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Fims vector #517

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Dec 13, 2023
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314a4a8
added fims vector
msupernaw Oct 26, 2023
fddb9e9
updates
msupernaw Oct 26, 2023
dd50459
Update fims_vector.hpp
msupernaw Oct 26, 2023
37c40d8
fully wrapped std::vector
msupernaw Oct 30, 2023
26533e5
Update fims_vector.hpp
msupernaw Oct 30, 2023
e50c35e
Update fims_vector.hpp
msupernaw Oct 30, 2023
3f6160e
added fims::Vector to population.
msupernaw Oct 30, 2023
940c8a3
use new fims::vector for fleet agecomp nll
ChristineStawitz-NOAA Oct 30, 2023
ec0a10c
add constructor for fims_vector
ChristineStawitz-NOAA Oct 31, 2023
c0d56b1
Update fims_vector.hpp
msupernaw Nov 1, 2023
da128c9
Update fims_vector.hpp
msupernaw Nov 1, 2023
21b7abc
Update fims_vector.hpp
msupernaw Nov 1, 2023
236bfaf
Update fims_vector.hpp
msupernaw Nov 1, 2023
3e2506a
Update fims_vector.hpp
msupernaw Nov 1, 2023
37a71f6
Update fims_vector.hpp
msupernaw Nov 1, 2023
62075c7
Update fims_vector.hpp
msupernaw Nov 1, 2023
69ab198
Update fims_vector.hpp
msupernaw Nov 1, 2023
6d4b460
Update fims_vector.hpp
msupernaw Nov 1, 2023
fa2648c
resolve merge conflict errors
ChristineStawitz-NOAA Nov 3, 2023
bb260c5
remove parametervector calls in fleet and pop
ChristineStawitz-NOAA Nov 8, 2023
aa9e76b
use fims::Vector<Type> for recruitment deviations
ChristineStawitz-NOAA Nov 8, 2023
f528887
remove ParameterVector from modeltraits
ChristineStawitz-NOAA Nov 8, 2023
3f0cf18
remove unecessary using call
ChristineStawitz-NOAA Nov 8, 2023
c7ea618
fix recruitment tests
ChristineStawitz-NOAA Nov 8, 2023
27a5d3e
Added documentation.
msupernaw Nov 8, 2023
9f583dd
Update fims_vector.hpp
msupernaw Nov 8, 2023
26907e3
Update fims_vector.hpp
msupernaw Nov 8, 2023
eb17321
Update model.hpp
msupernaw Nov 8, 2023
9b21864
update fims::Vector to work with TMB dmultinorm
msupernaw Nov 9, 2023
830ccbe
Remove references to ModelTraits and delete
ChristineStawitz-NOAA Nov 9, 2023
d280a93
remove tmbutils:: and replace int with size_t
ChristineStawitz-NOAA Nov 9, 2023
f4e390f
Merge branch 'main' into fims_vector
ChristineStawitz-NOAA Nov 15, 2023
972c221
fix merge cnflicts
ChristineStawitz-NOAA Nov 15, 2023
e86259e
another merge conflict
ChristineStawitz-NOAA Nov 15, 2023
60c3372
add log to documentation on recdevs
ChristineStawitz-NOAA Nov 16, 2023
13253b2
add 0 to end of recdevs
ChristineStawitz-NOAA Nov 16, 2023
28a87df
remove prop_female
ChristineStawitz-NOAA Nov 16, 2023
91fefa8
resize recdev vector
ChristineStawitz-NOAA Nov 16, 2023
2614278
special case last year of recdevs
ChristineStawitz-NOAA Nov 17, 2023
fe72c9d
fix comparison
ChristineStawitz-NOAA Nov 17, 2023
e8c9561
removes devtools
ChristineStawitz-NOAA Nov 17, 2023
2e6004f
Merge branch 'main' into fims_vector
ChristineStawitz-NOAA Nov 17, 2023
5c88595
Merge branch 'main' into fims_vector
ChristineStawitz-NOAA Nov 24, 2023
f276290
replace fims::Vector with vector<Type> in tmbdist
ChristineStawitz-NOAA Nov 24, 2023
1af00f2
change x to integervector and remove Rcpp warning
ChristineStawitz-NOAA Nov 27, 2023
8ee554d
fix gradient warning
ChristineStawitz-NOAA Nov 27, 2023
6959754
Merge branch 'main' into fims_vector
ChristineStawitz-NOAA Nov 28, 2023
d3f31be
fix fims::Vector to tmbutils::vector conversion
Andrea-Havron-NOAA Nov 29, 2023
d3acf76
add documentation
Andrea-Havron-NOAA Nov 30, 2023
7c3320f
Update fims_vector.hpp
msupernaw Dec 4, 2023
b878114
Update integration_class.hpp
msupernaw Dec 5, 2023
6dc3985
Update fims_vector.hpp
msupernaw Dec 5, 2023
e33f89a
Update rcpp_tmb_distribution.hpp
msupernaw Dec 6, 2023
7146751
Update fims_vector.hpp
msupernaw Dec 7, 2023
9229cfc
Update fims_vector.hpp
msupernaw Dec 7, 2023
1e45e97
Update integration_class.hpp
msupernaw Dec 7, 2023
aa2dcb0
Update integration_class.hpp
msupernaw Dec 7, 2023
8073c39
Update integration_class.hpp
msupernaw Dec 7, 2023
f65e43e
Update integration_class.hpp
msupernaw Dec 7, 2023
468959b
Update integration_class.hpp
msupernaw Dec 7, 2023
48bd94e
Update integration_class.hpp
msupernaw Dec 7, 2023
06fc54a
Update integration_class.hpp
msupernaw Dec 7, 2023
664eed7
cleanup of commented code and dox
ChristineStawitz-NOAA Dec 12, 2023
19eb97c
make log_obs_error a vector
ChristineStawitz-NOAA Dec 12, 2023
69dda10
make log_obs_error a vector (#532)
ChristineStawitz-NOAA Dec 12, 2023
b945e85
remove begin() and end() for const iterator
ChristineStawitz-NOAA Dec 12, 2023
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20 changes: 0 additions & 20 deletions inst/include/common/def.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -72,26 +72,6 @@ class fims_log {

std::map<std::string, std::ofstream> fims_log::FIMS_LOGS;

#ifdef STD_LIB

/**
* @brief Default trait. These are "T" specific
* traits that depend on modeling platform.
*/
template <typename Type>
struct ModelTraits {
typedef double real_t; /**< The real type */
typedef double variable_t; /**< The variable type */
typedef typename std::vector<double> DataVector; /**< The data vector type */
typedef typename std::vector<double> ParameterVector; /**< The variable vector
type */
typedef typename std::vector<std::vector<double> > DataMatrix; /**< The
data matrix type */
typedef typename std::vector<std::vector<double> > VariableMatrix; /**< The
variable matrix type */
};

#endif
} // namespace fims

#endif /* TRAITS_HPP */
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