MEIGOR: MEIGO - MEtaheuristics for bIoinformatics Global Optimization

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Global Optimization

Author
Jose Egea, David Henriques, Alexandre Fdez. Villaverde, Thomas Cokelaer
Date of publication
None
Maintainer
Jose Egea <josea.egea@upct.es>
License
GPL-3
Version
1.8.0

View on Bioconductor

Man pages

BayesFit
BayesFit
CeSSR
Global optimization algorithm for MINLPs based on Scatter...
CeVNSR
Global optimization algorithm for MINLPs based on VNS using a...
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...
essR-MEIGOR
Global optimization algorithm for MINLPs based on Scatter...
essR_multistart
Multistart function for eSS
eucl_dist
Computes the euclidean distance between the rows of two...
ith_essR
Auxiliary function to perform parallel runs
ith_VNSR
Auxiliary function to perform parallel runs
MEIGO
MEIGO main function
MEIGOR-package
Global optimization Toolbox
model
A model from CellNoptR
nls_fobj
Auxiliary function to evaluate constraints
optim_fobj
Gateway function to evaluate the objective function when the...
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_fobj
Gateway function to evaluate the objective function when...
solnp_ineq
Gateway function to evaluate the inequality constraints when...
ssm_beyond
Function that expands the search direction when a good...
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...
ssm_round_int
Rounds variables declared as integer of binary
vns_defaults
Default options for VNS
vns_optset
Set VNS options

Files in this package

MEIGOR/DESCRIPTION
MEIGOR/NAMESPACE
MEIGOR/R
MEIGOR/R/BayesFit-package.r
MEIGOR/R/CeSSR.R
MEIGOR/R/CeVNSR.R
MEIGOR/R/MEIGO.R
MEIGOR/R/accept_move.R
MEIGOR/R/calculate_hessian.R
MEIGOR/R/calculate_likelihood.R
MEIGOR/R/calculate_posterior.R
MEIGOR/R/calculate_prior.R
MEIGOR/R/convergence.R
MEIGOR/R/cur_params.R
MEIGOR/R/dhc.R
MEIGOR/R/essR.R
MEIGOR/R/essR_multistart.R
MEIGOR/R/estimate.R
MEIGOR/R/eucl_dist.R
MEIGOR/R/generate_new_position.R
MEIGOR/R/get_mixed_accepts.R
MEIGOR/R/initialize.R
MEIGOR/R/multichain.R
MEIGOR/R/nls_fobj.R
MEIGOR/R/optim_fobj.R
MEIGOR/R/prune.R
MEIGOR/R/reject_move.R
MEIGOR/R/run.R
MEIGOR/R/runBayesFit.R
MEIGOR/R/rvnds_hamming.R
MEIGOR/R/rvnds_local.R
MEIGOR/R/solnp_eq.R
MEIGOR/R/solnp_fobj.R
MEIGOR/R/solnp_ineq.R
MEIGOR/R/ssm_beyond.R
MEIGOR/R/ssm_defaults.R
MEIGOR/R/ssm_evalfc.R
MEIGOR/R/ssm_isdif2.R
MEIGOR/R/ssm_localsolver.R
MEIGOR/R/ssm_optset.R
MEIGOR/R/ssm_penalty_function.R
MEIGOR/R/ssm_round_int.R
MEIGOR/R/validate.R
MEIGOR/R/vns_defaults.R
MEIGOR/R/vns_optset.R
MEIGOR/build
MEIGOR/build/vignette.rds
MEIGOR/data
MEIGOR/data/CNORodeExample.RData
MEIGOR/data/CellNOptR_example.RData
MEIGOR/data/bayesFitExample.RData
MEIGOR/data/simpleExample.RData
MEIGOR/inst
MEIGOR/inst/NEWS
MEIGOR/inst/benchmarks
MEIGOR/inst/benchmarks/ex1.R
MEIGOR/inst/benchmarks/ex2.R
MEIGOR/inst/benchmarks/ex3.R
MEIGOR/inst/benchmarks/ex4.R
MEIGOR/inst/benchmarks/ex5.R
MEIGOR/inst/benchmarks/ex5_dynamics.R
MEIGOR/inst/benchmarks/f10.R
MEIGOR/inst/benchmarks/f17.R
MEIGOR/inst/benchmarks/f20.R
MEIGOR/inst/benchmarks/main_CeVNSR_example.R
MEIGOR/inst/benchmarks/main_ex1.R
MEIGOR/inst/benchmarks/main_ex2.R
MEIGOR/inst/benchmarks/main_ex3.R
MEIGOR/inst/benchmarks/main_ex4.R
MEIGOR/inst/benchmarks/main_ex5.R
MEIGOR/inst/benchmarks/main_ex5_Rsolnp.R
MEIGOR/inst/benchmarks/main_f10.R
MEIGOR/inst/benchmarks/main_f17.R
MEIGOR/inst/benchmarks/main_f20.R
MEIGOR/inst/benchmarks/main_multistart_ex3.R
MEIGOR/inst/benchmarks/main_rosen10_meigo.R
MEIGOR/inst/benchmarks/rosen10.R
MEIGOR/inst/doc
MEIGOR/inst/doc/MEIGOR-vignette.R
MEIGOR/inst/doc/MEIGOR-vignette.Rnw
MEIGOR/inst/doc/MEIGOR-vignette.pdf
MEIGOR/man
MEIGOR/man/BayesFit.Rd
MEIGOR/man/CeSSR.Rd
MEIGOR/man/CeVNSR.Rd
MEIGOR/man/MEIGO.Rd
MEIGOR/man/MEIGOR-package.Rd
MEIGOR/man/cnolist.Rd
MEIGOR/man/cur_params.Rd
MEIGOR/man/dhc.Rd
MEIGOR/man/essR-MEIGOR.Rd
MEIGOR/man/essR.Rd
MEIGOR/man/essR_multistart.Rd
MEIGOR/man/eucl_dist.Rd
MEIGOR/man/ith_VNSR.Rd
MEIGOR/man/ith_essR.Rd
MEIGOR/man/model.Rd
MEIGOR/man/nls_fobj.Rd
MEIGOR/man/optim_fobj.Rd
MEIGOR/man/paramsOpt.Rd
MEIGOR/man/runBayesFit.Rd
MEIGOR/man/rvnds_hamming.Rd
MEIGOR/man/rvnds_local.Rd
MEIGOR/man/solnp_eq.Rd
MEIGOR/man/solnp_fobj.Rd
MEIGOR/man/solnp_ineq.Rd
MEIGOR/man/ssm_beyond.Rd
MEIGOR/man/ssm_defaults.Rd
MEIGOR/man/ssm_evalfc.Rd
MEIGOR/man/ssm_isdif2.Rd
MEIGOR/man/ssm_localsolver.Rd
MEIGOR/man/ssm_optset.Rd
MEIGOR/man/ssm_penalty_function.Rd
MEIGOR/man/ssm_round_int.Rd
MEIGOR/man/vns_defaults.Rd
MEIGOR/man/vns_optset.Rd
MEIGOR/vignettes
MEIGOR/vignettes/MEIGOR-vignette.Rnw
MEIGOR/vignettes/MEIGO_refs.bib
MEIGOR/vignettes/logo_CSIC.eps
MEIGOR/vignettes/logo_EBI.eps
MEIGOR/vignettes/logo_UPCT.eps