The PIMs are kind of weird so posting to the forum in case anybody else has a similar question in the future. The oddness arises for how to match up the years for the first couple of transitions because they are orphaned in a model with full time-dependence (see parameters 16 to 18 in the PIMs). The relevant section of the Mark manual is Section 7.3 Using data where both young and adults are marked. The example on page 7-27 of the manual shows an example of coding for 2 age-classes and 4 transitions. The PIMs in the example below have 3 age-classes and 6 transitions for apparent survival. Both models are ignoring possible time-since-marking effects.
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Marked as second-year SY (transitions are SY to TY to ATY)
INPUT --- group=1 Phi rows=6 cols=6 Triang;
INPUT --- 1 7 12 13 14 15;
INPUT --- 2 8 13 14 15;
INPUT --- 3 9 14 15;
INPUT --- 4 10 15;
INPUT --- 5 11;
INPUT --- 6;
Marked as third-year TY (transitions are TY to ATY to ATY)
INPUT --- group=2 Phi rows=6 cols=6 Triang;
INPUT --- 16 17 12 13 14 15;
INPUT --- 7 12 13 14 15;
INPUT --- 8 13 14 15;
INPUT --- 9 14 15;
INPUT --- 10 15;
INPUT --- 11;
Marked as after-third-year ATY (all transitions are ATY to ATY)
INPUT --- group=3 Phi rows=6 cols=6 Triang;
INPUT --- 18 17 12 13 14 15;
INPUT --- 17 12 13 14 15;
INPUT --- 12 13 14 15;
INPUT --- 13 14 15;
INPUT --- 14 15;
INPUT --- 15;