MEIGOR: MEIGO - MEtaheuristics for bIoinformatics Global Optimization

Global Optimization

AuthorJose Egea, David Henriques, Alexandre Fdez. Villaverde, Thomas Cokelaer
Date of publicationNone
MaintainerJose Egea <josea.egea@upct.es>
LicenseGPL-3
Version1.8.0

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

Functions

BayesFit Man page
BayesFit-package Man page
CeSSR Man page
CeVNSR Man page
cnolist Man page
cur_params Man page
dhc Man page
essR Man page
essR_multistart Man page
essR-package Man page
eucl_dist Man page
ith_essR Man page
ith_VNSR Man page
MEIGO Man page
MEIGOR-package Man page
model Man page
nls_fobj Man page
optim_fobj Man page
paramsOpt Man page
runBayesFit Man page
rvnds_hamming Man page
rvnds_local Man page
solnp_eq Man page
solnp_fobj Man page
solnp_ineq Man page
ssm_beyond Man page
ssm_defaults Man page
ssm_evalfc Man page
ssm_isdif2 Man page
ssm_localsolver Man page
ssm_optset Man page
ssm_penalty_function Man page
ssm_round_int Man page
vns_defaults Man page
vns_optset Man page

Files

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

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