6.3. Calibration settings

The user must create a CSV file that contains informations about the data that will be used in the calibration process (see Table 6.4). This file will be read by the calibrar package.

Table 6.4 Calibration settings

variable

type

calibrate

weights

useData

TrachurusTrachurus.biomass

lnorm2

TRUE

12.5

TRUE

SardinaPilchardus.biomass

lnorm2

TRUE

12.5

TRUE

SardinellaAurita.biomass

lnorm2

TRUE

12.5

TRUE

EngraulisEncrasicolus.biomass

lnorm2

TRUE

12.5

TRUE

OctopusVulgaris.landings

lnorm2

TRUE

22.22

TRUE

MelicertusKerathurus.landings

lnorm2

TRUE

22.22

TRUE

MetapenaeusMonoceros.landings

lnorm2

TRUE

22.22

TRUE

TrachurusTrachurus.landings

lnorm2

TRUE

22.22

TRUE

SardinaPilchardus.landings

lnorm2

TRUE

22.22

TRUE

SardinellaAurita.landings

lnorm2

TRUE

22.22

TRUE

EngraulisEncrasicolus.landings

lnorm2

TRUE

22.22

TRUE

DiplodusAnnularis.landings

lnorm2

TRUE

22.22

TRUE

MustelusMustelus.landings

lnorm2

TRUE

22.22

TRUE

MerlucciusMerluccius.landings

lnorm2

TRUE

22.22

TRUE

PagellusErythrinus.landings

lnorm2

TRUE

22.22

TRUE

OctopusVulgaris.thr

minmaxt

TRUE

1

TRUE

MelicertusKerathurus.thr

minmaxt

TRUE

1

TRUE

MetapenaeusMonoceros.thr

minmaxt

TRUE

1

TRUE

TrachurusTrachurus.thr

minmaxt

TRUE

1

TRUE

SardinaPilchardus.thr

minmaxt

TRUE

1

TRUE

SardinellaAurita.thr

minmaxt

TRUE

1

TRUE

EngraulisEncrasicolus.thr

minmaxt

TRUE

1

TRUE

DiplodusAnnularis.thr

minmaxt

TRUE

1

TRUE

MustelusMustelus.thr

minmaxt

TRUE

1

TRUE

MerlucciusMerluccius.thr

minmaxt

TRUE

1

TRUE

PagellusErythrinus.thr

minmaxt

TRUE

1

TRUE

The table columns are:

  • variable is the list of the variables that will be fit the model with observations.

  • type is the likelyhood function that will be used in the fitting. It can either be a native function of the calibrar package or a user defined function.

  • calibrate indicates whether the data is used in the calibration.

  • weigthts provides the relative weights used to combine the partial objective values obtained for each variable.

  • useData indicates whether data are read from the disk. If useData=FALSE, the observed value is set to NULL and the likelyhood function is expected to use simulated data only. The latter option can be particularly useful to set penalties in the model outputs or parameters, where no observed data are needed.

Warning

If useData = TRUE, the name of the CSV file must be consistent with the name of the variable. For instance, if the variable is PagellusErythrinus.thr, the data file must be PagellusErythrinus.thr.csv

Danger

The column names (i.e. the header) are important and must be as shown in Table 6.4.