type: Type of group to create. One of penalty, understocking, catchstatistics, catchdistribution, stockdistribution.
name: A descriptive name for the component
weight: A numeric weighting
likelihoodfile: The likelihood file this component should end up in
...: Extra parameters for the group. See details.

Details

In addition, penalty understands:

data: A data.frame with 2 columns, "switch" and "power"

catchstatistics understands:

data_function: The function Gadget should use, by default guesses based on the function that generated data
data: A data.frame probably generated by mfdb_sample_meanlength_stddev
area: An list of areas, taken from attr(data, "area") if not supplied
age: An list of ages, taken from attr(data, "age") if not supplied
fleetnames: List of fleet names
stocknames: List of stock names

catchdistribution understands:

data_function: The function Gadget should use, by default uses sumofsquares
data_function_params: Extra parameters to supply to gadget, based on the function
aggregationlevel: TRUE or FALSE, defaults to FALSE
overconsumption: TRUE or FALSE, defaults to FALSE
epsilon: Numeric, defaults to 10
data: A data.frame probably generated by mfdb_sample_meanlength_stddev
area: An list of areas, taken from attr(data, "area") if not supplied
age: An list of ages, taken from attr(data, "age") if not supplied
length: An list of lengths, taken from attr(data, "length") if not supplied
fleetnames: List of fleet names
stocknames: List of stock names

stockdistribution understands:

data_function: The function Gadget should use, by default uses sumofsquares
overconsumption: TRUE or FALSE, defaults to FALSE
epsilon: Numeric, defaults to 10
data: A data.frame probably generated by mfdb_sample_meanlength_stddev
area: An list of areas, taken from attr(data, "area") if not supplied
age: An list of ages, taken from attr(data, "age") if not supplied
length: An list of lengths, taken from attr(data, "length") if not supplied
fleetnames: List of fleet names
stocknames: List of stock names

surveydistribution understands:

data: A data.frame probably generated by mfdb_sample_meanlength_stddev
area: An list of areas, taken from attr(data, "area") if not supplied
length: An list of lengths, taken from attr(data, "length") if not supplied
age: An list of ages, taken from attr(data, "age") if not supplied
stocknames: List of stock names
fittype, slope, intercept: Fit options, see GADGET manual
parameters: A vector of length 2
suitability: A single suitability function
epsilon: Numeric, defaults to 10
likelihoodtype: String, see GADGET manual

surveyindices understands:

sitype: What data the component is based on, see GADGET manual
biomass: 0 or 1, defaults to 0
data: A data.frame probably generated by mfdb_sample_meanlength_stddev
area: An list of areas, taken from attr(data, "area") if not supplied
age: An list of ages, taken from attr(data, "age") if not supplied
length: An list of lengths, taken from attr(data, "length") if not supplied
fleetnames: List of fleet names
stocknames: List of stock names
surveynames: List of acoustic survey names
fittype, slope, intercept: Fit options, see GADGET manual

stomachcontent understands:

data_function: Function GADGET will use
epsilon: To be used when calculated probability is low
prey_labels: Either a vector of stock names to be used for all preys, or a list to match preys, see below
prey_digestion_coefficients: Optional. Either a vector of coefficients fo be used for all preys, or a list to match preys, see below
predator_names: Vector of predator stock names
data: A data.frame probably generated by mfdb_sample_meanlength_stddev

Both prey_labels and prey_digestion_coefficients allow you to match parts of prey labels and use repetition. For instance, list("cod.mat" = "mature_cod", "cod" = "cod", "other") will give "cod.mat" the label "mature_cod", "cod.imm" the label "cod", and anything else will get "other". You can also use regular expression syntax, for example "cod[0-9]".

migrationpenalty understands:

stockname: Stock name
powercoeffs: 2 power coefficients

Value

A gadget_likelihood_component object that can then be written to a likelihood file with gadget_dir_write

Examples

# Create a penalty component
component <- gadget_likelihood_component("penalty",
        name = "bounds",
        weight = "0.5",
        data = data.frame(
            switch = c("default"),
            power = c(2),
            stringsAsFactors = FALSE))
component
#> $name
#> [1] "bounds"
#> 
#> $weight
#> [1] "0.5"
#> 
#> $type
#> [1] "penalty"
#> 
#> $datafile
#> ; Generated by mfdb 7.3.99
#> ; -- data --
#> ; switch	power
#> default	2
#> 
#> attr(,"likelihoodfile")
#> [1] "likelihood"
#> attr(,"class")
#> [1] "gadget_penalty_component"    "gadget_likelihood_component"

# Create an understocking component
component <- gadget_likelihood_component("understocking", name ="understock")
component
#> $name
#> [1] "understock"
#> 
#> $weight
#> [1] 0
#> 
#> $type
#> [1] "understocking"
#> 
#> attr(,"likelihoodfile")
#> [1] "likelihood"
#> attr(,"class")
#> [1] "gadget_understocking_component" "gadget_likelihood_component"   

# Any example could be added to a file with the following:-
gd <- gadget_directory(tempfile())
gadget_dir_write(gd, component)