Ecological Archives E096-229-A3
Christoffer Moesgaard Albertsen, Kim Whoriskey, David Yurkowski, Anders Nielsen, and Joanna Mills Flemming. 2015. Fast fitting of non-Gaussian state-space models to animal movement data via Template Model Builder. Ecology 96:2598–2604. http://dx.doi.org/10.1890/14-2101.1
Appendix C. Parameter estimates obtained using TMB for models fitted to the ringed seal data.
Table C1 shows the number of observations in each location class for the two data sets. Table C2-C5 shows the parameter estimates for the TMB-g and TMB-t fits for the subadult and adult ringed seal data. For both data sets, the measurement errors are estimated to be close to a Gaussian distribution for location class 3 and 2. For the adult ringed seal data, the Z class is also estimated to be close to a normal distribution.
Table C1. Number of observations per location class for the subadult and adult ringed seal data.
| 3 | 2 | 1 | 0 | A | B | Z | |
|---|---|---|---|---|---|---|---|
| Subadult | 92 | 209 | 392 | 263 | 854 | 1773 | 3 |
| Adult | 181 | 204 | 147 | 202 | 542 | 1412 | 10 |
Table C2. Estimates from the TMB-g model for the subadult data.
| Estimate | Std. Error | |
|---|---|---|
| log(β) | -0.6272 | 0.0915 |
| log(σ1) | -4.2909 | 0.0759 |
| log(σ2) | -3.5709 | 0.0733 |
| τ1,3 | 0.0030 | 0.0007 |
| τ2,3 | 0.0062 | 0.0017 |
| τ1,2 | 0.0026 | 0.0004 |
| τ2,2 | 0.0069 | 0.0009 |
| τ1,1 | 0.0059 | 0.0004 |
| τ2,1 | 0.0164 | 0.0010 |
| τ1,0 | 0.0234 | 0.0013 |
| τ2,0 | 0.0521 | 0.0028 |
| τ1,A | 0.0254 | 0.0008 |
| τ2,A | 0.0714 | 0.0020 |
| τ1,B | 0.0751 | 0.0013 |
| τ2,B | 0.1846 | 0.0032 |
| τ1,Z | 0.4036 | 0.1284 |
| τ2,Z | 0.9286 | 0.2567 |
Table C3. Estimates from the TMB-t model for the subadult data.
| Estimate | Std. Error | |
|---|---|---|
| log(β) | -0.8423 | 0.0617 |
| log(σ1) | -4.4811 | 0.0459 |
| log(σ2) | -3.7488 | 0.0482 |
| τ1,3 | 0.0031 | 0.0007 |
| τ2,3 | 0.0053 | 0.0012 |
| τ1,2 | 0.0026 | 0.0003 |
| τ2,2 | 0.0071 | 0.0008 |
| τ1,1 | 0.0050 | 0.0004 |
| τ2,1 | 0.0142 | 0.0009 |
| τ1,0 | 0.0102 | 0.0007 |
| τ2,0 | 0.0275 | 0.0018 |
| τ1,A | 0.0087 | 0.0004 |
| τ2,A | 0.0247 | 0.0011 |
| τ1,B | 0.0147 | 0.0004 |
| τ2,B | 0.0365 | 0.0010 |
| τ1,Z | 0.0782 | 0.0506 |
| τ2,Z | 0.2403 | 0.1289 |
| d3 | 93.4358 | 88.5858 |
| d2 | 121.1430 | 123.7133 |
| d1 | 7.6560 | 1.5786 |
| d0 | 3.2276 | 0.1674 |
| dA | 3.0899 | 0.0420 |
| dB | 3.0324 | 0.0137 |
| dZ | 3.9284 | 0.9744 |
Table C4. Estimates from the TMB-g model for the adult data.
| Estimate | Std. Error | |
|---|---|---|
| log(β) | -1.6428 | 0.1131 |
| log(σ1) | -5.5498 | 0.0856 |
| log(σ2) | -5.1676 | 0.0927 |
| τ1,3 | 0.0010 | 0.0002 |
| τ2,3 | 0.0034 | 0.0006 |
| τ1,2 | 0.0029 | 0.0005 |
| τ2,2 | 0.0076 | 0.0008 |
| τ1,1 | 0.0099 | 0.0013 |
| τ2,1 | 0.0324 | 0.0028 |
| τ1,0 | 0.0327 | 0.0019 |
| τ2,0 | 0.0752 | 0.0042 |
| τ1,A | 0.0441 | 0.0016 |
| τ2,A | 0.0899 | 0.0031 |
| τ1,B | 0.1231 | 0.0024 |
| τ2,B | 0.2489 | 0.0048 |
| τ1,Z | 0.1594 | 0.0337 |
| τ2,Z | 0.6493 | 0.1258 |
Table C5. Estimates from the TMB-t model for the adult data.
| Estimate | Std. Error | |
|---|---|---|
| log(β) | -1.6572 | 0.0953 |
| log(σ1) | -5.5224 | 0.0683 |
| log(σ2) | -5.1755 | 0.0753 |
| τ1,3 | 0.0010 | 0.0002 |
| τ2,3 | 0.0033 | 0.0005 |
| τ1,2 | 0.0028 | 0.0004 |
| τ2,2 | 0.0066 | 0.0007 |
| τ1,1 | 0.0068 | 0.0008 |
| τ2,1 | 0.0168 | 0.0018 |
| τ1,0 | 0.0190 | 0.0015 |
| τ2,0 | 0.0368 | 0.0029 |
| τ1,A | 0.0167 | 0.0009 |
| τ2,A | 0.0349 | 0.0018 |
| τ1,B | 0.0281 | 0.0009 |
| τ2,B | 0.0615 | 0.0019 |
| τ1,Z | 0.1785 | 0.0350 |
| τ2,Z | 0.6972 | 0.1191 |
| d3 | 477.1810 | 663.0708 |
| d2 | 12.5629 | 3.2426 |
| d1 | 4.1049 | 0.7763 |
| d0 | 3.2015 | 0.1937 |
| dA | 3.0534 | 0.0394 |
| dB | 3.0201 | 0.0112 |
| dZ | 32.4697 |