asreml.control | R Documentation

## Set control parameters for asreml()

### Description

Set various constants and additional arguments for `asreml`.

### Usage

    asreml.control(knots = 50, nsppoints = 21, splinepoints = list(),
                   predictpoints = list(), grid = TRUE, splinescale = -1,
                   spline.step = list(dev = 10000, pol = 10000),
                   pwrpoints = list(), ginverse = list(), mbf = list(),
                   group = list(), Cfixed = FALSE, Csparse = formula("~NULL"),
                   aom = FALSE, equate.levels = character(0), trace = TRUE,
                   maxiter = 13, stepsize = 0.1, workspace = 8e+06,
                   pworkspace = 8e+06, ...)

### Arguments

`knots` | default number of knot points for a spline. The number of knot points used is `min(unique( levels, knots))`.
`nsppoints` | influences the number of points used when predicting splines and polynomials. The design matrix generated by the `pol()` and `spl()` functions are modified to include extra rows used for prediction. The range of the data is divided by n-1 to give a step size i. For each point p in the list, a predict point is inserted at p+i if there is no data value in the interval [p, p+1.1i]. `nsppoints` is ignored if `splinepoints` is set. This process also affects the number of levels identified by `dev()`.
`splinepoints` | a list with named components where each component is a vector of user supplied knot points for a particular spline and the component name is the factor named in the `spl()` function.
`predictpoints` | a list with named components where each component is a list (for two dimensions) or vector (single dimension) of user supplied predict points for `spl(), pol(), dev()`, power or Matern models. If a component of this list is in turn a list of length 2 then the first vector is taken as the x coordinates and the second as the y coordinates. The names of the components of the predictpoints list must match exactly those used in the model functions.
`grid` | a vector controlling the expansion of `predictpoints` lists for 2 dimensional kriging. For a given term, the coordinates for prediction in 2 dimensions are given as component vectors in a list argument within the `predictpoints` tree. If TRUE (the default), the x and y coordinates are expanded to form an (x,y) grid of all possible combinations, otherwise the x and y vectors must be of equal length and are taken in parallel.
`splinescale` | when forming a design matrix for a `spl()` term, a standardised scale (`splinescale = -1`) is used. `splinescale = 1` forces `ASReml` to use the scale of the variable. The default is recommended in most cases.
`spline.step` | a list with components named `dev` and `pol` specifying the resolution for spline deviations and polynomial functions respectively. The default is `list(dev=10000,pol=10000)`. Points closer together than `1/(group.step)` of the range will be treated as a single point.
`pwrpoints` | a named list with each component containing the vector of distances to be used in a one-dimensional power model. The names of the components must match the corresponding model term named in the model formula.
`ginverse` | a named list with each component identifying a G-inverse matrix to include in the analysis. Each matrix can be included in the analysis as: 1. a data frame of three columns containing the non-zero elements of the lower triangle of the matrix. The first two columns of the data frame are the row and column indices and must be named row and column, respectively. This is the structure returned by `ASReml.Ainverse()`. 2. a matrix object. Only the lower triangle is used and NAs are ignored. 3. the complete lower triangle in vector form stored row by row; NAs are ignored. in all cases every diagonal element must be present.
`mbf` | a list specifying a set of covariates to be included with one or more `mbf()` model functions. Each component of the list must in turn contain components named `key` and `dataFrame`, where `dataFrame` is a character string naming the data frame holding the covariates and `key` is a character vector of length 2 naming the columns in `data` and `dataFrame` to match the records.
`group` | a list object with named components where each component is a numeric vector specifying contiguous fields in the data frame that are to be considered as a single term. The component names can then appear in asreml model formulae.
`Cfixed` | if TRUE then the part of the C-inverse matrix that is calculated is returned in component `Cfixed` of the `ASReml` object. `ASReml` does not compute the whole C-inverse matrix but only that which is sufficient to calculate the REML solution.
`Csparse` | if not NULL then a formula object nominating the terms in the sparse component of the model for which available elements of C-inverse are required. A data frame giving the row, column and non-zero element of C-inverse for the nominated terms is returned in component `Csparse` of the `ASReml` object.
`aom` | if TRUE, invokes research results in progress on Alternate Outlier Models and returns standardized conditional residuals and standardized conditional BLUPs in the asreml object.
`equate.levels` | a character vector of factor names whose levels are to be equated. If factor `A` has levels a,b,c,d and factor `B` has levels a,b,c,e, the effect of `equate.levels` is that both `A` and `B` have 5 levels and `as.numeric(A)` = 1,2,3,4 and `as.numeric(B)` = 1,2,3,5. See the `and` model function in the asreml reference manual.
`trace` | if TRUE then partial iteration details are displayed in the console. The component `monitor` of the `ASReml` object is a data frame containing the full convergence sequence. The `tr` method generates a graphical trace of each parameter's convergence sequence.
`maxiter` | maximum number of iterations (default is 10).
`stepsize` | update shrinkage factor. The step size actually used is `sqrt(stepsize)`.
`workspace` | size of workspace for the REML routines measured in double precision words (groups of 8 bytes). The default is `workspace=8e6` (or 64,000,000 bytes).
`pworkspace` | size of workspace for prediction from the linear model measured in double precision words (groups of 8 bytes). The default is `workspace=8e6` (or 64,000,000 bytes).

### Details

The `asreml.control()` argument/value pairs can be given directly in an `ASReml` call. These are then filtered through `asreml.control()` inside `asreml()`.

### Value

a list with components that correspond to each of the above arguments. See the `control` argument of `ASReml`.

### Author(s)

David Butler

### See Also

asreml