The ini block controls initial conditions for 'theta' (fixed effects), 'omega' (random effects), and 'sigma' (residual error) elements of the model.
ini(ini, ...)Ini block or nlmixr model object
Other arguments parsed by nlmixr
bounds expression or parsed ui object
'theta' and 'sigma' can be set using either <- or = such as
tvCL <- 1 or equivalently tvCL = 1. 'omega' can be set with a
~.
Parameters can be named or unnamed (though named parameters are preferred).
A named parameter is set using the name on the left of the assignment while
unnamed parameters are set without an assignment operator. tvCL <- 1
would set a named parameter of tvCL to 1. Unnamed parameters
are set using just the value, such as 1.
For some estimation methods, lower and upper bounds can be set for 'theta'
and 'sigma' values. To set a lower and/or upper bound, use a vector of
values. The vector is c(lower, estimate, upper). The vector may be
given with just the estimate (c(estimate)), the lower bound and
estimate (c(lower, estimate)), or all three (c(lower, estimate,
upper)). To set an estimate and upper bound without a lower bound, set the
lower bound to -Inf, c(-Inf, estimate, upper). When an
estimation method does not support bounds, the bounds will be ignored with a
warning.
'omega' values can be set as a single value or as the values of a
lower-triangular matrix. The values may be set as either a
variance-covariance matrix (the default) or as a correlation matrix for the
off-diagonals with the standard deviations on the diagonals. Names may be
set on the left side of the ~. To set a variance-covariance matrix
with variance values of 2 and 3 and a covariance of -2.5 use ~c(2, 2.5,
3). To set the same matrix with names of iivKa and iivCL, use
iivKa + iivCL~c(2, 2.5, 3). To set a correlation matrix with standard
deviations on the diagonal, use cor() like iivKa + iivCL~cor(2,
-0.5, 3).
Values may be fixed (and therefore not estimated) using either the name
fixed at the end of the assignment or by calling fixed() as a
function for the value to fix. For 'theta' and 'sigma', either the estimate
or the full definition (including lower and upper bounds) may be included in
the fixed setting. For example, the following are all effectively equivalent
to set a 'theta' or 'sigma' to a fixed value (because the lower and upper
bounds are ignored for a fixed value): tvCL <- fixed(1), tvCL <-
fixed(0, 1), tvCL <- fixed(0, 1, 2), tvCL <- c(0, fixed(1),
2), or tvCL <- c(0, 1, fixed). For 'omega' assignment, the full
block or none of the block must be set as fixed. Examples of setting
an 'omega' value as fixed are: iivKa~fixed(1), iivKa +
iivCL~fixed(1, 2, 3), or iivKa + iivCL~c(1, 2, 3, fixed). Anywhere
that fixed is used, FIX, FIXED, or fix may be
used equivalently.
For any value, standard mathematical operators or functions may be used to
define the value. For example, exp(2) and 24*30 may be used to
define a value anywhere that a number can be used (e.g. lower bound,
estimate, upper bound, variance, etc.).
Values may be labeled using the label() function after the assignment.
Labels are are used to make reporting easier by giving a human-readable
description of the parameter, but the labels do not have any effect on
estimation. The typical way to set a label so that the parameter tvCL
has a label of "Typical Value of Clearance (L/hr)" is tvCL <- 1;
label("Typical Value of Clearance (L/hr)").
nlmixr will attempt to determine some back-transformations for the
user. For example, CL <- exp(tvCL) will detect that tvCL must
be back-transformed by exp() for easier interpretation. When you want
to control the back-transformation, you can specify the back-transformation
using backTransform() after the assignment. For example, to set the
back-transformation to exp(), you can use tvCL <- 1;
backTransform(exp()).