1 #ifndef SPATIALSEIR_INCLUDEFILES
2 #define SPATIALSEIR_INCLUDEFILES
8 #ifndef LSS_SAMPLERS_INC
9 #define LSS_SAMPLERS_INC
11 #define COMPARTMENT_METROPOLIS_SAMPLER 1
12 #define COMPARTMENT_IDX_METROPOLIS_SAMPLER 2
13 #define COMPARTMENT_IDX_SLICE_SAMPLER 3
14 #define COMPARTMENT_BINOM_PROPOSAL_METROPOLIS_SAMPLER 14
15 #define COMPARTMENT_BINOM_PROPOSAL_SLICE_SAMPLER 15
16 #define COMPARTMENT_BINOM_IDX_METROPOLIS_SAMPLER 16
17 #define INITCOMPARTMENT_METROPOLIS_SAMPLER 4
18 #define INITCOMPARTMENT_IDX_METROPOLIS_SAMPLER 5
19 #define INITCOMPARTMENT_IDX_SLICE_SAMPLER 6
20 #define PARAMETER_SINGLE_METROPOLIS_SAMPLER 7
21 #define PARAMETER_JOINT_METROPOLIS_SAMPLER 8
22 #define PARAMETER_JOINT_SLICE_SAMPLER 9
23 #define PARAMETER_DECORR_SAMPLER 10
25 #define COMPARTMENT_METROPOLIS_SAMPLER_OCL 11
26 #define INITCOMPARTMENT_METROPOLIS_SAMPLER_OCL 12
27 #define PARAMETER_JOINT_METROPOLIS_SAMPLER_OCL 13
28 #define PARAMETER_NULL_SAMPLER 17
29 #define HYBRID_SAMPLER_BETA_P_EI 18
34 class FullConditional;
35 class CompartmentFullConditional;
36 class InitCompartmentFullConditional;
37 class ParameterFullConditional;
39 class CompartmentalModelMatrix;
40 class CovariateMatrix;
41 class RandomNumberProvider;
Definition: LSS_FullConditional.hpp:115
int ** initCompartmentData
Definition: LSS_Samplers.hpp:322
int ** indexList
Definition: LSS_Samplers.hpp:321
ModelContext ** context
Definition: LSS_Samplers.hpp:241
CompartmentBinomialSliceSampler(ModelContext *context, CompartmentFullConditional *compartmentFC, int *compartmentData, int *compartmentFrom, int *compartmentTo, double *probabilityVector, int probabilityVectorLen)
~InitCompartmentMetropolisSampler()
ModelContext ** context
Definition: LSS_Samplers.hpp:415
IndexedInitCompartmentMetropolisSampler(ModelContext *context, InitCompartmentFullConditional *initCompartmentFC, int *initCompartmentData)
int ** compartmentData
Definition: LSS_Samplers.hpp:214
int ** compartmentData
Definition: LSS_Samplers.hpp:185
int ** indexLength
Definition: LSS_Samplers.hpp:301
int ** compartmentData
Definition: LSS_Samplers.hpp:103
CompartmentFullConditional ** compartmentFC
Definition: LSS_Samplers.hpp:120
CompartmentMetropolisSampler_OCL(ModelContext *context, CompartmentFullConditional *compartmentFC, int *compartmentData)
ParameterHybridSampler(ModelContext *context, std::vector< ParameterFullConditional * > parameterFullConditionals, std::vector< double * > parameters, int samplerType)
int ** indexList
Definition: LSS_Samplers.hpp:142
int ** indexList
Definition: LSS_Samplers.hpp:213
ParameterFullConditional ** paramFC
Definition: LSS_Samplers.hpp:340
int ** compartmentFrom
Definition: LSS_Samplers.hpp:244
ModelContext ** context
Definition: LSS_Samplers.hpp:119
Definition: LSS_Samplers.hpp:365
Definition: LSS_FullConditional.hpp:177
CompartmentFullConditional ** compartmentFC
Definition: LSS_Samplers.hpp:184
Definition: LSS_Samplers.hpp:59
double * proposalCache
Definition: LSS_Samplers.hpp:413
Definition: LSS_Samplers.hpp:273
CompartmentMetropolisSampler(ModelContext *context, CompartmentFullConditional *compartmentFC, int *compartmentData)
Definition: LSS_FullConditional.hpp:147
ParameterFullConditional ** paramFC
Definition: LSS_Samplers.hpp:416
~IndexedInitCompartmentMetropolisSampler()
double ** param
Definition: LSS_Samplers.hpp:356
Definition: CovariateMatrix.hpp:29
ParameterJointMetropolisSampler_OCL(ModelContext *context, ParameterFullConditional *paramFC, double *param)
int ** indexLength
Definition: LSS_Samplers.hpp:212
ModelContext ** context
Definition: LSS_Samplers.hpp:318
Definition: LSS_Samplers.hpp:195
virtual ~Sampler()
Definition: LSS_Samplers.hpp:49
std::vector< ParameterFullConditional * > * parameterFullConditionals
Definition: LSS_Samplers.hpp:84
Definition: LSS_Samplers.hpp:289
IndexedCompartmentMetropolisSampler(ModelContext *context, CompartmentFullConditional *compartmentFC, int *compartmentData)
int ** compartmentData
Definition: LSS_Samplers.hpp:141
int ** initCompartmentData
Definition: LSS_Samplers.hpp:285
~CompartmentBinomialSliceSampler()
~IndexedCompartmentMetropolisSampler()
CompartmentFullConditional ** compartmentFC
Definition: LSS_Samplers.hpp:159
int ** initCompartmentData
Definition: LSS_Samplers.hpp:303
ModelContext ** context
Definition: LSS_Samplers.hpp:299
virtual int getSamplerType()=0
double ** param
Definition: LSS_Samplers.hpp:338
int ** indexLength
Definition: LSS_Samplers.hpp:160
ModelContext ** context
Definition: LSS_Samplers.hpp:79
~IndexedCompartmentBinomialMetropolisSampler()
Definition: LSS_Samplers.hpp:91
ParameterFullConditional ** paramFC
Definition: LSS_Samplers.hpp:358
double ** param
Definition: LSS_Samplers.hpp:375
int ** indexLength
Definition: LSS_Samplers.hpp:140
int ** initCompartmentData
Definition: LSS_Samplers.hpp:268
ModelContext ** context
Definition: LSS_Samplers.hpp:394
int * probabilityVectorLen
Definition: LSS_Samplers.hpp:189
ModelContext ** context
Definition: LSS_Samplers.hpp:101
IndexedCompartmentBinomialMetropolisSampler(ModelContext *context, CompartmentFullConditional *compartmentFC, int *compartmentData, int *compartmentFrom, int *compartmentTo, double *probabilityVector, int probabilityVectorLen)
Definition: LSS_Samplers.hpp:346
ModelContext ** context
Definition: LSS_Samplers.hpp:158
~InitCompartmentMetropolisSampler_OCL()
~ParameterSingleMetropolisSampler()
int * samplerType
Definition: LSS_Samplers.hpp:80
int ** compartmentTo
Definition: LSS_Samplers.hpp:216
Definition: LSS_Samplers.hpp:128
~ParameterDecorrelationSampler()
ModelContext ** context
Definition: LSS_Samplers.hpp:376
Definition: LSS_Samplers.hpp:328
CompartmentFullConditional ** compartmentFC
Definition: LSS_Samplers.hpp:242
ParameterDecorrelationSampler(ModelContext *context, ParameterFullConditional *paramFC, double *param, CovariateMatrix *proposalMatrix)
~ParameterJointMetropolisSampler()
ModelContext ** context
Definition: LSS_Samplers.hpp:283
double * proposalCache2
Definition: LSS_Samplers.hpp:414
int ** compartmentData
Definition: LSS_Samplers.hpp:243
Definition: LSS_Samplers.hpp:109
InitCompartmentMetropolisSampler(ModelContext *context, InitCompartmentFullConditional *initCompartmentFC, int *initCompartmentData)
CompartmentFullConditional ** compartmentFC
Definition: LSS_Samplers.hpp:139
~CompartmentBinomialMetropolisSampler()
double ** probabilityVector
Definition: LSS_Samplers.hpp:217
Definition: LSS_Samplers.hpp:383
Definition: LSS_Samplers.hpp:308
double ** param
Definition: LSS_Samplers.hpp:412
CovariateMatrix ** proposalMatrix
Definition: LSS_Samplers.hpp:417
ParameterFullConditional ** paramFC
Definition: LSS_Samplers.hpp:395
ModelContext ** context
Definition: LSS_Samplers.hpp:138
InitCompartmentFullConditional ** initCompartmentFC
Definition: LSS_Samplers.hpp:300
Definition: LSS_Samplers.hpp:148
ModelContext ** context
Definition: LSS_Samplers.hpp:183
IndexedCompartmentSliceSampler(ModelContext *context, CompartmentFullConditional *compartmentFC, int *compartmentData)
int ** compartmentData
Definition: LSS_Samplers.hpp:121
InitCompartmentFullConditional ** initCompartmentFC
Definition: LSS_Samplers.hpp:284
~IndexedInitCompartmentSliceSampler()
~IndexedCompartmentSliceSampler()
ModelContext ** context
Definition: LSS_Samplers.hpp:266
CompartmentFullConditional ** compartmentFC
Definition: LSS_Samplers.hpp:102
CompartmentBinomialMetropolisSampler(ModelContext *context, CompartmentFullConditional *compartmentFC, int *compartmentData, int *compartmentFrom, int *compartmentTo, double *probabilityVector, int probabilityVectorLen)
~ParameterHybridSampler()
Definition: LSS_Samplers.hpp:168
ParameterJointSliceSampler(ModelContext *context, ParameterFullConditional *paramFC, double *param)
InitCompartmentFullConditional ** initCompartmentFC
Definition: LSS_Samplers.hpp:319
Definition: LSS_Samplers.hpp:46
Definition: LSS_Samplers.hpp:226
ParameterSingleMetropolisSampler(ModelContext *context, ParameterFullConditional *paramFC, double *param)
double ** probabilityVector
Definition: LSS_Samplers.hpp:246
int ** indexList
Definition: LSS_Samplers.hpp:162
virtual void drawSample()=0
int ** compartmentTo
Definition: LSS_Samplers.hpp:245
int ** compartmentTo
Definition: LSS_Samplers.hpp:187
int * totalParamSize
Definition: LSS_Samplers.hpp:81
double ** param
Definition: LSS_Samplers.hpp:393
int ** compartmentData
Definition: LSS_Samplers.hpp:161
~ParameterJointMetropolisSampler_OCL()
int * probabilityVectorLen
Definition: LSS_Samplers.hpp:247
int ** compartmentFrom
Definition: LSS_Samplers.hpp:186
~CompartmentMetropolisSampler()
IndexedInitCompartmentSliceSampler(ModelContext *context, InitCompartmentFullConditional *initCompartmentFC, int *initCompartmentData)
InitCompartmentMetropolisSampler_OCL(ModelContext *context, InitCompartmentFullConditional *initCompartmentFC, int *initCompartmentData)
Definition: LSS_Samplers.hpp:256
std::vector< double * > * parameters
Definition: LSS_Samplers.hpp:85
ModelContext ** context
Definition: LSS_Samplers.hpp:357
ParameterFullConditional ** paramFC
Definition: LSS_Samplers.hpp:377
~CompartmentMetropolisSampler_OCL()
double * parameterCache
Definition: LSS_Samplers.hpp:82
double ** probabilityVector
Definition: LSS_Samplers.hpp:188
int * probabilityVectorLen
Definition: LSS_Samplers.hpp:218
ParameterJointMetropolisSampler(ModelContext *context, ParameterFullConditional *paramFC, double *param)
int ** indexList
Definition: LSS_Samplers.hpp:302
Definition: LSS_Samplers.hpp:70
ModelContext ** context
Definition: LSS_Samplers.hpp:339
Definition: ModelContext.hpp:82
ModelContext ** context
Definition: LSS_Samplers.hpp:210
int ** indexLength
Definition: LSS_Samplers.hpp:320
InitCompartmentFullConditional ** initCompartmentFC
Definition: LSS_Samplers.hpp:267
CompartmentFullConditional ** compartmentFC
Definition: LSS_Samplers.hpp:211
Definition: LSS_Samplers.hpp:401
~ParameterJointSliceSampler()
int ** compartmentFrom
Definition: LSS_Samplers.hpp:215