The ini block controls initial conditions for 'theta' (fixed effects), 'omega' (random effects), and 'sigma' (residual error) elements of the model.

## Usage

```
# S3 method for rxUi
ini(x, ..., envir = parent.frame(), append = NULL)
# S3 method for `function`
ini(x, ..., envir = parent.frame(), append = NULL)
# S3 method for rxode2
ini(x, ..., envir = parent.frame(), append = NULL)
# S3 method for rxModelVars
ini(x, ..., envir = parent.frame(), append = NULL)
ini(x, ..., envir = parent.frame(), append = NULL)
# S3 method for default
ini(x, ...)
```

## Arguments

- x
expression

- ...
Other expressions for

`ini()`

function- envir
the

`environment`

in which unevaluated model expressions is to be evaluated. May also be`NULL`

, a list, a data frame, a pairlist or an integer as specified to`sys.call`

.- append
Reorder theta parameters.

`NULL`

means no change to parameter order. A parameter name (as a character string) means to put the new parameter after the named parameter. A number less than or equal to zero means to put the parameter at the beginning of the list. A number greater than the last parameter number means to put the parameter at the end of the list.

## Details

'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)")
```

.

`rxode2`

/`nlmixr2`

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())
```

.