SSB Indices are not handled propery by catchabilities, obs_var accessor functions

ices-eg / wg_HAWG

Herring Assessment Working Group for the Area South of 62°N

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SSB Indices are not handled propery by catchabilities, obs_var accessor functions #12

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

Obs_var and catchabilities function do not return SSB indicies properly at the 
moment. Should also return SSB in addition to numbers at age indicies

Original issue reported on code.google.com by markpayn...@gmail.com on 27 Oct 2011 at 2:08

GoogleCodeExporter commented 9 years ago

Original comment by markpayn...@gmail.com on 27 Oct 2011 at 3:04

Added labels: Milestone-Release0.40, Priority-Critical

GoogleCodeExporter commented 9 years ago

Original comment by markpayn...@gmail.com on 2 Nov 2011 at 2:53

Added labels: FLSAM

GoogleCodeExporter commented 9 years ago

Clarification.

At the moment there are two accessor functions, obs_var(), and catchabilities() 
that work on an FLSAM object to return a data.frame with the estimates of the 
correspond parameters e.g.

library(FLSAM)
data(NSH.sam)
catchabilites(NSH.sam)

These functions work by looking at the <FLSAM>@ctrl@catchabilities slot to work 
out how to map the parameters fitted to the individual survey-at-age values ie 
via the bindings matrix.

The problem is that the current setup can returns the values for numbers-at-age 
surveys. We also need to return it for SSB surveys. This is a relatively simple 
modification to the code to extract the catchabilities and observation errors 
for the SSB indices, in addition to the numbers at age.

Original comment by markpayn...@gmail.com on 2 Nov 2011 at 3:34

GoogleCodeExporter commented 9 years ago

Original comment by markpayn...@gmail.com on 4 Nov 2011 at 8:02

GoogleCodeExporter commented 9 years ago

Original comment by markpayn...@gmail.com on 4 Nov 2011 at 8:07

GoogleCodeExporter commented 9 years ago

This is a bit tricky at the moment, as there is no uniformity in the way that 
the indices are specified in the configuration file. I'm not sure I can do this 
correctly, and would prefer Anders to unify the interface a bit.

At the moment, the easiest solution is to push it out into the future...

Original comment by markpayn...@gmail.com on 4 Nov 2011 at 3:08

Added labels: Priority-Low
Removed labels: Priority-Critical

GoogleCodeExporter commented 9 years ago

Original comment by markpayn...@gmail.com on 4 Nov 2011 at 3:09

Removed labels: Milestone-Release0.40

GoogleCodeExporter commented 9 years ago

Original comment by markpayn...@gmail.com on 8 Nov 2011 at 3:38

Added labels: Milestone-Release0.40, Priority-Critical
Removed labels: Priority-Low

GoogleCodeExporter commented 9 years ago

Implemented around about revision 1410 somewhere

Original comment by markpayn...@gmail.com on 9 Nov 2011 at 9:39

Changed state: Done