nlminbControl {nlmixr2} | R Documentation |
nlmixr2 nlminb defaults
Description
nlmixr2 nlminb defaults
Usage
nlminbControl(
eval.max = 200,
iter.max = 150,
trace = 0,
abs.tol = 0,
rel.tol = 1e-10,
x.tol = 1.5e-08,
xf.tol = 2.2e-14,
step.min = 1,
step.max = 1,
sing.tol = rel.tol,
scale = 1,
scale.init = NULL,
diff.g = NULL,
rxControl = NULL,
optExpression = TRUE,
sumProd = FALSE,
literalFix = TRUE,
returnNlminb = FALSE,
solveType = c("hessian", "grad", "fun"),
stickyRecalcN = 4,
maxOdeRecalc = 5,
odeRecalcFactor = 10^(0.5),
eventType = c("central", "forward"),
shiErr = (.Machine$double.eps)^(1/3),
shi21maxFD = 20L,
optimHessType = c("central", "forward"),
hessErr = (.Machine$double.eps)^(1/3),
shi21maxHess = 20L,
useColor = crayon::has_color(),
printNcol = floor((getOption("width") - 23)/12),
print = 1L,
normType = c("rescale2", "mean", "rescale", "std", "len", "constant"),
scaleType = c("nlmixr2", "norm", "mult", "multAdd"),
scaleCmax = 1e+05,
scaleCmin = 1e-05,
scaleC = NULL,
scaleTo = 1,
gradTo = 1,
addProp = c("combined2", "combined1"),
calcTables = TRUE,
compress = TRUE,
covMethod = c("r", "nlminb", ""),
adjObf = TRUE,
ci = 0.95,
sigdig = 4,
sigdigTable = NULL,
...
)
Arguments
eval.max |
Maximum number of evaluations of the objective function allowed. Defaults to 200. |
iter.max |
Maximum number of iterations allowed. Defaults to 150. |
trace |
The value of the objective function and the parameters is printed every trace'th iteration. When 0 no trace information is to be printed |
abs.tol |
Absolute tolerance. Defaults to 0 so the absolute convergence test is not used. If the objective function is known to be non-negative, the previous default of '1e-20' would be more appropriate |
rel.tol |
Relative tolerance. Defaults to '1e-10'. |
x.tol |
X tolerance. Defaults to '1.5e-8'. |
xf.tol |
false convergence tolerance. Defaults to '2.2e-14'. |
step.min |
Minimum step size. Default to ‘1.’. |
step.max |
Maximum step size. Default to ‘1.’. |
sing.tol |
singular convergence tolerance; defaults to 'rel.tol;. |
scale |
See PORT documentation (or leave alone). |
scale.init |
... probably need to check PORT documentation |
diff.g |
an estimated bound on the relative error in the objective function value |
rxControl |
'rxode2' ODE solving options during fitting, created with 'rxControl()' |
optExpression |
Optimize the rxode2 expression to speed up calculation. By default this is turned on. |
sumProd |
Is a boolean indicating if the model should change
multiplication to high precision multiplication and sums to
high precision sums using the PreciseSums package. By default
this is |
literalFix |
boolean, substitute fixed population values as literals and re-adjust ui and parameter estimates after optimization; Default is 'TRUE'. |
returnNlminb |
logical; when TRUE this will return the nlminb result instead of the nlmixr2 fit object |
solveType |
tells if ‘nlm' will use nlmixr2’s analytical gradients when available (finite differences will be used for event-related parameters like parameters controlling lag time, duration/rate of infusion, and modeled bioavailability). This can be: - '"hessian"' which will use the analytical gradients to create a Hessian with finite differences. - '"gradient"' which will use the gradient and let 'nlm' calculate the finite difference hessian - '"fun"' where nlm will calculate both the finite difference gradient and the finite difference Hessian When using nlmixr2's finite differences, the "ideal" step size for either central or forward differences are optimized for with the Shi2021 method which may give more accurate derivatives |
stickyRecalcN |
The number of bad ODE solves before reducing the atol/rtol for the rest of the problem. |
maxOdeRecalc |
Maximum number of times to reduce the ODE tolerances and try to resolve the system if there was a bad ODE solve. |
odeRecalcFactor |
The ODE recalculation factor when ODE solving goes bad, this is the factor the rtol/atol is reduced |
eventType |
Event gradient type for dosing events; Can be "central" or "forward" |
shiErr |
This represents the epsilon when optimizing the ideal step size for numeric differentiation using the Shi2021 method |
shi21maxFD |
The maximum number of steps for the optimization of the forward difference step size when using dosing events (lag time, modeled duration/rate and bioavailability) |
optimHessType |
The hessian type for when calculating the individual hessian by numeric differences (in generalized log-likelihood estimation). The options are "central", and "forward". The central differences is what R's 'optimHess()' uses and is the default for this method. (Though the "forward" is faster and still reasonable for most cases). The Shi21 cannot be changed for the Gill83 algorithm with the optimHess in a generalized likelihood problem. |
hessErr |
This represents the epsilon when optimizing the Hessian step size using the Shi2021 method. |
shi21maxHess |
Maximum number of times to optimize the best step size for the hessian calculation |
useColor |
Boolean indicating if focei can use ASCII color codes |
printNcol |
Number of columns to printout before wrapping parameter estimates/gradient |
print |
Integer representing when the outer step is printed. When this is 0 or do not print the iterations. 1 is print every function evaluation (default), 5 is print every 5 evaluations. |
normType |
This is the type of parameter
normalization/scaling used to get the scaled initial values
for nlmixr2. These are used with With the exception of In general, all all scaling formula can be described by:
= (
)/
Where The other data normalization approaches follow the following formula
= (
)/
|
scaleType |
The scaling scheme for nlmixr2. The supported types are:
|
scaleCmax |
Maximum value of the scaleC to prevent overflow. |
scaleCmin |
Minimum value of the scaleC to prevent underflow. |
scaleC |
The scaling constant used with
These parameter scaling coefficients are chose to try to keep similar slopes among parameters. That is they all follow the slopes approximately on a log-scale. While these are chosen in a logical manner, they may not always apply. You can specify each parameters scaling factor by this parameter if you wish. |
scaleTo |
Scale the initial parameter estimate to this value. By default this is 1. When zero or below, no scaling is performed. |
gradTo |
this is the factor that the gradient is scaled to before optimizing. This only works with scaleType="nlmixr2". |
addProp |
specifies the type of additive plus proportional errors, the one where standard deviations add (combined1) or the type where the variances add (combined2). The combined1 error type can be described by the following equation:
The combined2 error model can be described by the following equation:
Where: - y represents the observed value - f represents the predicted value - a is the additive standard deviation - b is the proportional/power standard deviation - c is the power exponent (in the proportional case c=1) |
calcTables |
This boolean is to determine if the foceiFit
will calculate tables. By default this is |
compress |
Should the object have compressed items |
covMethod |
Method for calculating covariance. In this discussion, R is the Hessian matrix of the objective function. The S matrix is the sum of individual gradient cross-product (evaluated at the individual empirical Bayes estimates).
|
adjObf |
is a boolean to indicate if the objective function
should be adjusted to be closer to NONMEM's default objective
function. By default this is |
ci |
Confidence level for some tables. By default this is 0.95 or 95% confidence. |
sigdig |
Optimization significant digits. This controls:
|
sigdigTable |
Significant digits in the final output table. If not specified, then it matches the significant digits in the 'sigdig' optimization algorithm. If 'sigdig' is NULL, use 3. |
... |
Additional arguments passed to |
Author(s)
Matthew L. Fidler
Examples
# A logit regression example with emax model
dsn <- data.frame(i=1:1000)
dsn$time <- exp(rnorm(1000))
dsn$DV=rbinom(1000,1,exp(-1+dsn$time)/(1+exp(-1+dsn$time)))
mod <- function() {
ini({
E0 <- 0.5
Em <- 0.5
E50 <- 2
g <- fix(2)
})
model({
v <- E0+Em*time^g/(E50^g+time^g)
ll(bin) ~ DV * v - log(1 + exp(v))
})
}
fit2 <- nlmixr(mod, dsn, est="nlminb")
print(fit2)
# you can also get the nlm output with fit2$nlminb
fit2$nlminb