rxSolve.Rd
This uses RxODE family of objects, file, or model specification to solve a ODE system.
rxControl( scale = NULL, method = c("liblsoda", "lsoda", "dop853"), transitAbs = NULL, atol = 1e08, rtol = 1e06, maxsteps = 70000L, hmin = 0L, hmax = NA, hmaxSd = 0, hini = 0, maxordn = 12L, maxords = 5L, ..., cores, covsInterpolation = c("locf", "linear", "nocb", "midpoint"), addCov = FALSE, matrix = FALSE, sigma = NULL, sigmaDf = NULL, sigmaLower = Inf, sigmaUpper = Inf, nCoresRV = 1L, sigmaIsChol = FALSE, nDisplayProgress = 10000L, amountUnits = NA_character_, timeUnits = "hours", stiff, theta = NULL, thetaLower = Inf, thetaUpper = Inf, eta = NULL, addDosing = FALSE, stateTrim = Inf, updateObject = FALSE, omega = NULL, omegaDf = NULL, omegaIsChol = FALSE, omegaLower = Inf, omegaUpper = Inf, nSub = 1L, thetaMat = NULL, thetaDf = NULL, thetaIsChol = FALSE, nStud = 1L, dfSub = 0, dfObs = 0, returnType = c("rxSolve", "matrix", "data.frame", "data.frame.TBS", "data.table", "tbl", "tibble"), seed = NULL, nsim = NULL, minSS = 10L, maxSS = 1000L, infSSstep = 12, strictSS = TRUE, params = NULL, events = NULL, istateReset = TRUE, subsetNonmem = TRUE, linLog = FALSE, maxAtolRtolFactor = 0.1, from = NULL, to = NULL, by = NULL, length.out = NULL, iCov = NULL, keep = NULL, drop = NULL, idFactor = TRUE, mxhnil = 0, hmxi = 0, warnIdSort = TRUE, warnDrop = TRUE, ssAtol = 1e08, ssRtol = 1e06, safeZero = TRUE ) rxSolve(object, ...) # S3 method for default rxSolve(object, params = NULL, events = NULL, inits = NULL, ...) # S3 method for rxSolve update(object, ...) # S3 method for RxODE predict(object, ...) # S3 method for rxSolve predict(object, ...) # S3 method for rxEt predict(object, ...) # S3 method for rxParams predict(object, ...) # S3 method for RxODE simulate(object, nsim = 1L, seed = NULL, ...) # S3 method for rxSolve simulate(object, nsim = 1L, seed = NULL, ...) # S3 method for rxParams simulate(object, nsim = 1L, seed = NULL, ...) # S3 method for rxSolve solve(a, b, ...) # S3 method for RxODE solve(a, b, ...) # S3 method for rxParams solve(a, b, ...) # S3 method for rxEt solve(a, b, ...)
scale  a numeric named vector with scaling for ode
parameters of the system. The names must correspond to the
parameter identifiers in the ODE specification. Each of the
ODE variables will be divided by the scaling factor. For
example 

method  The method for solving ODEs. Currently this supports:

transitAbs  boolean indicating if this is a transit compartment absorption 
atol  a numeric absolute tolerance (1e8 by default) used by the ODE solver to determine if a good solution has been achieved; This is also used in the solved linear model to check if prior doses do not add anything to the solution. 
rtol  a numeric relative tolerance (1e6 by default) used by the ODE solver to determine if a good solution has been achieved. This is also used in the solved linear model to check if prior doses do not add anything to the solution. 
maxsteps  maximum number of (internally defined) steps allowed during one call to the solver. (5000 by default) 
hmin  The minimum absolute step size allowed. The default value is 0. 
hmax  The maximum absolute step size allowed. When

hmaxSd  The number of standard deviations of the time difference to add to hmax. The default is 0 
hini  The step size to be attempted on the first step. The default value is determined by the solver (when hini = 0) 
maxordn  The maximum order to be allowed for the nonstiff (Adams) method. The default is 12. It can be between 1 and 12. 
maxords  The maximum order to be allowed for the stiff (BDF) method. The default value is 5. This can be between 1 and 5. 
...  Other arguments including scaling factors for each compartment. This includes S# = numeric will scale a compartment # by a dividing the compartment amount by the scale factor, like NONMEM. 
cores  Number of cores used in parallel ODE solving. This
defaults to the number or system cores determined by

covsInterpolation  specifies the interpolation method for
timevarying covariates. When solving ODEs it often samples
times outside the sampling time specified in

addCov  A boolean indicating if covariates should be added to the output matrix or data frame. By default this is disabled. 
matrix  A boolean indicating if a matrix should be returned instead of the RxODE's solved object. 
sigma  Named sigma covariance or Cholesky decomposition of a covariance matrix. The names of the columns indicate parameters that are simulated. These are simulated for every observation in the solved system. 
sigmaDf  Degrees of freedom of the sigma tdistribution. By
default it is equivalent to 
sigmaLower  Lower bounds for simulated unexplained variability (by default Inf) 
sigmaUpper  Upper bounds for simulated unexplained variability (by default Inf) 
nCoresRV  Number of cores used for the simulation of the
sigma variables. By default this is 1. This uses the package

sigmaIsChol  Boolean indicating if the sigma is in the Cholesky decomposition instead of a symmetric covariance 
nDisplayProgress  An integer indicating the minimum number of cbased solves before a progress bar is shown. By default this is 10,000. 
amountUnits  This supplies the dose units of a data frame supplied instead of an event table. This is for importing the data as an RxODE event table. 
timeUnits  This supplies the time units of a data frame supplied instead of an event table. This is for importing the data as an RxODE event table. 
stiff  a logical ( For stiff ODE systems ( For nonstiff systems ( 
theta  A vector of parameters that will be named THETA[#] and added to parameters 
thetaLower  Lower bounds for simulated population parameter variability (by default Inf) 
thetaUpper  Upper bounds for simulated population unexplained variability (by default Inf) 
eta  A vector of parameters that will be named ETA[#] and added to parameters 
addDosing  Boolean indicating if the solve should add RxODE
EVID and related columns. This will also include dosing
information and estimates at the doses. Be default, RxODE
only includes estimates at the observations. (default

stateTrim  When amounts/concentrations in one of the states are above this value, trim them to be this value. By default Inf. Also trims to stateTrim for large negative amounts/concentrations. If you want to trim between a range say `c(0, 2000000)` you may specify 2 values with a lower and upper range to make sure all state values are in the reasonable range. 
updateObject  This is an internally used flag to update the
RxODE solved object (when supplying an RxODE solved object) as
well as returning a new object. You probably should not
modify it's 
omega  Estimate of Covariance matrix. When omega is a list, assume it is a block matrix and convert it to a full matrix for simulations. 
omegaDf  The degrees of freedom of a tdistribution for
simulation. By default this is 
omegaIsChol  Indicates if the 
omegaLower  Lower bounds for simulated ETAs (by default Inf) 
omegaUpper  Upper bounds for simulated ETAs (by default Inf) 
nSub  Number between subject variabilities (ETAs) simulated for every realization of the parameters. 
thetaMat  Named theta matrix. 
thetaDf  The degrees of freedom of a tdistribution for
simulation. By default this is 
thetaIsChol  Indicates if the 
nStud  Number virtual studies to characterize uncertainty in estimated parameters. 
dfSub  Degrees of freedom to sample the between subject variability matrix from the inverse Wishart distribution (scaled) or scaled inverse chi squared distribution. 
dfObs  Degrees of freedom to sample the unexplained variability matrix from the inverse Wishart distribution (scaled) or scaled inverse chi squared distribution. 
returnType  This tells what type of object is returned. The currently supported types are:

seed  an object specifying if and how the random number generator should be initialized 
nsim  represents the number of simulations. For RxODE, if you supply single subject event tables (created with eventTable) 
minSS  Minimum number of iterations for a steadystate dose 
maxSS  Maximum number of iterations for a steadystate dose 
infSSstep  Step size for determining if a constant infusion has reached steady state. By default this is large value, 420. 
strictSS  Boolean indicating if a strict steadystate is
required. If a strict steadystate is ( 
params  a numeric named vector with values for every parameter in the ODE system; the names must correspond to the parameter identifiers used in the ODE specification; 
events  an 
istateReset  When 
subsetNonmem  subset to NONMEM compatible EVIDs only. By default TRUE. 
linLog  Boolean indicating if linear compartment models be
calculated more accurately in the logspace (slower) By
default this is off ( 
maxAtolRtolFactor  The maximum 
from  When there is no observations in the event table, start observations at this value. By default this is zero. 
to  When there is no observations in the event table, end observations at this value. By default this is 24 + maximum dose time. 
by  When there are no observations in the event table, this
is the amount to increment for the observations between 
length.out  The number of observations to create if there isn't any observations in the event table. By default this is 200. 
iCov  A data frame of individual nontime varying covariates
to combine with the 
keep  Columns to keep from either the input dataset or the

drop  Columns to drop from the output 
idFactor  This boolean indicates if original ID values should be maintained. This changes the default sequentially ordered ID to a factor with the original ID values in the original dataset. By default this is enabled. 
mxhnil  maximum number of messages printed (per problem) warning that T + H = T on a step (H = step size). This must be positive to result in a nondefault value. The default value is 0 (or infinite). 
hmxi  inverse of the maximum absolute value of H to be used. hmxi = 0.0 is allowed and corresponds to an infinite hmax (default). hmin and hmxi may be changed at any time, but will not take effect until the next change of H is considered. This option is only considered with method=liblsoda. 
warnIdSort  Warn if the ID is not present and RxODE assumes the order of the parameters/iCov are the same as the order of the parameters in the input dataset. 
warnDrop  Warn if column(s) were supposed to be dropped, but were not present. 
ssAtol  Steady state atol convergence factor. Can be a vector based on each state. 
ssRtol  Steady state rtol convergence factor. Can be a vector based on each state. 
safeZero  Use safe zero divide and log routines. By default this is turned on but you may turn it off if you wish. 
object  is a either a RxODE family of objects, or a filename with a RxODE model specification, or a string with a RxODE model specification. 
inits  a vector of initial values of the state variables (e.g., amounts in each compartment), and the order in this vector must be the same as the state variables (e.g., PK/PD compartments); 
a  when using 
b  when using 
An “rxSolve” solve object that stores the solved value in a matrix with as many rows as there are sampled time points and as many columns as system variables (as defined by the ODEs and additional assignments in the RxODE model code). It also stores information about the call to allow dynamic updating of the solved object.
The operations for the object are similar to a dataframe, but
expand the $
and [[""]]
access operators and
assignment operators to resolve based on different parameter
values, initial conditions, solver parameters, or events (by
updating the time
variable).
You can call the eventTable
methods on the solved
object to update the event table and resolve the system of
equations.
Hindmarsh, A. C. ODEPACK, A Systematized Collection of ODE Solvers. Scientific Computing, R. S. Stepleman et al. (Eds.), NorthHolland, Amsterdam, 1983, pp. 5564.
Petzold, L. R. Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations. Siam J. Sci. Stat. Comput. 4 (1983), pp. 136148.
Hairer, E., Norsett, S. P., and Wanner, G. Solving ordinary differential equations I, nonstiff problems. 2nd edition, Springer Series in Computational Mathematics, SpringerVerlag (1993).