PTAGIS - PitPro data formats
PIT tag data is available from the PIT Tag Information System (PTAGIS) of the Pacific States Marine Fisheries Commission (PSMFC). To access the PTAGIS database and download data from it you will need to create an account. The information about PTAGIS found in this document is valid at the time of writing, but is subject to change.
Instructions for creating an account and for running queries can be found at:
Generally the process is as follows: select a data source, select the fields for your query, select a filter for the query that restricts the output to a particular set of values, select sorting, choose any desired summaries, choose what type of headers or footers are desired, and finally, give the “query” a name and save it. Once a query has been saved, it can be “run”, and upon completion of the run, the data will be available for download.
For PitPro, it is important to select the correct fields in the correct order. Screen shots of the PTAGIS field definition page for each of the data input types, or data sources, are provided below. The four data source used by PitPro are tagging data, interrogation data, recapture data, and mortality data. See the PitPro documentation for more about PitPro data sourcse:
http://www.cbr.washington.edu/paramest/pitpro/manual/pitpro_v4_manual/pitpro4_manual.pdf
It is necessary to sort the interrogation by “Tag id,” but no sorting is required for the tagging, recapture or mortality data. Data summaries are not used by PitPro, and should not be selected. Headers and footers, and sql query information is also not used by PitPro, and should be left out, unless required for other applications. In general, if PitPro does not find a valid tag id in the correct field for a line of data in a particular data file, the line is ignored. This should lead to any of these summary and meta data to be ignored, but to be safe, it is best to leave any of these data out of the files. Also, any extra fields at the end of a data line are ignored.
Once the query is run, the data will be available for download. Data downloaded from PTAGIS is in a format that is suitable for PitPro, and no post-processing is required. It is a good practice, although not necessary, to rename the files, giving them the suffix that PitPro expects for each particular data type. This will allow PitPro to sort the data folder files and only display the proper data type in each of the data menus. See the list below for the required suffixes.
| Interrogation data: | “.obs” |
|---|---|
| Tagging data: | “.tag” |
| Recapture data: | “.rcp” |
| Mortality data: | “.mrt” |
Notes on each data type follow:
- Interrogation data: Interrogation data can be downloaded either from the Interrogation Detail or the Interrgoation Summary PTAGIS data source. The difference between these data sources is that the Interrogation Detail provides the entire observation history for a fish while the Interrogation Summary provides only the last observation. In most cases the last observation is sufficient. There are two known exceptions. At McNary it is possible for a sampled fish to be subsequently observed on raceway or river monitors leading to a last detection that doesn't reflect the sample. PitPro censors any sampled fish so this may lead to an innacurate capture history for the fish. The other exception is when the fish are sorted out of order due to a clock error, or a fast moving fish is detected on multiple detectors giving the same time, resulting an incorrect last detection. Again the result is an innacurate capture history. The advantage to using last detection is much smaller data files and faster runs. In either case, the data must be sorted by PIT-tag.
- Tagging data: Tagging data need not be sorted.
- Recapture data: Recapture data need not be sorted. The recapture river kilometer is optional. If it is not provided, the program will use the river kilometer defined for the recapture site. This is for backwards compatibility. It is best to provide river kilometer.
- Mortality data: Se recapture data.
If the data is to be processed by a relational database, such as Access, or a spreadsheet, such as Excel, care must be taken to preserve the correct field order and format.
Once the files have the correct suffix, they must folder defined in the PitPro interface as the Data directory. The following four screen shots are taken from the PTAGIS data system and show the correct field selection for each type of data.
Interrogation Detail data
Fig. 1 - PTAGIS interrogation detail data field selection example.
Interrogation Suummary data
Fig. 2 - PTAGIS interrogation summary data field selection example.
Tagging data
Fig. 3 - PTAGIS tagging data field selection example.
Recapture data
Fig. 4 - PTAGIS recapture data field selection example.
Mortality data
Fig. 5 - PTAGIS mortality data field selection example.