amici.amici.ReturnData

class amici.amici.ReturnData(*args)

Stores all data to be returned by amici.amici.runAmiciSimulation().

NOTE: multidimensional arrays are stored in row-major order (FORTRAN-style)

__init__(*args)

Overload 1:

default constructor

Overload 2:

ReturnData

Parameters

• ts (DoubleVector) – see amici::SimulationParameters::ts

• model_dimensions (ModelDimensions) – Model dimensions

• nplist (int) – see amici::ModelDimensions::nplist

• nmaxevent (int) – see amici::ModelDimensions::nmaxevent

• nt (int) – see amici::ModelDimensions::nt

• newton_maxsteps (int) – see amici::Solver::newton_maxsteps

• pscale (ParameterScalingVector >) – see amici::SimulationParameters::pscale

• o2mode (int) – see amici::SimulationParameters::o2mode

• sensi (int) – see amici::Solver::sensi

• sensi_meth (int) – see amici::Solver::sensi_meth

• rdrm (int) – see amici::Solver::rdata_reporting

• quadratic_llh (boolean) – whether model defines a quadratic nllh and computing res, sres and FIM makes sense

Overload 3:

constructor that uses information from model and solver to appropriately initialize fields

Parameters

• solver (Solver) – solver instance

• model (Model) – model instance

Methods Summary

__init__(*args)

Overload 1:

Attributes

FIM	fisher information matrix (shape nplist x nplist, row-major)
J	Jacobian of differential equation right hand side (shape nx x nx, row-major)
chi2	chi2 value
cpu_time	computation time of forward solve [ms]
cpu_timeB	computation time of backward solve [ms]
lbw	Lower bandwidth of the Jacobian
llh	loglikelihood value
nJ	Dimension of the augmented objective function for 2nd order ASA
ndJydy	Number of nonzero elements in the \(derivative of\f$dJy\) (dimension nytrue)
ndwdp	Number of nonzero elements in the p derivative of the repeating elements
ndwdw	Number of nonzero elements in the w derivative of the repeating elements
ndwdx	Number of nonzero elements in the x derivative of the repeating elements
ndxdotdw	Number of nonzero elements in the \(derivative of \f$xdot\)
ne	Number of events
newton_maxsteps	maximal number of newton iterations for steady state calculation
nk	Number of constants
nmaxevent	maximal number of occurring events (for every event type)
nnz	Number of nonzero entries in Jacobian
np	Number of parameters
nplist	number of parameter for which sensitivities were requested
nt	number of considered timepoints
numerrtestfails	number of error test failures forward problem (shape nt)
numerrtestfailsB	number of error test failures backward problem (shape nt)
numnonlinsolvconvfails	number of linear solver convergence failures forward problem (shape nt)
numnonlinsolvconvfailsB	number of linear solver convergence failures backward problem (shape nt)
numrhsevals	number of right hand side evaluations forward problem (shape nt)
numrhsevalsB	number of right hand side evaluations backward problem (shape nt)
numsteps	number of integration steps forward problem (shape nt)
numstepsB	number of integration steps backward problem (shape nt)
nw	Number of common expressions
nx	number of states (alias nx_rdata, kept for backward compatibility)
nx_rdata	Number of states
nx_solver	Number of states with conservation laws applied
nx_solver_reinit	Number of solver states subject to reinitialization
nxtrue	number of states in the unaugmented system (alias nxtrue_rdata, kept for backward compatibility)
nxtrue_rdata	Number of states in the unaugmented system
nxtrue_solver	Number of states in the unaugmented system with conservation laws applied
ny	Number of observables
nytrue	Number of observables in the unaugmented system
nz	Number of event outputs
nztrue	Number of event outputs in the unaugmented system
o2mode	flag indicating whether second order sensitivities were requested
order	employed order forward problem (shape nt)
posteq_cpu_time	computation time of the steady state solver [ms] (postequilibration)
posteq_cpu_timeB	computation time of the steady state solver of the backward problem [ms] (postequilibration)
posteq_numlinsteps	number of linear steps by Newton step for steady state problem.
posteq_numsteps	number of Newton steps for steady state problem (preequilibration) [newton, simulation, newton] (shape 3) (postequilibration)
posteq_numstepsB	number of simulation steps for adjoint steady state problem (postequilibration) [== 0 if analytical solution worked, > 0 otherwise]
posteq_status	flags indicating success of steady state solver (postequilibration)
posteq_t	time when steadystate was reached via simulation (postequilibration)
posteq_wrms	weighted root-mean-square of the rhs when steadystate was reached (postequilibration)
preeq_cpu_time	computation time of the steady state solver [ms] (preequilibration)
preeq_cpu_timeB	computation time of the steady state solver of the backward problem [ms] (preequilibration)
preeq_numlinsteps	number of linear steps by Newton step for steady state problem.
preeq_numsteps	number of Newton steps for steady state problem (preequilibration) [newton, simulation, newton] (length = 3)
preeq_numstepsB	number of simulation steps for adjoint steady state problem (preequilibration) [== 0 if analytical solution worked, > 0 otherwise]
preeq_status	flags indicating success of steady state solver (preequilibration)
preeq_t	time when steadystate was reached via simulation (preequilibration)
preeq_wrms	weighted root-mean-square of the rhs when steadystate was reached (preequilibration)
pscale	scaling of parameterization (lin,log,log10)
rdata_reporting	reporting mode
res	observable (shape nt*ny, row-major)
rz	event trigger output (shape nmaxevent x nz, row-major)
s2llh	second order parameter derivative of loglikelihood (shape nJ-1 x nplist, row-major)
s2rz	second order parameter derivative of event trigger output (shape nmaxevent x nztrue x nplist x nplist, row-major)
sensi	sensitivity order
sensi_meth	sensitivity method
sigmay	observable standard deviation (shape nt x ny, row-major)
sigmaz	event output sigma standard deviation (shape nmaxevent x nz, row-major)
sllh	parameter derivative of loglikelihood (shape nplist)
sres	parameter derivative of residual (shape nt*ny x nplist, row-major)
srz	parameter derivative of event trigger output (shape nmaxevent x nz x nplist, row-major)
ssigmay	parameter derivative of observable standard deviation (shape nt x nplist x ny, row-major)
ssigmaz	parameter derivative of event output standard deviation (shape nmaxevent x nz, row-major)
status	status code
sx	parameter derivative of state (shape nt x nplist x nx, row-major)
sx0	initial sensitivities (shape nplist x nx, row-major)
sx_ss	preequilibration sensitivities found by Newton solver (shape nplist x nx, row-major)
sy	parameter derivative of observable (shape nt x nplist x ny, row-major)
sz	parameter derivative of event output (shape nmaxevent x nz, row-major)
ts	timepoints (shape nt)
ubw	Upper bandwidth of the Jacobian
w	w data from the model (recurring terms in xdot, for imported SBML models from python, this contains the flux vector) (shape nt x nw, row major)
x	state (shape nt x nx, row-major)
x0	initial state (shape nx)
x_ss	preequilibration steady state found by Newton solver (shape nx)
xdot	time derivative (shape nx)
y	observable (shape nt x ny, row-major)
z	event output (shape nmaxevent x nz, row-major)

Methods

__init__(*args)

Overload 1:

default constructor

Overload 2:

ReturnData

Parameters

• ts (DoubleVector) – see amici::SimulationParameters::ts

• model_dimensions (ModelDimensions) – Model dimensions

• nplist (int) – see amici::ModelDimensions::nplist

• nmaxevent (int) – see amici::ModelDimensions::nmaxevent

• nt (int) – see amici::ModelDimensions::nt

• newton_maxsteps (int) – see amici::Solver::newton_maxsteps

• pscale (ParameterScalingVector >) – see amici::SimulationParameters::pscale

• o2mode (int) – see amici::SimulationParameters::o2mode

• sensi (int) – see amici::Solver::sensi

• sensi_meth (int) – see amici::Solver::sensi_meth

• rdrm (int) – see amici::Solver::rdata_reporting

• quadratic_llh (boolean) – whether model defines a quadratic nllh and computing res, sres and FIM makes sense

Overload 3:

constructor that uses information from model and solver to appropriately initialize fields

Parameters

• solver (Solver) – solver instance

• model (Model) – model instance