admb_real:admb_real
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admb_real:admb_real [2010/05/04 08:41] – lennartfr | admb_real:admb_real [2010/09/09 08:39] (current) – lennartfr | ||
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- | For 2, 4, and 5 cohorts, the trajectories | + | For 2, 4, and 5 cohorts, the trajectories |
2 cohorts: ({{: | 2 cohorts: ({{: | ||
Line 487: | Line 487: | ||
Note that the scale of the y-axis is different for the case of five cohorts. | Note that the scale of the y-axis is different for the case of five cohorts. | ||
+ | |||
+ | ===== Model with sigmoid function for catchability ===== | ||
+ | |||
+ | Since the estimates for the catchability q are very low, we try to model it with a sigmoid function. That is, | ||
+ | |||
+ | ^ Catchability ^ = ^ q0 exp(a x + b)/(1+exp(a x + b)) ^ | ||
+ | |||
+ | where the x represents the age of the cohort. | ||
+ | |||
+ | :!: **NOTE** this means that instead of one q per survey, there are now three parameters, q, a, and b (called q0, q_alpha and q_beta in the code), // | ||
+ | |||
+ | The model is implemented in {{: | ||
+ | <file txt cod.pin> | ||
+ | # N0 | ||
+ | 1.000000 | ||
+ | |||
+ | # q alpha beta | ||
+ | 0.60 1 1 | ||
+ | |||
+ | # log(s) | ||
+ | 0.1 | ||
+ | |||
+ | # M | ||
+ | 0.2 | ||
+ | </ | ||
+ | |||
+ | We run the model on the same dataset as before, and get: | ||
+ | | {{: | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | </ | ||
+ | | {{: | ||
+ | |||
+ | As one can see, the effective catchability is very low, due to the fact that q0 is at its lower bound of 0.05. Therefore we set the lower bound to be 0.5, (which requires editing of the .tpl file and recompilation), | ||
+ | |||
+ | |{{: | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |{{: | ||
+ | |||
+ | As one can see, q is still at its lower bound, which seems to be the most important parameter for this model on this dataset. | ||
+ | |||
+ | ===== Model with two separate catchabilities ===== | ||
+ | |||
+ | This model has two q variables for each survey, one which is applied to age groups 0-2, and one which is applied to age group 3 and up. It is implemented in {{: | ||
+ | <file txt cod.pin> | ||
+ | # N0 | ||
+ | 3.07 2.95 2.9 | ||
+ | # q02 | ||
+ | 0.20 | ||
+ | # q3plus | ||
+ | 0.2 | ||
+ | # log(s) | ||
+ | 0.1 | ||
+ | # M | ||
+ | 0.1 | ||
+ | </ | ||
+ | |||
+ | We run it on the usual data set, and get: | ||
+ | |||
+ | |{{: | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |||
+ | As one can see the catchability for the classes age 3 and up is larger than for 0-2 year olds, which is consistent with our expectations. | ||
+ | |||
+ | ===== Model with two separate catchabilities and two mortalities ===== | ||
+ | |||
+ | This model is a combination of the models with two Ms and two qs. The .tpl file can be found {{: | ||
+ | <file txt cod.pin> | ||
+ | # N0 | ||
+ | 3.07 2.95 2.9 | ||
+ | # q02 | ||
+ | 0.20 | ||
+ | # q3plus | ||
+ | 0.2 | ||
+ | # log(s) | ||
+ | 0.1 | ||
+ | # M | ||
+ | 0.1 | ||
+ | # Mvec | ||
+ | 0 | ||
+ | </ | ||
+ | |||
+ | We run it on the standard dataset and get: | ||
+ | |||
+ | | {{: | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |||
+ | Note that the catchability for 0-2 year olds, q02, is at its lower bound of 0.05, whereas the catchability q3plus is not. |
admb_real/admb_real.1272962507.txt.gz · Last modified: 2010/05/04 08:41 by lennartfr