Class ExpData
Defined in File edata.h
Inheritance Relationships
Base Type
public amici::SimulationParameters
(Class SimulationParameters)
Class Documentation
-
class amici::ExpData : public amici::SimulationParameters
ExpData carries all information about experimental or condition-specific data.
Public Functions
-
ExpData() = default
default constructor
-
ExpData(int nytrue, int nztrue, int nmaxevent)
constructor that only initializes dimensions
- Parameters
nytrue – Number of observables
nztrue – Number of event outputs
nmaxevent – Maximal number of events to track
-
ExpData(int nytrue, int nztrue, int nmaxevent, std::vector<realtype> ts)
constructor that initializes timepoints from vectors
- Parameters
nytrue – Number of observables
nztrue – Number of event outputs
nmaxevent – Maximal number of events to track
ts – Timepoints (dimension: nt)
-
ExpData(int nytrue, int nztrue, int nmaxevent, std::vector<realtype> ts, std::vector<realtype> fixedParameters)
constructor that initializes timepoints and fixed parameters from vectors
- Parameters
nytrue – Number of observables
nztrue – Number of event outputs
nmaxevent – Maximal number of events to track
ts – Timepoints (dimension: nt)
fixedParameters – Model constants (dimension: nk)
-
ExpData(int nytrue, int nztrue, int nmaxevent, std::vector<realtype> ts, std::vector<realtype> const &observedData, std::vector<realtype> const &observedDataStdDev, std::vector<realtype> const &observedEvents, std::vector<realtype> const &observedEventsStdDev)
constructor that initializes timepoints and data from vectors
- Parameters
nytrue – Number of observables
nztrue – Number of event outputs
nmaxevent – Maximal number of events to track
ts – Timepoints (dimension: nt)
observedData – observed data (dimension: nt x nytrue, row-major)
observedDataStdDev – standard deviation of observed data (dimension: nt x nytrue, row-major)
observedEvents – observed events (dimension: nmaxevents x nztrue, row-major)
observedEventsStdDev – standard deviation of observed events/roots (dimension: nmaxevents x nztrue, row-major)
-
explicit ExpData(const Model &model)
constructor that initializes with Model
- Parameters
model – pointer to model specification object
-
ExpData(const ReturnData &rdata, realtype sigma_y, realtype sigma_z)
constructor that initializes with returnData, adds noise according to specified sigmas
- Parameters
rdata – return data pointer with stored simulation results
sigma_y – scalar standard deviations for all observables
sigma_z – scalar standard deviations for all event observables
-
ExpData(const ReturnData &rdata, std::vector<realtype> sigma_y, std::vector<realtype> sigma_z)
constructor that initializes with returnData, adds noise according to specified sigmas
- Parameters
rdata – return data pointer with stored simulation results
sigma_y – vector of standard deviations for observables (dimension: nytrue or nt x nytrue, row-major)
sigma_z – vector of standard deviations for event observables (dimension: nztrue or nmaxevent x nztrue, row-major)
-
~ExpData() = default
-
int nytrue() const
number of observables of the non-augmented model
- Returns
number of observables of the non-augmented model
-
int nztrue() const
number of event observables of the non-augmented model
- Returns
number of event observables of the non-augmented model
-
int nmaxevent() const
maximal number of events to track
- Returns
maximal number of events to track
-
int nt() const
number of timepoints
- Returns
number of timepoints
-
void setTimepoints(const std::vector<realtype> &ts)
Set function that copies data from input to ExpData::ts.
- Parameters
ts – timepoints
-
std::vector<realtype> const &getTimepoints() const
get function that copies data from ExpData::ts to output
- Returns
ExpData::ts
-
realtype getTimepoint(int it) const
get function that returns timepoint at index
- Parameters
it – timepoint index
- Returns
timepoint timepoint at index
-
void setObservedData(const std::vector<realtype> &observedData)
set function that copies data from input to ExpData::my
- Parameters
observedData – observed data (dimension: nt x nytrue, row-major)
-
void setObservedData(const std::vector<realtype> &observedData, int iy)
set function that copies observed data for specific observable
- Parameters
observedData – observed data (dimension: nt)
iy – observed data index
-
bool isSetObservedData(int it, int iy) const
get function that checks whether data at specified indices has been set
- Parameters
it – time index
iy – observable index
- Returns
boolean specifying if data was set
-
std::vector<realtype> const &getObservedData() const
get function that copies data from ExpData::observedData to output
- Returns
observed data (dimension: nt x nytrue, row-major)
-
const realtype *getObservedDataPtr(int it) const
get function that returns a pointer to observed data at index
- Parameters
it – timepoint index
- Returns
pointer to observed data at index (dimension: nytrue)
-
void setObservedDataStdDev(const std::vector<realtype> &observedDataStdDev)
set function that copies data from input to ExpData::observedDataStdDev
- Parameters
observedDataStdDev – standard deviation of observed data (dimension: nt x nytrue, row-major)
-
void setObservedDataStdDev(realtype stdDev)
set function that sets all ExpData::observedDataStdDev to the input value
- Parameters
stdDev – standard deviation (dimension: scalar)
-
void setObservedDataStdDev(const std::vector<realtype> &observedDataStdDev, int iy)
set function that copies standard deviation of observed data for specific observable
- Parameters
observedDataStdDev – standard deviation of observed data (dimension: nt)
iy – observed data index
-
void setObservedDataStdDev(realtype stdDev, int iy)
set function that sets all standard deviation of a specific observable to the input value
- Parameters
stdDev – standard deviation (dimension: scalar)
iy – observed data index
-
bool isSetObservedDataStdDev(int it, int iy) const
get function that checks whether standard deviation of data at specified indices has been set
- Parameters
it – time index
iy – observable index
- Returns
boolean specifying if standard deviation of data was set
-
std::vector<realtype> const &getObservedDataStdDev() const
get function that copies data from ExpData::observedDataStdDev to output
- Returns
standard deviation of observed data
-
const realtype *getObservedDataStdDevPtr(int it) const
get function that returns a pointer to standard deviation of observed data at index
- Parameters
it – timepoint index
- Returns
pointer to standard deviation of observed data at index
-
void setObservedEvents(const std::vector<realtype> &observedEvents)
set function that copies observed event data from input to ExpData::observedEvents
- Parameters
observedEvents – observed data (dimension: nmaxevent x nztrue, row-major)
-
void setObservedEvents(const std::vector<realtype> &observedEvents, int iz)
set function that copies observed event data for specific event observable
- Parameters
observedEvents – observed data (dimension: nmaxevent)
iz – observed event data index
-
bool isSetObservedEvents(int ie, int iz) const
get function that checks whether event data at specified indices has been set
- Parameters
ie – event index
iz – event observable index
- Returns
boolean specifying if data was set
-
std::vector<realtype> const &getObservedEvents() const
get function that copies data from ExpData::mz to output
- Returns
observed event data
-
const realtype *getObservedEventsPtr(int ie) const
get function that returns a pointer to observed data at ieth occurrence
- Parameters
ie – event occurrence
- Returns
pointer to observed event data at ieth occurrence
-
void setObservedEventsStdDev(const std::vector<realtype> &observedEventsStdDev)
set function that copies data from input to ExpData::observedEventsStdDev
- Parameters
observedEventsStdDev – standard deviation of observed event data
-
void setObservedEventsStdDev(realtype stdDev)
set function that sets all ExpData::observedDataStdDev to the input value
- Parameters
stdDev – standard deviation (dimension: scalar)
-
void setObservedEventsStdDev(const std::vector<realtype> &observedEventsStdDev, int iz)
set function that copies standard deviation of observed data for specific observable
- Parameters
observedEventsStdDev – standard deviation of observed data (dimension: nmaxevent)
iz – observed data index
-
void setObservedEventsStdDev(realtype stdDev, int iz)
set function that sets all standard deviation of a specific observable to the input value
- Parameters
stdDev – standard deviation (dimension: scalar)
iz – observed data index
-
bool isSetObservedEventsStdDev(int ie, int iz) const
get function that checks whether standard deviation of even data at specified indices has been set
- Parameters
ie – event index
iz – event observable index
- Returns
boolean specifying if standard deviation of event data was set
Public Members
-
std::string id
Arbitrary (not necessarily unique) identifier.
Protected Functions
-
void applyDimensions()
resizes observedData, observedDataStdDev, observedEvents and observedEventsStdDev
-
void applyDataDimension()
resizes observedData and observedDataStdDev
-
void applyEventDimension()
resizes observedEvents and observedEventsStdDev
-
ExpData() = default