spam (version 2.11-0)

options: Options Settings

Description

Allow the user to set and examine a variety of options which affect the way in which R computes and displays sparse matrix results.

Value

For getOption, the current value set for option x, or

NULL if the option is unset.

For options(), a list of all set options sorted by category. For

options(name), a list of length one containing the set value, or NULL if it is unset. For uses setting one or more options, a list with the previous values of the options changed (returned invisibly).

Options used for the package <code>spam</code>

A short description with the default values follows.

spam.eps=.Machine$double.eps:

values smaller than this are considered as zero. This is only used when creating spam objects.

spam.drop=FALSE:

default parameter for drop when subsetting

spam.printsize=100:

the max number of elements of a matrix which we display as regular matrix.

spam.imagesize=10000:

the max number of elements of a matrix we display as regular matrix with image or display. Larger matrices are represented as dots only.

spam.cex=1200:

default dot size for image or display.

spam.structurebased=FALSE:

should operations be carried out on the nonzero entries (the structure) or including the zeros.

spam.inefficiencywarning=1e6:

issue a warning when inefficient operations are performed and the matrix exceeds the specified size. Valid value is a postive integer or a logical. TRUE corresponds to 1 (always), FALSE to Inf.

spam.trivalues=FALSE:

a flag whether to return the structure (FALSE) or the values themselves (TRUE) when returning the upper and lower triangular part of a matrix.

spam.listmethod="PE":

algorithm for spam.list. Default is suggestion by Paul Eilers (thanks). Any other specification uses a bubble sort algorithm which is only slightly faster for very sparse matrices.

spam.dopivoting=TRUE:

default parameter for "solve" routines. FALSE would solve the system without using the permutation.

spam.NAOK=FALSE:

logical determines if NA, NaN and Inf are allowed to Fortan. Setting to TRUE allows to work with these but full functionality has not been tested.

spam.safemodevalidity=TRUE:

logical determines if sanity check is peformed when constructing sparse matrices. Default is safer but somewhat slower.

spam.cholsymmetrycheck=TRUE:

for the Cholesky factorization, verify if the matrix is symmetric.

spam.cholpivotcheck=TRUE:

for the Cholesky factorization, when passing a permutation, should a minimum set of checks be performed?

spam.cholupdatesingular="warning":

for a Cholesky update, what happens if the matrix is singular: "warning" only and returning the not updated factor, "error" or return simply "NULL".

spam.cholincreasefactor=c(1.25,1.25):

If not enought memory could be allocated, these are the steps to increase it.

spam.nnznearestdistnnz=c(400^2,400):

Memory allocation parameters for nearest.dist.

spam.nearestdistincreasefactor=1.25:

If not enought memory could be allocated, this is the step to increase it.

Details

Invoking options() with no arguments returns a list with the current values of the options. To access the value of a single option, one should use getOption("spam.eps"), e.g., rather than options("spam.eps") which is a list of length one.

Of course, printing is still subordinate to getOption("max.print") or similar options.

See Also

Functions influenced by these options include: print.spam, display.spam, image.spam, upper.tri.spam, chol.spam, nearest.dist, etc.
powerboost

Examples

smat <- diag.spam( 1:8)
smat
options(spam.printsize=49)
smat

# List all spam options:
options()[grep("spam",names(options()))]

# Reset to default values:
options(spam.eps=.Machine$double.eps,
        spam.drop=FALSE,
        spam.printsize=100,
        spam.imagesize=10000,
        spam.cex=1200,
        spam.structurebased=FALSE,
        spam.inefficiencywarning=1e6,
        spam.trivalues=FALSE,
        spam.listmethod="PE",
        spam.NAOK=FALSE,
        spam.safemodevalidity=TRUE,
        spam.dopivoting=TRUE,
        spam.cholsymmetrycheck=TRUE,
        spam.cholpivotcheck=TRUE,
        spam.cholupdatesingular="warning",
        spam.cholincreasefactor=c(1.25,1.25),
        spam.nearestdistincreasefactor=1.25,
        spam.nearestdistnnz=c(400^2,400))