modelFunctions {asreml} | R Documentation

## Model term constructor functions.

### Description

This class of special functions constructs model terms with specific properties.

### Usage

    con(obj)

    lin(obj)

    pow(obj, p=1, offset=0)

    pol(obj, t=1, init=NA)

    leg(obj,t=1,init=NA)

    spl(obj, k=0, init=NA)

    dev(obj, init=NA)

    ma(obj)

    at(obj,lvls)

    and(obj, times=1)

    mbf(obj)

    grp(obj)

    dsum(model, levels=NULL, outer=FALSE)

    C(obj, contr)

### Arguments

`obj` | An object in the data frame. `mbf` A component name from the `asreml()` `mbf` list argument. `grp` A component name from the `asreml()` `group` list argument.
`p` | The exponent in a power function term (`pow`).
`offset` | Constant added to `obj`; default 0.
`t` | pol: The maximum degree of a set of orthogonal polynomials formed from `obj`. If negative, the intercept polynomial is omitted. leg: The maximum degree of a set of Legendre polynomials formed from `obj`. If negative, the intercept polynomial is omitted.
`k` | The number of equally spaced knot points for a cubic smoothing spline. If zero or omitted, `k` is set to `asreml.options()$knots` (default 50).
`init` | Optional initial value for the default identity variance model (`idv`) when used in the `random` formula.
`lvls` | Vector of levels of the conditioning factor (`obj`) that define the conditioning covariates formed by `at`. If numeric, `lvls` indexes the levels vector of `obj`; that is, `levels(obj)[lvls]`.
`times` | Multiples (may be non-integer) of the design matrix for `obj` are added to the preceeding design matrix.
`model` | A formula of the form `~A+B+...|Z`, where `A` and `B` define variance matrices for simple or compound model terms, and `Z` is a simple conditioning factor whose levels identify and determine the number of sub-matrices in the direct sum. The `"|"` operator is applied associatively and operates with all terms on its left; that is, `A+B|C` implies `(A+B)|C` and is equivalent to `A|C+B|C`.
`levels` | A list of length the number of terms in the left hand side of `model` that are separated by `"+"`. The components of `levels` are vectors of unique values of `Z`. If there is only one term in the left hand side of `model` (or if the context allows, see examples) then `levels` may be a vector. If `levels` is numeric, then these are ordinal numbers that refer to the sections defined by Z in `unique(Z)` order. If `NULL`, the default is to use `unique(Z)`.
`outer` | if `TRUE`, independent blocks of correlated observations are modelled with common variance and correlation parameters; the blocks can be of different sizes.
`contr` | An integer vector of contrast coefficients parallel to `levels(obj)`.

### Functions

- `asr_con`: Sum to zero constraints.

- `asr_lin`: Create a variate from `obj`.

- `asr_pow`: Creates the model term `(obj+offset)`^p.

- `asr_pol`: Orthogonal polynomials.

- `asr_leg`: Legendre polynomials.

- `asr_spl`: Cubic smoothing spline, random component.

- `asr_dev`: Spline deviations; create a factor from the variate `obj`.

- `asr_ma`: Construct a term with a moving-average order 1 design matrix from `obj`.

- `asr_at`: Form a conditioning covariable from `obj` for each level of `obj` specified in the `lvls` argument.

- `asr_and`: Multiply the design matrix for `obj` by `times` and add it to the preceeding design matrix.

- `asr_mbf`: Create a model term from covariates not stored in `data`.

- `asr_grp`: Create a model term from covariates held in columns of `data`.

- `asr_dsum`: Direct sum structures for residual models.

- `asr_C`: Treatment contrasts

### Examples

    ## Not run:

    ## separable autoregressive residual model at each level of Site
    residual = ~ dsum(~ ar1(Column):ar1(Row) | Site)

    ## different residual models at different levels of site
    ## the ordinals in the levels list refer to the unique values of
    ## Site in unique(Site) order.
    residual = ~ dsum(~ ar1(Column):ar1(Row) + id(Column):ar1(Row) | Site,
                    levels = list(c(1,3), c(2,4)))

    ## equivalent
    residual = ~ dsum(~ ar1(Column):ar1(Row) | Site, levels=c(1,3))
              + dsum(~ id(Column):ar1(Row)  | Site, levels=c(2,4))

    ## "biological" Date within Plot
    residual = ~ dsum(~ ar1(Date) | Plot, outer=TRUE)

    ## "explicit" times
    residual = ~ dsum(~ exp(Date) | Plot, outer=TRUE)

    ## End(Not run)

[Package asreml version 4.1.0.176 Index]