amici.amici.ReturnData¶
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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)
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__init__
(*args)[source] Overload 1:
Default constructor
Overload 2:
Constructor
- Parameters
ts (DoubleVector) – see amici::SimulationParameters::ts
model_dimensions (
ModelDimensions
) – Model dimensionsnplist (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
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 dimensionsnplist (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
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