Class ExpData¶
Defined in File edata.h
Class Documentation¶
-
class
amici
::
ExpData
¶ 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
:nztrue
:nmaxevent
:
-
ExpData
(int nytrue, int nztrue, int nmaxevent, std::vector<realtype> ts)¶ constructor that initializes timepoints from vectors
- Parameters
nytrue
: (dimension: scalar)nztrue
: (dimension: scalar)nmaxevent
: (dimension: scalar)ts
: (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
: (dimension: scalar)nztrue
: (dimension: scalar)nmaxevent
: (dimension: scalar)ts
: (dimension: nt)fixedParameters
: (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
: (dimension: scalar)nztrue
: (dimension: scalar)nmaxevent
: (dimension: scalar)ts
: (dimension: nt)observedData
: (dimension: nt x nytrue, row-major)observedDataStdDev
: (dimension: nt x nytrue, row-major)observedEvents
: (dimension: nmaxevent x nztrue, row-major)observedEventsStdDev
: (dimension: nmaxevent x nztrue, row-major)
-
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 resultssigma_y
: scalar standard deviations for all observablessigma_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 resultssigma_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
- Return
number of observables of the non-augmented model
-
int
nztrue
() const¶ number of event observables of the non-augmented model
- Return
number of event observables of the non-augmented model
-
int
nmaxevent
() const¶ maximal number of events to track
- Return
maximal number of events to track
-
int
nt
() const¶ number of timepoints
- Return
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
- Return
ExpData::ts
-
realtype
getTimepoint
(int it) const¶ get function that returns timepoint at index
- Return
timepoint timepoint at index
- Parameters
it
: timepoint 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
: oberved data index
-
bool
isSetObservedData
(int it, int iy) const¶ get function that checks whether data at specified indices has been set
- Return
boolean specifying if data was set
- Parameters
it
: time indexiy
: observable index
-
std::vector<realtype> const &
getObservedData
() const¶ get function that copies data from ExpData::observedData to output
- Return
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
- Return
pointer to observed data at index (dimension: nytrue)
- Parameters
it
: timepoint index
-
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
- Return
boolean specifying if standard deviation of data was set
- Parameters
it
: time indexiy
: observable index
-
std::vector<realtype> const &
getObservedDataStdDev
() const¶ get function that copies data from ExpData::observedDataStdDev to output
- Return
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
- Return
pointer to standard deviation of observed data at index
- Parameters
it
: timepoint 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
- Return
boolean specifying if data was set
- Parameters
ie
: event indexiz
: event observable index
-
std::vector<realtype> const &
getObservedEvents
() const¶ get function that copies data from ExpData::mz to output
- Return
observed event data
-
const realtype *
getObservedEventsPtr
(int ie) const¶ get function that returns a pointer to observed data at ieth occurrence
- Return
pointer to observed event data at ieth occurrence
- Parameters
ie
: event 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
- Return
boolean specifying if standard deviation of event data was set
- Parameters
ie
: event indexiz
: event observable index
Public Members
-
std::vector<realtype>
fixedParameters
¶ condition-specific fixed parameters of size Model::nk() or empty
-
std::vector<realtype>
fixedParametersPreequilibration
¶ condition-specific fixed parameters for pre-equilibration of size Model::nk() or empty. Overrides Solver::newton_preeq
-
std::vector<realtype>
fixedParametersPresimulation
¶ condition-specific fixed parameters for pre-simulation of size Model::nk() or empty.
-
std::vector<realtype>
parameters
¶ condition-specific parameters of size Model::np() or empty
-
std::vector<realtype>
sx0
¶ condition-specific initial condition sensitivities of size Model::nx() * Model::nplist(), Model::nx() * ExpData::plist.size(), if ExpData::plist is not empty, or empty
-
std::vector<ParameterScaling>
pscale
¶ condition-specific parameter scales of size Model::np()
-
std::vector<int>
plist
¶ condition-specific parameter list
-
realtype
t_presim
= 0¶ duration of pre-simulation if this is > 0, presimulation will be performed from (model->t0 - t_presim) to model->t0 using the fixedParameters in fixedParametersPresimulation
-
bool
reinitializeFixedParameterInitialStates
= false¶ flag indicating whether reinitialization of states depending on fixed parameters is activated
Protected Functions
-
void
applyDimensions
()¶ resizes observedData, observedDataStdDev, observedEvents and observedEventsStdDev
-
void
applyDataDimension
()¶ resizes observedData and observedDataStdDev
-
void
applyEventDimension
()¶ resizes observedEvents and observedEventsStdDev
-