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Issue42 #44

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bd2d832
Added qdev parameters
smartell Mar 29, 2015
2723e76
Implemented time-varying q with random walk parameters estimated, rev…
smartell Mar 30, 2015
54f27aa
q_dev parameters now estimable
smartell Mar 30, 2015
9cef226
Extended nlvec to accomodate process errors in catchability
smartell Mar 30, 2015
dad1c07
Time varying q, close #37
smartell Mar 30, 2015
5dd148f
Fixed array out of bounds error
smartell Mar 30, 2015
fffd56d
Control file change
smartell Mar 30, 2015
ad781e4
added compositionLikelihoods.hpp
smartell Mar 30, 2015
f262f63
Working on compositionLikelihoods.hpp
smartell Mar 30, 2015
4e0ef7a
Still working out methods for abstract base class
smartell Mar 30, 2015
a1113a8
Creating DATA and DVAR typenames for composition likelihoods
smartell Mar 31, 2015
72e61cd
Still developing negLogLikelihood abstract class
smartell Mar 31, 2015
6602b55
Fixed minor error in getRaggedVectors
smartell Apr 1, 2015
9fc0b02
More progress on the multivariateLogistic derived class
smartell Apr 1, 2015
c1843f3
More progress on the multivariateLogistic derived class
smartell Apr 1, 2015
689b828
Now have an actual likelihood from the derived class multivariateLogi…
smartell Apr 1, 2015
f2c99bc
removed old code
smartell Apr 1, 2015
459360c
Have aggregation working for dmvlogistic and abstract base class, res…
smartell Apr 1, 2015
b8a9d8a
Now have multivariateLogistic producing the same results with aggrega…
smartell Apr 1, 2015
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -279,3 +279,6 @@ _____________________________________________________________
Last changed on:
Source code: https://github.com/smartell/iSCAM
_____________________________________________________________

## Code Changes
- March 30, 2015. Added time varying catchbility options (random walk).
28 changes: 15 additions & 13 deletions fba/HALIBUT/DATA/DMVL1988/Halibut2014.ctl
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Expand Up @@ -83,7 +83,7 @@
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##
##
## ———————————————————————————————————————————————————————————————————————————————————— ##
## TIME VARYING NATURAL MORTALIIY RATES ##
## ———————————————————————————————————————————————————————————————————————————————————— ##
Expand All @@ -104,18 +104,20 @@
## ———————————————————————————————————————————————————————————————————————————————————— ##
##
##
## ------------------------------------------------------------------------- ##
## PRIORS FOR SURVEY Q ##
## Prior type: ##
## 0 - uninformative prior ##
## 1 - normal prior density for log(q) ##
## 2 - random walk in q ##
## ------------------------------------------------------------------------- ##
2 # -number of surveys (nits)
0 0 # -prior type (see legend above
0 0 # -prior log(mean)
0 0 # -prior sd
## ------------------------------------------------------------------------- ##
## ———————————————————————————————————————————————————————————————————————————————————— ##
## ABUNDANCE OBSERVATION MODELS
## ———————————————————————————————————————————————————————————————————————————————————— ##
## QTYPE:
## 0 = FIXED SURVEY Q (specify log(mean) for prior log(mean))
## 1 = CONSTANT Q (use MLE for q and optional informative prior)
## 2 = RANDOM WALK Q (use prior mean & sd for penalized random walk)
## ———————————————————————————————————————————————————————————————————————————————————— ##
2 # -number of surveys (n_it_nobs)
2 2 # -QTYPE (see legend above)
0 0 # -prior log(mean)
0 0 # -prior sd (set to 0 for uniformative prior)
1 1 # -Estimation phase
## ———————————————————————————————————————————————————————————————————————————————————— ##
##

## ------------------------------------------------------------------------- ##
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216 changes: 108 additions & 108 deletions fba/HALIBUT/DATA/Halibut2014.dat
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Expand Up @@ -384,123 +384,123 @@
## commercial_data:
## survey
## iyr index(it) gear area group sex log(SE) log(PE) timing
1907 280 1 1 1 0 0.100 0.010 0.5
1910 271 1 1 1 0 0.100 0.010 0.5
1911 237 1 1 1 0 0.100 0.010 0.5
1912 176 1 1 1 0 0.100 0.010 0.5
1913 129 1 1 1 0 0.100 0.010 0.5
1914 124 1 1 1 0 0.100 0.010 0.5
1915 118 1 1 1 0 0.100 0.010 0.5
1916 137 1 1 1 0 0.100 0.010 0.5
1917 98 1 1 1 0 0.100 0.010 0.5
1918 96 1 1 1 0 0.100 0.010 0.5
1919 93 1 1 1 0 0.100 0.010 0.5
1920 96 1 1 1 0 0.100 0.010 0.5
1921 88 1 1 1 0 0.100 0.010 0.5
1922 73 1 1 1 0 0.100 0.010 0.5
1923 78 1 1 1 0 0.100 0.010 0.5
1924 74 1 1 1 0 0.100 0.010 0.5
1925 68 1 1 1 0 0.100 0.010 0.5
1926 67 1 1 1 0 0.100 0.010 0.5
1927 65 1 1 1 0 0.100 0.010 0.5
1928 58 1 1 1 0 0.100 0.010 0.5
1929 51 1 1 1 0 0.100 0.010 0.5
1930 46 1 1 1 0 0.100 0.010 0.5
1931 50 1 1 1 0 0.100 0.010 0.5
1932 60 1 1 1 0 0.100 0.010 0.5
1933 63 1 1 1 0 0.100 0.010 0.5
1934 62 1 1 1 0 0.100 0.010 0.5
1935 76 1 1 1 0 0.100 0.010 0.5
1936 71 1 1 1 0 0.100 0.010 0.5
1937 80 1 1 1 0 0.100 0.010 0.5
1938 88 1 1 1 0 0.100 0.010 0.5
1939 80 1 1 1 0 0.100 0.010 0.5
1940 81 1 1 1 0 0.100 0.010 0.5
1941 85 1 1 1 0 0.100 0.010 0.5
1942 90 1 1 1 0 0.100 0.010 0.5
1943 95 1 1 1 0 0.100 0.010 0.5
1944 110 1 1 1 0 0.100 0.010 0.5
1945 102 1 1 1 0 0.100 0.010 0.5
1946 101 1 1 1 0 0.100 0.010 0.5
1947 99 1 1 1 0 0.100 0.010 0.5
1948 99 1 1 1 0 0.100 0.010 0.5
1949 95 1 1 1 0 0.100 0.010 0.5
1950 95 1 1 1 0 0.100 0.010 0.5
1951 96 1 1 1 0 0.100 0.010 0.5
1952 110 1 1 1 0 0.100 0.010 0.5
1953 131 1 1 1 0 0.100 0.010 0.5
1954 133 1 1 1 0 0.100 0.010 0.5
1955 119 1 1 1 0 0.100 0.010 0.5
1956 129 1 1 1 0 0.100 0.010 0.5
1957 110 1 1 1 0 0.100 0.010 0.5
1958 121 1 1 1 0 0.100 0.010 0.5
1959 129 1 1 1 0 0.100 0.010 0.5
1960 132 1 1 1 0 0.100 0.010 0.5
1961 127 1 1 1 0 0.100 0.010 0.5
1962 115 1 1 1 0 0.100 0.010 0.5
1963 105 1 1 1 0 0.100 0.010 0.5
1964 100 1 1 1 0 0.100 0.010 0.5
1965 99 1 1 1 0 0.100 0.010 0.5
1966 100 1 1 1 0 0.100 0.010 0.5
1967 101 1 1 1 0 0.100 0.010 0.5
1968 103 1 1 1 0 0.100 0.010 0.5
1969 95 1 1 1 0 0.100 0.010 0.5
1970 91 1 1 1 0 0.100 0.010 0.5
1971 89 1 1 1 0 0.100 0.010 0.5
1972 78 1 1 1 0 0.100 0.010 0.5
1973 63 1 1 1 0 0.100 0.010 0.5
1974 61 1 1 1 0 0.100 0.010 0.5
1975 61 1 1 1 0 0.100 0.010 0.5
1976 55 1 1 1 0 0.100 0.010 0.5
1977 63 1 1 1 0 0.100 0.010 0.5
1978 71 1 1 1 0 0.100 0.010 0.5
1979 75 1 1 1 0 0.100 0.010 0.5
1980 94 1 1 1 0 0.100 0.010 0.5
1981 111 1 1 1 0 0.100 0.010 0.5
1982 127 1 1 1 0 0.100 0.010 0.5
1984 291 1 1 1 0 0.100 0.010 0.5
1985 357 1 1 1 0 0.036 0.010 0.5
1986 320 1 1 1 0 0.041 0.010 0.5
1987 321 1 1 1 0 0.040 0.010 0.5
1988 368 1 1 1 0 0.035 0.010 0.5
1989 358 1 1 1 0 0.025 0.010 0.5
1990 319 1 1 1 0 0.028 0.010 0.5
1991 318 1 1 1 0 0.038 0.010 0.5
1992 319 1 1 1 0 0.034 0.010 0.5
1993 373 1 1 1 0 0.099 0.010 0.5
1994 306 1 1 1 0 0.072 0.010 0.5
1995 330 1 1 1 0 0.036 0.010 0.5
1996 392 1 1 1 0 0.038 0.010 0.5
1997 405 1 1 1 0 0.025 0.010 0.5
1998 408 1 1 1 0 0.025 0.010 0.5
1999 393 1 1 1 0 0.023 0.010 0.5
2000 403 1 1 1 0 0.022 0.010 0.5
2001 362 1 1 1 0 0.041 0.010 0.5
2002 360 1 1 1 0 0.019 0.010 0.5
2003 329 1 1 1 0 0.018 0.010 0.5
2004 319 1 1 1 0 0.019 0.010 0.5
2005 296 1 1 1 0 0.017 0.010 0.5
2006 270 1 1 1 0 0.019 0.010 0.5
2007 252 1 1 1 0 0.020 0.010 0.5
2008 232 1 1 1 0 0.017 0.010 0.5
2009 222 1 1 1 0 0.018 0.010 0.5
2010 204 1 1 1 0 0.020 0.010 0.5
2011 198 1 1 1 0 0.015 0.010 0.5
2012 195 1 1 1 0 0.021 0.010 0.5
2013 179 1 1 1 0 0.017 0.010 0.5
2014 191 1 1 1 0 0.052 0.010 0.5
1907 280 1 1 1 0 0.100 0.050 0.5
1910 271 1 1 1 0 0.100 0.050 0.5
1911 237 1 1 1 0 0.100 0.050 0.5
1912 176 1 1 1 0 0.100 0.050 0.5
1913 129 1 1 1 0 0.100 0.050 0.5
1914 124 1 1 1 0 0.100 0.050 0.5
1915 118 1 1 1 0 0.100 0.050 0.5
1916 137 1 1 1 0 0.100 0.050 0.5
1917 98 1 1 1 0 0.100 0.050 0.5
1918 96 1 1 1 0 0.100 0.050 0.5
1919 93 1 1 1 0 0.100 0.050 0.5
1920 96 1 1 1 0 0.100 0.050 0.5
1921 88 1 1 1 0 0.100 0.050 0.5
1922 73 1 1 1 0 0.100 0.050 0.5
1923 78 1 1 1 0 0.100 0.050 0.5
1924 74 1 1 1 0 0.100 0.050 0.5
1925 68 1 1 1 0 0.100 0.050 0.5
1926 67 1 1 1 0 0.100 0.050 0.5
1927 65 1 1 1 0 0.100 0.050 0.5
1928 58 1 1 1 0 0.100 0.050 0.5
1929 51 1 1 1 0 0.100 0.050 0.5
1930 46 1 1 1 0 0.100 0.050 0.5
1931 50 1 1 1 0 0.100 0.050 0.5
1932 60 1 1 1 0 0.100 0.050 0.5
1933 63 1 1 1 0 0.100 0.050 0.5
1934 62 1 1 1 0 0.100 0.050 0.5
1935 76 1 1 1 0 0.100 0.050 0.5
1936 71 1 1 1 0 0.100 0.050 0.5
1937 80 1 1 1 0 0.100 0.050 0.5
1938 88 1 1 1 0 0.100 0.050 0.5
1939 80 1 1 1 0 0.100 0.050 0.5
1940 81 1 1 1 0 0.100 0.050 0.5
1941 85 1 1 1 0 0.100 0.050 0.5
1942 90 1 1 1 0 0.100 0.050 0.5
1943 95 1 1 1 0 0.100 0.050 0.5
1944 110 1 1 1 0 0.100 0.050 0.5
1945 102 1 1 1 0 0.100 0.050 0.5
1946 101 1 1 1 0 0.100 0.050 0.5
1947 99 1 1 1 0 0.100 0.050 0.5
1948 99 1 1 1 0 0.100 0.050 0.5
1949 95 1 1 1 0 0.100 0.050 0.5
1950 95 1 1 1 0 0.100 0.050 0.5
1951 96 1 1 1 0 0.100 0.050 0.5
1952 110 1 1 1 0 0.100 0.050 0.5
1953 131 1 1 1 0 0.100 0.050 0.5
1954 133 1 1 1 0 0.100 0.050 0.5
1955 119 1 1 1 0 0.100 0.050 0.5
1956 129 1 1 1 0 0.100 0.050 0.5
1957 110 1 1 1 0 0.100 0.050 0.5
1958 121 1 1 1 0 0.100 0.050 0.5
1959 129 1 1 1 0 0.100 0.050 0.5
1960 132 1 1 1 0 0.100 0.050 0.5
1961 127 1 1 1 0 0.100 0.050 0.5
1962 115 1 1 1 0 0.100 0.050 0.5
1963 105 1 1 1 0 0.100 0.050 0.5
1964 100 1 1 1 0 0.100 0.050 0.5
1965 99 1 1 1 0 0.100 0.050 0.5
1966 100 1 1 1 0 0.100 0.050 0.5
1967 101 1 1 1 0 0.100 0.050 0.5
1968 103 1 1 1 0 0.100 0.050 0.5
1969 95 1 1 1 0 0.100 0.050 0.5
1970 91 1 1 1 0 0.100 0.050 0.5
1971 89 1 1 1 0 0.100 0.050 0.5
1972 78 1 1 1 0 0.100 0.050 0.5
1973 63 1 1 1 0 0.100 0.050 0.5
1974 61 1 1 1 0 0.100 0.050 0.5
1975 61 1 1 1 0 0.100 0.050 0.5
1976 55 1 1 1 0 0.100 0.050 0.5
1977 63 1 1 1 0 0.100 0.050 0.5
1978 71 1 1 1 0 0.100 0.050 0.5
1979 75 1 1 1 0 0.100 0.050 0.5
1980 94 1 1 1 0 0.100 0.050 0.5
1981 111 1 1 1 0 0.100 0.050 0.5
1982 127 1 1 1 0 0.100 0.050 0.5
1984 291 1 1 1 0 0.100 1.000 0.5
1985 357 1 1 1 0 0.036 0.050 0.5
1986 320 1 1 1 0 0.041 0.050 0.5
1987 321 1 1 1 0 0.040 0.050 0.5
1988 368 1 1 1 0 0.035 0.050 0.5
1989 358 1 1 1 0 0.025 0.050 0.5
1990 319 1 1 1 0 0.028 0.050 0.5
1991 318 1 1 1 0 0.038 0.050 0.5
1992 319 1 1 1 0 0.034 0.050 0.5
1993 373 1 1 1 0 0.099 0.050 0.5
1994 306 1 1 1 0 0.072 0.050 0.5
1995 330 1 1 1 0 0.036 0.050 0.5
1996 392 1 1 1 0 0.038 0.050 0.5
1997 405 1 1 1 0 0.025 0.050 0.5
1998 408 1 1 1 0 0.025 0.050 0.5
1999 393 1 1 1 0 0.023 0.050 0.5
2000 403 1 1 1 0 0.022 0.050 0.5
2001 362 1 1 1 0 0.041 0.050 0.5
2002 360 1 1 1 0 0.019 0.050 0.5
2003 329 1 1 1 0 0.018 0.050 0.5
2004 319 1 1 1 0 0.019 0.050 0.5
2005 296 1 1 1 0 0.017 0.050 0.5
2006 270 1 1 1 0 0.019 0.050 0.5
2007 252 1 1 1 0 0.020 0.050 0.5
2008 232 1 1 1 0 0.017 0.050 0.5
2009 222 1 1 1 0 0.018 0.050 0.5
2010 204 1 1 1 0 0.020 0.050 0.5
2011 198 1 1 1 0 0.015 0.050 0.5
2012 195 1 1 1 0 0.021 0.050 0.5
2013 179 1 1 1 0 0.017 0.050 0.5
2014 191 1 1 1 0 0.052 0.050 0.5
## survey_data:
1977 1.4713 6 1 1 0 0.100 0.010 0.5
1978 1.1112 6 1 1 0 0.100 0.010 0.5
1980 2.0090 6 1 1 0 0.100 0.010 0.5
1981 2.6670 6 1 1 0 0.100 0.010 0.5
1982 2.8739 6 1 1 0 0.100 0.010 0.5
1982 2.8739 6 1 1 0 0.100 1.000 0.5
1983 2.8816 6 1 1 0 0.100 0.010 0.5
1984 9.3014 6 1 1 0 0.100 0.010 0.5
1984 9.3014 6 1 1 0 0.100 1.000 0.5
1985 8.9419 6 1 1 0 0.100 0.010 0.5
1986 6.2568 6 1 1 0 0.100 0.010 0.5
1996 12.8858 6 1 1 0 0.100 0.010 0.5
1997 7.7841 6 1 1 0 0.034 0.010 0.5
1997 7.7841 6 1 1 0 0.034 1.000 0.5
1998 6.9727 6 1 1 0 0.034 0.010 0.5
1999 6.2649 6 1 1 0 0.034 0.010 0.5
2000 6.6265 6 1 1 0 0.034 0.010 0.5
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