Model test related methods
BiochemNetABC.change_simulation_stop_criteria
— Methodchange_simulation_stop_criteria(m::ContinuousTimeModel, isabsorbing_func::Symbol)
Change the simulation of the model m
by adding a stop criteria based on the function named isabsorbing_func::Symbol
. isabsorbing_func
must have the type signature isabsorbing_func(p::Vector{Float64}, x::Vector{Int})
where p
is the parameter vector of the model and x
a state (not an observed state) of the model.
BiochemNetABC.distribute_mean_value_lha
— Methoddistribute_mean_value_lha(sm::SynchronizedModel, sym_var::Symbol, nbr_stim::Int)
Distribute over workers the computation of the mean value of an LHA over nbr_sim
simulations of the model.
BiochemNetABC.draw!
— Methoddraw!(mat_p, pm)
Draw size(mat_p)[2]
(number of columns of mat_p
) parameters from the prior distribution defined in pm
and stores it in mat_p
.
BiochemNetABC.draw!
— Methoddraw!(vec_p, pm)
Draw a parameter from the prior distribution defined in pm and stores it in vec_p
.
BiochemNetABC.draw_model!
— Methoddraw_model!(pm::ParametricModel)
Draw a parameter from the prior disitribution defined in pm::ParametricModel
and save it in the model contained in pm
.
BiochemNetABC.prior_pdf!
— Methodprior_pdf(res_pdf, mat_p, pm)
Computes the density for each column of mat_p
of the prior distribution defined in pm
. Stores it in res_pdf
. (length(vec_res) == size(mat_p)[2]
)
BiochemNetABC.prior_pdf
— Methodprior_pdf(p_prior, pm)
Computes the density at p_prior
of the prior distribution defined in pm
.
BiochemNetABC.probability_var_value_lha
— Methoddistribute_var_value_lha(sm::SynchronizedModel, nbr_sim::Int, value = 0, sym_var = :d)
Compute the probability that the variable sym_var
is equal to value
of an LHA over nbr_sim
simulations of the model.
BiochemNetABC.simulate
— Methodsimulate(pm::ParametricModel, p_prior::AbstractVector{Float64})
Simulates the model contained in the parametric model pm
with the p_prior
parameters. It simulates the model by taking the parameters contained in get_proba_model(pm).p
and replace the 1D parameters pm.params with p_prior
.
BiochemNetABC.volatile_simulate
— Methodvolatile_simulate(pm::ParametricModel, p_prior::AbstractVector{Float64})
A volatile version of simulate(pm::ParametricModel, p_prior::AbstractVector{Float64})
. The model in pm
should be of type SynchronizedModel (typeof(pm.m) <: SynchronizedModel
). It returns S::StateLHA
, not a trajectory.
BiochemNetABC.volatile_simulate
— Methodvolatile_simulate(sm::SynchronizedModel; p, verbose)
Simulates a model synchronized with an automaton but does not store the values of the simulation in order to improve performance. It returns the last state of the simulation S::StateLHA
not a trajectory σ::SynchronizedTrajectory
.