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.


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


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