I'm analysing survival of bats since 2003. The individuals in the dataset belong to six different colonies. Not each colony is captured from the beginning of the dataset.
When I process the data, I define one of the colonies which is captured from the beginning to be used as intercept.
- Code: Select all
Mnat_ch$colony<-relevel(Mnat_ch$colony,ref = "WT1")
However, I'm a bit confused about the output:
92:p gMAAWB c2003 a1 t2 0.4998699 34.103246 0.7632867E-116 1.0000000
93:p gMAAWB c2003 a2 t2 0.5005587 57.331560 0.6227126E-195 1.0000000
94:p gMAAWB c2003 a3 t2 0.4999241 49.479929 0.3366644E-168 1.0000000
95:p gMAAWB c2003 a4 t2 0.4999636 24.706158 0.7563297E-84 1.0000000
96:p gMAAWB c2003 a5 t2 0.4992349 50.101268 0.2570549E-170 1.0000000
97:p gMAAWB c2003 a6 t2 0.4992148 54.512895 0.2448618E-185 1.0000000
98:p gMAAWB c2003 a7 t2 0.5559716 43.368219 0.3636272E-149 1.0000000
99:p gMAAWB c2003 a8 t2 0.4994105 58.036799 0.2460450E-197 1.0000000
100:p gMAAWB c2003 a9 t2 1.0000000 0.9207331E-05 0.9999819 1.0000180
101:p gMAAWB c2003 a10 t 0.9562008 0.0421730 0.7520690 0.9936758
102:p gMAAWB c2003 a11 t 1.0000000 0.2680045E-05 0.9999947 1.0000053
103:p gMAAWB c2003 a12 t 0.9838998 0.0159068 0.8951579 0.9977190
104:p gMAAWB c2003 a13 t 0.8964622 0.0362678 0.8010174 0.9490382
105:p gMAAWB c2003 a14 t 0.9005783 0.0372112 0.8004483 0.9533911
106:p gMAAWB c2003 a15 t 0.6572732 0.0550997 0.5428326 0.7559461
c2003 is the cohort marked at 2003, with age 1 at time t2.. i assume there should stand the year of recapture (2003,2004 ... ).
But what tells me that? The colony WB enters the data since 2011 so 2003 as a reference wouldn't be the best idea.
The output comes from the model Phi(~1)p(~-1 + colony:time), so the colony WB should have it's own intercept and I think that Mark correctly detects that the WB colony starts at 2011.
Thanks