fdyn {dynafluxr} | R Documentation |
Retrieve flux dynamics from metabolic kinetics
Description
Retrieve flux dynamics from metabolic kinetics
Usage
fdyn(
mf,
stofull,
nsp = 4L,
nki = 5L,
lieq = NULL,
monotone = 0,
dls = FALSE,
atomlen = NULL,
npi = 300L,
wsd = FALSE,
nmsf = character(0L),
sderr = NULL,
tol = 1e-10,
regular_grid = TRUE
)
Arguments
mf |
Data-frame or matrix, specie kinetic measurements. Columns must be named with specie names and 'Time'. |
stofull |
Full stoichiometric matrix, |
nsp |
Integer, polynomial order of B-spline to use for species (default 4) |
nki |
Integer, number of internal knots for B-splines (default 5) |
lieq |
List, equality constraints on species (default NULL, i.e. no equality constraint) |
monotone |
Numeric scalar or vector, 1=species are monotonically increasing; -1=monotonically decreasing; 0=no constraint. If vector, each value constraints (or not) a corresponding data column in mf ('Time' column is excluded from counting) (default 0, i.e. no monotonicity constraint) |
dls |
Logical scalar, if TRUE, indicates that differential least squares should be resolved instead of integral least squares. (default FALSE, i.e. ILS will be used) |
atomlen |
Numerical named vector, indicates what is label length
of a given specie used a vector item name. If provided, results
will contain |
npi |
Integer scalar, indicates a number of plot intervals to produce smooth plots. (default 300) |
wsd |
Logical scalar, if TRUE, indicates that differential least squares should be resolved with residuals weighted by a factor of covariance matrix. (default FALSE, i.e. no weighting is used) |
nmsf |
Character vector, list of species for which scaling factor maust be estimated for –dls. |
sderr |
Numeric vector, use this SD of measured metabolites instead of automatically estimated. The name of each vector component is metabolite name, tha value is SD vale, e.g. |
tol |
Double scalar, tolerance for detecting singular matrices and solving linear systems |
regular_grid |
Logical scalar, use regular knot grid (default: TRUE) |
Details
Each item in lieq
corresponds to a specie and is a
2 column matrix (Time, Value). Each
row of this matrix indicates what 'Value' must take corresponding
specie at what 'Time'. Typically, it can be used to impose
starting values at Time=0 for some species.
All specie fits are constraint to have values >= 0.
Value
List with following components:
- mf:
specie data frame used for fitting
- tp:
vector of time points for used measurements
- tpp:
vector of time points for plot (fine time resolution)
- sto:
stoichiometric matrix used for fitting
- stofull:
stoichiometric matrix before a possible NA elimination
- stoinv:
pseudo-inverse of sto
- msp:
measured specie spline function
- vsp:
estimated rates spline function
- fsp:
estimated total flux (S*v) spline function
- dsp:
first derivative of measured spline function
- isp:
integrated specie spline function
- asp:
atom balance over msp spline function
- iasp:
atom balance over isp spline function
- vsp:
flux spline function
- dsp:
measured specie first derivative spline function
- rsp:
residual
dM/dt - S%*%v
spline function- risp:
integral residual
M - \u222bS%*%v dt
spline function- sdrate:
matrix of SD values for flux B-spline coefficients, of size (
ncoef x nrate
)- chi2tab:
data-frame with chi2-test results
- sf:
named scale factor vector
- internal_knot_ref:
number of internal knots used for estimation of var_ref