readSBMLR: Convert an SBMLR file into an R model object of class SBMLR

Description Usage Arguments Details Value Note Author(s) See Also Examples

Description

This function converts an SBMLR model file into a corresponding SBMLR model object. This is more than a source-ing: the file is simpler than the object since things are generated, such as, rate law and rule R expressions and functions, and mathML.

Usage

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readSBMLR(filename)

Arguments

filename

An SBMLR model definition file.

Details

A limited subset of SBML level 2 models is currently supported, e.g. events and function definitions are not covered.

Value

A corresponding SBMLR model object.

Note

This function replaces the use of source in older versions of SBMLR. It converts rate law and rule strings to R functions and expressions and to MathML.

Author(s)

Tom Radivoyevitch

See Also

readSBML

Examples

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library(SBMLR)
curtoX=readSBML(file.path(system.file(package="SBMLR"), "models/curto.xml"))  
curtoR=readSBMLR(file.path(system.file(package="SBMLR"), "models/curto.r"))  
curtoX==curtoR

Example output

Loading required package: XML
Loading required package: deSolve
$species
     index initialConcentrations boundaryConditions
PRPP  TRUE                  TRUE               TRUE
IMP   TRUE                  TRUE               TRUE
SAMP  TRUE                  TRUE               TRUE
ATP   TRUE                  TRUE               TRUE
SAM   TRUE                  TRUE               TRUE
Ade   TRUE                  TRUE               TRUE
XMP   TRUE                  TRUE               TRUE
GTP   TRUE                  TRUE               TRUE
dATP  TRUE                  TRUE               TRUE
dGTP  TRUE                  TRUE               TRUE
RNA   TRUE                  TRUE               TRUE
DNA   TRUE                  TRUE               TRUE
HX    TRUE                  TRUE               TRUE
Xa    TRUE                  TRUE               TRUE
Gua   TRUE                  TRUE               TRUE
UA    TRUE                  TRUE               TRUE
R5P   TRUE                  TRUE               TRUE
Pi    TRUE                  TRUE               TRUE

$reactions
       index Laws initialFluxes
ada     TRUE TRUE          TRUE
ade     TRUE TRUE          TRUE
adna    TRUE TRUE          TRUE
adrnr   TRUE TRUE          TRUE
ampd    TRUE TRUE          TRUE
aprt    TRUE TRUE          TRUE
arna    TRUE TRUE          TRUE
asuc    TRUE TRUE          TRUE
asli    TRUE TRUE          TRUE
dada    TRUE TRUE          TRUE
den     TRUE TRUE          TRUE
dgnuc   TRUE TRUE          TRUE
dnaa    TRUE TRUE          TRUE
dnag    TRUE TRUE          TRUE
gdna    TRUE TRUE          TRUE
gdrnr   TRUE TRUE          TRUE
gmpr    TRUE TRUE          TRUE
gmps    TRUE TRUE          TRUE
gnuc    TRUE TRUE          TRUE
gprt    TRUE TRUE          TRUE
grna    TRUE TRUE          TRUE
gua     TRUE TRUE          TRUE
hprt    TRUE TRUE          TRUE
hx      TRUE TRUE          TRUE
hxd     TRUE TRUE          TRUE
impd    TRUE TRUE          TRUE
inuc    TRUE TRUE          TRUE
mat     TRUE TRUE          TRUE
polyam  TRUE TRUE          TRUE
prpps   TRUE TRUE          TRUE
pyr     TRUE TRUE          TRUE
rnaa    TRUE TRUE          TRUE
rnag    TRUE TRUE          TRUE
trans   TRUE TRUE          TRUE
ua      TRUE TRUE          TRUE
x       TRUE TRUE          TRUE
xd      TRUE TRUE          TRUE

SBMLR documentation built on Nov. 17, 2017, 10:07 a.m.