amici.amici.ReturnData

class amici.amici.ReturnData(*args)[source]

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

NOTE: multi-dimensional arrays are stored in row-major order (C-style)

__init__(*args)[source]

Overload 1:

Default constructor


Overload 2:

Constructor

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

\(\chi^2\) value

cpu_time

computation time of forward solve [ms]

cpu_timeB

computation time of backward solve [ms]

lbw

Lower bandwidth of the Jacobian

llh

log-likelihood 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

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 log-likelihood (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 log-likelihood (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)[source]

Overload 1:

Default constructor


Overload 2:

Constructor

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