| Title: | R Functions for Solving Stoichiometric Equations |
|---|---|
| Description: | Given a list of substance compositions, a list of substances involved in a process, and a list of constraints in addition to mass conservation of elementary constituents, the package contains functions to build the substance composition matrix, to analyze the uniqueness of process stoichiometry, and to calculate stoichiometric coefficients if process stoichiometry is unique. (See Reichert, P. and Schuwirth, N., A generic framework for deriving process stoichiometry in enviromental models, Environmental Modelling and Software 25, 1241-1251, 2010 for more details.) |
| Authors: | Peter Reichert |
| Maintainer: | Peter Reichert <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.1-5 |
| Built: | 2024-11-21 04:49:28 UTC |
| Source: | https://github.com/cran/stoichcalc |
Given a list of substance compositions, a list of substances involved in a process, and a list of constraints in addition to mass conservation of elementary constituents, the package contains functions to build the substance composition matrix, to analyze the uniqueness of process stoichiometry, and to calculate stoichiometric coefficients if process stoichiometry is unique (see reference given below for more details).
| Package: | stoichcalc |
| Type: | Package |
| Version: | 1.1-5 |
| Date: | 2023-08-28 |
| License: | GPL >= 2 |
| LazyLoad: | yes |
The package contains the following three functions:calc.comp.matrix
constructs the substance composition matrix
froma a list of substance composition vectors,calc.stoich.basis calculates the basis of the stoichiometry space
that is compatible with mass balances of elementary constituents
and additional constraints,
calc.stoich.coef calculates the stoichiometric coefficients
of a process from involved substances, their composition and constraints.
Peter Reichert <[email protected]>
Reichert, P. and Schuwirth, N., A generic framework for deriving process stoichiometry in environmental models, Environmental Modelling and Software 25, 1241-1251, 2010.
calc.comp.matrix,
calc.stoich.basis,
calc.stoich.coef
subst.comp <- list(NH4 = c(H = 4*1/14, # gH/gNH4-N N = 1, # gN/gNH4-N charge = 1/14), # chu/gNH4-N NO3 = c(O = 3*16/14, # gO/gNO3-N N = 1, # gN/gNO3-N charge = -1/14), # chu/gNO3-N HPO4 = c(O = 4*16/31, # gO/gHPO4-P H = 1*1/31, # gH/gHPO4-P P = 1, # gP/gHPO4-P charge = -2/31), # chu/gHPO4-P HCO3 = c(C = 1, # gC/gHCO3-C O = 3*16/12, # gO/gHCO3-C H = 1*1/12, # gH/gHCO3-C charge = -1/12), # chu/gHCO3-C O2 = c(O = 1), # gO/gO2-O H = c(H = 1, # gH/molH charge = 1), # chu/molH H2O = c(O = 1*12, # gO/molH2O H = 2*1), # gH/molH2O ALG = c(N = 0.06, # gN/gALG P = 0.005, # gP/gALG O = 0.50, # gO/gALG H = 0.07, # gH/gALG C = 0.365), # gC/gALG ZOO = c(N = 0.06, # gN/gZOO P = 0.01, # gP/gZOO O = 0.50, # gO/gZOO H = 0.07, # gH/gZOO C = 0.36), # gC/gZOO POM = c(N = 0.04, # gN/gPOM P = 0.007, # gP/gPOM O = 0.40, # gO/gPOM H = 0.07, # gH/gPOM C = 0.483), # gC/gPOM DOM = c(N = 0.04, # gN/gDOM P = 0.007, # gP/gDOM O = 0.40, # gO/gDOM H = 0.07, # gH/gDOM C = 0.483)) # gC/gDOM Y.ZOO <- 0.2; f.POM <- 0.2; f.DOM <- 0.1 alpha <- calc.comp.matrix(subst.comp) subst.gro.ALG.NO3 <- c("NO3","HPO4","HCO3", "O2","H","H2O","ALG") basis.gro.ALG.NO3 <- calc.stoich.basis(alpha,subst.gro.ALG.NO3) nu.gro.ALG.NO3 <- calc.stoich.coef(alpha = alpha, name = "gro.ALG.NO3", subst = subst.gro.ALG.NO3, subst.norm = "ALG", nu.norm = 1) subst.gro.ZOO <- c("NH4","HPO4","HCO3","O2","H", "H2O","ALG","ZOO","POM","DOM") basis.gro.ZOO <- calc.stoich.basis(alpha,subst.gro.ZOO) const.gro.ZOO <- list(c("ZOO" = 1,"ALG" = Y.ZOO), c("POM" = 1,"ALG" = f.POM), c("DOM" = 1,"ALG" = f.DOM)) nu.gro.ZOO <- calc.stoich.coef(alpha = alpha, name = "gro.ZOO", subst = subst.gro.ZOO, subst.norm = "ZOO", nu.norm = 1, constraints = const.gro.ZOO) nu <- rbind(nu.gro.ALG.NO3, nu.gro.ZOO) print(nu,digits=2)subst.comp <- list(NH4 = c(H = 4*1/14, # gH/gNH4-N N = 1, # gN/gNH4-N charge = 1/14), # chu/gNH4-N NO3 = c(O = 3*16/14, # gO/gNO3-N N = 1, # gN/gNO3-N charge = -1/14), # chu/gNO3-N HPO4 = c(O = 4*16/31, # gO/gHPO4-P H = 1*1/31, # gH/gHPO4-P P = 1, # gP/gHPO4-P charge = -2/31), # chu/gHPO4-P HCO3 = c(C = 1, # gC/gHCO3-C O = 3*16/12, # gO/gHCO3-C H = 1*1/12, # gH/gHCO3-C charge = -1/12), # chu/gHCO3-C O2 = c(O = 1), # gO/gO2-O H = c(H = 1, # gH/molH charge = 1), # chu/molH H2O = c(O = 1*12, # gO/molH2O H = 2*1), # gH/molH2O ALG = c(N = 0.06, # gN/gALG P = 0.005, # gP/gALG O = 0.50, # gO/gALG H = 0.07, # gH/gALG C = 0.365), # gC/gALG ZOO = c(N = 0.06, # gN/gZOO P = 0.01, # gP/gZOO O = 0.50, # gO/gZOO H = 0.07, # gH/gZOO C = 0.36), # gC/gZOO POM = c(N = 0.04, # gN/gPOM P = 0.007, # gP/gPOM O = 0.40, # gO/gPOM H = 0.07, # gH/gPOM C = 0.483), # gC/gPOM DOM = c(N = 0.04, # gN/gDOM P = 0.007, # gP/gDOM O = 0.40, # gO/gDOM H = 0.07, # gH/gDOM C = 0.483)) # gC/gDOM Y.ZOO <- 0.2; f.POM <- 0.2; f.DOM <- 0.1 alpha <- calc.comp.matrix(subst.comp) subst.gro.ALG.NO3 <- c("NO3","HPO4","HCO3", "O2","H","H2O","ALG") basis.gro.ALG.NO3 <- calc.stoich.basis(alpha,subst.gro.ALG.NO3) nu.gro.ALG.NO3 <- calc.stoich.coef(alpha = alpha, name = "gro.ALG.NO3", subst = subst.gro.ALG.NO3, subst.norm = "ALG", nu.norm = 1) subst.gro.ZOO <- c("NH4","HPO4","HCO3","O2","H", "H2O","ALG","ZOO","POM","DOM") basis.gro.ZOO <- calc.stoich.basis(alpha,subst.gro.ZOO) const.gro.ZOO <- list(c("ZOO" = 1,"ALG" = Y.ZOO), c("POM" = 1,"ALG" = f.POM), c("DOM" = 1,"ALG" = f.DOM)) nu.gro.ZOO <- calc.stoich.coef(alpha = alpha, name = "gro.ZOO", subst = subst.gro.ZOO, subst.norm = "ZOO", nu.norm = 1, constraints = const.gro.ZOO) nu <- rbind(nu.gro.ALG.NO3, nu.gro.ZOO) print(nu,digits=2)
Construct substance composition matrix from list of substance composition vectors
calc.comp.matrix(subst.comp,verbose=TRUE)calc.comp.matrix(subst.comp,verbose=TRUE)
subst.comp |
Named list of named composition vectors. The list must contain entries labelled by the substance names containing vectors of the mass fractions of elementary constituents (typically chemical elements, charge or COD resp. ThOD) that characterize the composition of the substance. Each element of these vectors must be labelled by the name of the corresponding elementary constituent. |
verbose |
indicator for whether or not to write basic information to the console. |
This function compiles the substance composition matrix used in the other functions of the stoichcalc package. It can alternatively be composed manually or by a user-defined function. The main advantage of the use of this function is that substance compositions can be maintained in lists. This makes it much easier to remove and add substances and elementary constituents.
Composition matrix of all substances (labelled columns) and mass fractions of elementary constituents (labelled rows).
Peter Reichert <[email protected]>
Reichert, P. and Schuwirth, N., A generic framework for deriving process stoichiometry in environmental models, Environmental Modelling and Software 25, 1241-1251, 2010.
calc.stoich.basis, calc.stoich.coef
subst.comp <- list(NH4 = c(H = 4*1/14, # gH/gNH4-N N = 1, # gN/gNH4-N charge = 1/14), # chu/gNH4-N NO3 = c(O = 3*16/14, # gO/gNO3-N N = 1, # gN/gNO3-N charge = -1/14), # chu/gNO3-N HPO4 = c(O = 4*16/31, # gO/gHPO4-P H = 1*1/31, # gH/gHPO4-P P = 1, # gP/gHPO4-P charge = -2/31), # chu/gHPO4-P HCO3 = c(C = 1, # gC/gHCO3-C O = 3*16/12, # gO/gHCO3-C H = 1*1/12, # gH/gHCO3-C charge = -1/12), # chu/gHCO3-C O2 = c(O = 1), # gO/gO2-O H = c(H = 1, # gH/molH charge = 1), # chu/molH H2O = c(O = 1*12, # gO/molH2O H = 2*1), # gH/molH2O ALG = c(N = 0.06, # gN/gALG P = 0.005, # gP/gALG O = 0.50, # gO/gALG H = 0.07, # gH/gALG C = 0.365), # gC/gALG ZOO = c(N = 0.06, # gN/gZOO P = 0.01, # gP/gZOO O = 0.50, # gO/gZOO H = 0.07, # gH/gZOO C = 0.36), # gC/gZOO POM = c(N = 0.04, # gN/gPOM P = 0.007, # gP/gPOM O = 0.40, # gO/gPOM H = 0.07, # gH/gPOM C = 0.483), # gC/gPOM DOM = c(N = 0.04, # gN/gDOM P = 0.007, # gP/gDOM O = 0.40, # gO/gDOM H = 0.07, # gH/gDOM C = 0.483)) # gC/gDOM alpha <- calc.comp.matrix(subst.comp) print(alpha)subst.comp <- list(NH4 = c(H = 4*1/14, # gH/gNH4-N N = 1, # gN/gNH4-N charge = 1/14), # chu/gNH4-N NO3 = c(O = 3*16/14, # gO/gNO3-N N = 1, # gN/gNO3-N charge = -1/14), # chu/gNO3-N HPO4 = c(O = 4*16/31, # gO/gHPO4-P H = 1*1/31, # gH/gHPO4-P P = 1, # gP/gHPO4-P charge = -2/31), # chu/gHPO4-P HCO3 = c(C = 1, # gC/gHCO3-C O = 3*16/12, # gO/gHCO3-C H = 1*1/12, # gH/gHCO3-C charge = -1/12), # chu/gHCO3-C O2 = c(O = 1), # gO/gO2-O H = c(H = 1, # gH/molH charge = 1), # chu/molH H2O = c(O = 1*12, # gO/molH2O H = 2*1), # gH/molH2O ALG = c(N = 0.06, # gN/gALG P = 0.005, # gP/gALG O = 0.50, # gO/gALG H = 0.07, # gH/gALG C = 0.365), # gC/gALG ZOO = c(N = 0.06, # gN/gZOO P = 0.01, # gP/gZOO O = 0.50, # gO/gZOO H = 0.07, # gH/gZOO C = 0.36), # gC/gZOO POM = c(N = 0.04, # gN/gPOM P = 0.007, # gP/gPOM O = 0.40, # gO/gPOM H = 0.07, # gH/gPOM C = 0.483), # gC/gPOM DOM = c(N = 0.04, # gN/gDOM P = 0.007, # gP/gDOM O = 0.40, # gO/gDOM H = 0.07, # gH/gDOM C = 0.483)) # gC/gDOM alpha <- calc.comp.matrix(subst.comp) print(alpha)
Calculate the basis of the stoichiometry space that is compatible with mass balances of elementary constituents and additional constraints
calc.stoich.basis(alpha, subst = NA, constraints = list(), eps = 1e-5, verbose = TRUE)calc.stoich.basis(alpha, subst = NA, constraints = list(), eps = 1e-5, verbose = TRUE)
alpha |
Substance composition matrix of all substances (labelled columns)
and mass fractions of elementary constituents (labelled rows).
Typically calculated by the function |
subst |
Character vector of names of substances to be used for analysis (this must be a subset of the column names of alpha). |
constraints |
list of stoichiometric constraints in addition to mass conservation of elementary constituents. Each stoichiometric constraint must be stored as a vector containing the coefficients of the linear equation in elementary constituents that defines the constraint. The elements of this vector must be labelled by the names of the corresponding elementary constituents. |
eps |
relative tolerance for checking ratios of stoichiometric coefficients (only used for informing user about substance pairs with fixed stoichiometric ratio) |
verbose |
indicator for whether or not to write basic information to the console. |
This function is primarily used in the function calc.stoich.coef.
However, it can also be used to check the number of required stoichiometric
constraints in addition to mass conservation of elementary constituents
for a given process.
In this case the composition matrix should only contain the substances
relevant for this process.
The number of required constraints is then equal to the row dimension of the
output matrix minus 1.
Matrix of basis vectors (in rows) that span the compatible stoichiometric space.
Peter Reichert <[email protected]>
Reichert, P. and Schuwirth, N., A generic framework for deriving process stoichiometry in environmental models, Environmental Modelling and Software 25, 1241-1251, 2010.
calc.comp.matrix, calc.stoich.coef
subst.comp <- list(NH4 = c(H = 4*1/14, # gH/gNH4-N N = 1, # gN/gNH4-N charge = 1/14), # chu/gNH4-N NO3 = c(O = 3*16/14, # gO/gNO3-N N = 1, # gN/gNO3-N charge = -1/14), # chu/gNO3-N HPO4 = c(O = 4*16/31, # gO/gHPO4-P H = 1*1/31, # gH/gHPO4-P P = 1, # gP/gHPO4-P charge = -2/31), # chu/gHPO4-P HCO3 = c(C = 1, # gC/gHCO3-C O = 3*16/12, # gO/gHCO3-C H = 1*1/12, # gH/gHCO3-C charge = -1/12), # chu/gHCO3-C O2 = c(O = 1), # gO/gO2-O H = c(H = 1, # gH/molH charge = 1), # chu/molH H2O = c(O = 1*12, # gO/molH2O H = 2*1), # gH/molH2O ALG = c(N = 0.06, # gN/gALG P = 0.005, # gP/gALG O = 0.50, # gO/gALG H = 0.07, # gH/gALG C = 0.365), # gC/gALG ZOO = c(N = 0.06, # gN/gZOO P = 0.01, # gP/gZOO O = 0.50, # gO/gZOO H = 0.07, # gH/gZOO C = 0.36), # gC/gZOO POM = c(N = 0.04, # gN/gPOM P = 0.007, # gP/gPOM O = 0.40, # gO/gPOM H = 0.07, # gH/gPOM C = 0.483), # gC/gPOM DOM = c(N = 0.04, # gN/gDOM P = 0.007, # gP/gDOM O = 0.40, # gO/gDOM H = 0.07, # gH/gDOM C = 0.483)) # gC/gDOM Y.ZOO <- 0.2; f.POM <- 0.2; f.DOM <- 0.1 alpha <- calc.comp.matrix(subst.comp) subst.gro.ALG.NO3 <- c("NO3","HPO4","HCO3", "O2","H","H2O","ALG") basis.gro.ALG.NO3 <- calc.stoich.basis(alpha,subst.gro.ALG.NO3) subst.gro.ZOO <- c("NH4","HPO4","HCO3","O2","H", "H2O","ALG","ZOO","POM","DOM") basis.gro.ZOO <- calc.stoich.basis(alpha,subst.gro.ZOO) const.gro.ZOO <- list(c("ZOO" = 1,"ALG" = Y.ZOO), c("POM" = 1,"ALG" = f.POM), c("DOM" = 1,"ALG" = f.DOM)) basis.gro.ZOO <- calc.stoich.basis(alpha,subst.gro.ZOO,const.gro.ZOO)subst.comp <- list(NH4 = c(H = 4*1/14, # gH/gNH4-N N = 1, # gN/gNH4-N charge = 1/14), # chu/gNH4-N NO3 = c(O = 3*16/14, # gO/gNO3-N N = 1, # gN/gNO3-N charge = -1/14), # chu/gNO3-N HPO4 = c(O = 4*16/31, # gO/gHPO4-P H = 1*1/31, # gH/gHPO4-P P = 1, # gP/gHPO4-P charge = -2/31), # chu/gHPO4-P HCO3 = c(C = 1, # gC/gHCO3-C O = 3*16/12, # gO/gHCO3-C H = 1*1/12, # gH/gHCO3-C charge = -1/12), # chu/gHCO3-C O2 = c(O = 1), # gO/gO2-O H = c(H = 1, # gH/molH charge = 1), # chu/molH H2O = c(O = 1*12, # gO/molH2O H = 2*1), # gH/molH2O ALG = c(N = 0.06, # gN/gALG P = 0.005, # gP/gALG O = 0.50, # gO/gALG H = 0.07, # gH/gALG C = 0.365), # gC/gALG ZOO = c(N = 0.06, # gN/gZOO P = 0.01, # gP/gZOO O = 0.50, # gO/gZOO H = 0.07, # gH/gZOO C = 0.36), # gC/gZOO POM = c(N = 0.04, # gN/gPOM P = 0.007, # gP/gPOM O = 0.40, # gO/gPOM H = 0.07, # gH/gPOM C = 0.483), # gC/gPOM DOM = c(N = 0.04, # gN/gDOM P = 0.007, # gP/gDOM O = 0.40, # gO/gDOM H = 0.07, # gH/gDOM C = 0.483)) # gC/gDOM Y.ZOO <- 0.2; f.POM <- 0.2; f.DOM <- 0.1 alpha <- calc.comp.matrix(subst.comp) subst.gro.ALG.NO3 <- c("NO3","HPO4","HCO3", "O2","H","H2O","ALG") basis.gro.ALG.NO3 <- calc.stoich.basis(alpha,subst.gro.ALG.NO3) subst.gro.ZOO <- c("NH4","HPO4","HCO3","O2","H", "H2O","ALG","ZOO","POM","DOM") basis.gro.ZOO <- calc.stoich.basis(alpha,subst.gro.ZOO) const.gro.ZOO <- list(c("ZOO" = 1,"ALG" = Y.ZOO), c("POM" = 1,"ALG" = f.POM), c("DOM" = 1,"ALG" = f.DOM)) basis.gro.ZOO <- calc.stoich.basis(alpha,subst.gro.ZOO,const.gro.ZOO)
Calculate stoichiometric coefficients of a process from involved substances, their composition and constraints
calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)
alpha |
Substance composition matrix of all substances (labelled columns)
and mass fractions of elementary constituents (labelled rows).
Typically calculated by the function |
name |
Name of the process |
subst |
Character vector of names of substances affected by the process (this must be a subset of the column names of alpha) |
subst.norm |
Name of the substance that should have a normalized (given) stoichiometric coefficient |
nu.norm |
Stoichiometric coefficient of the substance the name of which is specified in the argument subst.norm |
constraints |
List of stoichiometric constraints in addition to mass conservation of elementary constituents. Each stoichiometric constraint must be stored as a vector containing the coefficients of the linear equation in elementary constituents that defines the constraint. The elements of this vector must be labelled by the names of the corresponding elementary constituents. |
eps |
relative tolerance for checking ratios of stoichiometric coefficients (only used for informing user about substance pairs with fixed stoichiometric ratio) |
verbose |
indicator for whether or not to write basic information to the console. |
This is the key function of the package for the calculation of stoichiometric coefficients of individual processes. The results for different processes can easily be bound to the comprehensive stoichiometric matrix of all processes by using rbind.
Matrix consisting of one row of stoichiometric coefficients of the process or an error message if the process stoichiometry is not uniquely defined. The row name of the matrix is equal to the process name specified as an argument (to allow binding the stoichiometries of several processes to a comprehensive stoichiometric matrix), the column names are equal to the substance names provided by the substance composition matrix alpha.
Peter Reichert <[email protected]>
Reichert, P. and Schuwirth, N., A generic framework for deriving process stoichiometry in environmental models, Environmental Modelling and Software 25, 1241-1251, 2010.
calc.comp.matrix, calc.stoich.basis
subst.comp <- list(NH4 = c(H = 4*1/14, # gH/gNH4-N N = 1, # gN/gNH4-N charge = 1/14), # chu/gNH4-N NO3 = c(O = 3*16/14, # gO/gNO3-N N = 1, # gN/gNO3-N charge = -1/14), # chu/gNO3-N HPO4 = c(O = 4*16/31, # gO/gHPO4-P H = 1*1/31, # gH/gHPO4-P P = 1, # gP/gHPO4-P charge = -2/31), # chu/gHPO4-P HCO3 = c(C = 1, # gC/gHCO3-C O = 3*16/12, # gO/gHCO3-C H = 1*1/12, # gH/gHCO3-C charge = -1/12), # chu/gHCO3-C O2 = c(O = 1), # gO/gO2-O H = c(H = 1, # gH/molH charge = 1), # chu/molH H2O = c(O = 1*12, # gO/molH2O H = 2*1), # gH/molH2O ALG = c(N = 0.06, # gN/gALG P = 0.005, # gP/gALG O = 0.50, # gO/gALG H = 0.07, # gH/gALG C = 0.365), # gC/gALG ZOO = c(N = 0.06, # gN/gZOO P = 0.01, # gP/gZOO O = 0.50, # gO/gZOO H = 0.07, # gH/gZOO C = 0.36), # gC/gZOO POM = c(N = 0.04, # gN/gPOM P = 0.007, # gP/gPOM O = 0.40, # gO/gPOM H = 0.07, # gH/gPOM C = 0.483), # gC/gPOM DOM = c(N = 0.04, # gN/gDOM P = 0.007, # gP/gDOM O = 0.40, # gO/gDOM H = 0.07, # gH/gDOM C = 0.483)) # gC/gDOM Y.ZOO <- 0.2; f.POM <- 0.2; f.DOM <- 0.1 alpha <- calc.comp.matrix(subst.comp) subst.gro.ALG.NO3 <- c("NO3","HPO4","HCO3", "O2","H","H2O","ALG") basis.gro.ALG.NO3 <- calc.stoich.basis(alpha,subst.gro.ALG.NO3) nu.gro.ALG.NO3 <- calc.stoich.coef(alpha = alpha, name = "gro.ALG.NO3", subst = subst.gro.ALG.NO3, subst.norm = "ALG", nu.norm = 1) subst.gro.ZOO <- c("NH4","HPO4","HCO3","O2","H", "H2O","ALG","ZOO","POM","DOM") basis.gro.ZOO <- calc.stoich.basis(alpha,subst.gro.ZOO) const.gro.ZOO <- list(c("ZOO" = 1,"ALG" = Y.ZOO), c("POM" = 1,"ALG" = f.POM), c("DOM" = 1,"ALG" = f.DOM)) nu.gro.ZOO <- calc.stoich.coef(alpha = alpha, name = "gro.ZOO", subst = subst.gro.ZOO, subst.norm = "ZOO", nu.norm = 1, constraints = const.gro.ZOO) nu <- rbind(nu.gro.ALG.NO3, nu.gro.ZOO) print(nu,digits=2)subst.comp <- list(NH4 = c(H = 4*1/14, # gH/gNH4-N N = 1, # gN/gNH4-N charge = 1/14), # chu/gNH4-N NO3 = c(O = 3*16/14, # gO/gNO3-N N = 1, # gN/gNO3-N charge = -1/14), # chu/gNO3-N HPO4 = c(O = 4*16/31, # gO/gHPO4-P H = 1*1/31, # gH/gHPO4-P P = 1, # gP/gHPO4-P charge = -2/31), # chu/gHPO4-P HCO3 = c(C = 1, # gC/gHCO3-C O = 3*16/12, # gO/gHCO3-C H = 1*1/12, # gH/gHCO3-C charge = -1/12), # chu/gHCO3-C O2 = c(O = 1), # gO/gO2-O H = c(H = 1, # gH/molH charge = 1), # chu/molH H2O = c(O = 1*12, # gO/molH2O H = 2*1), # gH/molH2O ALG = c(N = 0.06, # gN/gALG P = 0.005, # gP/gALG O = 0.50, # gO/gALG H = 0.07, # gH/gALG C = 0.365), # gC/gALG ZOO = c(N = 0.06, # gN/gZOO P = 0.01, # gP/gZOO O = 0.50, # gO/gZOO H = 0.07, # gH/gZOO C = 0.36), # gC/gZOO POM = c(N = 0.04, # gN/gPOM P = 0.007, # gP/gPOM O = 0.40, # gO/gPOM H = 0.07, # gH/gPOM C = 0.483), # gC/gPOM DOM = c(N = 0.04, # gN/gDOM P = 0.007, # gP/gDOM O = 0.40, # gO/gDOM H = 0.07, # gH/gDOM C = 0.483)) # gC/gDOM Y.ZOO <- 0.2; f.POM <- 0.2; f.DOM <- 0.1 alpha <- calc.comp.matrix(subst.comp) subst.gro.ALG.NO3 <- c("NO3","HPO4","HCO3", "O2","H","H2O","ALG") basis.gro.ALG.NO3 <- calc.stoich.basis(alpha,subst.gro.ALG.NO3) nu.gro.ALG.NO3 <- calc.stoich.coef(alpha = alpha, name = "gro.ALG.NO3", subst = subst.gro.ALG.NO3, subst.norm = "ALG", nu.norm = 1) subst.gro.ZOO <- c("NH4","HPO4","HCO3","O2","H", "H2O","ALG","ZOO","POM","DOM") basis.gro.ZOO <- calc.stoich.basis(alpha,subst.gro.ZOO) const.gro.ZOO <- list(c("ZOO" = 1,"ALG" = Y.ZOO), c("POM" = 1,"ALG" = f.POM), c("DOM" = 1,"ALG" = f.DOM)) nu.gro.ZOO <- calc.stoich.coef(alpha = alpha, name = "gro.ZOO", subst = subst.gro.ZOO, subst.norm = "ZOO", nu.norm = 1, constraints = const.gro.ZOO) nu <- rbind(nu.gro.ALG.NO3, nu.gro.ZOO) print(nu,digits=2)