MEIGOR: MEIGO - MEtaheuristics for bIoinformatics Global Optimization

Global Optimization

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MEIGOR")
AuthorJose Egea, David Henriques, Alexandre Fdez. Villaverde, Thomas Cokelaer
Bioconductor views SystemsBiology
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

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

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