From 9b45ba2b474cc23cb46d128eef1aa9d60aa70321 Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Thu, 28 Jan 2016 15:46:39 +0100
Subject: [PATCH] non working maximum total flux
---
R/sysBiolAlg_mtfClass.R | 28 ++++++++++++++++++++++------
inst/NEWS.Rd | 7 +++++++
man/sysBiolAlg_mtf-class.Rd | 5 +++++
3 files changed, 34 insertions(+), 6 deletions(-)
diff --git a/R/sysBiolAlg_mtfClass.R b/R/sysBiolAlg_mtfClass.R
index 362d339..cacd177 100644
--- a/R/sysBiolAlg_mtfClass.R
+++ b/R/sysBiolAlg_mtfClass.R
@@ -47,6 +47,7 @@ setMethod(f = "initialize",
react = NULL, lb = NULL, ub = NULL,
costcoefbw = NULL,
costcoeffw = NULL,
+ lpdir = "min",
absMAX = SYBIL_SETTINGS("MAXIMUM"),
useNames = SYBIL_SETTINGS("USE_NAMES"),
cnames = NULL,
@@ -65,6 +66,7 @@ setMethod(f = "initialize",
stopifnot(is(model, "modelorg"),
is(wtobj, "numeric"),
is(absMAX, "numeric"))
+ stopifnot(lpdir %in% c("min", "max"))
# If wtobj is longer than 1, mtf algorithm has to run several
# times. In that case, wtobj is not written in the problem
@@ -102,6 +104,8 @@ setMethod(f = "initialize",
# | | |
# obj 0 | 1 | 1 |
+ # NOTE: if lpdir == "max" the 2nd and 3rd block
+ # will be <= instead of >= and signs change.
# ---------------------------------------------
# problem dimensions
@@ -131,10 +135,18 @@ setMethod(f = "initialize",
fi <- c(1:nc)
# rows for the delta match matrix
- diag(LHS[(nr+1) :(nr+nc) ,1 :nc ]) <- 1
- diag(LHS[(nr+1) :(nr+nc) ,(nc+1) :(2*nc)]) <- 1
- diag(LHS[(nr+nc+1):(nr+2*nc),1 :nc ]) <- -1
- diag(LHS[(nr+nc+1):(nr+2*nc),(2*nc+1):(3*nc)]) <- 1
+ if(lpdir=="min"){
+ diag(LHS[(nr+1) :(nr+nc) ,1 :nc ]) <- 1
+ diag(LHS[(nr+1) :(nr+nc) ,(nc+1) :(2*nc)]) <- 1
+ diag(LHS[(nr+nc+1):(nr+2*nc),1 :nc ]) <- -1
+ diag(LHS[(nr+nc+1):(nr+2*nc),(2*nc+1):(3*nc)]) <- 1
+ }else{
+ diag(LHS[(nr+1) :(nr+nc) ,1 :nc ]) <- 1
+ diag(LHS[(nr+1) :(nr+nc) ,(nc+1) :(2*nc)]) <- -1
+ diag(LHS[(nr+nc+1):(nr+2*nc),1 :nc ]) <- -1
+ diag(LHS[(nr+nc+1):(nr+2*nc),(2*nc+1):(3*nc)]) <- 1
+ }
+
# fix the value of the objective function
LHS[(nr+2*nc+1),1:nc] <- obj_coef(model)
@@ -156,7 +168,11 @@ setMethod(f = "initialize",
#rupper <- c(rhs(model), rep(absMAX, 2*nc + 1))
rlower <- c(rep(0, nr), rep(0, 2*nc), currmo)
rupper <- c(rep(0, nr), rep(absMAX, 2*nc + 1))
- rtype <- c(rep("E", nr), rep("L", 2*nc + 1))
+ if(lpdir == "min"){
+ rtype <- c(rep("E", nr), rep("L", 2*nc), "L")
+ }else{
+ rtype <- c(rep("E", nr), rep("U", 2*nc), "L")
+ }
# ---------------------------------------------
# objective function
@@ -252,7 +268,7 @@ setMethod(f = "initialize",
rlb = rlower,
rub = rupper,
rtype = rtype,
- lpdir = "min",
+ lpdir = lpdir,
ctype = NULL,
cnames = colNames,
rnames = rowNames,
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 2875c43..8c6c333 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -6,6 +6,13 @@
\newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+\section{Changes in version 1.3.4 2016-01-27}{
+ \itemize{
+ \item \code{sysBiolAlg_mtfClass} got option to be used as maximum total
+ flux, too.
+ }
+}
+% ---------------------------------------------------------------------------- %
\section{Changes in version 1.3.3 2015-11-25}{
\itemize{
\item \code{addReact} crashed for irreversible models.
diff --git a/man/sysBiolAlg_mtf-class.Rd b/man/sysBiolAlg_mtf-class.Rd
index baf906d..397adb5 100644
--- a/man/sysBiolAlg_mtf-class.Rd
+++ b/man/sysBiolAlg_mtf-class.Rd
@@ -111,6 +111,11 @@
values given in \code{costcoeffw}.\cr
Default: \code{NULL}.
}
+ \item{\code{lpdir}:}{Object of class \code{"character"}
+ giving the direction of optimization. with \code{max} this class can be
+ used to optimize maximum total flux. Cavetas: Because of changes in the
+ linear problem, this cannot be changed later. Default: \code{min}.
+ }
\item{absMAX}{
A single numerical value used as a maximum value for upper variable
and contraint bounds.\cr
--
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