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tmb__core_8hpp_source.html | 2 +- tmb__enable__header__only_8hpp.html | 2 +- tmb__enable__header__only_8hpp_source.html | 2 +- tmb__enable__precompile_8hpp.html | 2 +- tmb__enable__precompile_8hpp_source.html | 2 +- tmbad__allow__comparison_8hpp_source.html | 2 +- tmbad__atomic__macro_8hpp_source.html | 2 +- tmbutils_2vectorize_8hpp.html | 2 +- tmbutils_2vectorize_8hpp_source.html | 2 +- tmbutils_8hpp.html | 2 +- tmbutils_8hpp_source.html | 2 +- tmbutils__extra_8hpp_source.html | 2 +- toggle__thread__safe__R_8hpp.html | 2 +- toggle__thread__safe__R_8hpp_source.html | 2 +- toms708_8cpp_source.html | 2 +- transform2_8cpp-example.html | 2 +- transform_8cpp-example.html | 2 +- transform_parallel_8cpp-example.html | 2 +- tweedie_8cpp-example.html | 2 +- tweedie_8cpp_source.html | 2 +- tweedie_8hpp_source.html | 2 +- validation_2MVRandomWalkValidation_8cpp-example.html | 2 +- validation_2randomwalkvalidation_8cpp-example.html | 2 +- validation_2rickervalidation_8cpp-example.html | 2 +- vector_8hpp.html | 2 +- vector_8hpp_source.html | 2 +- 523 files changed, 524 insertions(+), 524 deletions(-) diff --git a/01-Introduction_8md_source.html b/01-Introduction_8md_source.html index 5e9208fee..99cf2a1e8 100644 --- a/01-Introduction_8md_source.html +++ b/01-Introduction_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/02-ModelObject_8md_source.html b/02-ModelObject_8md_source.html index 7410266fe..54e5a2cb4 100644 --- a/02-ModelObject_8md_source.html +++ b/02-ModelObject_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/03-Sparsity_8md_source.html b/03-Sparsity_8md_source.html index de507774f..8cbbf9dfd 100644 --- a/03-Sparsity_8md_source.html +++ b/03-Sparsity_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/04-CovStruct_8md_source.html b/04-CovStruct_8md_source.html index 430d77204..7a338dad9 100644 --- a/04-CovStruct_8md_source.html +++ b/04-CovStruct_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/05-Simulation_8md_source.html b/05-Simulation_8md_source.html index 52dc53971..4bf8d286c 100644 --- a/05-Simulation_8md_source.html +++ b/05-Simulation_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/06-Validation_8md_source.html b/06-Validation_8md_source.html index 73b753fe6..3229c3748 100644 --- a/06-Validation_8md_source.html +++ b/06-Validation_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/07-AtomicFunctions_8md_source.html b/07-AtomicFunctions_8md_source.html index f7b41ca61..ba1ae9d30 100644 --- a/07-AtomicFunctions_8md_source.html +++ b/07-AtomicFunctions_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/08-Parallelization_8md_source.html b/08-Parallelization_8md_source.html index f0359a40e..e15c9a2d2 100644 --- a/08-Parallelization_8md_source.html +++ b/08-Parallelization_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/09-Appendix_8md_source.html b/09-Appendix_8md_source.html index 6c66d8c75..da90a6baa 100644 --- a/09-Appendix_8md_source.html +++ b/09-Appendix_8md_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/Appendix.html b/Appendix.html index ec9f4a63b..7329d9b1d 100644 --- a/Appendix.html +++ b/Appendix.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/AtomicFunctions.html b/AtomicFunctions.html index 89fb7e35a..2210b5de7 100644 --- a/AtomicFunctions.html +++ b/AtomicFunctions.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/Introduction.html b/Introduction.html index cb0292767..6b4f15d7b 100644 --- a/Introduction.html +++ b/Introduction.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/ModelObject.html b/ModelObject.html index 32752620b..30dc63497 100644 --- a/ModelObject.html +++ b/ModelObject.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/R__inla_8hpp.html b/R__inla_8hpp.html index a545fcdc0..e89c22747 100644 --- a/R__inla_8hpp.html +++ b/R__inla_8hpp.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/R__inla_8hpp_source.html b/R__inla_8hpp_source.html index 73187976e..a648ac2e3 100644 --- a/R__inla_8hpp_source.html +++ b/R__inla_8hpp_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/Rstream_8hpp_source.html b/Rstream_8hpp_source.html index a33d911e5..cff71f0b4 100644 --- a/Rstream_8hpp_source.html +++ b/Rstream_8hpp_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/Simulation.html b/Simulation.html index 84e23fef4..7cd5abf5d 100644 --- a/Simulation.html +++ b/Simulation.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/Sparsity.html b/Sparsity.html index bea7ac9e9..40be20a52 100644 --- a/Sparsity.html +++ b/Sparsity.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/TMB_2inst_2include_2tiny__ad_2gamma_2gamma_8cpp_source.html b/TMB_2inst_2include_2tiny__ad_2gamma_2gamma_8cpp_source.html index d6e51ea0a..0d41cadb6 100644 --- a/TMB_2inst_2include_2tiny__ad_2gamma_2gamma_8cpp_source.html +++ b/TMB_2inst_2include_2tiny__ad_2gamma_2gamma_8cpp_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/TMB_8hpp.html b/TMB_8hpp.html index 9ecfe03fd..96f28b28e 100644 --- a/TMB_8hpp.html +++ b/TMB_8hpp.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
diff --git a/TMB_8hpp_source.html b/TMB_8hpp_source.html index d22ead486..9a1d83f98 100644 --- a/TMB_8hpp_source.html +++ b/TMB_8hpp_source.html @@ -28,7 +28,7 @@
TMB Documentation -  v1.9.9 +  v1.9.10
@@ -73,7 +73,7 @@
TMB.hpp
-Go to the documentation of this file.
1 // Copyright (C) 2013-2015 Kasper Kristensen
2 // License: GPL-2
3 /* Utility: Compile time test for Type=double */
4 template<class Type>
5 struct isDouble{
6  enum{value=false};
7 };
8 template<>
9 struct isDouble<double>{
10  enum{value=true};
11 };
12 
16 /* To be removed */
17 #define TMB_DEBUG 0
18 #define TMB_PRINT(x)std::cout << #x << ": " << x << "\n"; std::cout.flush();
19 
20 /* Conditionally skip compilation */
21 #ifdef WITH_LIBTMB
22 #define CSKIP(...) ;
23 #define TMB_EXTERN extern
24 #else
25 #define CSKIP(...) __VA_ARGS__
26 #define TMB_EXTERN
27 #endif
28 #ifdef TMB_PRECOMPILE_ATOMICS
29 #define IF_TMB_PRECOMPILE_ATOMICS(...) __VA_ARGS__
30 #else
31 #define IF_TMB_PRECOMPILE_ATOMICS(...)
32 #endif
33 #ifdef HAVE_PRECOMPILED_ATOMICS
34 #define CSKIP_ATOMIC(...) ;
35 #else
36 #define CSKIP_ATOMIC(...) __VA_ARGS__
37 #endif
38 
39 /* Must come before Rinternals.h */
40 #ifdef _OPENMP
41 #include <omp.h>
42 #endif
43 
44 /* Early inclusion of Rprintf and REprintf */
45 #include <R_ext/Print.h>
46 #include "Rstream.hpp"
47 
48 /* Flag to bypass abort() */
49 #ifndef TMB_ABORT
50 #define TMB_ABORT abort()
51 #endif
52 
53 /* Include the Eigen library. */
54 #ifdef TMB_SAFEBOUNDS
55 #undef NDEBUG
56 #undef eigen_assert
57 void eigen_REprintf(const char* x);
58 #define eigen_assert(x) if (!(x)) { eigen_REprintf("TMB has received an error from Eigen. "); \
59  eigen_REprintf("The following condition was not met:\n"); \
60  eigen_REprintf(#x); \
61  eigen_REprintf("\nPlease check your matrix-vector bounds etc., "); \
62  eigen_REprintf("or run your program through a debugger.\n"); \
63  TMB_ABORT;}
64 #define TMBAD_ASSERT2(x,msg) \
65 if (!(x)) { \
66  Rcerr << "TMBad assertion failed.\n"; \
67  Rcerr << "The following condition was not met: " << #x << "\n"; \
68  Rcerr << "Possible reason: " msg << "\n"; \
69  Rcerr << "For more info run your program through a debugger.\n"; \
70  TMB_ABORT; \
71 }
72 #define TMBAD_ASSERT(x) TMBAD_ASSERT2(x,"Unknown")
73 #else
74 #undef NDEBUG
75 #define NDEBUG 1
76 #define TMBAD_ASSERT2(x,msg) (void) (x);
77 #define TMBAD_ASSERT(x) (void) (x);
78 #endif
79 /* Provide access to file 'DisableStupidWarnings.h' which has been
80  patched by RcppEigen to satisfy CRAN policy. This file may need
81  regular updating. The renaming is to aviod a CRAN note. */
82 #ifdef TMB_EIGEN_DISABLE_WARNINGS
83 #ifndef EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
84 #define EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS 1
85 #endif
86 #include "EigenWarnings/DisableStupidWarnings"
87 #endif
88 #include <Eigen/Dense>
89 
90 // Default: Include Eigen/Sparse normally
91 #ifndef TMB_SPARSE_STORAGE_INDEX
92 #include <Eigen/Sparse>
93 #else
94 // Alternative: Include Eigen/Sparse with custom sparse matrix integer type
95 #define SparseMatrix SparseMatrix_rename
96 #include <Eigen/Sparse>
97 #undef SparseMatrix
98 namespace Eigen {
99 template<class T, int Flags = 0, class StorageIndex = TMB_SPARSE_STORAGE_INDEX>
100 using SparseMatrix = SparseMatrix_rename<T, Flags, StorageIndex>;
101 }
102 #endif
103 
104 /* Workaround side effect when -DEIGEN_USE_LAPACKE is set */
105 #undef I
106 
107 /* Select AD framework: TMBAD or CPPAD */
108 #ifndef CPPAD_FRAMEWORK
109 #ifndef TMBAD_FRAMEWORK
110 #define CPPAD_FRAMEWORK
111 #endif
112 #endif
113 
114 /* Include the CppAD library. (Always turn off debug for cppad) */
115 #undef NDEBUG
116 #define NDEBUG 1
117 #include "cppad/cppad.hpp"
118 #ifdef TMBAD_FRAMEWORK
119 #include "TMBad/TMBad.hpp"
120 #include "TMBad/tmbad_allow_comparison.hpp"
121 #include "TMBad/eigen_numtraits.hpp"
122 #undef error
123 #include "TMBad/compile.hpp"
124 #include "TMBad/graph2dot.hpp"
125 #include "TMBad/compression.hpp"
126 #include "TMBad/ad_blas.hpp"
127 #ifndef WITH_LIBTMB
128 #include "TMBad/TMBad.cpp"
129 #endif
130 #define error Rf_error
131 // Workaround to make CppAD::Integer working with TMBad
132 namespace CppAD {
133 int Integer(const TMBad::ad_aug &x) CSKIP ({ return (int) x.Value(); })
134 TMBad::ad_aug abs(const TMBad::ad_aug &x) CSKIP ({ return TMBad::fabs(x); })
135 #define TMBAD_CONDEXP(NAME) \
136 TMBad::ad_aug CondExp ## NAME( \
137  const TMBad::ad_aug &x0, \
138  const TMBad::ad_aug &x1, \
139  const TMBad::ad_aug &x2, \
140  const TMBad::ad_aug &x3) CSKIP ( { \
141  return TMBad::CondExp ## NAME(x0, x1, x2, x3); \
142 })
143 TMBAD_CONDEXP(Eq)
144 TMBAD_CONDEXP(Ne)
145 TMBAD_CONDEXP(Lt)
146 TMBAD_CONDEXP(Gt)
147 TMBAD_CONDEXP(Le)
148 TMBAD_CONDEXP(Ge)
149 #undef TMBAD_CONDEXP
150 bool Variable(const TMBad::ad_aug &x) CSKIP ({ return !x.constant(); })
151 }
152 // FIXME: Move to TMBad source?
153 namespace TMBad {
154  /* Add 'isfinite', 'isinf' and 'isnan' to TMBad */
155  using std::isfinite;
156  bool isfinite(const TMBad::ad_aug &x)CSKIP({ return isfinite(x.Value()); })
157  using std::isinf;
158  bool isinf(const TMBad::ad_aug &x)CSKIP({ return isinf(x.Value()); })
159  using std::isnan;
160  bool isnan(const TMBad::ad_aug &x)CSKIP({ return isnan(x.Value()); })
161 }
162 #endif
163 
164 /* Include the R library _after_ Eigen and CppAD. Otherwise, the R
165  macros can cause conflicts (as they do not respect the Eigen and
166  CppAD namespace limits). E.g., the 'length' macro conflicts with
167  CppAD when compiling with '-std=c++11'. */
168 #include <R.h>
169 #include <Rinternals.h>
170 #include "toggle_thread_safe_R.hpp"
171 void eigen_REprintf(const char* x)CSKIP({REprintf("%s",x);})
172 
173 #include "tmbutils/tmbutils.hpp"
174 #include "tmbutils/vectorize.hpp"
175 using tmbutils::matrix;
176 using tmbutils::vector;
177 using CppAD::AD;
178 using CppAD::ADFun;
179 namespace CppAD{
180  /* Add to CppAD so that 'Variable' works for any 'Type' */
181  bool Variable(double x)CSKIP({ return false; })
182  /* Add 'isfinite', 'isinf' and 'isnan' to CppAD */
183  using std::isfinite;
184  template <class T>
185  bool isfinite(const AD<T> &x)CSKIP({ return isfinite(Value(x)); })
186  using std::isinf;
187  template <class T>
188  bool isinf(const AD<T> &x)CSKIP({ return isinf(Value(x)); })
189  using std::isnan;
190  template <class T>
191  bool isnan(const AD<T> &x)CSKIP({ return isnan(Value(x)); })
192 }
193 #include "convert.hpp" // asSEXP, asMatrix, asVector
194 #include "config.hpp"
195 #include "tmbutils/getListElement.hpp"
196 #include "atomic_math.hpp"
197 #include "expm.hpp"
198 #include "atomic_convolve.hpp"
199 #include "tiny_ad/atomic.hpp"
200 #include "tiny_ad/integrate/integrate.hpp"
201 #include "dynamic_data.hpp" // Requires atomic namespace
202 #include "Vectorize.hpp"
203 #include "dnorm.hpp" // harmless
204 #include "lgamma.hpp" // harmless
205 #include "start_parallel.hpp"
206 #include "tmbutils/newton.hpp" // Newton solver + Laplace used by TransformADFunObject
207 #include "tmb_core.hpp"
208 #include "distributions_R.hpp"
209 #include "convenience.hpp" // Requires besselK
210 #include "tmbutils/tmbutils_extra.hpp"
211 #include "tmbutils/R_inla.hpp"
212 #include "tmbutils/sparse_matrix_exponential.hpp"
213 #include "tmbutils/concat.hpp"
214 #include "precompile.hpp" // Must come last
215 using tmbutils::array;
216 using Eigen::Matrix;
217 using Eigen::Array;
218 
219 /* Cleanup */
220 
221 // Nothing more to precompile
222 #undef CSKIP
223 #define CSKIP(...) __VA_ARGS__
224 #undef CSKIP_ATOMIC
225 #define CSKIP_ATOMIC(...) __VA_ARGS__
Automatic differentiation library designed for TMB.
Definition: TMB.hpp:153
+Go to the documentation of this file.
1 // Copyright (C) 2013-2015 Kasper Kristensen
2 // License: GPL-2
3 /* Utility: Compile time test for Type=double */
4 template<class Type>
5 struct isDouble{
6  enum{value=false};
7 };
8 template<>
9 struct isDouble<double>{
10  enum{value=true};
11 };
12 
16 /* To be removed */
17 #define TMB_DEBUG 0
18 #define TMB_PRINT(x)std::cout << #x << ": " << x << "\n"; std::cout.flush();
19 
20 /* Conditionally skip compilation */
21 #ifdef WITH_LIBTMB
22 #define CSKIP(...) ;
23 #define TMB_EXTERN extern
24 #else
25 #define CSKIP(...) __VA_ARGS__
26 #define TMB_EXTERN
27 #endif
28 #ifdef TMB_PRECOMPILE_ATOMICS
29 #define IF_TMB_PRECOMPILE_ATOMICS(...) __VA_ARGS__
30 #else
31 #define IF_TMB_PRECOMPILE_ATOMICS(...)
32 #endif
33 #ifdef HAVE_PRECOMPILED_ATOMICS
34 #define CSKIP_ATOMIC(...) ;
35 #else
36 #define CSKIP_ATOMIC(...) __VA_ARGS__
37 #endif
38 
39 /* Must come before Rinternals.h */
40 #ifdef _OPENMP
41 #include <omp.h>
42 #endif
43 
44 /* Early inclusion of Rprintf and REprintf */
45 #include <R_ext/Print.h>
46 #include "Rstream.hpp"
47 
48 /* Flag to bypass abort() */
49 #ifndef TMB_ABORT
50 #define TMB_ABORT abort()
51 #endif
52 
53 /* Include the Eigen library. */
54 #ifdef TMB_SAFEBOUNDS
55 #undef NDEBUG
56 #undef eigen_assert
57 void eigen_REprintf(const char* x);
58 #define eigen_assert(x) if (!(x)) { eigen_REprintf("TMB has received an error from Eigen. "); \
59  eigen_REprintf("The following condition was not met:\n"); \
60  eigen_REprintf(#x); \
61  eigen_REprintf("\nPlease check your matrix-vector bounds etc., "); \
62  eigen_REprintf("or run your program through a debugger.\n"); \
63  TMB_ABORT;}
64 #define TMBAD_ASSERT2(x,msg) \
65 if (!(x)) { \
66  Rcerr << "TMBad assertion failed.\n"; \
67  Rcerr << "The following condition was not met: " << #x << "\n"; \
68  Rcerr << "Possible reason: " msg << "\n"; \
69  Rcerr << "For more info run your program through a debugger.\n"; \
70  TMB_ABORT; \
71 }
72 #define TMBAD_ASSERT(x) TMBAD_ASSERT2(x,"Unknown")
73 #else
74 #undef NDEBUG
75 #define NDEBUG 1
76 #define TMBAD_ASSERT2(x,msg) (void) (x);
77 #define TMBAD_ASSERT(x) (void) (x);
78 #endif
79 /* Provide access to file 'DisableStupidWarnings.h' which has been
80  patched by RcppEigen to satisfy CRAN policy. This file may need
81  regular updating. The renaming is to aviod a CRAN note. */
82 #ifdef TMB_EIGEN_DISABLE_WARNINGS
83 #ifndef EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
84 #define EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS 1
85 #endif
86 #include "EigenWarnings/DisableStupidWarnings"
87 #endif
88 #include <Eigen/Dense>
89 
90 // Default: Include Eigen/Sparse normally
91 #ifndef TMB_SPARSE_STORAGE_INDEX
92 #include <Eigen/Sparse>
93 #else
94 // Alternative: Include Eigen/Sparse with custom sparse matrix integer type
95 #define SparseMatrix SparseMatrix_rename
96 #include <Eigen/Sparse>
97 #undef SparseMatrix
98 namespace Eigen {
99 template<class T, int Flags = 0, class StorageIndex = TMB_SPARSE_STORAGE_INDEX>
100 using SparseMatrix = SparseMatrix_rename<T, Flags, StorageIndex>;
101 }
102 #endif
103 
104 /* Workaround side effect when -DEIGEN_USE_LAPACKE is set */
105 #undef I
106 
107 /* Select AD framework: TMBAD or CPPAD */
108 #ifndef CPPAD_FRAMEWORK
109 #ifndef TMBAD_FRAMEWORK
110 #define CPPAD_FRAMEWORK
111 #endif
112 #endif
113 
114 /* Include the CppAD library. (Always turn off debug for cppad) */
115 #undef NDEBUG
116 #define NDEBUG 1
117 #include "cppad/cppad.hpp"
118 #ifdef TMBAD_FRAMEWORK
119 #include "TMBad/TMBad.hpp"
120 #include "TMBad/tmbad_allow_comparison.hpp"
121 #include "TMBad/eigen_numtraits.hpp"
122 #undef error
123 #include "TMBad/compile.hpp"
124 #include "TMBad/graph2dot.hpp"
125 #include "TMBad/compression.hpp"
126 #include "TMBad/ad_blas.hpp"
127 #ifndef WITH_LIBTMB
128 #include "TMBad/TMBad.cpp"
129 #endif
130 #define error Rf_error
131 // Workaround to make CppAD::Integer working with TMBad
132 namespace CppAD {
133 int Integer(const TMBad::ad_aug &x) CSKIP ({ return (int) x.Value(); })
134 TMBad::ad_aug abs(const TMBad::ad_aug &x) CSKIP ({ return TMBad::fabs(x); })
135 #define TMBAD_CONDEXP(NAME) \
136 TMBad::ad_aug CondExp ## NAME( \
137  const TMBad::ad_aug &x0, \
138  const TMBad::ad_aug &x1, \
139  const TMBad::ad_aug &x2, \
140  const TMBad::ad_aug &x3) CSKIP ( { \
141  return TMBad::CondExp ## NAME(x0, x1, x2, x3); \
142 })
143 TMBAD_CONDEXP(Eq)
144 TMBAD_CONDEXP(Ne)
145 TMBAD_CONDEXP(Lt)
146 TMBAD_CONDEXP(Gt)
147 TMBAD_CONDEXP(Le)
148 TMBAD_CONDEXP(Ge)
149 #undef TMBAD_CONDEXP
150 bool Variable(const TMBad::ad_aug &x) CSKIP ({ return !x.constant(); })
151 }
152 // FIXME: Move to TMBad source?
153 namespace TMBad {
154  /* Add 'isfinite', 'isinf' and 'isnan' to TMBad */
155  using std::isfinite;
156  bool isfinite(const TMBad::ad_aug &x)CSKIP({ return isfinite(x.Value()); })
157  using std::isinf;
158  bool isinf(const TMBad::ad_aug &x)CSKIP({ return isinf(x.Value()); })
159  using std::isnan;
160  bool isnan(const TMBad::ad_aug &x)CSKIP({ return isnan(x.Value()); })
161 }
162 #endif
163 
164 /* Include the R library _after_ Eigen and CppAD. Otherwise, the R
165  macros can cause conflicts (as they do not respect the Eigen and
166  CppAD namespace limits). E.g., the 'length' macro conflicts with
167  CppAD when compiling with '-std=c++11'. */
168 #include <R.h>
169 #include <Rinternals.h>
170 #include "toggle_thread_safe_R.hpp"
171 void eigen_REprintf(const char* x)CSKIP({REprintf("%s",x);})
172 
173 #include "tmbutils/tmbutils.hpp"
174 #include "tmbutils/vectorize.hpp"
175 using tmbutils::matrix;
176 using tmbutils::vector;
177 using CppAD::AD;
178 using CppAD::ADFun;
179 namespace CppAD{
180  /* Add to CppAD so that 'Variable' works for any 'Type' */
181  bool Variable(double x)CSKIP({ return false; })
182  /* Add 'isfinite', 'isinf' and 'isnan' to CppAD */
183  using std::isfinite;
184  template <class T>
185  bool isfinite(const AD<T> &x)CSKIP({ return isfinite(Value(x)); })
186  using std::isinf;
187  template <class T>
188  bool isinf(const AD<T> &x)CSKIP({ return isinf(Value(x)); })
189  using std::isnan;
190  template <class T>
191  bool isnan(const AD<T> &x)CSKIP({ return isnan(Value(x)); })
192 }
193 #include "convert.hpp" // asSEXP, asMatrix, asVector
194 #include "config.hpp"
195 #include "tmbutils/getListElement.hpp"
196 #include "atomic_math.hpp"
197 #include "expm.hpp"
198 #include "atomic_convolve.hpp"
199 #include "tiny_ad/atomic.hpp"
200 #include "tiny_ad/integrate/integrate.hpp"
201 #include "dynamic_data.hpp" // Requires atomic namespace
202 #include "Vectorize.hpp"
203 #include "dnorm.hpp" // harmless
204 #include "lgamma.hpp" // harmless
205 #include "start_parallel.hpp"
206 #include "tmbutils/newton.hpp" // Newton solver + Laplace used by TransformADFunObject
207 #ifndef TMB_SKINNY
208 #include "tmb_core.hpp"
209 #endif
210 #include "distributions_R.hpp"
211 #include "convenience.hpp" // Requires besselK
212 #include "tmbutils/tmbutils_extra.hpp"
213 #include "tmbutils/R_inla.hpp"
214 #include "tmbutils/sparse_matrix_exponential.hpp"
215 #include "tmbutils/concat.hpp"
216 #include "precompile.hpp" // Must come last
217 using tmbutils::array;
218 using Eigen::Matrix;
219 using Eigen::Array;
220 
221 /* Cleanup */
222 
223 // Nothing more to precompile
224 #undef CSKIP
225 #define CSKIP(...) __VA_ARGS__
226 #undef CSKIP_ATOMIC
227 #define CSKIP_ATOMIC(...) __VA_ARGS__
Automatic differentiation library designed for TMB.
Definition: TMB.hpp:153
Array class used by TMB.
Definition: tmbutils.hpp:23
Augmented AD type.
Definition: global.hpp:2831
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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TMB Documentation -  v1.9.9 +  v1.9.10
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