View source: R/plainMethods_stoiBuild_stoiCheck.r
stoiCreate | R Documentation |
Creates a stoichiometry matrix from a set of reaction equations.
stoiCreate(
reactions,
eval = FALSE,
env = globalenv(),
toRight = "_forward",
toLeft = "_backward"
)
reactions |
A named vector of character strings, each representing a (chemical) reaction. See syntax details below. |
eval |
Logical. If |
env |
Only relevant if |
toRight |
Only relevant for reversible reactions. The passed character
string is appended to the name of the respective element of
|
toLeft |
Like |
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
.
The syntax rules for reaction equations are as follows (see examples):
There must be a left hand side and a right hand side. Sides must be separated by one of the arrows '->', '<-', or '<->' with the latter indicating a reversible reaction.
Names of component(s) must appear at each side of the reaction. These must be legal row/column names in R. If multiple components are consumed or produced, they must be separated by '+'.
Any stoichiometric factors need to appear before the respective component name using '*' as the separating character. Stoichiometric factors being equal to unity can be omitted.
A stoichiometric factor is treated as a mathematical expression. In common cases, it is just a numeric constant. However, the expression can also involve references to variables or functions. If such an expression contains math operators '*' or '+' it needs to be enclosed in parenthesis.
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.