From 5b2ab491e801cb866a305630c78b5f264d682a99 Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Mon, 19 Oct 2015 16:31:19 +0200
Subject: [PATCH] easyconstraint documentation and implementation
---
DESCRIPTION | 10 +-
R/sysBiolAlg_fbaEasyConstraintClass.R | 55 ++++++--
man/sysBiolAlg_fbaEasyConstraint-class.Rd | 152 ++++++++++++++++++++++
3 files changed, 200 insertions(+), 17 deletions(-)
create mode 100644 man/sysBiolAlg_fbaEasyConstraint-class.Rd
diff --git a/DESCRIPTION b/DESCRIPTION
index 18a0246..833d777 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling in R
-Version: 1.3.1
-Date: 2015-06-17
+Version: 1.3.2
+Date: 2015-10-19
Authors@R: c(
person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut")),
@@ -48,9 +48,11 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
optsol_optimizeProbClass.R optsol_fluxVarClass.R
optsol_fluxdelClass.R optsol_robAnaClass.R optsol_phppClass.R
optsol_genedelClass.R checksolClass.R summaryOptsolClass.R
- sysBiolAlgClass.R sysBiolAlg_fbaClass.R sysBiolAlg_fvClass.R
+ sysBiolAlgClass.R sysBiolAlg_fbaClass.R
+ sysBiolAlg_fbaEasyConstraintClass.R sysBiolAlg_fvClass.R
sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R
- sysBiolAlg_mtfClass.R sysBiolAlg_roomClass.R sybilLogClass.R
+ sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
+ sysBiolAlg_roomClass.R sybilLogClass.R
Packaged: 2014-11-19 20:39:37 UTC; gabriel
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
diff --git a/R/sysBiolAlg_fbaEasyConstraintClass.R b/R/sysBiolAlg_fbaEasyConstraintClass.R
index bdd97cb..676240b 100644
--- a/R/sysBiolAlg_fbaEasyConstraintClass.R
+++ b/R/sysBiolAlg_fbaEasyConstraintClass.R
@@ -100,32 +100,61 @@ setMethod(f = "initialize",
mat <- S(model)
rtype <- rep("E", nRows)
+ rlb <- rep(0, nRows)
+ rub <- rep(0, nRows)
#add easyConstraints:
if(!is.null(easyConstraint)){
- if( length(easyConstraint$nz) == length(easyConstraint$x)
- | length(easyConstraint$nz) == length(easyConstraint$rtype)){
+ if( length(easyConstraint$react) != length(easyConstraint$x)
+ | length(easyConstraint$react) != length(easyConstraint$rtype)
+ ){
stop("easyConstraint elements have to have equal lengths")
}
- stopifnot(is.list(easyConstraints$nz))
- stopifnot(is.list(easyConstraints$x))
- stopifnot(all(easyConstraints$rtype %in% c("F", "L", "U", "D", "E")))
+ stopifnot(is.list(easyConstraint$react))
+ stopifnot(is.list(easyConstraint$x))
+ stopifnot(all(easyConstraint$rtype %in% c("F", "L", "U", "D", "E")))
- m <- Matrix(0, ncol=nCols, nrow=length(easyConstraint))
+ # setting and checking rlb
+ if(is.null(easyConstraint$lb)){
+ rlb <- c(rlb, rep(0, length(easyConstraint$react)))
+ }else{
+ if(length(easyConstraint$react) != length(easyConstraint$lb)){
+ stop("easyConstraint$lb length has to match length of react argument")
+ }else{
+ stopifnot(is.numeric(easyConstraint$lb))
+ rlb <- c(rlb, easyConstraint$lb)
+ }
+ }
+
+ # setting and checking rub
+ if(is.null(easyConstraint$ub)){
+ rub <- c(rub, rep(0, length(easyConstraint$react)))
+ }else{
+ if(length(easyConstraint$react) != length(easyConstraint$ub)){
+ stop("easyConstraint$ub length has to match length of react argument")
+ }else{
+ stopifnot(is.numeric(easyConstraint$ub))
+ rub <- c(rub, easyConstraint$ub)
+ }
+ }
+ browser()
+
+ m <- Matrix(0, ncol=nCols, nrow=length(easyConstraint$react))
- for(i in 1:length(easyConstraint)){
- m[i, easyConstraint$nz] <- easyConstraint$x
+ for(i in 1:length(easyConstraint$react)){
+ m[i, easyConstraint$react[[i]]] <- easyConstraint$x[[i]]
}
+
mat <- rbind2(mat, m)
rtype <- c(rtype, easyConstraint$rtype)
- nRow <- nRow + length(easyConstraint)
+ nRows <- nRows + length(easyConstraint$react)
if(!is.null(rowNames)){
- c(rowNames, paste0("easyConstraint", 1:length(easyConstraint)))
+ c(rowNames, paste0("easyConstraint", 1:length(easyConstraint$react)))
}
}
-
+
# generate problem object
.Object <- callNextMethod(.Object,
sbalg = "fba",
@@ -138,10 +167,10 @@ setMethod(f = "initialize",
ub = uppbnd(model),
lb = lowbnd(model),
obj = obj_coef(model),
- rlb = rep(0, nRows),
+ rlb = rlb,
rtype = rtype,
lpdir = lpdir,
- rub = NULL,
+ rub = rub,
ctype = NULL,
cnames = colNames,
rnames = rowNames,
diff --git a/man/sysBiolAlg_fbaEasyConstraint-class.Rd b/man/sysBiolAlg_fbaEasyConstraint-class.Rd
new file mode 100644
index 0000000..00f9381
--- /dev/null
+++ b/man/sysBiolAlg_fbaEasyConstraint-class.Rd
@@ -0,0 +1,152 @@
+\name{sysBiolAlg_fba-class}
+
+\Rdversion{1.1}
+\encoding{utf8}
+
+\docType{class}
+
+\alias{sysBiolAlg_fbaEasyConstraint-class}
+\alias{sysBiolAlg_fbaEasyConstraint}
+\alias{sysBiolAlg_mtfEasyConstraint-class}
+\alias{sysBiolAlg_mtfEasyConstraint}
+\alias{mtfEasyConstraint}
+\alias{fbaEasyConstraint}
+
+\title{Class \code{"sysBiolAlg_fbaEasyConstraint"} and \code{"sysBiolAlg_mtfEasyConstraint"}}
+
+\description{
+ The classes \code{sysBiolAlg_fbaEasyConstraint} \code{sysBiolAlg_mtfEasyConstraint} hold an object of class
+ \code{\linkS4class{optObj}} which is generated to meet the
+ requirements of the FBA/MTF algorithm. \cr
+ In Addition to this, it is very easy to add
+ additional linear constraints to that linear problem. Each constraints is
+ defined by the affected reaction, the coefficient, lower and upper bounds, and
+ the constraint type.
+}
+
+\section{Objects from the Class}{
+ Objects can be created by calls of the form
+
+ \code{sysBiolAlg(model, algorithm = "fba", ...)}.
+
+ Arguments to \code{...} which are passed to method \code{initialize} of class
+ \code{sysBiolAlg_fba} are described in the Details section.
+}
+
+\section{Slots}{
+ \describe{
+ Slots are the same as in the original MTF/FBA classes.
+
+ In addition, this slot is implemented:
+
+ \item{\code{easyConstraint}:}{
+ List holding the information for the constraints (see details):
+ \itemize{
+ \item{\code{react}}{
+ List of numeric vectors. Values indicate, to which reaction the
+ constraint applys.
+ }
+ \item{\code{x}}{
+ List of numeric vectors. Values indicate coefficients of the
+ constraint. Lengths have to be equal to \code{react}-field.
+ }
+ \item{\code{lb}}{
+ Numeric vector of lower bounds for constraints. If not given, a
+ default bound of 0 will be used.
+ }
+ \item{\code{ub}}{
+ Numeric vector of lower bounds for constraints. If not given, a
+ default bound of 0 will be used. Only needed for constraints,
+ that need two bounds.
+ }
+ \item{\code{rtype}}{
+ Character vector defining the type of constraint.
+
+ \tabular{lll}{
+ \code{"F"}: \tab free constraint (GLPK only) \tab \eqn{-\infty < x < \infty}{-INF < x < INF} \cr
+ \code{"L"}: \tab constraint with lower bound \tab \eqn{\mathrm{lb} \leq x < \infty}{lb <= x < INF} \cr
+ \code{"U"}: \tab constraint with upper bound \tab \eqn{-\infty < x \leq \mathrm{ub}}{-INF < x <= ub} \cr
+ \code{"D"}: \tab double-bounded (ranged) constraint \tab \eqn{\mathrm{lb} \leq x \leq \mathrm{ub}}{lb <= x <= ub} \cr
+ \code{"E"}: \tab fixed (equality) constraint \tab \eqn{\mathrm{lb} = x = \mathrm{ub}}{lb = x = ub} \cr
+ }
+ If \code{rtype[i]} is not one of \code{"F"}, \code{"L"}, \code{"U"},
+ \code{"D"} or \code{"E"}, the value of \code{rtype[i]} will be set to
+ \code{"E"}. See Details of \code{\link{loadLPprob}}.
+ }
+ }
+ }
+ }
+}
+
+\section{Extends}{
+ Class \code{"\linkS4class{sysBiolAlg}"}, directly.
+}
+
+\section{Methods}{
+ No methods defined with class "sysBiolAlg_fbaEasyConstraint" in the signature.
+}
+
+\details{
+ The problem object is built to be capable to perform flux balance analysis
+ (FBA) with a given model, which is basically the solution of a linear
+ programming problem
+ \deqn{%
+ \begin{array}{rll}%
+ \max & \mbox{\boldmath$c$\unboldmath}^{\mathrm{T}}
+ \mbox{\boldmath$v$\unboldmath} \\[1ex]
+ \mathrm{s.\,t.} & \mbox{\boldmath$Sv$\unboldmath} = 0 \\[1ex]
+ & \alpha_i \leq v_i \leq \beta_i
+ & \quad \forall i \in \{1, \ldots, n\} \\[1ex]
+ \end{array}%
+ }{
+ max c^T v
+ s.t. Sv = 0
+ a_i <= v_i <= b_i for i = 1, ..., n
+ }
+ with \eqn{\bold{S}}{S} being the stoichiometric matrix, \eqn{\alpha_i}{a_i}
+ and \eqn{\beta_i}{b_i} being the lower and upper bounds for flux (variable)
+ \eqn{i} respectively. The total number of variables of the optimization
+ problem is denoted by \eqn{n}. The solution of the optimization is a flux
+ distribution maximizing the objective function
+ \eqn{
+ \mbox{\boldmath$c$\unboldmath}^{\mathrm{T}}
+ \mbox{\boldmath$v$\unboldmath}
+ }{c^T v} under the a given environment and the assumption of steady state.
+ The optimization can be executed by using \code{\link{optimizeProb}}.
+
+ The additional i-th EasyConstraint will be added as follows to the problem: \emph{to be checked.}
+ \deqn{
+ \begin{array}{l}%
+ \code{lb} <= v_\code{react\[\[i\]\]} * (x_i)^T <= \code{ub}
+ \end{array}%
+ }{
+ \code{lb} <= v_{\code{react\[\[i\]\]}} * (x_i)^T <= \code{ub}
+ }
+
+}
+
+\references{
+ Edwards, J. S., Covert, M and Palsson, B. Ø. (2002) Metabolic modelling of
+ microbes: the flux-balance approach. \emph{Environ Microbiol} \bold{4},
+ 133--140.
+
+ Edwards, J. S., Ibarra, R. U. and Palsson, B. Ø. (2001) In silico predictions
+ of \emph{Escherichia coli} metabolic capabilities are consistent with
+ experimental data. \emph{Nat Biotechnol} \bold{19}, 125--130.
+}
+
+\author{
+ Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\seealso{
+ Constructor function \code{\link{sysBiolAlg}} and
+ superclass \code{\linkS4class{sysBiolAlg}}.
+}
+
+\examples{
+ showClass("sysBiolAlg_fba")
+}
+
+\keyword{classes}
--
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