MEIGO - MEtaheuristics for bIoinformatics Global Optimization


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Documentation for package ‘MEIGOR’ version 1.33.0

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BayesFit-package BayesFit
essR-package Global optimization algorithm for MINLPs based on Scatter Search
MEIGOR-package Global optimization Toolbox
BayesFit BayesFit
CeSSR Global optimization algorithm for MINLPs based on Scatter Search using a Cooperative Strategy
CeVNSR Global optimization algorithm for MINLPs based on VNS using a Cooperative Strategy
cnolist A CNOlist from CellNOptR paclage
cur_params Current values of all model parameters
dhc Local search algorithm within eSS
essR Global optimization algorithm for MINLPs based on Scatter Search
essR_multistart Multistart function for eSS
eucl_dist Computes the euclidean distance between the rows of two different matrices
ith_essR Auxiliary function to perform parallel runs
ith_VNSR Auxiliary function to perform parallel runs
MEIGO MEIGO main function
model A model from CellNoptR
nls_fobj Auxiliary function to evaluate constraints
optim_fobj Gateway function to evaluate the objective function when the local solvers are invoked.
paramsOpt Optimal parameters for simulation with CNORode
runBayesFit Running the BayesFit optimisation
rvnds_hamming Main VNS function
rvnds_local Local search in VNS
solnp_eq Gateway function to evaluate the equality constraints when solnp is invoked as local solver
solnp_fobj Gateway function to evaluate the objective function when solnp is invoked as local solver
solnp_ineq Gateway function to evaluate the inequality constraints when solnp is invoked as local solver
ssm_beyond Function that expands the search direction when a good offspring solution has been found
ssm_defaults Sets the default options for eSSR
ssm_evalfc Gateway function to evaluate the objective function in essR
ssm_isdif2 Calculates relative errors between two vectors
ssm_localsolver Configure local solver
ssm_optset Assigns values to the options defined by the user
ssm_penalty_function Calculates the penalized objective function in constrained problems
ssm_round_int Rounds variables declared as integer of binary
vns_defaults Default options for VNS
vns_optset Set VNS options