====== Computational Biology and Ecology ======

===== Current Projects =====

===== Parsimonious Fish Stock Assessment =====
[[Background:Background|Background to Methodologies]]

[[Collaboration:Collaboration|Collaboration]]
==== Work done April/May 2010 ====
  * Automatic Differentiation Model Builder ([[admb:admb|ADMB]])
  * [[admb_Synthetic:admb_Synthtetic|ADMB Synthetic Data]]
  * [[admb_Real:admb_Real|ADMB Real Data]]
     * [[admb_discussions:admb_discussions|ADMB Discussions]]
     * Hjelp med [[wiki:syntax|wiki-syntaksen]]
  * [[mfiles:mfiles|Matlab/Octave Utilities]]

==== Work done September --- December 2010 ====
=== Models estimating 0 year olds and older ===
== Models with assumed exact catch data == 
  * [[admb_real:sdreport_and_vpa|Comparing the models with VPA estimates]]
  * [[admb_real:two_qs_cohorts_per_run|Designing experiments: Choosing the number of cohorts per run]]
    * [[admb_real:monotonizing_surveys|Monotonic survey data]]
== Models with errors in the catch data == 
  * [[admb_real:uncertain_catch|Model with latent variables]] (**Obsolete**, see below instead)

=== Model estimating only 3 year olds and older===
== Models with assumed exact catch data == 

  * [[admb_real:N3_cohorts_per_run|Choosing the number of cohorts per run]]
    * [[admb_real:n3_cohorts_per_run_monotonic|Monotonic survey data]] ( :!: **NOTE** The plots in this section contain an error)
== Models with errors in the catch data == 
  * [[admb_real:n3_re_catch:catch_sigma_levels:catch_sigma_levels|Testing different levels of sigma for catch --- no variables locked]]
  * [[admb_real:n3_re_catch:misfit:misfit_testing|Testing of misfit as a function of catch standard deviations (q, s, M locked)]]
  * [[admb_real:n3_re_catch:locking_variables:locking_tests|Testing the effect of fixing different variables]]
  * [[admb_real:n3_re_catch:various_experiments|Various experiments]] **(Obsolete)**

=== Model following all cohorts in any given year ===
[[admb_real:all_cohorts:model_description|Description of the model]]
== Models with assumed exact catch data == 
  * [[admb_real:all_cohorts:preliminary_experiments|Preliminary experiments]]
== Models with errors in the catch data == 
  * TBD