Efficient Constrained Based Modelling


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Documentation for package ‘sybil’ version 2.2.0

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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"'