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# ==============================================================================
# STOICHCALC - R-Routines for Solving Stoichiometric Equations
# ==============================================================================
#
# Example corresponding to section 5.1 of the paper cited below 22.02.2010
# =============================================================
#
# Literature: Peter Reichert and Nele Schuwirth
# A generic framework for deriving process stoichiometry
# in environmental models
# submitted to Environmental Modelling and Software
#
# ==============================================================================
# load library functions:
# =======================
library("stoichcalc")
# Define composition:
# ===================
# define composition parameters:
# ------------------------------
param <- list(a.N.ALG = 0.06, # gN/gALG
a.P.ALG = 0.01) # gP/gALG
# define composition vectors of substances:
# -----------------------------------------
NH4 <- c(N = 1) # gN/gNH4-N
HPO4 <- c(P = 1) # gP/gHPO4-P
ALG <- c(N = param$a.N.ALG, # gN/gALG
P = param$a.P.ALG) # gP/gALG
# define list of composition vectors:
# -----------------------------------
subst.comp <- list(NH4 = NH4,
HPO4 = HPO4,
ALG = ALG)
# compile and print composition matrix:
# -------------------------------------
alpha <- calc.comp.matrix(subst.comp)
print(alpha,digits=2)
# Derivation of Process Stoichiometry:
# ====================================
# calculate stoichiometries of growth and respiration processes:
# --------------------------------------------------------------
# growth of algae:
subst.gro.ALG.NH4 <- c("NH4","HPO4","ALG")
basis <- calc.stoich.basis(alpha = alpha,
subst = subst.gro.ALG.NH4)
nu.gro.ALG.NH4 <- calc.stoich.coef(alpha = alpha,
name = "gro.ALG.NH4",
subst = subst.gro.ALG.NH4,
subst.norm = "ALG",
nu.norm = 1)
# respiration of algae:
subst.resp.ALG <- c("NH4","HPO4","ALG")
basis <- calc.stoich.basis(alpha = alpha,
subst = subst.resp.ALG)
nu.resp.ALG <- calc.stoich.coef(alpha = alpha,
name = "resp.ALG",
subst = subst.resp.ALG,
subst.norm = "ALG",
nu.norm = -1)
# compile and print stoichiometric matrix of all processes:
# ---------------------------------------------------------
nu <- rbind(nu.gro.ALG.NH4,
nu.resp.ALG)
print(nu,digits=2)
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