5 Tag Files

The tag files contain the information about the tagging experiments that are to be included in the Gadget model. Gadget will keep track of the number, and proportion, of fish in an age-length cell that have been tagged for a tagging experiment. This information can then be compared to the recaptures from that tagging experiment when calculating a likelihood score (see Recaptures, section 8.9).

To define tagged populations in the Gadget model, the “main” file must contain a list of the data files that contain the description of the tagging experiments, and the format for this is shown below:

[tagging]
tagfiles               <names of the tag files>

The main tag file lists the tagging experiments, along with basic information about the experiments and the name of the datafile that contains information about the number of fish tagged for the tagging experiment. The format for this file shown below, with each new tagging experiment starting with the keyword [component]:

[component]
tagid                  <name of the tagging experiment>
stock                  <name of the tagged stock>
tagarea                <area that the tagging took place>
endyear                <year of last recapture>
tagloss                <proportion of tagged fish that are lost>
numbers                <see Tagging Numbers>

Each tagging experiment is defined by specifying the name of the tagging experiment, the stock that is tagged for the tagging experiment, and the area that the tagging took place on. Note that it is currently possible to only tag one stock, on one area, for each tagging experiment.

The optional \(<\)endyear\(>\) value is used to define the end of a tagging experiment, and should be set to the year of the last expected recapture from the tagging experiment. This can be used to reduce the calculation time. If this is not specified, then it is assumed that the tagging experiment will run until the end of the simulation.

The \(<\)tagloss\(>\) value is used to remove tagged fish from the model. For each time step, a number of tags can be lost from the tagging experiment. The number of tagged fish that remain in the tagging experiment is given by the equation (5.1) below:

\[\begin{equation} \tag{5.1} N = N (e^{-t})\end{equation}\]

where: \(<\) N \(>\) is the number of tagged fish in an age-length group \(<t>\) is the proportion of tagged fish that are lost, as specified in the input file

5.1 Tagging Numbers

The numbers section of the tag file gives the number of fish tagged for the tagging experiment. This is given in a column format in a separate file, so the main tag file simply gives the name of this tag data file, as shown in the example below:

numbers                <name of data file>

For the tag datafile, this is a simple list of tag identifier, timestep, length and then the number of fish tagged, for that tag/timestep/length combination. This format is shown below:

<tagid>  <year>  <step>  <length>  <number>

Note that the \(<\)length\(>\) value refers to the minimum length of the length cell that the tagged fish will be put into.