diff --git a/docs/annotated.html b/docs/annotated.html index b312c14..d62c454 100644 --- a/docs/annotated.html +++ b/docs/annotated.html @@ -113,8 +113,8 @@  CFleetInterfaceBaseRcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherited and not called from R directly  CGrowthInterfaceBaseRcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly  CIndexDataInterfaceRcpp interface for data as an S4 object. To instantiate from R: fleet <- new(fims$Index) - CJsonParserParses JSON strings and generates JSON values - CJsonValueRepresents a JSON value + CJsonParser + CJsonValue  CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(fims$logistic_maturity)  CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)  CMaturityInterfaceBaseMaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function diff --git a/docs/classBevertonHoltRecruitmentInterface-members.html b/docs/classBevertonHoltRecruitmentInterface-members.html index 707deb7..f71bac6 100644 --- a/docs/classBevertonHoltRecruitmentInterface-members.html +++ b/docs/classBevertonHoltRecruitmentInterface-members.html @@ -89,7 +89,7 @@ log_rzeroBevertonHoltRecruitmentInterface log_sigma_recruitBevertonHoltRecruitmentInterface logit_steepBevertonHoltRecruitmentInterface - RecruitmentInterfaceBase()RecruitmentInterfaceBaseinline + RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinline ~BevertonHoltRecruitmentInterface() (defined in BevertonHoltRecruitmentInterface)BevertonHoltRecruitmentInterfaceinlinevirtual ~RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinlinevirtual diff --git a/docs/classBevertonHoltRecruitmentInterface.html b/docs/classBevertonHoltRecruitmentInterface.html index a8ee8c7..068b074 100644 --- a/docs/classBevertonHoltRecruitmentInterface.html +++ b/docs/classBevertonHoltRecruitmentInterface.html @@ -105,9 +105,6 @@ virtual double evaluate_nll ()  evaluate recruitment nll More...
  -- Public Member Functions inherited from RecruitmentInterfaceBase - RecruitmentInterfaceBase () -  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () diff --git a/docs/classGrowthInterfaceBase.html b/docs/classGrowthInterfaceBase.html index 6193cc6..13c0d87 100644 --- a/docs/classGrowthInterfaceBase.html +++ b/docs/classGrowthInterfaceBase.html @@ -126,6 +126,7 @@

Detailed Description

Rcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly.

+

Growth Rcpp interface *

Member Data Documentation

◆ id

diff --git a/docs/classJsonParser.html b/docs/classJsonParser.html index 711a916..3758bd0 100644 --- a/docs/classJsonParser.html +++ b/docs/classJsonParser.html @@ -76,21 +76,15 @@
-

Parses JSON strings and generates JSON values. - More...

-

#include <fims_json.hpp>

- - -

Public Member Functions

JsonValue Parse (const std::string &json)
 Parse a JSON string and return the corresponding JSON value. More...
 
void WriteToFile (const std::string &filename, JsonValue jsonValue)
 Write a JSON value to a file. More...
 
void Show (JsonValue jsonValue)
 Display a JSON value to the standard output. More...
 

Detailed Description

@@ -111,8 +105,7 @@

- -

Parse a JSON string and return the corresponding JSON value.

+

Parse a JSON string and return the corresponding JSON value.

Parse a JSON string and return the corresponding JSON value.

Parameters
@@ -138,8 +131,7 @@

- -

Display a JSON value to the standard output.

+

Display a JSON value to the standard output.

Display a JSON value to the standard output.

Parameters

jsonThe JSON string to parse.
@@ -174,8 +166,7 @@

- -

Write a JSON value to a file.

+

Write a JSON value to a file.

Write a JSON value to an output file.

Parameters

jsonValueThe JSON value to display.
@@ -183,6 +174,7 @@

-

Represents a JSON value. - More...

-

#include <fims_json.hpp>

filenameThe name of the output file.
- - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - +

Public Member Functions

- JsonValue ()
 Default constructor, initializes to Null value.
 JsonValue ()
 
- JsonValue (int num)
 Constructor for numeric JSON value (i.e., integer).
 JsonValue (int num)
 
- JsonValue (double num)
 Constructor for numeric JSON value (i.e., double).
 JsonValue (double num)
 
- JsonValue (const std::string &str)
 Constructor for string JSON value.
 JsonValue (const std::string &str)
 
- JsonValue (bool b)
 Constructor for boolean JSON value.
 JsonValue (bool b)
 
- JsonValue (const JsonObject &obj)
 Constructor for JSON object value.
 JsonValue (const JsonObject &obj)
 
- JsonValue (const JsonArray &arr)
 Constructor for JSON array value.
 JsonValue (const JsonArray &arr)
 
-JsonValueType GetType () const
 Get the type of the JSON value.
JsonValueType GetType () const
 
-int GetInt () const
 Get the numeric value as an integer.
int GetInt () const
 
-double GetDouble () const
 Get the numeric value as a double.
double GetDouble () const
 
-const std::string & GetString () const
 Get the string value.
const std::string & GetString () const
 
-bool GetBool () const
 Get the boolean value.
bool GetBool () const
 
-JsonObject & GetObject ()
 Get the JSON object.
JsonObject & GetObject ()
 
-JsonArray & GetArray ()
 Get the JSON array.
JsonArray & GetArray ()
 

Detailed Description

Represents a JSON value.

-
The documentation for this class was generated from the following file:
    +

Constructor & Destructor Documentation

+ +

◆ JsonValue() [1/7]

+ +
+
+ + + + + +
+ + + + + + + +
JsonValue::JsonValue ()
+ 		+inline
+
+

Default constructor, initializes to Null value.

+ +
+
+ +

◆ JsonValue() [2/7]

+ +
+
+ + + + + +
+ + + + + + + + +
JsonValue::JsonValue (int num)
+ 		+inline
+
+

Constructor for numeric JSON value (i.e., integer).

+ +
+
+ +

◆ JsonValue() [3/7]

+ +
+
+ + + + + +
+ + + + + + + + +
JsonValue::JsonValue (double num)
+ 		+inline
+
+

Constructor for numeric JSON value (i.e., double).

+ +
+
+ +

◆ JsonValue() [4/7]

+ +
+
+ + + + + +
+ + + + + + + + +
JsonValue::JsonValue (const std::string & str)
+ 		+inline
+
+

Constructor for string JSON value.

+ +
+
+ +

◆ JsonValue() [5/7]

+ +
+
+ + + + + +
+ + + + + + + + +
JsonValue::JsonValue (bool b)
+ 		+inline
+
+

Constructor for boolean JSON value.

+ +
+
+ +

◆ JsonValue() [6/7]

+ +
+
+ + + + + +
+ + + + + + + + +
JsonValue::JsonValue (const JsonObject & obj)
+ 		+inline
+
+

Constructor for JSON object value.

+ +
+
+ +

◆ JsonValue() [7/7]

+ +
+
+ + + + + +
+ + + + + + + + +
JsonValue::JsonValue (const JsonArray & arr)
+ 		+inline
+
+

Constructor for JSON array value.

+ +
+
+

Member Function Documentation

+ +

◆ GetArray()

+ +
+
+ + + + + +
+ + + + + + + +
JsonArray& JsonValue::GetArray ()
+ 		+inline
+
+

Get the JSON array.

+ +
+
+ +

◆ GetBool()

+ +
+
+ + + + + +
+ + + + + + + +
bool JsonValue::GetBool () const
+ 		+inline
+
+

Get the boolean value.

+ +
+
+ +

◆ GetDouble()

+ +
+
+ + + + + +
+ + + + + + + +
double JsonValue::GetDouble () const
+ 		+inline
+
+

Get the numeric value as a double.

+ +
+
+ +

◆ GetInt()

+ +
+
+ + + + + +
+ + + + + + + +
int JsonValue::GetInt () const
+ 		+inline
+
+

Get the numeric value as an integer.

+ +
+
+ +

◆ GetObject()

+ +
+
+ + + + + +
+ + + + + + + +
JsonObject& JsonValue::GetObject ()
+ 		+inline
+
+

Get the JSON object.

+ +
+
+ +

◆ GetString()

+ +
+
+ + + + + +
+ + + + + + + +
const std::string& JsonValue::GetString () const
+ 		+inline
+
+

Get the string value.

+ +
+
+ +

◆ GetType()

+ +
+
+ + + + + +
+ + + + + + + +
JsonValueType JsonValue::GetType () const
+ 		+inline
+
+

Get the type of the JSON value.

+ +
+
+
The documentation for this class was generated from the following file: diff --git a/docs/classMaturityInterfaceBase.html b/docs/classMaturityInterfaceBase.html index dfa6620..94db030 100644 --- a/docs/classMaturityInterfaceBase.html +++ b/docs/classMaturityInterfaceBase.html @@ -126,6 +126,7 @@

Detailed Description

MaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function.

+

maturity Rcpp interface

Member Data Documentation

◆ id

diff --git a/docs/classPopulationInterfaceBase.html b/docs/classPopulationInterfaceBase.html index 5704f07..8f3bad9 100644 --- a/docs/classPopulationInterfaceBase.html +++ b/docs/classPopulationInterfaceBase.html @@ -122,6 +122,7 @@

Detailed Description

PopulationInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Population function.

+

Population Rcpp interface

Member Data Documentation

◆ id

diff --git a/docs/classRecruitmentInterfaceBase-members.html b/docs/classRecruitmentInterfaceBase-members.html index f8d90e1..cea405f 100644 --- a/docs/classRecruitmentInterfaceBase-members.html +++ b/docs/classRecruitmentInterfaceBase-members.html @@ -83,7 +83,7 @@ idRecruitmentInterfaceBase id_gRecruitmentInterfaceBasestatic live_objectsRecruitmentInterfaceBasestatic - RecruitmentInterfaceBase()RecruitmentInterfaceBaseinline + RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinline ~RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinlinevirtual diff --git a/docs/classRecruitmentInterfaceBase.html b/docs/classRecruitmentInterfaceBase.html index 48d8fc8..8bdcea8 100644 --- a/docs/classRecruitmentInterfaceBase.html +++ b/docs/classRecruitmentInterfaceBase.html @@ -95,8 +95,6 @@ - - @@ -131,34 +129,8 @@

Public Member Functions

 RecruitmentInterfaceBase ()
 
virtual uint32_t get_id ()=0
 get the ID of the interface base object

Detailed Description

RecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Recruitment function.

-

Constructor & Destructor Documentation

- -

◆ RecruitmentInterfaceBase()

- -
-
- - - - - -
- - - - - - - -
RecruitmentInterfaceBase::RecruitmentInterfaceBase ()
- 		-inline
-
-

static bool constrain_deviations; /‍**< whether or not the rec devs are constrained*‍/

- -
-
-

Member Function Documentation

+

Recruitment Rcpp interface

+

Member Function Documentation

◆ evaluate_nll()

diff --git a/docs/classSelectivityInterfaceBase.html b/docs/classSelectivityInterfaceBase.html index 13c5632..88258c2 100644 --- a/docs/classSelectivityInterfaceBase.html +++ b/docs/classSelectivityInterfaceBase.html @@ -127,6 +127,7 @@

Detailed Description

SelectivityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Selectivity function.

+

Selectivity Rcpp interface

Member Data Documentation

◆ id

diff --git a/docs/fims__json_8hpp.html b/docs/fims__json_8hpp.html index b9d2eba..903f0cb 100644 --- a/docs/fims__json_8hpp.html +++ b/docs/fims__json_8hpp.html @@ -95,21 +95,15 @@

Classes

class  JsonValue - Represents a JSON value. More...
  class  JsonParser - Parses JSON strings and generates JSON values. More...
  - - + - - +

Typedefs

-using JsonObject = std::map< std::string, JsonValue >
 Alias for a JSON object, mapping strings to JSON values.
using JsonObject = std::map< std::string, JsonValue >
 
-using JsonArray = std::vector< JsonValue >
 Alias for a JSON array, containing a sequence of JSON values.
using JsonArray = std::vector< JsonValue >
 
-

@@ -124,13 +118,43 @@ , Array
}

 Represents different types of JSON values. More...
 

Detailed Description

A simple JSON parsing and generation library.

This library provides classes and functions for parsing JSON strings and generating JSON data structures.

-

Enumeration Type Documentation

+

Typedef Documentation

+ +

◆ JsonArray

+ +
+
+ + + + +
using JsonArray = std::vector<JsonValue>
+
+

Alias for a JSON array, containing a sequence of JSON values.

+ +
+
+ +

◆ JsonObject

+ +
+
+ + + + +
using JsonObject = std::map<std::string, JsonValue>
+
+

Alias for a JSON object, mapping strings to JSON values.

+ +
+
+

Enumeration Type Documentation

◆ JsonValueType

@@ -142,7 +166,6 @@

-

Represents different types of JSON values.

- - + + diff --git a/docs/population_8hpp_source.html b/docs/population_8hpp_source.html index dc5ca31..26cfdd5 100644 --- a/docs/population_8hpp_source.html +++ b/docs/population_8hpp_source.html @@ -145,6 +145,7 @@
83  std::vector<Type> expected_numbers_at_age;
85  std::vector<Type> expected_catch;
86  std::vector<Type> expected_recruitment;
+
87  // recruitment
88  int recruitment_id = -999;
89  std::shared_ptr<RecruitmentBase<Type>>
90  recruitment;
@@ -669,7 +670,7 @@
fims_popdy::Population::spawning_biomass
std::vector< Type > spawning_biomass
Definition: population.hpp:76
fims_popdy::Population::fleet_id
int fleet_id
Definition: population.hpp:103
fims_popdy::Population::mortality_F
ParameterVector mortality_F
Definition: population.hpp:60
-
fims_popdy::Population::recruitment_id
int recruitment_id
recruitment
Definition: population.hpp:88
+
fims_popdy::Population::recruitment_id
int recruitment_id
Definition: population.hpp:88
fims_popdy::Population::CalculateUnfishedBiomass
void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age)
Adds to existing yearly unfished biomass estimates the biomass for a specified year and age.
Definition: population.hpp:306
fims_popdy::Population::recruitment
std::shared_ptr< RecruitmentBase< Type > > recruitment
Definition: population.hpp:90
fims_popdy::Population::log_M
ParameterVector log_M
Definition: population.hpp:53
diff --git a/docs/rcpp__growth_8hpp_source.html b/docs/rcpp__growth_8hpp_source.html index 16fbea6..5d0dede 100644 --- a/docs/rcpp__growth_8hpp_source.html +++ b/docs/rcpp__growth_8hpp_source.html @@ -89,10 +89,6 @@
11 #include "../../../population_dynamics/growth/growth.hpp"
12 #include "rcpp_interface_base.hpp"
13 
-
14 /****************************************************************
-
15  * Growth Rcpp interface *
-
16  ***************************************************************/
-
17 
24 class GrowthInterfaceBase : public FIMSRcppInterfaceBase {
25  public:
26  static uint32_t id_g;
diff --git a/docs/rcpp__interface_8hpp_source.html b/docs/rcpp__interface_8hpp_source.html index 026935b..636346c 100644 --- a/docs/rcpp__interface_8hpp_source.html +++ b/docs/rcpp__interface_8hpp_source.html @@ -499,14 +499,14 @@
466 #endif /* RCPP_INTERFACE_HPP */
AgeCompDataInterface::age_comp_data
Rcpp::NumericVector age_comp_data
Definition: rcpp_data.hpp:65
AgeCompDataInterface::get_id
virtual uint32_t get_id()
get the ID of the interface base object
Definition: rcpp_data.hpp:82
-
BevertonHoltRecruitmentInterface::evaluate_nll
virtual double evaluate_nll()
evaluate recruitment nll
Definition: rcpp_recruitment.hpp:101
-
BevertonHoltRecruitmentInterface::logit_steep
Parameter logit_steep
Definition: rcpp_recruitment.hpp:73
-
BevertonHoltRecruitmentInterface::deviations
Rcpp::NumericVector deviations
Definition: rcpp_recruitment.hpp:76
-
BevertonHoltRecruitmentInterface::evaluate
virtual double evaluate(double spawners, double ssbzero)
evaluate method for child recruitment interface objects to inherit
Definition: rcpp_recruitment.hpp:86
-
BevertonHoltRecruitmentInterface::get_id
virtual uint32_t get_id()
get the ID of the interface base object
Definition: rcpp_recruitment.hpp:84
-
BevertonHoltRecruitmentInterface::estimate_deviations
bool estimate_deviations
Definition: rcpp_recruitment.hpp:77
-
BevertonHoltRecruitmentInterface::log_sigma_recruit
Parameter log_sigma_recruit
Definition: rcpp_recruitment.hpp:75
-
BevertonHoltRecruitmentInterface::log_rzero
Parameter log_rzero
Definition: rcpp_recruitment.hpp:74
+
BevertonHoltRecruitmentInterface::evaluate_nll
virtual double evaluate_nll()
evaluate recruitment nll
Definition: rcpp_recruitment.hpp:100
+
BevertonHoltRecruitmentInterface::logit_steep
Parameter logit_steep
Definition: rcpp_recruitment.hpp:72
+
BevertonHoltRecruitmentInterface::deviations
Rcpp::NumericVector deviations
Definition: rcpp_recruitment.hpp:75
+
BevertonHoltRecruitmentInterface::evaluate
virtual double evaluate(double spawners, double ssbzero)
evaluate method for child recruitment interface objects to inherit
Definition: rcpp_recruitment.hpp:85
+
BevertonHoltRecruitmentInterface::get_id
virtual uint32_t get_id()
get the ID of the interface base object
Definition: rcpp_recruitment.hpp:83
+
BevertonHoltRecruitmentInterface::estimate_deviations
bool estimate_deviations
Definition: rcpp_recruitment.hpp:76
+
BevertonHoltRecruitmentInterface::log_sigma_recruit
Parameter log_sigma_recruit
Definition: rcpp_recruitment.hpp:74
+
BevertonHoltRecruitmentInterface::log_rzero
Parameter log_rzero
Definition: rcpp_recruitment.hpp:73
DataInterfaceBase::live_objects
static std::map< uint32_t, DataInterfaceBase * > live_objects
Definition: rcpp_data.hpp:27
DataInterfaceBase::id_g
static uint32_t id_g
Definition: rcpp_data.hpp:23
DistributionsInterfaceBase::live_objects
static std::map< uint32_t, DistributionsInterfaceBase * > live_objects
Definition: rcpp_tmb_distribution.hpp:26
diff --git a/docs/rcpp__maturity_8hpp_source.html b/docs/rcpp__maturity_8hpp_source.html index 30a5a22..20e79b6 100644 --- a/docs/rcpp__maturity_8hpp_source.html +++ b/docs/rcpp__maturity_8hpp_source.html @@ -91,10 +91,6 @@
13 #include "../../../population_dynamics/maturity/maturity.hpp"
14 #include "rcpp_interface_base.hpp"
15 
-
16 /****************************************************************
-
17  * maturity Rcpp interface *
-
18  ***************************************************************/
-
19 
24 class MaturityInterfaceBase : public FIMSRcppInterfaceBase {
25  public:
26  static uint32_t id_g;
diff --git a/docs/rcpp__population_8hpp_source.html b/docs/rcpp__population_8hpp_source.html index 4deb0df..99ca982 100644 --- a/docs/rcpp__population_8hpp_source.html +++ b/docs/rcpp__population_8hpp_source.html @@ -89,10 +89,6 @@
11 #include "../../../population_dynamics/population/population.hpp"
12 #include "rcpp_interface_base.hpp"
13 
-
14 /****************************************************************
-
15  * Population Rcpp interface *
-
16  ***************************************************************/
-
17 
22 class PopulationInterfaceBase : public FIMSRcppInterfaceBase {
23  public:
24  static uint32_t id_g;
diff --git a/docs/rcpp__recruitment_8hpp_source.html b/docs/rcpp__recruitment_8hpp_source.html index e11cb75..f9e0091 100644 --- a/docs/rcpp__recruitment_8hpp_source.html +++ b/docs/rcpp__recruitment_8hpp_source.html @@ -90,10 +90,6 @@
12 #include "../../../population_dynamics/recruitment/recruitment.hpp"
13 #include "rcpp_interface_base.hpp"
14 
-
15 /****************************************************************
-
16  * Recruitment Rcpp interface *
-
17  ***************************************************************/
-
18 
23 class RecruitmentInterfaceBase : public FIMSRcppInterfaceBase {
24  public:
25  static uint32_t id_g;
@@ -102,148 +98,149 @@
28  static std::map<uint32_t, RecruitmentInterfaceBase*> live_objects;
31  // static std::vector<double> recruit_deviations; /**< vector of recruitment
32  // deviations*/
-
35 
-
36  RecruitmentInterfaceBase() {
-
37  this->id = RecruitmentInterfaceBase::id_g++;
-
38  /* Create instance of map: key is id and value is pointer to
-
39  RecruitmentInterfaceBase */
-
40  RecruitmentInterfaceBase::live_objects[this->id] = this;
-
41  FIMSRcppInterfaceBase::fims_interface_objects.push_back(this);
-
42  }
-
43 
-
44  virtual ~RecruitmentInterfaceBase() {}
-
45 
-
48  virtual uint32_t get_id() = 0;
-
49 
-
52  virtual double evaluate(double spawners, double ssbzero) = 0;
-
53 
-
59  virtual double evaluate_nll() = 0;
-
60 };
-
61 
-
62 uint32_t RecruitmentInterfaceBase::id_g = 1;
-
63 std::map<uint32_t, RecruitmentInterfaceBase*>
-
64  RecruitmentInterfaceBase::live_objects;
-
65 
-
71 class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
-
72  public:
-
73  Parameter logit_steep;
-
74  Parameter log_rzero;
-
75  Parameter log_sigma_recruit;
-
76  Rcpp::NumericVector deviations;
-
77  bool estimate_deviations =
-
78  false;
-
80  BevertonHoltRecruitmentInterface() : RecruitmentInterfaceBase() {}
-
81 
-
82  virtual ~BevertonHoltRecruitmentInterface() {}
-
83 
-
84  virtual uint32_t get_id() { return this->id; }
-
85 
-
86  virtual double evaluate(double spawners, double ssbzero) {
-
87  fims_popdy::SRBevertonHolt<double> BevHolt;
-
88 
-
89  BevHolt.logit_steep = this->logit_steep.value_m;
-
90  if (this->logit_steep.value_m == 1.0) {
-
91  warning(
-
92  "Steepness is subject to a logit transformation, so its value is "
-
93  "0.7848469. Fixing it at 1.0 is not currently possible.");
-
94  }
-
95 
-
96  BevHolt.log_rzero = this->log_rzero.value_m;
-
97 
-
98  return BevHolt.evaluate(spawners, ssbzero);
-
99  }
-
100 
-
101  virtual double evaluate_nll() {
-
102  fims_popdy::SRBevertonHolt<double> NLL;
-
103 
-
104  NLL.log_sigma_recruit = this->log_sigma_recruit.value_m;
-
105  NLL.recruit_deviations.resize(deviations.size()); // Vector from TMB
-
106  for (int i = 0; i < deviations.size(); i++) {
-
107  NLL.recruit_deviations[i] = deviations[i];
-
108  }
-
109  RECRUITMENT_LOG << "Rec devs being passed to C++ are " << deviations
-
110  << std::endl;
-
111  NLL.estimate_recruit_deviations = this->estimate_deviations;
-
112  return NLL.evaluate_nll();
-
113  }
-
114 
-
115 #ifdef TMB_MODEL
-
116 
-
117  template <typename Type>
-
118  bool add_to_fims_tmb_internal() {
-
119  std::shared_ptr<fims_info::Information<Type> > info =
-
120  fims_info::Information<Type>::GetInstance();
-
121 
-
122  std::shared_ptr<fims_popdy::SRBevertonHolt<Type> > recruitment =
-
123  std::make_shared<fims_popdy::SRBevertonHolt<Type> >();
-
124 
-
125  // set relative info
-
126  recruitment->id = this->id;
-
127  recruitment->logit_steep = this->logit_steep.value_m;
-
128  if (this->logit_steep.estimated_m) {
-
129  if (this->logit_steep.is_random_effect_m) {
-
130  info->RegisterRandomEffect(recruitment->logit_steep);
-
131  } else {
-
132  info->RegisterParameter(recruitment->logit_steep);
-
133  }
-
134  }
-
135  recruitment->log_rzero = this->log_rzero.value_m;
-
136  if (this->log_rzero.estimated_m) {
-
137  if (this->log_rzero.is_random_effect_m) {
-
138  info->RegisterRandomEffect(recruitment->log_rzero);
-
139  } else {
-
140  info->RegisterParameter(recruitment->log_rzero);
-
141  }
-
142  }
-
143  recruitment->log_sigma_recruit = this->log_sigma_recruit.value_m;
-
144  if (this->log_sigma_recruit.estimated_m) {
-
145  if (this->log_sigma_recruit.is_random_effect_m) {
-
146  info->RegisterRandomEffect(recruitment->log_sigma_recruit);
-
147  } else {
-
148  info->RegisterParameter(recruitment->log_sigma_recruit);
-
149  }
-
150  }
-
151 
-
152  recruitment->recruit_deviations.resize(this->deviations.size());
-
153  if (this->estimate_deviations) {
-
154  for (size_t i = 0; i < recruitment->recruit_deviations.size(); i++) {
-
155  recruitment->recruit_deviations[i] = this->deviations[i];
-
156  info->RegisterParameter(recruitment->recruit_deviations[i]);
-
157  }
-
158  } else {
-
159  for (size_t i = 0; i < recruitment->recruit_deviations.size(); i++) {
-
160  recruitment->recruit_deviations[i] = this->deviations[i];
-
161  }
-
162  }
-
163 
-
164  // add to Information
-
165  info->recruitment_models[recruitment->id] = recruitment;
-
166 
-
167  return true;
-
168  }
-
169 
-
172  virtual bool add_to_fims_tmb() {
-
173  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
-
174  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
-
175  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
-
176  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
-
177 
-
178  return true;
-
179  }
-
180 
-
181 #endif
-
182 };
-
183 
-
184 #endif
-
BevertonHoltRecruitmentInterface
Rcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(fims$be...
Definition: rcpp_recruitment.hpp:71
-
BevertonHoltRecruitmentInterface::evaluate_nll
virtual double evaluate_nll()
evaluate recruitment nll
Definition: rcpp_recruitment.hpp:101
-
BevertonHoltRecruitmentInterface::logit_steep
Parameter logit_steep
Definition: rcpp_recruitment.hpp:73
-
BevertonHoltRecruitmentInterface::deviations
Rcpp::NumericVector deviations
Definition: rcpp_recruitment.hpp:76
-
BevertonHoltRecruitmentInterface::evaluate
virtual double evaluate(double spawners, double ssbzero)
evaluate method for child recruitment interface objects to inherit
Definition: rcpp_recruitment.hpp:86
-
BevertonHoltRecruitmentInterface::get_id
virtual uint32_t get_id()
get the ID of the interface base object
Definition: rcpp_recruitment.hpp:84
-
BevertonHoltRecruitmentInterface::estimate_deviations
bool estimate_deviations
Definition: rcpp_recruitment.hpp:77
-
BevertonHoltRecruitmentInterface::log_sigma_recruit
Parameter log_sigma_recruit
Definition: rcpp_recruitment.hpp:75
-
BevertonHoltRecruitmentInterface::log_rzero
Parameter log_rzero
Definition: rcpp_recruitment.hpp:74
+
33  // static bool constrain_deviations; /**< whether or not the rec devs are constrained*/
+
34 
+
35  RecruitmentInterfaceBase() {
+
36  this->id = RecruitmentInterfaceBase::id_g++;
+
37  /* Create instance of map: key is id and value is pointer to
+
38  RecruitmentInterfaceBase */
+
39  RecruitmentInterfaceBase::live_objects[this->id] = this;
+
40  FIMSRcppInterfaceBase::fims_interface_objects.push_back(this);
+
41  }
+
42 
+
43  virtual ~RecruitmentInterfaceBase() {}
+
44 
+
47  virtual uint32_t get_id() = 0;
+
48 
+
51  virtual double evaluate(double spawners, double ssbzero) = 0;
+
52 
+
58  virtual double evaluate_nll() = 0;
+
59 };
+
60 
+
61 uint32_t RecruitmentInterfaceBase::id_g = 1;
+
62 std::map<uint32_t, RecruitmentInterfaceBase*>
+
63  RecruitmentInterfaceBase::live_objects;
+
64 
+
70 class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
+
71  public:
+
72  Parameter logit_steep;
+
73  Parameter log_rzero;
+
74  Parameter log_sigma_recruit;
+
75  Rcpp::NumericVector deviations;
+
76  bool estimate_deviations =
+
77  false;
+
79  BevertonHoltRecruitmentInterface() : RecruitmentInterfaceBase() {}
+
80 
+
81  virtual ~BevertonHoltRecruitmentInterface() {}
+
82 
+
83  virtual uint32_t get_id() { return this->id; }
+
84 
+
85  virtual double evaluate(double spawners, double ssbzero) {
+
86  fims_popdy::SRBevertonHolt<double> BevHolt;
+
87 
+
88  BevHolt.logit_steep = this->logit_steep.value_m;
+
89  if (this->logit_steep.value_m == 1.0) {
+
90  warning(
+
91  "Steepness is subject to a logit transformation, so its value is "
+
92  "0.7848469. Fixing it at 1.0 is not currently possible.");
+
93  }
+
94 
+
95  BevHolt.log_rzero = this->log_rzero.value_m;
+
96 
+
97  return BevHolt.evaluate(spawners, ssbzero);
+
98  }
+
99 
+
100  virtual double evaluate_nll() {
+
101  fims_popdy::SRBevertonHolt<double> NLL;
+
102 
+
103  NLL.log_sigma_recruit = this->log_sigma_recruit.value_m;
+
104  NLL.recruit_deviations.resize(deviations.size()); // Vector from TMB
+
105  for (int i = 0; i < deviations.size(); i++) {
+
106  NLL.recruit_deviations[i] = deviations[i];
+
107  }
+
108  RECRUITMENT_LOG << "Rec devs being passed to C++ are " << deviations
+
109  << std::endl;
+
110  NLL.estimate_recruit_deviations = this->estimate_deviations;
+
111  return NLL.evaluate_nll();
+
112  }
+
113 
+
114 #ifdef TMB_MODEL
+
115 
+
116  template <typename Type>
+
117  bool add_to_fims_tmb_internal() {
+
118  std::shared_ptr<fims_info::Information<Type> > info =
+
119  fims_info::Information<Type>::GetInstance();
+
120 
+
121  std::shared_ptr<fims_popdy::SRBevertonHolt<Type> > recruitment =
+
122  std::make_shared<fims_popdy::SRBevertonHolt<Type> >();
+
123 
+
124  // set relative info
+
125  recruitment->id = this->id;
+
126  recruitment->logit_steep = this->logit_steep.value_m;
+
127  if (this->logit_steep.estimated_m) {
+
128  if (this->logit_steep.is_random_effect_m) {
+
129  info->RegisterRandomEffect(recruitment->logit_steep);
+
130  } else {
+
131  info->RegisterParameter(recruitment->logit_steep);
+
132  }
+
133  }
+
134  recruitment->log_rzero = this->log_rzero.value_m;
+
135  if (this->log_rzero.estimated_m) {
+
136  if (this->log_rzero.is_random_effect_m) {
+
137  info->RegisterRandomEffect(recruitment->log_rzero);
+
138  } else {
+
139  info->RegisterParameter(recruitment->log_rzero);
+
140  }
+
141  }
+
142  recruitment->log_sigma_recruit = this->log_sigma_recruit.value_m;
+
143  if (this->log_sigma_recruit.estimated_m) {
+
144  if (this->log_sigma_recruit.is_random_effect_m) {
+
145  info->RegisterRandomEffect(recruitment->log_sigma_recruit);
+
146  } else {
+
147  info->RegisterParameter(recruitment->log_sigma_recruit);
+
148  }
+
149  }
+
150 
+
151  recruitment->recruit_deviations.resize(this->deviations.size());
+
152  if (this->estimate_deviations) {
+
153  for (size_t i = 0; i < recruitment->recruit_deviations.size(); i++) {
+
154  recruitment->recruit_deviations[i] = this->deviations[i];
+
155  info->RegisterParameter(recruitment->recruit_deviations[i]);
+
156  }
+
157  } else {
+
158  for (size_t i = 0; i < recruitment->recruit_deviations.size(); i++) {
+
159  recruitment->recruit_deviations[i] = this->deviations[i];
+
160  }
+
161  }
+
162 
+
163  // add to Information
+
164  info->recruitment_models[recruitment->id] = recruitment;
+
165 
+
166  return true;
+
167  }
+
168 
+
171  virtual bool add_to_fims_tmb() {
+
172  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
+
173  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
+
174  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
+
175  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
+
176 
+
177  return true;
+
178  }
+
179 
+
180 #endif
+
181 };
+
182 
+
183 #endif
+
BevertonHoltRecruitmentInterface
Rcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(fims$be...
Definition: rcpp_recruitment.hpp:70
+
BevertonHoltRecruitmentInterface::evaluate_nll
virtual double evaluate_nll()
evaluate recruitment nll
Definition: rcpp_recruitment.hpp:100
+
BevertonHoltRecruitmentInterface::logit_steep
Parameter logit_steep
Definition: rcpp_recruitment.hpp:72
+
BevertonHoltRecruitmentInterface::deviations
Rcpp::NumericVector deviations
Definition: rcpp_recruitment.hpp:75
+
BevertonHoltRecruitmentInterface::evaluate
virtual double evaluate(double spawners, double ssbzero)
evaluate method for child recruitment interface objects to inherit
Definition: rcpp_recruitment.hpp:85
+
BevertonHoltRecruitmentInterface::get_id
virtual uint32_t get_id()
get the ID of the interface base object
Definition: rcpp_recruitment.hpp:83
+
BevertonHoltRecruitmentInterface::estimate_deviations
bool estimate_deviations
Definition: rcpp_recruitment.hpp:76
+
BevertonHoltRecruitmentInterface::log_sigma_recruit
Parameter log_sigma_recruit
Definition: rcpp_recruitment.hpp:74
+
BevertonHoltRecruitmentInterface::log_rzero
Parameter log_rzero
Definition: rcpp_recruitment.hpp:73
FIMSRcppInterfaceBase
Base class for all interface objects.
Definition: rcpp_interface_base.hpp:61
FIMSRcppInterfaceBase::fims_interface_objects
static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
Definition: rcpp_interface_base.hpp:64
FIMSRcppInterfaceBase::add_to_fims_tmb
virtual bool add_to_fims_tmb()
virtual method to inherit to add objects to the TMB model
Definition: rcpp_interface_base.hpp:67
@@ -256,7 +253,6 @@
RecruitmentInterfaceBase::id
uint32_t id
Definition: rcpp_recruitment.hpp:26
RecruitmentInterfaceBase::get_id
virtual uint32_t get_id()=0
get the ID of the interface base object
RecruitmentInterfaceBase::evaluate
virtual double evaluate(double spawners, double ssbzero)=0
evaluate method for child recruitment interface objects to inherit
-
RecruitmentInterfaceBase::RecruitmentInterfaceBase
RecruitmentInterfaceBase()
Definition: rcpp_recruitment.hpp:36
RecruitmentInterfaceBase::id_g
static uint32_t id_g
Definition: rcpp_recruitment.hpp:25
RecruitmentInterfaceBase::evaluate_nll
virtual double evaluate_nll()=0
evaluate recruitment nll
fims_info::Information::GetInstance
static std::shared_ptr< Information< Type > > GetInstance()
Definition: information.hpp:125
diff --git a/docs/rcpp__selectivity_8hpp_source.html b/docs/rcpp__selectivity_8hpp_source.html index b606dbe..7035c5e 100644 --- a/docs/rcpp__selectivity_8hpp_source.html +++ b/docs/rcpp__selectivity_8hpp_source.html @@ -90,10 +90,6 @@
12 #include "../../../population_dynamics/selectivity/selectivity.hpp"
13 #include "rcpp_interface_base.hpp"
14 
-
15 /****************************************************************
-
16  * Selectivity Rcpp interface *
-
17  ***************************************************************/
-
18 
23 class SelectivityInterfaceBase : public FIMSRcppInterfaceBase {
24  public:
25  static uint32_t id_g;
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+215,6 @@ - @@ -1525,8 +1524,6 @@

- -

recruitment

id of recruitment model object

Enumerator
Null 

Null JSON value.

diff --git a/docs/fims__json_8hpp_source.html b/docs/fims__json_8hpp_source.html index 981087c..8d18874 100644 --- a/docs/fims__json_8hpp_source.html +++ b/docs/fims__json_8hpp_source.html @@ -76,355 +76,354 @@
fims_json.hpp
-Go to the documentation of this file.
1 #include <cctype>
-
6 #include <iostream>
-
7 #include <map>
-
8 #include <sstream>
-
9 #include <string>
-
10 #include <vector>
-
11 
-
12 class JsonValue;
+Go to the documentation of this file.
1 
+
7 #include <cctype>
+
8 #include <iostream>
+
9 #include <map>
+
10 #include <sstream>
+
11 #include <string>
+
12 #include <vector>
13 
-
15 using JsonObject = std::map<std::string, JsonValue>;
-
16 
-
18 using JsonArray = std::vector<JsonValue>;
-
19 
-
21 enum JsonValueType {
-
22  Null = 0,
-
23  Number,
-
24  String,
-
25  Bool,
-
26  Object,
-
27  Array
-
28 };
-
29 
-
31 class JsonValue {
-
32  public:
-
34  JsonValue() : type(JsonValueType::Null) {}
-
35 
-
37  JsonValue(int num) : type(JsonValueType::Number), number(num) {}
-
38 
-
40  JsonValue(double num) : type(JsonValueType::Number), number(num) {}
-
41 
-
43  JsonValue(const std::string& str) : type(JsonValueType::String), str(str) {}
-
44 
-
46  JsonValue(bool b) : type(JsonValueType::Bool), boolean(b) {}
-
47 
-
49  JsonValue(const JsonObject& obj) : type(JsonValueType::Object), object(obj) {}
-
50 
-
52  JsonValue(const JsonArray& arr) : type(JsonValueType::Array), array(arr) {}
-
53 
-
55  JsonValueType GetType() const { return type; }
-
56 
-
58  int GetInt() const { return static_cast<int>(number); }
-
59 
-
61  double GetDouble() const { return number; }
-
62 
-
64  const std::string& GetString() const { return str; }
-
65 
-
67  bool GetBool() const { return boolean; }
-
68 
-
70  JsonObject& GetObject() { return object; }
-
71 
-
73  JsonArray& GetArray() { return array; }
-
74 
-
75  private:
-
76  JsonValueType type;
-
77  double number;
-
78  std::string str;
-
79  bool boolean;
-
80  JsonObject object;
-
81  JsonArray array;
-
82 };
-
83 
-
85 class JsonParser {
-
86  public:
-
88  JsonValue Parse(const std::string& json);
-
90  void WriteToFile(const std::string& filename, JsonValue jsonValue);
-
92  void Show(JsonValue jsonValue);
+
14 class JsonValue;
+
15 
+
19 using JsonObject = std::map<std::string, JsonValue>;
+
20 
+
24 using JsonArray = std::vector<JsonValue>;
+
25 
+
29 enum JsonValueType {
+
30  Null = 0,
+
31  Number,
+
32  String,
+
33  Bool,
+
34  Object,
+
35  Array
+
36 };
+
37 
+
41 class JsonValue {
+
42  public:
+
44  JsonValue() : type(JsonValueType::Null) {}
+
45 
+
47  JsonValue(int num) : type(JsonValueType::Number), number(num) {}
+
48 
+
50  JsonValue(double num) : type(JsonValueType::Number), number(num) {}
+
51 
+
53  JsonValue(const std::string& str) : type(JsonValueType::String), str(str) {}
+
54 
+
56  JsonValue(bool b) : type(JsonValueType::Bool), boolean(b) {}
+
57 
+
59  JsonValue(const JsonObject& obj) : type(JsonValueType::Object), object(obj) {}
+
60 
+
62  JsonValue(const JsonArray& arr) : type(JsonValueType::Array), array(arr) {}
+
63 
+
65  JsonValueType GetType() const { return type; }
+
66 
+
68  int GetInt() const { return static_cast<int>(number); }
+
69 
+
71  double GetDouble() const { return number; }
+
72 
+
74  const std::string& GetString() const { return str; }
+
75 
+
77  bool GetBool() const { return boolean; }
+
78 
+
80  JsonObject& GetObject() { return object; }
+
81 
+
83  JsonArray& GetArray() { return array; }
+
84 
+
85  private:
+
86  JsonValueType type;
+
87  double number;
+
88  std::string str;
+
89  bool boolean;
+
90  JsonObject object;
+
91  JsonArray array;
+
92 };
93 
-
94  private:
-
96  void SkipWhitespace();
-
98  JsonValue ParseValue();
-
100  JsonValue ParseNumber();
-
102  JsonValue ParseString();
-
104  JsonValue ParseBool();
-
106  JsonValue ParseNull();
-
108  JsonValue ParseObject();
-
110  JsonValue ParseArray();
-
112  void WriteJsonValue(std::ofstream& outputFile, JsonValue jsonValue);
-
114  void PrintJsonValue(std::ostream& outputFile, JsonValue jsonValue);
-
116  void Indent(std::ostream& outputFile, int level);
-
118  void Indent(std::ofstream& outputFile, int level);
-
119 
-
120  std::string data;
-
121  size_t position;
-
122 };
-
123 
-
127 JsonValue JsonParser::Parse(const std::string& json) {
-
128  data = json;
-
129  position = 0;
-
130  return ParseValue();
-
131 }
-
132 
-
133 void JsonParser::SkipWhitespace() {
-
134  while (position < data.length() && std::isspace(data[position])) {
-
135  position++;
-
136  }
-
137 }
-
138 
-
141 JsonValue JsonParser::ParseValue() {
-
143  SkipWhitespace();
-
144  char current = data[position];
-
145  if (current == '{') {
-
146  return ParseObject();
-
147  } else if (current == '[') {
-
148  return ParseArray();
-
149  } else if (current == '"') {
-
150  return ParseString();
-
151  } else if (current == 't' || current == 'f') {
-
152  return ParseBool();
-
153  } else if (current == 'n') {
-
154  return ParseNull();
-
155  } else {
-
156  return ParseNumber();
-
157  }
-
158 }
-
159 
-
162 JsonValue JsonParser::ParseNumber() {
-
163  size_t end_pos = position;
-
164  bool is_float = false;
-
165  while (end_pos < data.length() &&
-
166  (std::isdigit(data[end_pos]) || data[end_pos] == '.' ||
-
167  data[end_pos] == '-' || data[end_pos] == 'e' ||
-
168  data[end_pos] == 'E')) {
-
169  if (data[end_pos] == '.' || data[end_pos] == 'e' || data[end_pos] == 'E') {
-
170  is_float = true;
-
171  }
-
172  end_pos++;
+
97 class JsonParser {
+
98  public:
+
100  JsonValue Parse(const std::string& json);
+
102  void WriteToFile(const std::string& filename, JsonValue jsonValue);
+
104  void Show(JsonValue jsonValue);
+
105 
+
106  private:
+
108  void SkipWhitespace();
+
110  JsonValue ParseValue();
+
112  JsonValue ParseNumber();
+
114  JsonValue ParseString();
+
116  JsonValue ParseBool();
+
118  JsonValue ParseNull();
+
120  JsonValue ParseObject();
+
122  JsonValue ParseArray();
+
124  void WriteJsonValue(std::ofstream& outputFile, JsonValue jsonValue);
+
126  void PrintJsonValue(std::ostream& outputFile, JsonValue jsonValue);
+
128  void Indent(std::ostream& outputFile, int level);
+
130  void Indent(std::ofstream& outputFile, int level);
+
131 
+
132  std::string data;
+
133  size_t position;
+
134 };
+
135 
+
141 JsonValue JsonParser::Parse(const std::string& json) {
+
142  data = json;
+
143  position = 0;
+
144  return ParseValue();
+
145 }
+
146 
+
147 void JsonParser::SkipWhitespace() {
+
148  while (position < data.length() && std::isspace(data[position])) {
+
149  position++;
+
150  }
+
151 }
+
152 
+
157 JsonValue JsonParser::ParseValue() {
+
159  SkipWhitespace();
+
160  char current = data[position];
+
161  if (current == '{') {
+
162  return ParseObject();
+
163  } else if (current == '[') {
+
164  return ParseArray();
+
165  } else if (current == '"') {
+
166  return ParseString();
+
167  } else if (current == 't' || current == 'f') {
+
168  return ParseBool();
+
169  } else if (current == 'n') {
+
170  return ParseNull();
+
171  } else {
+
172  return ParseNumber();
173  }
-
174 
-
175  std::string num_str = data.substr(position, end_pos - position);
-
176  position = end_pos;
-
177 
-
178  if (is_float) {
-
179  double num;
-
180  std::istringstream(num_str) >> num;
-
181  return JsonValue(num);
-
182  } else {
-
183  int num;
-
184  std::istringstream(num_str) >> num;
-
185  return JsonValue(num);
-
186  }
-
187 }
-
188 
-
191 JsonValue JsonParser::ParseString() {
-
192  position++; // Skip the initial '"'
-
193  size_t end_pos = data.find('"', position);
-
194  std::string str = data.substr(position, end_pos - position);
-
195  position = end_pos + 1;
-
196  return JsonValue(str);
-
197 }
-
198 
-
201 JsonValue JsonParser::ParseBool() {
-
202  if (data.compare(position, 4, "true") == 0) {
-
203  position += 4;
-
204  return JsonValue(true);
-
205  } else if (data.compare(position, 5, "false") == 0) {
-
206  position += 5;
-
207  return JsonValue(false);
-
208  } else {
-
209  // Invalid boolean value
-
210  return JsonValue();
-
211  }
-
212 }
-
213 
-
216 JsonValue JsonParser::ParseNull() {
-
217  if (data.compare(position, 4, "null") == 0) {
-
218  position += 4;
-
219  return JsonValue();
-
220  } else {
-
221  // Invalid null value
-
222  return JsonValue();
-
223  }
-
224 }
-
225 
-
228 JsonValue JsonParser::ParseObject() {
-
229  JsonObject obj;
-
230  position++; // Skip the initial '{'
-
231 
-
232  while (data[position] != '}') {
-
233  SkipWhitespace();
-
234  std::string key = ParseString().GetString();
+
174 }
+
175 
+
180 JsonValue JsonParser::ParseNumber() {
+
181  size_t end_pos = position;
+
182  bool is_float = false;
+
183  while (end_pos < data.length() &&
+
184  (std::isdigit(data[end_pos]) || data[end_pos] == '.' ||
+
185  data[end_pos] == '-' || data[end_pos] == 'e' ||
+
186  data[end_pos] == 'E')) {
+
187  if (data[end_pos] == '.' || data[end_pos] == 'e' || data[end_pos] == 'E') {
+
188  is_float = true;
+
189  }
+
190  end_pos++;
+
191  }
+
192 
+
193  std::string num_str = data.substr(position, end_pos - position);
+
194  position = end_pos;
+
195 
+
196  if (is_float) {
+
197  double num;
+
198  std::istringstream(num_str) >> num;
+
199  return JsonValue(num);
+
200  } else {
+
201  int num;
+
202  std::istringstream(num_str) >> num;
+
203  return JsonValue(num);
+
204  }
+
205 }
+
206 
+
211 JsonValue JsonParser::ParseString() {
+
212  position++; // Skip the initial '"'
+
213  size_t end_pos = data.find('"', position);
+
214  std::string str = data.substr(position, end_pos - position);
+
215  position = end_pos + 1;
+
216  return JsonValue(str);
+
217 }
+
218 
+
223 JsonValue JsonParser::ParseBool() {
+
224  if (data.compare(position, 4, "true") == 0) {
+
225  position += 4;
+
226  return JsonValue(true);
+
227  } else if (data.compare(position, 5, "false") == 0) {
+
228  position += 5;
+
229  return JsonValue(false);
+
230  } else {
+
231  // Invalid boolean value
+
232  return JsonValue();
+
233  }
+
234 }
235 
-
236  position++; // Skip the ':'
-
237  SkipWhitespace();
-
238  JsonValue value = ParseValue();
-
239  obj[key] = value;
-
240 
-
241  SkipWhitespace();
-
242  if (data[position] == ',') {
-
243  position++;
-
244  }
-
245  }
-
246 
-
247  position++; // Skip the trailing '}'
-
248  return JsonValue(obj);
-
249 }
-
250 
-
253 JsonValue JsonParser::ParseArray() {
-
254  JsonArray arr;
-
255  position++; // Skip the initial '['
-
256 
-
257  while (data[position] != ']') {
-
258  SkipWhitespace();
-
259  JsonValue value = ParseValue();
-
260  arr.push_back(value);
+
240 JsonValue JsonParser::ParseNull() {
+
241  if (data.compare(position, 4, "null") == 0) {
+
242  position += 4;
+
243  return JsonValue();
+
244  } else {
+
245  // Invalid null value
+
246  return JsonValue();
+
247  }
+
248 }
+
249 
+
254 JsonValue JsonParser::ParseObject() {
+
255  JsonObject obj;
+
256  position++; // Skip the initial '{'
+
257 
+
258  while (data[position] != '}') {
+
259  SkipWhitespace();
+
260  std::string key = ParseString().GetString();
261 
-
262  SkipWhitespace();
-
263  if (data[position] == ',') {
-
264  position++;
-
265  }
-
266  }
-
267 
-
268  position++; // Skip the trailing ']'
-
269  return JsonValue(arr);
-
270 }
-
271 
-
275 void JsonParser::WriteToFile(const std::string& filename, JsonValue jsonValue) {
-
276  std::ofstream outputFile(filename);
-
277  if (!outputFile) {
-
278  std::cerr << "Error: Unable to open file " << filename << " for writing."
-
279  << std::endl;
-
280  return;
-
281  }
-
282 
-
283  // Call a private helper function to write JSON values recursively
-
284  WriteJsonValue(outputFile, jsonValue);
-
285 }
-
286 
-
288 // Private helper function to write JSON values recursively
-
291 void JsonParser::WriteJsonValue(std::ofstream& outputFile,
-
292  JsonValue jsonValue) {
-
293  switch (jsonValue.GetType()) {
-
294  case JsonValueType::Null:
-
295  outputFile << "null";
-
296  break;
-
297  case JsonValueType::Number:
-
298  outputFile << jsonValue.GetDouble();
-
299  break;
-
300  case JsonValueType::String:
-
301  outputFile << "\"" << jsonValue.GetString() << "\"";
-
302  break;
-
303  case JsonValueType::Bool:
-
304  outputFile << (jsonValue.GetBool() ? "true" : "false");
-
305  break;
-
306  case JsonValueType::Object: {
-
307  JsonObject& obj = jsonValue.GetObject();
-
308  outputFile << "{";
-
309  bool first = true;
-
310  for (const auto& pair : obj) {
-
311  if (!first) {
-
312  outputFile << ",";
-
313  }
-
314  first = false;
-
315  outputFile << "\"" << pair.first << "\":";
-
316  WriteJsonValue(outputFile, pair.second);
-
317  }
-
318  outputFile << "}";
-
319  } break;
-
320  case JsonValueType::Array: {
-
321  JsonArray& arr = jsonValue.GetArray();
-
322  outputFile << "[";
-
323  bool first = true;
-
324  for (const auto& value : arr) {
-
325  if (!first) {
-
326  outputFile << ",";
-
327  }
-
328  first = false;
-
329  WriteJsonValue(outputFile, value);
-
330  }
-
331  outputFile << "]";
-
332  } break;
-
333  }
-
334 }
-
335 
-
338 void JsonParser::Show(JsonValue jsonValue) {
-
339  this->PrintJsonValue(std::cout, jsonValue);
-
340  std::cout << std::endl;
-
341 }
-
342 
-
346 void JsonParser::PrintJsonValue(std::ostream& output, JsonValue jsonValue) {
-
347  switch (jsonValue.GetType()) {
-
348  case JsonValueType::Null:
-
349  output << "null";
-
350  break;
-
351  case JsonValueType::Number:
-
352  output << jsonValue.GetDouble();
-
353  break;
-
354  case JsonValueType::String:
-
355  output << "\"" << jsonValue.GetString() << "\"";
-
356  break;
-
357  case JsonValueType::Bool:
-
358  output << (jsonValue.GetBool() ? "true" : "false");
-
359  break;
-
360  case JsonValueType::Object: {
-
361  JsonObject& obj = jsonValue.GetObject();
-
362  output << "{";
-
363  bool first = true;
-
364  for (const auto& pair : obj) {
-
365  if (!first) {
-
366  output << ",";
-
367  }
-
368  first = false;
-
369  output << "\"" << pair.first << "\":";
-
370  PrintJsonValue(output, pair.second);
-
371  }
-
372  output << "}";
-
373  } break;
-
374  case JsonValueType::Array: {
-
375  JsonArray& arr = jsonValue.GetArray();
-
376  output << "[";
-
377  bool first = true;
-
378  for (const auto& value : arr) {
-
379  if (!first) {
-
380  output << ",";
-
381  }
-
382  first = false;
-
383  PrintJsonValue(output, value);
-
384  }
-
385  output << "]";
-
386  } break;
-
387  }
-
388 }
-
JsonParser
Parses JSON strings and generates JSON values.
Definition: fims_json.hpp:85
-
JsonParser::Parse
JsonValue Parse(const std::string &json)
Parse a JSON string and return the corresponding JSON value.
Definition: fims_json.hpp:127
-
JsonParser::Show
void Show(JsonValue jsonValue)
Display a JSON value to the standard output.
Definition: fims_json.hpp:338
-
JsonParser::WriteToFile
void WriteToFile(const std::string &filename, JsonValue jsonValue)
Write a JSON value to a file.
Definition: fims_json.hpp:275
-
JsonValue
Represents a JSON value.
Definition: fims_json.hpp:31
-
JsonValue::GetDouble
double GetDouble() const
Get the numeric value as a double.
Definition: fims_json.hpp:61
-
JsonValue::JsonValue
JsonValue(double num)
Constructor for numeric JSON value (i.e., double).
Definition: fims_json.hpp:40
-
JsonValue::GetType
JsonValueType GetType() const
Get the type of the JSON value.
Definition: fims_json.hpp:55
-
JsonValue::JsonValue
JsonValue(int num)
Constructor for numeric JSON value (i.e., integer).
Definition: fims_json.hpp:37
-
JsonValue::GetBool
bool GetBool() const
Get the boolean value.
Definition: fims_json.hpp:67
-
JsonValue::JsonValue
JsonValue(bool b)
Constructor for boolean JSON value.
Definition: fims_json.hpp:46
-
JsonValue::GetObject
JsonObject & GetObject()
Get the JSON object.
Definition: fims_json.hpp:70
-
JsonValue::GetArray
JsonArray & GetArray()
Get the JSON array.
Definition: fims_json.hpp:73
-
JsonValue::JsonValue
JsonValue()
Default constructor, initializes to Null value.
Definition: fims_json.hpp:34
-
JsonValue::GetInt
int GetInt() const
Get the numeric value as an integer.
Definition: fims_json.hpp:58
-
JsonValue::GetString
const std::string & GetString() const
Get the string value.
Definition: fims_json.hpp:64
-
JsonValue::JsonValue
JsonValue(const JsonObject &obj)
Constructor for JSON object value.
Definition: fims_json.hpp:49
-
JsonValue::JsonValue
JsonValue(const JsonArray &arr)
Constructor for JSON array value.
Definition: fims_json.hpp:52
-
JsonValue::JsonValue
JsonValue(const std::string &str)
Constructor for string JSON value.
Definition: fims_json.hpp:43
-
JsonArray
std::vector< JsonValue > JsonArray
Alias for a JSON array, containing a sequence of JSON values.
Definition: fims_json.hpp:18
-
JsonObject
std::map< std::string, JsonValue > JsonObject
Alias for a JSON object, mapping strings to JSON values.
Definition: fims_json.hpp:15
-
JsonValueType
JsonValueType
Represents different types of JSON values.
Definition: fims_json.hpp:21
-
Bool
@ Bool
Boolean JSON value.
Definition: fims_json.hpp:25
-
Object
@ Object
JSON object.
Definition: fims_json.hpp:26
-
Null
@ Null
Null JSON value.
Definition: fims_json.hpp:22
-
String
@ String
String JSON value.
Definition: fims_json.hpp:24
-
Array
@ Array
JSON array.
Definition: fims_json.hpp:27
-
Number
@ Number
Numeric JSON value.
Definition: fims_json.hpp:23
+
262  position++; // Skip the ':'
+
263  SkipWhitespace();
+
264  JsonValue value = ParseValue();
+
265  obj[key] = value;
+
266 
+
267  SkipWhitespace();
+
268  if (data[position] == ',') {
+
269  position++;
+
270  }
+
271  }
+
272 
+
273  position++; // Skip the trailing '}'
+
274  return JsonValue(obj);
+
275 }
+
276 
+
281 JsonValue JsonParser::ParseArray() {
+
282  JsonArray arr;
+
283  position++; // Skip the initial '['
+
284 
+
285  while (data[position] != ']') {
+
286  SkipWhitespace();
+
287  JsonValue value = ParseValue();
+
288  arr.push_back(value);
+
289 
+
290  SkipWhitespace();
+
291  if (data[position] == ',') {
+
292  position++;
+
293  }
+
294  }
+
295 
+
296  position++; // Skip the trailing ']'
+
297  return JsonValue(arr);
+
298 }
+
299 
+
305 void JsonParser::WriteToFile(const std::string& filename, JsonValue jsonValue) {
+
306  std::ofstream outputFile(filename);
+
307  if (!outputFile) {
+
308  std::cerr << "Error: Unable to open file " << filename << " for writing."
+
309  << std::endl;
+
310  return;
+
311  }
+
312 
+
314  WriteJsonValue(outputFile, jsonValue);
+
315 }
+
316 
+
323 void JsonParser::WriteJsonValue(std::ofstream& outputFile,
+
324  JsonValue jsonValue) {
+
325  switch (jsonValue.GetType()) {
+
326  case JsonValueType::Null:
+
327  outputFile << "null";
+
328  break;
+
329  case JsonValueType::Number:
+
330  outputFile << jsonValue.GetDouble();
+
331  break;
+
332  case JsonValueType::String:
+
333  outputFile << "\"" << jsonValue.GetString() << "\"";
+
334  break;
+
335  case JsonValueType::Bool:
+
336  outputFile << (jsonValue.GetBool() ? "true" : "false");
+
337  break;
+
338  case JsonValueType::Object: {
+
339  JsonObject& obj = jsonValue.GetObject();
+
340  outputFile << "{";
+
341  bool first = true;
+
342  for (const auto& pair : obj) {
+
343  if (!first) {
+
344  outputFile << ",";
+
345  }
+
346  first = false;
+
347  outputFile << "\"" << pair.first << "\":";
+
348  WriteJsonValue(outputFile, pair.second);
+
349  }
+
350  outputFile << "}";
+
351  } break;
+
352  case JsonValueType::Array: {
+
353  JsonArray& arr = jsonValue.GetArray();
+
354  outputFile << "[";
+
355  bool first = true;
+
356  for (const auto& value : arr) {
+
357  if (!first) {
+
358  outputFile << ",";
+
359  }
+
360  first = false;
+
361  WriteJsonValue(outputFile, value);
+
362  }
+
363  outputFile << "]";
+
364  } break;
+
365  }
+
366 }
+
367 
+
372 void JsonParser::Show(JsonValue jsonValue) {
+
373  this->PrintJsonValue(std::cout, jsonValue);
+
374  std::cout << std::endl;
+
375 }
+
376 
+
382 void JsonParser::PrintJsonValue(std::ostream& output, JsonValue jsonValue) {
+
383  switch (jsonValue.GetType()) {
+
384  case JsonValueType::Null:
+
385  output << "null";
+
386  break;
+
387  case JsonValueType::Number:
+
388  output << jsonValue.GetDouble();
+
389  break;
+
390  case JsonValueType::String:
+
391  output << "\"" << jsonValue.GetString() << "\"";
+
392  break;
+
393  case JsonValueType::Bool:
+
394  output << (jsonValue.GetBool() ? "true" : "false");
+
395  break;
+
396  case JsonValueType::Object: {
+
397  JsonObject& obj = jsonValue.GetObject();
+
398  output << "{";
+
399  bool first = true;
+
400  for (const auto& pair : obj) {
+
401  if (!first) {
+
402  output << ",";
+
403  }
+
404  first = false;
+
405  output << "\"" << pair.first << "\":";
+
406  PrintJsonValue(output, pair.second);
+
407  }
+
408  output << "}";
+
409  } break;
+
410  case JsonValueType::Array: {
+
411  JsonArray& arr = jsonValue.GetArray();
+
412  output << "[";
+
413  bool first = true;
+
414  for (const auto& value : arr) {
+
415  if (!first) {
+
416  output << ",";
+
417  }
+
418  first = false;
+
419  PrintJsonValue(output, value);
+
420  }
+
421  output << "]";
+
422  } break;
+
423  }
+
424 }
+
JsonParser
Definition: fims_json.hpp:97
+
JsonParser::Parse
JsonValue Parse(const std::string &json)
Definition: fims_json.hpp:141
+
JsonParser::Show
void Show(JsonValue jsonValue)
Definition: fims_json.hpp:372
+
JsonParser::WriteToFile
void WriteToFile(const std::string &filename, JsonValue jsonValue)
Definition: fims_json.hpp:305
+
JsonValue
Definition: fims_json.hpp:41
+
JsonValue::GetDouble
double GetDouble() const
Definition: fims_json.hpp:71
+
JsonValue::JsonValue
JsonValue(double num)
Definition: fims_json.hpp:50
+
JsonValue::GetType
JsonValueType GetType() const
Definition: fims_json.hpp:65
+
JsonValue::JsonValue
JsonValue(int num)
Definition: fims_json.hpp:47
+
JsonValue::GetBool
bool GetBool() const
Definition: fims_json.hpp:77
+
JsonValue::JsonValue
JsonValue(bool b)
Definition: fims_json.hpp:56
+
JsonValue::GetObject
JsonObject & GetObject()
Definition: fims_json.hpp:80
+
JsonValue::GetArray
JsonArray & GetArray()
Definition: fims_json.hpp:83
+
JsonValue::JsonValue
JsonValue()
Definition: fims_json.hpp:44
+
JsonValue::GetInt
int GetInt() const
Definition: fims_json.hpp:68
+
JsonValue::GetString
const std::string & GetString() const
Definition: fims_json.hpp:74
+
JsonValue::JsonValue
JsonValue(const JsonObject &obj)
Definition: fims_json.hpp:59
+
JsonValue::JsonValue
JsonValue(const JsonArray &arr)
Definition: fims_json.hpp:62
+
JsonValue::JsonValue
JsonValue(const std::string &str)
Definition: fims_json.hpp:53
+
JsonArray
std::vector< JsonValue > JsonArray
Definition: fims_json.hpp:24
+
JsonObject
std::map< std::string, JsonValue > JsonObject
Definition: fims_json.hpp:19
+
JsonValueType
JsonValueType
Definition: fims_json.hpp:29
+
Bool
@ Bool
Definition: fims_json.hpp:33
+
Object
@ Object
Definition: fims_json.hpp:34
+
Null
@ Null
Definition: fims_json.hpp:30
+
String
@ String
Definition: fims_json.hpp:32
+
Array
@ Array
Definition: fims_json.hpp:35
+
Number
@ Number
Definition: fims_json.hpp:31
diff --git a/docs/functions_func.html b/docs/functions_func.html index e456b4c..a5da32c 100644 --- a/docs/functions_func.html +++ b/docs/functions_func.html @@ -359,9 +359,6 @@

- r -

 CDoubleLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
 CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(fims$logistic_selectivity)
 Cfims_info::Information< Type >Stores FIMS model information and creates model. Contains all objects and data pre-model construction
 CJsonParserParses JSON strings and generates JSON values
 CJsonValueRepresents a JSON value
 CJsonParser
 CJsonValue
 Cfims_model::Model< Type >Model class. FIMS objective function
 CParameterRcppInterface class that defines the interface between R and C++ for parameter types
 Cfims_popdy::Subpopulation< Type >
std::vector< Type > expected_recruitment
 
int recruitment_id = -999
 recruitment More...
 
std::shared_ptr< RecruitmentBase< Type > > recruitment