diff --git a/docs/SS330_User_Manual_release.html b/docs/SS330_User_Manual_release.html index 98c9967b..b569595a 100644 --- a/docs/SS330_User_Manual_release.html +++ b/docs/SS330_User_Manual_release.html @@ -1642,209 +1642,204 @@
The transition matrix can depend upon weight-at-length which differs between sexes and can vary seasonally. Thus, the transition matrix is calculated internally for each sex and each season.
The ability to analyze tag-recapture data is available with SS3. Each released tag group is characterized by an area, time, sex and age at release. Each recapture event is characterized by a time and fleet. Fleets operate in only one area so it is not necessary to record the area of recapture. Fleets with tagging data needed to be specified as fishing fleets (e.g., fleet type 1 or 2)). Inside the model, the tagged cohort is apportioned across all growth patterns in a given area at a given time (with options to apportion to only one sex or to both). The tag cohort by growth pattern then behaves according to the movement and mortality of the growth pattern. The number of tagged fish is modeled as a negligible fraction of the total population. This means that a tagging event does not move fish from an untagged group to a tagged group. Instead, it acts as if the tags are seeded into the population with no impact at all on the total population abundance or mortality. The choice to require assignment of a predominant age at release for each tag group is a pragmatic coding and model efficiency choice. By assigning a tag group to a single age, rather than distributing it across all possible ages according to the size composition of the release group, it can be tracked as a single diagonal cohort through the age x time matrix with minimal overhead to the rest of the model. Tags are assumed to be released at the beginning of a season and recaptures follow the timing of the fleet that made the recapture.
+Each released tag group is characterized by an area, time, sex and age at release. Each recapture event is characterized by a time and fleet (since fleets operate in only one area, it is not necessary to specify the area of recapture). Fleets with tagging data must be fishing fleets (e.g., fleet type 1 or 2).
+Inside the model, the tagged cohort is apportioned across all growth patterns in a given area at a given time (with options to apportion to only one sex or to both). The tag cohort by growth pattern then behaves according to the movement and mortality of the growth pattern. The number of tagged fish is modeled as a negligible fraction of the total population, so a tagging event does not move fish from an untagged group to a tagged group. Instead, tagged fish are seeded into the population with no impact at all on the total population abundance or mortality.
+Predominant age at release for each tag group must be assigned; this requirement keeps SS3 efficient. By assigning a tag group to a single age rather than distributing it across all possible ages according to the size composition of the release group, the tag group can be tracked as a single cohort through the age by time matrix with minimal overhead to the rest of the model. Tags are released at the beginning of a season and recaptures follow the timing of the fleet that made the recapture.
1 | - | Do tags - if this value is 0, then omit all entries below. | +Do tags - 0/1/2. If this value is 0, then omit all entries below. | ||||||||||||||
COND = 1 All subsequent tag-recapture entries must be omitted if "Do Tags" = 0 | ++ | + | If value is 2, read 1 additional input. | ||||||||||||||
COND > 0 All subsequent tag-recapture entries must be omitted if "Do Tags" = 0 | +|||||||||||||||||
3 | Number of tag groups | ||||||||||||||||
7 | Number of recapture events | ||||||||||||||||
2 | -Mixing latency period: N periods to delay before comparing | +Mixing latency period: N periods to delay before comparing observed | |||||||||||||||
- | observed to expected recoveries (0 = release period) | +to expected recoveries (0 = release period). | |||||||||||||||
10 | Max periods (seasons) to track recoveries, after which tags enter | ||||||||||||||||
accumulator | |||||||||||||||||
COND = 2 | +|||||||||||||||||
+ | 2 | +Minimum recaptures. The number of recaptures >= mixperiod must be | +|||||||||||||||
+ | + | >= min tags recaptured specified to include tag group in log likelihood | +|||||||||||||||
Release Data | @@ -4018,7 +4033,8 @@