Creates a stoichiometry matrix from a set of reaction equations.
stoiCreate(
reactions,
eval = FALSE,
env = globalenv(),
toRight = "_forward",
toLeft = "_backward"
)A matrix with the following properties:
The number of columns equals the total number of components present
in reactions. The components' names are used as column names.
The number of rows equals the length of reactions plus the
number of reversible reactions. Thus, a single row is created for each
non-reversible reaction but two rows are created for reversible ones.
The latter represent the forward and backward reaction (in that order).
The row names are constructed from the names of reactions, making
use of the suffixes toRight and toLeft in the case of
reversible reactions.
The matrix is filled with the stoichiometric factors extracted from
reactions. Empty elements are set to zero.
The type of the matrix (character or
numeric) depends on the value of eval.
A named vector of character strings, each representing a (chemical) reaction. See syntax details below.
Logical. If FALSE (default), the returned matrix is of
type character and any mathematical expressions are
returned as text. If TRUE, an attempt is made to return a
numeric matrix by evaluating the expression making use
env.
Only relevant if eval is TRUE. Must be an
environment or list supplying constants, functions, and operators needed to
evaluate expressions in the generated matrix.
Only relevant for reversible reactions. The passed character
string is appended to the name of the respective element of
reactions to create a unique name for the forward reaction.
Like toRight, but this is the suffix for the backward
reaction.
David Kneis david.kneis@tu-dresden.de
Use stoiCheck to validate the mass balance of
the generated matrix.
# EXAMPLE 1: From https://en.wikipedia.org/wiki/Petersen_matrix (July 2016)
#
reactions <- c(
formS= "A + 2 * B -> S",
equiES= "E + S <-> ES",
decoES= "ES -> E + P"
)
stoi <- stoiCreate(reactions, eval=TRUE, toRight="_f", toLeft="_b")
print(stoi)
# EXAMPLE 2: Decomposition of organic matter (selected equations only)
#
# Eq. 1 and 2 are from Soetaert et al. (1996), Geochimica et Cosmochimica
# Acta, 60 (6), 1019-1040. 'OM' is organic matter. Constants 'nc' and 'pc'
# represent the nitrogen/carbon and phosphorus/carbon ratio, respectively.
reactions <- c(
oxicDegrad= "OM + O2 -> CO2 + nc * NH3 + pc * H3PO4 + H2O",
denitrific= "OM + 0.8*HNO3 -> CO2 + nc*NH3 + 0.4*N2 + pc*H3PO4 + 1.4*H2O",
dissPhosp1= "H3PO4 <-> H + H2PO4",
dissPhosp2= "H2PO4 <-> H + HPO4"
)
# Non-evaluated matrix
stoi <- stoiCreate(reactions, toRight="_f", toLeft="_b")
print(stoi)
# Evaluated matrix ('nc' and 'pc' according to Redfield ratio)
pars <- list(nc=16/106, pc=1/106)
stoi <- stoiCreate(reactions, eval=TRUE, env=pars, toRight="_f", toLeft="_b")
print(stoi)
Run the code above in your browser using DataLab