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Issue39#45

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smartell wants to merge 61 commits intoIPHCfrom
issue39
Open

Issue39#45
smartell wants to merge 61 commits intoIPHCfrom
issue39

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@smartell smartell commented Apr 13, 2015

Added new AgeBar plot.

smartell added 30 commits March 29, 2015 12:06
@smartell
Added qdev parameters
bd2d832
@smartell
Implemented time-varying q with random walk parameters estimated, rev…
2723e76 
…amped survey q controls
@smartell
q_dev parameters now estimable
54f27aa
@smartell
Extended nlvec to accomodate process errors in catchability
9cef226
@smartell
Time varying q, close #37
dad1c07
@smartell
Fixed array out of bounds error
5dd148f
@smartell
Control file change
fffd56d
@smartell
added compositionLikelihoods.hpp
ad781e4
@smartell
Working on compositionLikelihoods.hpp
f262f63
@smartell
Still working out methods for abstract base class
4e0ef7a
@smartell
Creating DATA and DVAR typenames for composition likelihoods
a1113a8
@smartell
Still developing negLogLikelihood abstract class
72e61cd
@smartell
Fixed minor error in getRaggedVectors
6602b55
@smartell
More progress on the multivariateLogistic derived class
9fc0b02
@smartell
More progress on the multivariateLogistic derived class
c1843f3
@smartell
Now have an actual likelihood from the derived class multivariateLogi…
689b828 
…stic
@smartell
removed old code
f2c99bc
@smartell
Have aggregation working for dmvlogistic and abstract base class, res…
459360c 
…ults are not the same however
@smartell
Now have multivariateLogistic producing the same results with aggrega…
b8a9d8a 
…tion method
@smartell
Commented out COUT statements from debugging
d7db409
@smartell
tsting multivariateLogistic, need to fix bug in residuals.
3fe5a26
@smartell
Deleted pointer for age comps likelihoods
2ba25e2
@smartell
Started multinomial base class
91a2bfd
@smartell
Started multinomial base class
5ea1ad6
@smartell
Appear to have multinomial working. But still needs testing.
e966ce6
@smartell
Added multinomial with effective sample size
46af58b
@smartell
Multinomial with effective sample size estimated
1017f1d
@smartell
Did some speed tests with compositionLikelihoods.hpp. 7X slower, so d…
594b59d 
…eprecated
@smartell
Modification to Halibut Data file to stirp 00s of age comps.
5b3583c
@smartell
Nearly fixed all age comp plots, need to fix age labels on plotAgeSum…
8ed8801 
…mary
smartell added 30 commits April 3, 2015 21:07
@smartell
FIxed more Rscrpts for autmated ploting. Parse Halibut age comps by a…
745d7ba 
…ge 20 and 25
@smartell
Stash
ebc13d2
@smartell
Fixed legend in plotageSummary
7135a1d
@smartell
trimed the number of qdev parameters when conducting prospective anal…
f7a8cc9 
…ysis
@smartell
Added retropsecitve adjustment to qdev_count
34a7310
@smartell
Fixed the data file, wrong years for jumps in Q.
74c8635
@smartell
Added qdeve plot
38904bf
@smartell
Better fits to the halibut model, fixed likelihood for first-differne…
50fe871 
…ce on log_q, not the deviates
@smartell
new Age Barplot
2a9edc5
@smartell
Adding lines to age bars
7a5f9c0
@smartell
PlotAgebars now available
bae2f68
@smartell
Added new controls to control file, and read in DATA_SECTION
11ac51c
@smartell
Implemented slx_log_par
639904e
@smartell
chk point
d574c45
@smartell
New Selex class interface now starting to work for Logistic only
a844b25
@smartell
annual cubic splines working
528f7f7
@smartell
Bicubic spline working
4cf8ba6
@smartell
Bicubic spline working
cba68f9
@smartell
Testing sex-specific selex curves
dbea682
@smartell
Added penalties to objective function for NEW_SELEX
31b24c0
@smartell
Stash with NEW_SELEX undefined
497dfdf
@smartell
Still working on penalties and constraints for new slx params.
e451a96
@smartell
commented out define NEW_SELEX. Issue with transposing the parameters…
37751db 
… for bicubic splines
@smartell
More tweaks to Selectivity and control file for halibut
06c9e31
@smartell
Run using bicubic splines for all fisheries.
35e5527
@smartell
Fixed bug in case 2 of calc_slx
e9523e0
@smartell
Fixed bug in case 2 of calc_slx
8274a99
@smartell
Updated template control file
7617264
@smartell
FIxed relative paths in R4iSCAM.R
3ed08fd
@smartell
Added new plotSelex.R script
23d947b
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