Package: MEIGOR 1.47.0

Jose A. Egea

MEIGOR: MEIGOR - MEtaheuristics for bIoinformatics Global Optimization

MEIGOR provides a comprehensive environment for performing global optimization tasks in bioinformatics and systems biology. It leverages advanced metaheuristic algorithms to efficiently search the solution space and is specifically tailored to handle the complexity and high-dimensionality of biological datasets. This package supports various optimization routines and is integrated with Bioconductor's infrastructure for a seamless analysis workflow.

Authors:Jose A. Egea [aut, cre], David Henriques [aut], Alexandre Fdez. Villaverde [aut], Thomas Cokelaer [aut]

MEIGOR_1.47.0.tar.gz
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MEIGOR_1.47.0.tgz(r-4.6-any)MEIGOR_1.47.0.tgz(r-4.5-any)
MEIGOR_1.47.0.tar.gz(r-4.7-any)MEIGOR_1.47.0.tar.gz(r-4.6-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MEIGOR/json (API)

# Install 'MEIGOR' in R:

install.packages('MEIGOR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

cnolist - A CNOlist from CellNOptR paclage
cnolist - A CNOlist from CellNOptR paclage
cnolist - A CNOlist from CellNOptR paclage
cnolist_cellnopt - A CNOlist from CellNOptR paclage
model - A model from CellNoptR
model - A model from CellNoptR
model - A model from CellNoptR
model_cellnopt - A model from CellNoptR
paramsOpt - Optimal parameters for simulation with CNORode

On BioConductor:MEIGOR-1.47.0(bioc 3.24)MEIGOR-1.46.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

systemsbiology optimization software

4.08 score 60 scripts 1 mentions 8 exports 71 dependencies

Last updated from:ed43619a02. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	173
linux-devel-x86_64	NOTE	293
source / vignettes	OK	219
linux-release-x86_64	NOTE	269
macos-release-arm64	NOTE	124
macos-oldrel-arm64	NOTE	143
windows-devel	NOTE	170
windows-release	NOTE	161
windows-oldrel	NOTE	166
wasm-release	OK	177

Exports:CeSSR CeVNSR cur_params essR essR_multistart MEIGO runBayesFit rvnds_hamming

Dependencies:base64enc BH BiocGenerics bitops bslib cachem CellNOptR cli CNORode codetools cpp11 deSolve digest evaluate farver fastmap fontawesome fs future future.apply genalg generics ggplot2 globals glue graph gtable highr htmltools igraph isoband jquerylib jsonlite knitr labeling lattice lifecycle listenv magrittr Matrix memoise mime numDeriv parallelly pkgconfig R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RCurl Rgraphviz rlang rmarkdown Rsolnp S7 sass scales snow snowfall stringi stringr tinytex truncnorm vctrs viridisLite withr xfun XML yaml

MEIGOR: a software suite based on metaheuristics for global optimization in systems biology and bioinformatics

Rendered fromMEIGOR-vignette.Rmdusingknitr::rmarkdown

Last update: 2024-03-12
Started: 2024-03-12

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

Package: MEIGOR 1.47.0

MEIGOR: MEIGOR - MEtaheuristics for bIoinformatics Global Optimization

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