- y
the initial (state) values for the ODE system. If y
has a name attribute, the names will be used to label the output
matrix.
- times
times at which explicit estimates for y are
desired. The first value in times must be the initial time.
- func
either an R-function that computes the values of the
derivatives in the ODE system (the model definition) at time
t, or a character string giving the name of a compiled function in a
dynamically loaded shared library, or a list of symbols returned by
checkDLL.
If func is an R-function, it must be defined as:
func <- function(t, y, parms,...). t is the current
time point in the integration, y is the current estimate of
the variables in the ODE system. If the initial values y has
a names attribute, the names will be available inside func.
parms is a vector or list of parameters; ... (optional) are
any other arguments passed to the function.
The return value of func should be a list, whose first
element is a vector containing the derivatives of y with
respect to time, and whose next elements are global values
that are required at each point in times. The derivatives
must be specified in the same order as the state variables y.
If func is a string, then dllname must give the name
of the shared library (without extension) which must be loaded
before lsoda() is called. See package vignette
"compiledCode" for more
details.
func can also be a list of symbols returned by checkDLL
to avoid overhead from repeated internal calls to this function. It
is an experimental feature for special situations, when a small compiled
model with a low number of integration steps is repeatedly called. It is
currently only available for the lsoda solver, see
example.
- parms
vector or list of parameters used in func or
jacfunc.
- rtol
relative error tolerance, either a scalar or an array as
long as y. See details.
- atol
absolute error tolerance, either a scalar or an array as
long as y. See details.
- jacfunc
if not NULL, an R function, that computes the
Jacobian of the system of differential equations
\(\partial\dot{y}_i/\partial y_j\), or
a string giving the name of a function or subroutine in
dllname that computes the Jacobian (see vignette
"compiledCode" for more about this option).
In some circumstances, supplying
jacfunc can speed up the computations, if the system is
stiff. The R calling sequence for jacfunc is identical to
that of func.
If the Jacobian is a full matrix, jacfunc should return a
matrix \(\partial\dot{y}/\partial y\), where the ith row contains the derivative of
\(dy_i/dt\) with respect to \(y_j\), or a vector containing the
matrix elements by columns (the way R and FORTRAN store matrices).
If the Jacobian is banded, jacfunc should return a matrix
containing only the nonzero bands of the Jacobian, rotated
row-wise. See first example of lsode.
- jactype
the structure of the Jacobian, one of "fullint",
"fullusr", "bandusr" or "bandint" - either
full or banded and estimated internally or by user.
- rootfunc
if not NULL, an R function that computes the
function whose root has to be estimated or a string giving the name
of a function or subroutine in dllname that computes the root
function. The R calling sequence for rootfunc is identical
to that of func. rootfunc should return a vector with
the function values whose root is sought. When rootfunc is
provided, then lsodar will be called.
- verbose
if TRUE: full output to the screen, e.g. will
print the diagnostiscs of the integration - see details.
- nroot
only used if dllname is specified: the number of
constraint functions whose roots are desired during the integration;
if rootfunc is an R-function, the solver estimates the number
of roots.
- tcrit
if not NULL, then lsoda cannot integrate
past tcrit. The FORTRAN routine lsoda overshoots its
targets (times points in the vector times), and interpolates
values for the desired time points. If there is a time beyond which
integration should not proceed (perhaps because of a singularity),
that should be provided in tcrit.
- hmin
an optional minimum value of the integration stepsize. In
special situations this parameter may speed up computations with the
cost of precision. Don't use hmin if you don't know why!
- hmax
an optional maximum value of the integration stepsize. If
not specified, hmax is set to the largest difference in
times, to avoid that the simulation possibly ignores
short-term events. If 0, no maximal size is specified.
- hini
initial step size to be attempted; if 0, the initial step
size is determined by the solver.
- ynames
logical, if FALSE: names of state variables are not
passed to function func; this may speed up the simulation especially
for large models.
- maxordn
the maximum order to be allowed in case the method is
non-stiff. Should be <= 12. Reduce maxord to save storage space.
- maxords
the maximum order to be allowed in case the method is
stiff. Should be <= 5. Reduce maxord to save storage space.
- bandup
number of non-zero bands above the diagonal, in case
the Jacobian is banded.
- banddown
number of non-zero bands below the diagonal, in case
the Jacobian is banded.
- maxsteps
maximal number of steps per output interval taken by the
solver.
- dllname
a string giving the name of the shared library
(without extension) that contains all the compiled function or
subroutine definitions refered to in func and
jacfunc. See package vignette "compiledCode".
- initfunc
if not NULL, the name of the initialisation function
(which initialises values of parameters), as provided in
dllname. See package vignette "compiledCode".
- initpar
only when dllname is specified and an
initialisation function initfunc is in the dll: the
parameters passed to the initialiser, to initialise the common
blocks (FORTRAN) or global variables (C, C++).
- rpar
only when dllname is specified: a vector with
double precision values passed to the dll-functions whose names are
specified by func and jacfunc.
- ipar
only when dllname is specified: a vector with
integer values passed to the dll-functions whose names are specified
by func and jacfunc.
- nout
only used if dllname is specified and the model is
defined in compiled code: the number of output variables calculated
in the compiled function func, present in the shared
library. Note: it is not automatically checked whether this is
indeed the number of output variables calculated in the dll - you have
to perform this check in the code. See package vignette
"compiledCode".
- outnames
only used if dllname is specified and
nout > 0: the names of output variables calculated in the
compiled function func, present in the shared library.
These names will be used to label the output matrix.
- forcings
only used if dllname is specified: a list with
the forcing function data sets, each present as a two-columned matrix,
with (time,value); interpolation outside the interval
[min(times), max(times)] is done by taking the value at
the closest data extreme.
See forcings or package vignette "compiledCode".
- initforc
if not NULL, the name of the forcing function
initialisation function, as provided in
dllname. It MUST be present if forcings has been given a
value.
See forcings or package vignette "compiledCode".
- fcontrol
A list of control parameters for the forcing functions.
See forcings or vignette compiledCode.
- events
A matrix or data frame that specifies events, i.e. when the value of a
state variable is suddenly changed. See events for more information.
- lags
A list that specifies timelags, i.e. the number of steps
that has to be kept. To be used for delay differential equations.
See timelags, dede for more information.
- ...
additional arguments passed to func and
jacfunc allowing this to be a generic function.