Efficient Constrained Based Modelling

---

Documentation for package ‘sybil’ version 2.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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A B C D E F G H I L M N O P R S T U V W Y misc

sybil-package

sybil - Efficient Constrained Based Modelling in R

-- A --

addAlgorithm	Add a New Algorithm Name to sybil
addCols	Add Columns to an Optimization Problem
addCols-method	Add Columns to an Optimization Problem
addCols-methods	Add Columns to an Optimization Problem
addColsToProb	Add New Columns (Variables) to an Optimization Problem
addColsToProb-method	Add New Columns (Variables) to an Optimization Problem
addColsToProb-methods	Add New Columns (Variables) to an Optimization Problem
addExchReact	Add Exchange Reactions to a Model
addReact	Add/Change Reactions in a Model
addReact-method	Add/Change Reactions in a Model
addRows	Add Rows to an Optimization Problem
addRows-method	Add Rows to an Optimization Problem
addRows-methods	Add Rows to an Optimization Problem
addRowsCols	Add Rows and Columns to an Optimization Problem
addRowsCols-method	Add Rows and Columns to an Optimization Problem
addRowsCols-methods	Add Rows and Columns to an Optimization Problem
addRowsToProb	Add New Rows (Constraints) to an Optimization Problem
addRowsToProb-method	Add New Rows (Constraints) to an Optimization Problem
addRowsToProb-methods	Add New Rows (Constraints) to an Optimization Problem
addSolver	Add a New Mathematical Programming Solver to sybil
ALGORITHM	Set and Get sybil Parameters
algorithm	Class optsol
algorithm-method	Class optsol
algorithm-method	Class '"sysBiolAlg"'
algorithm<-	Class optsol
algorithm<--method	Class optsol
algorithm<--method	Class '"sysBiolAlg"'
alg_par	Class '"sysBiolAlg"'
alg_par-method	Class optsol
alg_par-method	Class '"sysBiolAlg"'
alg_par<-	Class '"sysBiolAlg"'
alg_par<--method	Class optsol
alg_par<--method	Class '"sysBiolAlg"'
allGenes	Structure of Class "modelorg"
allGenes-method	Structure of Class "modelorg"
allGenes<-	Structure of Class "modelorg"
allGenes<--method	Structure of Class "modelorg"
applyChanges	Generic Function to Apply Changes to Objects of Class sysBiolAlg
applyChanges-method	Generic Function to Apply Changes to Objects of Class sysBiolAlg
applyChanges-methods	Generic Function to Apply Changes to Objects of Class sysBiolAlg

-- B --

backupProb	Copies a Problem Object to a New Problem Object
backupProb-method	Copies a Problem Object to a New Problem Object
backupProb-methods	Copies a Problem Object to a New Problem Object
blocked	Class '"optsol_blockedReact"'
blocked-method	Class '"optsol_blockedReact"'
blocked<-	Class '"optsol_blockedReact"'
blocked<--method	Class '"optsol_blockedReact"'
blockedReact	Find Blocked Reactions in a Metabolic Network
blReact	Class '"optsol_fluxVar"'
blReact-method	Class '"optsol_fluxVar"'

-- C --

changeBounds	Change Variable Bounds in a Metabolic Network
changeColsBnds	Change Column (Variable) Bounds in the Optimization Problem
changeColsBnds-method	Change Column (Variable) Bounds in the Optimization Problem
changeColsBnds-methods	Change Column (Variable) Bounds in the Optimization Problem
changeColsBndsObjCoefs	Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem
changeColsBndsObjCoefs-method	Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem
changeColsBndsObjCoefs-methods	Change Column (Variable) Bounds and Objective Coefficients in the Optimization Problem
changeGPR	Check and Change the GPR Rules
changeMatrixRow	Change a Row in the Constraint Matrix of the Optimization Problem
changeMatrixRow-method	Change a Row in the Constraint Matrix of the Optimization Problem
changeMatrixRow-methods	Change a Row in the Constraint Matrix of the Optimization Problem
changeMaxObj	Class '"sysBiolAlg_mtf"'
changeMaxObj-method	Class '"sysBiolAlg_mtf"'
changeObjCoefs	Change Column (Variable) Objective Coefficients in the Optimization Problem
changeObjCoefs-method	Change Column (Variable) Objective Coefficients in the Optimization Problem
changeObjCoefs-methods	Change Column (Variable) Objective Coefficients in the Optimization Problem
changeObjFunc	Sets/changes the Objective Function
changeRowsBnds	Change Row Bounds in the Optimization Problem
changeRowsBnds-method	Change Row Bounds in the Optimization Problem
changeRowsBnds-methods	Change Row Bounds in the Optimization Problem
changeUptake	Change Uptake Reactions
changeUptake-method	Change Uptake Reactions
changeUptake-methods	Change Uptake Reactions
checkAlgorithm	Check Algorithm
checkDefaultMethod	Validate Solver and Method
checkOptSol	Summarized Information About an Object of Class Optsol
checkOptSol-method	Summarized Information About an Object of Class Optsol
checkOptSol-methods	Summarized Information About an Object of Class Optsol
checkReactId	Check if a Reaction Id is Valid
checksol	Structure of the Class "checksol"
checksol-class	Structure of the Class "checksol"
checkSolStat	Class '"optObj"'
checkStat	Class optsol
checkStat-method	Class optsol
checkVersion	checks Version of modelorg
checkVersion,modelorg	checks Version of modelorg
checkVersion-method	checks Version of modelorg
checkVersion-methods	checks Version of modelorg
chlb	Class '"optsol_fluxdel"'
chlb-method	Class '"optsol_fluxdel"'
chlb<-	Class '"optsol_fluxdel"'
chlb<--method	Class '"optsol_fluxdel"'
chub	Class '"optsol_fluxdel"'
chub-method	Class '"optsol_fluxdel"'
chub<-	Class '"optsol_fluxdel"'
chub<--method	Class '"optsol_fluxdel"'
clpPtr-class	Class '"optObj"'
cmd	Class '"ppProc"'
cmd-method	Class '"ppProc"'
cmd<-	Class '"ppProc"'
cmd<--method	Class '"ppProc"'
comp_attr	Structure of Class "modelorg"
comp_attr-method	Structure of Class "modelorg"
comp_attr<-	Structure of Class "modelorg"
comp_attr<--method	Structure of Class "modelorg"
cplexPointer-class	Class '"optObj"'
cplexPtr-class	Class '"optObj"'
ctrlfl	Class '"optsol_robAna"'
ctrlfl-method	Class '"optsol_phpp"'
ctrlfl-method	Class '"optsol_robAna"'
ctrlfl<-	Class '"optsol_robAna"'
ctrlfl<--method	Class '"optsol_phpp"'
ctrlfl<--method	Class '"optsol_robAna"'
ctrlr	Class '"optsol_robAna"'
ctrlr-method	Class '"optsol_robAna"'
ctrlr<-	Class '"optsol_robAna"'
ctrlr<--method	Class '"optsol_robAna"'

-- D --

deadEndMetabolites	Identify Dead End Metabolites
deadEndMetabolites-method	Identify Dead End Metabolites
deadEndMetabolites-methods	Identify Dead End Metabolites
deleted	Class '"optsol_fluxdel"'
deleted-method	Class '"optsol_fluxdel"'
deleted-method	Class '"optsol_genedel"'
delProb	Free Memory Associated to the Pointer to the Problem Object
delProb-method	Free Memory Associated to the Pointer to the Problem Object
delProb-methods	Free Memory Associated to the Pointer to the Problem Object
dels	Class '"optsol_fluxdel"'
dels-method	Class '"optsol_fluxdel"'
dels<-	Class '"optsol_fluxdel"'
dels<--method	Class '"optsol_fluxdel"'
didFoot	Class '"sybilLog"'
didFoot-method	Class '"sybilLog"'
didFoot<-	Class '"sybilLog"'
didFoot<--method	Class '"sybilLog"'
dim-method	Structure of Class "modelorg"
dim-method	Class '"optObj"'
doubleFluxDel	Double Flux Deletion Experiment
doubleGeneDel	Double Gene Deletion Experiment
doubleReact	Identifies Identical Reactions

-- E --

EasyConstraint	Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
Ec_core	Escherichia coli Core Metabolic Model
editEnvir	Environment Editor for Metabolic Networks
emsg	Class '"sybilError"'
emsg-method	Class '"sybilError"'
emsg<-	Class '"sybilError"'
emsg<--method	Class '"sybilError"'
enum	Class '"sybilError"'
enum-method	Class '"sybilError"'
enum<-	Class '"sybilError"'
enum<--method	Class '"sybilError"'
exit_code	Structure of the Class "checksol"
exit_code-method	Structure of the Class "checksol"
exit_code<-	Structure of the Class "checksol"
exit_code<--method	Structure of the Class "checksol"
exit_meaning	Structure of the Class "checksol"
exit_meaning-method	Structure of the Class "checksol"
exit_meaning<-	Structure of the Class "checksol"
exit_meaning<--method	Structure of the Class "checksol"
exit_num	Structure of the Class "checksol"
exit_num-method	Structure of the Class "checksol"
exit_num<-	Structure of the Class "checksol"
exit_num<--method	Structure of the Class "checksol"
ex_met	Class '"summaryOptsol"'
ex_met-method	Class '"summaryOptsol"'
ex_val	Class '"summaryOptsol"'
ex_val-method	Class '"summaryOptsol"'

-- F --

fba	Class '"sysBiolAlg_fba"'
fbaEasyConstraint	Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
fenc	Class '"sybilLog"'
fenc-method	Class '"sybilLog"'
fenc<-	Class '"sybilLog"'
fenc<--method	Class '"sybilLog"'
fh	Class '"sybilLog"'
fh-method	Class '"sybilLog"'
fh<-	Class '"sybilLog"'
fh<--method	Class '"sybilLog"'
file-class	Class '"sybilLog"'
findExchReact	Find Exchange Reactions
fldind	Class optsol
fldind-method	Class optsol
fldind-method	Class '"sysBiolAlg"'
fldind<-	Class optsol
fldind<--method	Class optsol
fldind<--method	Class '"sysBiolAlg"'
fluxdels	Class '"optsol_genedel"'
fluxdels-method	Class '"optsol_genedel"'
fluxdels<-	Class '"optsol_genedel"'
fluxdels<--method	Class '"optsol_genedel"'
fluxdist	Class optsol
fluxdist-method	Class optsol
fluxdist<-	Class optsol
fluxdist<--method	Class optsol
fluxDistribution	Class '"fluxDistribution"'
fluxDistribution-class	Class '"fluxDistribution"'
fluxes	Class optsol
fluxes-method	Class '"fluxDistribution"'
fluxes-method	Class optsol
fluxes<-	Class optsol
fluxes<--method	Class '"fluxDistribution"'
fluxes<--method	Class optsol
fluxVar	Flux Variability Analysis
fname	Class '"sybilLog"'
fname-method	Class '"sybilLog"'
fname<-	Class '"sybilLog"'
fname<--method	Class '"sybilLog"'
fpath	Class '"sybilLog"'
fpath-method	Class '"sybilLog"'
fpath<-	Class '"sybilLog"'
fpath<--method	Class '"sybilLog"'
fv	Class '"sysBiolAlg_fv"'

-- G --

geneDel	Get Gene-Reaction Association
geneDeletion	Gene Deletion Experiments
genes	Structure of Class "modelorg"
genes-method	Structure of Class "modelorg"
genes<-	Structure of Class "modelorg"
genes<--method	Structure of Class "modelorg"
getColPrim	Get Primal Value of Variables After Optimization
getColPrim-method	Get Primal Value of Variables After Optimization
getColPrim-methods	Get Primal Value of Variables After Optimization
getColsLowBnds	Get Lower Bounds of the Columns (Variables) of the Optimization Problem
getColsLowBnds-method	Get Lower Bounds of the Columns (Variables) of the Optimization Problem
getColsLowBnds-methods	Get Lower Bounds of the Columns (Variables) of the Optimization Problem
getColsNames	Retrieve Variable Names
getColsNames-method	Retrieve Variable Names
getColsNames-methods	Retrieve Variable Names
getColsUppBnds	Get Upper Bounds of the Columns (Variables) of the Optimization Problem
getColsUppBnds-method	Get Upper Bounds of the Columns (Variables) of the Optimization Problem
getColsUppBnds-methods	Get Upper Bounds of the Columns (Variables) of the Optimization Problem
getFluxDist	Retrieve Flux Distribution
getFluxDist-method	Retrieve Flux Distribution
getFluxDist-methods	Retrieve Flux Distribution
getMeanReturn	Class '"optObj"'
getMeanStatus	Class '"optObj"'
getNetFlux	Class '"netFlux"'
getNumCols	Get Number of Columns (Variables) of the Optimization Problem
getNumCols-method	Get Number of Columns (Variables) of the Optimization Problem
getNumCols-methods	Get Number of Columns (Variables) of the Optimization Problem
getNumNnz	Retrieve the Number of Non-Zero Elements of the Constraint Matrix
getNumNnz-method	Retrieve the Number of Non-Zero Elements of the Constraint Matrix
getNumNnz-methods	Retrieve the Number of Non-Zero Elements of the Constraint Matrix
getNumRows	Get Number of Rows (Constraints) of the Optimization Problem
getNumRows-method	Get Number of Rows (Constraints) of the Optimization Problem
getNumRows-methods	Get Number of Rows (Constraints) of the Optimization Problem
getObjCoefs	Get Objective Coefficients of the Optimization Problem
getObjCoefs-method	Get Objective Coefficients of the Optimization Problem
getObjCoefs-methods	Get Objective Coefficients of the Optimization Problem
getObjDir	Get Direction of Optimization.
getObjDir-method	Get Direction of Optimization.
getObjDir-methods	Get Direction of Optimization.
getObjVal	Get Value of the Objective Function After Optimization
getObjVal-method	Get Value of the Objective Function After Optimization
getObjVal-methods	Get Value of the Objective Function After Optimization
getReaction	Functions to subset and merge modelorg objects.
getReaction-method	Functions to subset and merge modelorg objects.
getRedCosts	Get Reduced Costs of all Variables After Optimization
getRedCosts-method	Get Reduced Costs of all Variables After Optimization
getRedCosts-method	Class '"optsol_phpp"'
getRedCosts-methods	Get Reduced Costs of all Variables After Optimization
getRowsLowBnds	Get Lower Bounds of the Rows (Constraints) of the Optimization Problem
getRowsLowBnds-method	Get Lower Bounds of the Rows (Constraints) of the Optimization Problem
getRowsLowBnds-methods	Get Lower Bounds of the Rows (Constraints) of the Optimization Problem
getRowsNames	Retrieve Constraint Names
getRowsNames-method	Retrieve Constraint Names
getRowsNames-methods	Retrieve Constraint Names
getRowsUppBnds	Get Upper Bounds of the Rows (Constraints) of the Optimization Problem
getRowsUppBnds-method	Get Upper Bounds of the Rows (Constraints) of the Optimization Problem
getRowsUppBnds-methods	Get Upper Bounds of the Rows (Constraints) of the Optimization Problem
getSolStat	Get Solution Status After Optimization
getSolStat-method	Get Solution Status After Optimization
getSolStat-methods	Get Solution Status After Optimization
getSolverParm	Retrieve Current Parameter Settings Used By The Optimization Software
getSolverParm-method	Retrieve Current Parameter Settings Used By The Optimization Software
getSolverParm-methods	Retrieve Current Parameter Settings Used By The Optimization Software
getsybilenv	Print sybil Environment
glpkPtr-class	Class '"optObj"'
gpr	Structure of Class "modelorg"
gpr-method	Structure of Class "modelorg"
gpr<-	Structure of Class "modelorg"
gpr<--method	Structure of Class "modelorg"
gprRule	Structure of Class "modelorg"
gprRule-method	Structure of Class "modelorg"
gprRule<-	Structure of Class "modelorg"
gprRule<--method	Structure of Class "modelorg"
gprRules	Structure of Class "modelorg"
gprRules-method	Structure of Class "modelorg"
gprRules<-	Structure of Class "modelorg"
gprRules<--method	Structure of Class "modelorg"

-- H --

hasEffect	Class '"optsol_genedel"'
hasEffect-method	Class '"optsol_genedel"'
hasEffect<-	Class '"optsol_genedel"'
hasEffect<--method	Class '"optsol_genedel"'

-- I --

image-method	Class '"summaryOptsol"'
ind	Class '"ppProc"'
ind-method	Class '"ppProc"'
ind<-	Class '"ppProc"'
ind<--method	Class '"ppProc"'
initProb	Initialize Problem Object
initProb-method	Initialize Problem Object
initProb-methods	Initialize Problem Object
irrev	Class for Metabolic Networks in Irreversible Format.
irrev-method	Class for Metabolic Networks in Irreversible Format.
irrev2rev	Class for Metabolic Networks in Irreversible Format.
irrev2rev-method	Class for Metabolic Networks in Irreversible Format.
irrev2rev<-	Class for Metabolic Networks in Irreversible Format.
irrev2rev<--method	Class for Metabolic Networks in Irreversible Format.
irrev<-	Class for Metabolic Networks in Irreversible Format.
irrev<--method	Class for Metabolic Networks in Irreversible Format.

-- L --

length-method	Class '"netFlux"'
length-method	Class optsol
length-method	Structure of Class "reactId"
lethal	Class '"optsol_fluxdel"'
lethal-method	Class '"optsol_fluxdel"'
lmoma	Class '"sysBiolAlg_lmoma"'
loadLPprob	Load Data to Optimization Problem
loadLPprob-method	Load Data to Optimization Problem
loadLPprob-methods	Load Data to Optimization Problem
loadMatrixPerColumnLPSOLVE	Class '"optObj_lpSolveAPI"'
loadQobj	Load Quadratic Part of the Objective Function to the Optimization Problem
loadQobj-method	Load Quadratic Part of the Objective Function to the Optimization Problem
loadQobj-methods	Load Quadratic Part of the Objective Function to the Optimization Problem
logCall	Class '"sybilLog"'
logCall-method	Class '"sybilLog"'
logClose<-	Class '"sybilLog"'
logClose<--method	Class '"sybilLog"'
logComment	Class '"sybilLog"'
logComment-method	Class '"sybilLog"'
logError	Class '"sybilLog"'
logError-method	Class '"sybilLog"'
logFH	Class '"sybilLog"'
logFH-method	Class '"sybilLog"'
logFileFH	Class '"sybilLog"'
logFoot<-	Class '"sybilLog"'
logFoot<--method	Class '"sybilLog"'
logHead	Class '"sybilLog"'
logHead-method	Class '"sybilLog"'
loglevel	Class '"sybilLog"'
loglevel-method	Class '"sybilLog"'
loglevel<-	Class '"sybilLog"'
loglevel<--method	Class '"sybilLog"'
logMessage	Class '"sybilLog"'
logMessage-method	Class '"sybilLog"'
logOptimization	Class '"sybilLog"'
logOptimization-method	Class '"sybilLog"'
logOptimizationTH	Class '"sybilLog"'
logOptimizationTH-method	Class '"sybilLog"'
logStep<-	Class '"sybilLog"'
logStep<--method	Class '"sybilLog"'
logWarning	Class '"sybilLog"'
logWarning-method	Class '"sybilLog"'
lowbnd	Structure of Class "modelorg"
lowbnd-method	Structure of Class "modelorg"
lowbnd-method	Class '"reactId_Exch"'
lowbnd<-	Structure of Class "modelorg"
lowbnd<--method	Structure of Class "modelorg"
lowbnd<--method	Class '"reactId_Exch"'
lpExtPtr-class	Class '"optObj"'
lp_dir	Class optsol
lp_dir-method	Class optsol
lp_dir<-	Class optsol
lp_dir<--method	Class optsol
lp_num_cols	Class optsol
lp_num_cols-method	Class optsol
lp_num_cols<-	Class optsol
lp_num_cols<--method	Class optsol
lp_num_rows	Class optsol
lp_num_rows-method	Class optsol
lp_num_rows<-	Class optsol
lp_num_rows<--method	Class optsol
lp_obj	Class optsol
lp_obj-method	Class optsol
lp_obj<-	Class optsol
lp_obj<--method	Class optsol
lp_ok	Class optsol
lp_ok-method	Class optsol
lp_ok<-	Class optsol
lp_ok<--method	Class optsol
lp_stat	Class optsol
lp_stat-method	Class optsol
lp_stat<-	Class optsol
lp_stat<--method	Class optsol
lstname	Class '"sybilLog"'
lstname-method	Class '"sybilLog"'

-- M --

makeOptsolMO	Constructor Function for Objects of Class 'optsol_optimizeProb'.
matchrev	Class for Metabolic Networks in Irreversible Format.
matchrev-method	Class for Metabolic Networks in Irreversible Format.
matchrev<-	Class for Metabolic Networks in Irreversible Format.
matchrev<--method	Class for Metabolic Networks in Irreversible Format.
MAXIMUM	Set and Get sybil Parameters
maxSol	Class '"optsol_blockedReact"'
maxSol-method	Class '"optsol_blockedReact"'
maxSol-method	Class '"optsol_fluxVar"'
mergeReact2Modelorg	Functions to subset and merge modelorg objects.
METHOD	Set and Get sybil Parameters
method	Class optsol
method-method	Class '"optObj"'
method-method	Class optsol
method<-	Class optsol
method<--method	Class optsol
met_attr	Structure of Class "modelorg"
met_attr-method	Structure of Class "modelorg"
met_attr<-	Structure of Class "modelorg"
met_attr<--method	Structure of Class "modelorg"
met_comp	Structure of Class "modelorg"
met_comp-method	Structure of Class "modelorg"
met_comp<-	Structure of Class "modelorg"
met_comp<--method	Structure of Class "modelorg"
met_de	Structure of Class "modelorg"
met_de-method	Structure of Class "modelorg"
met_de<-	Structure of Class "modelorg"
met_de<--method	Structure of Class "modelorg"
met_id	Structure of Class "modelorg"
met_id-method	Structure of Class "modelorg"
met_id-method	Class '"reactId_Exch"'
met_id<-	Structure of Class "modelorg"
met_id<--method	Structure of Class "modelorg"
met_id<--method	Class '"reactId_Exch"'
met_name	Structure of Class "modelorg"
met_name-method	Structure of Class "modelorg"
met_name<-	Structure of Class "modelorg"
met_name<--method	Structure of Class "modelorg"
met_num	Structure of Class "modelorg"
met_num-method	Structure of Class "modelorg"
met_num<-	Structure of Class "modelorg"
met_num<--method	Structure of Class "modelorg"
met_pos	Class '"reactId_Exch"'
met_pos-method	Class '"reactId_Exch"'
met_pos<-	Class '"reactId_Exch"'
met_pos<--method	Class '"reactId_Exch"'
met_single	Structure of Class "modelorg"
met_single-method	Structure of Class "modelorg"
met_single<-	Structure of Class "modelorg"
met_single<--method	Structure of Class "modelorg"
minSol	Class '"optsol_blockedReact"'
minSol-method	Class '"optsol_blockedReact"'
minSol-method	Class '"optsol_fluxVar"'
mod2irrev	Produces a Model in Irreversible Format
modelorg	Structure of Class "modelorg"
modelorg-class	Structure of Class "modelorg"
modelorg2ExPA	Write an Instance of Class modelorg to File in ExPA Format
modelorg2tsv	Write an Instance of Class modelorg to File
modelorg_irrev	Class for Metabolic Networks in Irreversible Format.
modelorg_irrev-class	Class for Metabolic Networks in Irreversible Format.
mod_attr	Structure of Class "modelorg"
mod_attr-method	Structure of Class "modelorg"
mod_attr<-	Structure of Class "modelorg"
mod_attr<--method	Structure of Class "modelorg"
mod_compart	Structure of Class "modelorg"
mod_compart-method	Structure of Class "modelorg"
mod_compart<-	Structure of Class "modelorg"
mod_compart<--method	Structure of Class "modelorg"
mod_desc	Structure of Class "modelorg"
mod_desc-method	Structure of Class "modelorg"
mod_desc<-	Structure of Class "modelorg"
mod_desc<--method	Structure of Class "modelorg"
mod_id	Structure of Class "modelorg"
mod_id-method	Structure of Class "modelorg"
mod_id-method	Class optsol
mod_id-method	Structure of Class "reactId"
mod_id-method	Class '"summaryOptsol"'
mod_id<-	Structure of Class "modelorg"
mod_id<--method	Structure of Class "modelorg"
mod_id<--method	Class optsol
mod_id<--method	Structure of Class "reactId"
mod_id<--method	Class '"summaryOptsol"'
mod_key	Structure of Class "modelorg"
mod_key-method	Structure of Class "modelorg"
mod_key-method	Class optsol
mod_key-method	Structure of Class "reactId"
mod_key-method	Class '"summaryOptsol"'
mod_key<-	Structure of Class "modelorg"
mod_key<--method	Structure of Class "modelorg"
mod_key<--method	Class optsol
mod_key<--method	Structure of Class "reactId"
mod_key<--method	Class '"summaryOptsol"'
mod_name	Structure of Class "modelorg"
mod_name-method	Structure of Class "modelorg"
mod_name<-	Structure of Class "modelorg"
mod_name<--method	Structure of Class "modelorg"
mod_obj	Class optsol
mod_obj-method	Class optsol
mod_obj-method	Class '"summaryOptsol"'
mod_obj<-	Class '"summaryOptsol"'
mod_obj<--method	Class '"summaryOptsol"'
moma	Class '"sysBiolAlg_moma"'
mtf	Class '"sysBiolAlg_mtf"'
mtfEasyConstraint	Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
multiDel	Parallel Support for sybil

-- N --

nc	Class '"sysBiolAlg"'
nc-method	Class '"sysBiolAlg"'
nc<-	Class '"sysBiolAlg"'
nc<--method	Class '"sysBiolAlg"'
netFlux	Class '"netFlux"'
netFlux-class	Class '"netFlux"'
nfluxes	Class optsol
nfluxes-method	Class optsol
nnzero-method	Class '"fluxDistribution"'
nnzero-method	Class '"summaryOptsol"'
nr	Class '"sysBiolAlg"'
nr-method	Class '"sysBiolAlg"'
nr<-	Class '"sysBiolAlg"'
nr<--method	Class '"sysBiolAlg"'
num_of_fluxes	Class '"fluxDistribution"'
num_of_fluxes-method	Class '"fluxDistribution"'
num_of_prob	Class optsol
num_of_prob-method	Structure of the Class "checksol"
num_of_prob-method	Class optsol
num_of_prob<-	Class optsol
num_of_prob<--method	Structure of the Class "checksol"
num_of_prob<--method	Class optsol
nvar	Class '"fluxDistribution"'
nvar-method	Class '"fluxDistribution"'
nzeros	Class '"summaryOptsol"'
nzeros-method	Class '"summaryOptsol"'

-- O --

obj_coef	Structure of Class "modelorg"
obj_coef-method	Structure of Class "modelorg"
obj_coef-method	Class optsol
obj_coef<-	Structure of Class "modelorg"
obj_coef<--method	Structure of Class "modelorg"
obj_coef<--method	Class optsol
obj_func	Class optsol
obj_func-method	Class optsol
obj_func<-	Class optsol
obj_func<--method	Class optsol
oneFluxDel	Single Flux Deletion Experiment
oneGeneDel	Single Gene Deletion Experiment
onlyChangeGPR	Change the GPR Rules
onlyCheckGPR	Check the GPR Rules
optimizeProb	Optimize Problem Object
optimizeProb-method	Optimize Problem Object
optimizeProb-methods	Optimize Problem Object
optimizer	Performs Series of Optimizations
optObj	General Constructor Function For Objects of Class 'optObj'
optObj-class	Class '"optObj"'
optObj_clpAPI-class	Class '"optObj_clpAPI"'
optObj_cplexAPI-class	Class '"optObj_cplexAPI"'
optObj_glpkAPI-class	Class '"optObj_glpkAPI"'
optObj_lpSolveAPI-class	Class '"optObj_lpSolveAPI"'
optsol	Class optsol
optsol-class	Class optsol
optsol_blockedReact-class	Class '"optsol_blockedReact"'
optsol_fluxdel-class	Class '"optsol_fluxdel"'
optsol_fluxVar-class	Class '"optsol_fluxVar"'
optsol_genedel-class	Class '"optsol_genedel"'
optsol_optimizeProb-class	Class '"optsol_optimizeProb"'
optsol_phpp-class	Class '"optsol_phpp"'
optsol_robAna-class	Class '"optsol_robAna"'
OPT_DIRECTION	Set and Get sybil Parameters

-- P --

pa	Class '"ppProc"'
pa-method	Class '"ppProc"'
pa<-	Class '"ppProc"'
pa<--method	Class '"ppProc"'
PATH_TO_MODEL	Set and Get sybil Parameters
phpp	Phenotypic Phase Plane Analysis
plot-method	Class '"fluxDistribution"'
plot-method	Class optsol
plot-method	Class '"optsol_fluxVar"'
plot-method	Class '"optsol_phpp"'
plot-method	Class '"optsol_robAna"'
plot-method	Class '"summaryOptsol"'
plotRangeVar	Class '"optsol_fluxVar"'
plotRangeVar-method	Class '"optsol_fluxVar"'
pointerToProb	Class '"optObj"'
pointerToProb-class	Class '"optObj"'
postProc	Class '"optsol_optimizeProb"'
postProc-method	Class '"optsol_optimizeProb"'
postProc<-	Class '"optsol_optimizeProb"'
postProc<--method	Class '"optsol_optimizeProb"'
ppProc	Class '"ppProc"'
ppProc-class	Class '"ppProc"'
preProc	Class '"optsol_optimizeProb"'
preProc-method	Class '"optsol_optimizeProb"'
preProc<-	Class '"optsol_optimizeProb"'
preProc<--method	Class '"optsol_optimizeProb"'
printExchange	Class '"summaryOptsol"'
printExchange-method	Class '"summaryOptsol"'
printMetabolite	Print Rows of the Stoichiometric Matrix
printMetabolite-method	Print Rows of the Stoichiometric Matrix
printMetabolite-methods	Print Rows of the Stoichiometric Matrix
printObjFunc	Structure of Class "modelorg"
printObjFunc-method	Structure of Class "modelorg"
printReaction	Print Columns of the Stoichiometric Matrix
printReaction-method	Print Columns of the Stoichiometric Matrix
printReaction-methods	Print Columns of the Stoichiometric Matrix
problem	Class '"sysBiolAlg"'
problem-method	Class '"sysBiolAlg"'
probType	Class '"optObj"'
probType-method	Class '"optObj"'
promptSysBiolAlg	Generate A Skeletal Structure of Subclasses of sysBiolAlg

-- R --

rate	Class '"netFlux"'
rate-method	Class '"netFlux"'
react	Structure of Class "modelorg"
react-class	Structure of Class "modelorg"
react-method	Class '"optsol_blockedReact"'
react-method	Class '"optsol_fluxVar"'
react<-	Class '"optsol_blockedReact"'
react<--method	Class '"optsol_blockedReact"'
react<--method	Class '"optsol_fluxVar"'
reactId	Structure of Class "reactId"
reactId-class	Structure of Class "reactId"
reactId_Exch	Class '"reactId_Exch"'
reactId_Exch-class	Class '"reactId_Exch"'
react_attr	Structure of Class "modelorg"
react_attr-method	Structure of Class "modelorg"
react_attr<-	Structure of Class "modelorg"
react_attr<--method	Structure of Class "modelorg"
react_de	Structure of Class "modelorg"
react_de-method	Structure of Class "modelorg"
react_de<-	Structure of Class "modelorg"
react_de<--method	Structure of Class "modelorg"
react_id	Structure of Class "modelorg"
react_id-method	Structure of Class "modelorg"
react_id-method	Class '"netFlux"'
react_id-method	Class optsol
react_id-method	Structure of Class "reactId"
react_id<-	Structure of Class "modelorg"
react_id<--method	Structure of Class "modelorg"
react_id<--method	Class '"netFlux"'
react_id<--method	Class optsol
react_id<--method	Structure of Class "reactId"
react_name	Structure of Class "modelorg"
react_name-method	Structure of Class "modelorg"
react_name<-	Structure of Class "modelorg"
react_name<--method	Structure of Class "modelorg"
react_num	Structure of Class "modelorg"
react_num-method	Structure of Class "modelorg"
react_num<-	Structure of Class "modelorg"
react_num<--method	Structure of Class "modelorg"
react_pos	Structure of Class "reactId"
react_pos-method	Structure of Class "reactId"
react_pos<-	Structure of Class "reactId"
react_pos<--method	Structure of Class "reactId"
react_rev	Structure of Class "modelorg"
react_rev-method	Structure of Class "modelorg"
react_rev<-	Structure of Class "modelorg"
react_rev<--method	Structure of Class "modelorg"
react_single	Structure of Class "modelorg"
react_single-method	Structure of Class "modelorg"
react_single<-	Structure of Class "modelorg"
react_single<--method	Structure of Class "modelorg"
readProb	Read Problem Object From File
readProb-method	Read Problem Object From File
readProb-methods	Read Problem Object From File
readTSVmod	Read a Metabolic Network in a TSV (CSV) Format
resetChanges	Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg
resetChanges-method	Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg
resetChanges-methods	Generic Function to Reset Temporary Changes in Objects of Class sysBiolAlg
return_codeLPSOLVE	Class '"optObj_lpSolveAPI"'
rev2irrev	Class for Metabolic Networks in Irreversible Format.
rev2irrev-method	Class for Metabolic Networks in Irreversible Format.
rev2irrev<-	Class for Metabolic Networks in Irreversible Format.
rev2irrev<--method	Class for Metabolic Networks in Irreversible Format.
rmReact	Remove Reactions From a Model
robAna	Robustness Analysis
room	Class '"sysBiolAlg_room"'
rxnGeneMat	Structure of Class "modelorg"
rxnGeneMat-method	Structure of Class "modelorg"
rxnGeneMat<-	Structure of Class "modelorg"
rxnGeneMat<--method	Structure of Class "modelorg"

-- S --

S	Structure of Class "modelorg"
s	Structure of Class "modelorg"
S-method	Structure of Class "modelorg"
s-method	Structure of Class "modelorg"
S<-	Structure of Class "modelorg"
s<-	Structure of Class "modelorg"
S<--method	Structure of Class "modelorg"
s<--method	Structure of Class "modelorg"
scaleProb	Scaling of the Constraint Matrix of an Optimization Problem
scaleProb-method	Scaling of the Constraint Matrix of an Optimization Problem
scaleProb-methods	Scaling of the Constraint Matrix of an Optimization Problem
sensitivityAnalysis	Sensitivity Analysis
sensitivityAnalysis-method	Sensitivity Analysis
sensitivityAnalysis-methods	Sensitivity Analysis
setColsNames	Set/Change Variable Names
setColsNames-method	Set/Change Variable Names
setColsNames-methods	Set/Change Variable Names
setObjDir	Set Direction of Optimization
setObjDir-method	Set Direction of Optimization
setObjDir-methods	Set Direction of Optimization
setRhsZero	Set Right Hand Side of the Optimization Problem To Zero
setRhsZero-method	Set Right Hand Side of the Optimization Problem To Zero
setRhsZero-methods	Set Right Hand Side of the Optimization Problem To Zero
setRowsNames	Set/Change Constraint Names
setRowsNames-method	Set/Change Constraint Names
setRowsNames-methods	Set/Change Constraint Names
setSolverParm	Set Parameters Used By The Optimization Software
setSolverParm-method	Set Parameters Used By The Optimization Software
setSolverParm-methods	Set Parameters Used By The Optimization Software
show-method	Structure of the Class "checksol"
show-method	Structure of Class "modelorg"
show-method	Class optsol
shrinkMatrix	Get a Subset of Matrix Like Objects
shrinkMatrix-method	Get a Subset of Matrix Like Objects
shrinkMatrix-methods	Get a Subset of Matrix Like Objects
singletonMetabolites	Identify Singleton Metabolites
singletonMetabolites-method	Identify Singleton Metabolites
singletonMetabolites-methods	Identify Singleton Metabolites
Snnz	Structure of Class "modelorg"
Snnz-method	Structure of Class "modelorg"
solveLp	Optimize Problem Object
solveLp-method	Optimize Problem Object
solveLp-methods	Optimize Problem Object
SOLVER	Set and Get sybil Parameters
solver	Class optsol
solver-method	Class '"optObj"'
solver-method	Class optsol
solver<-	Class optsol
solver<--method	Class optsol
SOLVER_CTRL_PARM	Set and Get sybil Parameters
status_code	Structure of the Class "checksol"
status_code-method	Structure of the Class "checksol"
status_code<-	Structure of the Class "checksol"
status_code<--method	Structure of the Class "checksol"
status_meaning	Structure of the Class "checksol"
status_meaning-method	Structure of the Class "checksol"
status_meaning<-	Structure of the Class "checksol"
status_meaning<--method	Structure of the Class "checksol"
status_num	Structure of the Class "checksol"
status_num-method	Structure of the Class "checksol"
status_num<-	Structure of the Class "checksol"
status_num<--method	Structure of the Class "checksol"
stclear	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stexists	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stfirst	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stinit	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stlength	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stlist	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stpop	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stpush	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stseek	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stshift	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
stunshift	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
subSys	Structure of Class "modelorg"
subSys-method	Structure of Class "modelorg"
subSys<-	Structure of Class "modelorg"
subSys<--method	Structure of Class "modelorg"
summaryOptsol	Summarize Objects of Class Optsol
summaryOptsol-class	Class '"summaryOptsol"'
sybil	sybil - Efficient Constrained Based Modelling in R
sybil-deprecated	Deprecated Functions and Methods in Package 'sybil'
sybilError	Class '"sybilError"'
sybilError-class	Class '"sybilError"'
sybilLog	Class '"sybilLog"'
sybilLog-class	Class '"sybilLog"'
sybilStack	A Data Type Providing Stack (LIFO) And Queue (FIFO) Functionality
SYBIL_SETTINGS	Set and Get sybil Parameters
sysBiolAlg	General Constructor Function For Objects of Class 'sysBiolAlg'
sysBiolAlg-class	Class '"sysBiolAlg"'
sysBiolAlg_fba	Class '"sysBiolAlg_fba"'
sysBiolAlg_fba-class	Class '"sysBiolAlg_fba"'
sysBiolAlg_fbaEasyConstraint	Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
sysBiolAlg_fbaEasyConstraint-class	Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
sysBiolAlg_fv	Class '"sysBiolAlg_fv"'
sysBiolAlg_fv-class	Class '"sysBiolAlg_fv"'
sysBiolAlg_lmoma	Class '"sysBiolAlg_lmoma"'
sysBiolAlg_lmoma-class	Class '"sysBiolAlg_lmoma"'
sysBiolAlg_moma	Class '"sysBiolAlg_moma"'
sysBiolAlg_moma-class	Class '"sysBiolAlg_moma"'
sysBiolAlg_mtf	Class '"sysBiolAlg_mtf"'
sysBiolAlg_mtf-class	Class '"sysBiolAlg_mtf"'
sysBiolAlg_mtfEasyConstraint	Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
sysBiolAlg_mtfEasyConstraint-class	Class '"sysBiolAlg_fbaEasyConstraint"' and Class '"sysBiolAlg_mtfEasyConstraint"'
sysBiolAlg_room	Class '"sysBiolAlg_room"'
sysBiolAlg_room-class	Class '"sysBiolAlg_room"'

-- T --

TOLERANCE

Set and Get sybil Parameters

-- U --

upgradeModelorg	Upgrade modelorg to newer version.
uppbnd	Structure of Class "modelorg"
uppbnd-method	Structure of Class "modelorg"
uppbnd-method	Class '"reactId_Exch"'
uppbnd<-	Structure of Class "modelorg"
uppbnd<--method	Structure of Class "modelorg"
uppbnd<--method	Class '"reactId_Exch"'
uptake	Class '"reactId_Exch"'
uptake-method	Class '"reactId_Exch"'
uptake<-	Class '"reactId_Exch"'
uptake<--method	Class '"reactId_Exch"'
uptMet	Class '"reactId_Exch"'
uptMet-method	Class '"reactId_Exch"'
uptReact	Class '"reactId_Exch"'
uptReact-method	Class '"reactId_Exch"'
USE_NAMES	Set and Get sybil Parameters

-- V --

verblevel	Class '"sybilLog"'
verblevel-method	Class '"sybilLog"'
verblevel<-	Class '"sybilLog"'
verblevel<--method	Class '"sybilLog"'
version	Structure of Class "modelorg"
version-method	Structure of Class "modelorg"
version<-	Structure of Class "modelorg"
version<--method	Structure of Class "modelorg"

-- W --

writeProb	Write Problem Object to File
writeProb-method	Write Problem Object to File
writeProb-methods	Write Problem Object to File
wrong_solver_msg	Class '"optObj"'
wrong_type_msg	Class '"optObj"'

-- Y --

ypd	In Sillico YPD Medium

-- misc --

[-method	Class '"fluxDistribution"'
[-method	Class '"optsol_fluxdel"'
[-method	Structure of Class "reactId"
[-method	Class '"reactId_Exch"'