MEIGOR: MEIGO - MEtaheuristics for bIoinformatics Global Optimization
Version 1.10.0

Global Optimization

Browse man pages Browse package API and functions Browse package files

AuthorJose Egea, David Henriques, Alexandre Fdez. Villaverde, Thomas Cokelaer
Bioconductor views SystemsBiology
Date of publicationNone
MaintainerJose Egea <josea.egea@upct.es>
LicenseGPL-3
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MEIGOR")

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 Source code
CeVNSR Man page Source code
MEIGO Man page Source code
MEIGOR-package Man page
accept_move Source code
add_chain Source code
all_pruned Source code
between_chain_variances Source code
calculate_hessian Source code
calculate_likelihood Source code
calculate_posterior Source code
calculate_prior Source code
check_chain_lengths Source code
cnolist Man page
convergence_criterion Source code
cur_params Man page Source code
dhc Man page Source code
essR Man page Source code
essR-package Man page
essR_multistart Man page Source code
estimate Source code
eucl_dist Man page Source code
generate_new_position Source code
get_mixed_accepts Source code
get_sample_position Source code
initialize Source code
initialize_and_pool Source code
ith_VNSR Man page Source code
ith_essR Man page Source code
maximum_likelihood Source code
maximum_posterior Source code
model Man page
nls_fobj Man page Source code
optim_fobj Man page Source code
parameter_variance_estimates Source code
paramsOpt Man page
pool_chains Source code
prune Source code
prune_all_chains Source code
reject_move Source code
run Source code
runBayesFit Man page Source code
rvnds_hamming Man page Source code
rvnds_local Man page Source code
solnp_eq Man page Source code
solnp_fobj Man page Source code
solnp_ineq Man page Source code
ssm_beyond Man page Source code
ssm_defaults Man page Source code
ssm_evalfc Man page Source code
ssm_isdif2 Man page Source code
ssm_localsolver Man page Source code
ssm_optset Man page Source code
ssm_penalty_function Man page Source code
ssm_round_int Man page Source code
test_between_chain_variances Source code
test_convergence_criterion Source code
test_parameter_variance_estimates Source code
test_within_chain_variances Source code
validate Source code
vns_defaults Man page Source code
vns_optset Man page Source code
within_chain_variances Source code

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
MEIGOR documentation built on May 20, 2017, 9:24 p.m.