R: Set or return options of sm library

sm.options {sm} | R Documentation

## Set or return options of sm library

### Description

This function provides a means to control the behaviour of the `sm` library such as the colour of the plotted lines, the size of the grid in 2-d estimation, the set of evaluations points, and many others. A list may be given as the only argument, or any number of arguments may be in the `name=value` form. If no arguments are specified then the function returns the current settings of all the arguments.

### Usage

    sm.options(...)

### Arguments

`...` | A list may be given as the only argument, or any number of arguments may be in the `name=value` form. The valid names of the arguments are given below.

add

  a logical value which controls whether the estimate is added to the current plot. Its default value is `FALSE`, which creates a new plot. This argument applies only with one-dimensional data or to contour and `rgl` created from two-dimensional data.

alpha

  an parameter, lying between 0 and 1, which controls the transparency of the surface used to construct an `rgl` plot for regression with two covariates. The default value is `0.7`.

alpha.mesh

  an parameter, lying between 0 and 1, which controls the transparency of the mesh lines used to construct an `rgl` plot for regression with two covariates. The default value is `1`.

band

  a logical value which controls whether the distance between the nonparametric estimate and a reference model should be indicated as a band (one covariate), or through colour painting of the regression surface (two covariates). This is activated only when a model has been nominated through the `model` parameter. In the case of two covariates, the setting of the argument `col` has priority over `band`. The setting `se = TRUE` can also activate this feature.

col

  the colour used for plotting observed points and estimated curves. Where groups are used, with one covariate, `col` may be set to a vector of colours associated with the groups. In regression with two covariates using an `rgl` display, `col` may be set to a single colour, or to the values `"height"` or `"se"`. These letter two setting cause the surface to be painted according to its height or to standard error information; see the information on the parameters `se`, `se.breaks` and `model`. Default: `col=1`.

col.band

  the colour used for the reference band when a `model` is specified in regression with one covariate. Default: `col.band="cyan"`.

col.mesh

  the colour used for the ‘wire mesh’ representation plotting observed points in an rgl display for regression with two covariates. This can also be set by the second component of a vector of length two which is set for `col`. Default: `col.mesh="black"`.

col.palette

  the colours used for shading an image plot, or for surface painting in an rgl display, for regression with two covariates. Default: `col.palette=topo.colors(12)`.

col.points

  the colour used for plotting observed points in a regression with one covariate or an `rgl` display for regression with two covariates. Default: `col.points="black"`.

delta

  in `sm.density`, a value which will be added to the data before they are log transformed in the procedure to handle positive data. The value of `delta` is used only when `positive` takes the value `TRUE`. The default value is the smallest value observed in each dimension. This argument does not apply with three-dimensional data. Default: `delta=NA`

describe

  logical flag whiich affects the behaviour of `sm.script` and `provide.data`. If `describe=TRUE` (default), a data documentation file is printed.

df

  approximate degrees-of-freedom of the smoothing parameter used in `sm.regression`, when a numerical value of `h` is not specified. In this case, the equivalent value of `h` will be computed and included in the list returned on exit from `sm.regression`. Default value is 6 if `x` is a vector and 12 if `x` is a matrix.

diff.ord

  in `sm.regression`, an integer defining the degree of differencing to be applied in the estimation process. When this argument is set to 1, the method of Rice, based on the squared differences of pairs of neighbouring observations, is used. When the argument is set to 2 (deafult), the method of Gasser, Sroka and Jennen-Steinmetz, based on differences between each observation and a linear interplotation from its two neighbours, is used.

display

  This argument applies only with one- or two-dimensional data. The setting `"none"` will prevent any graphical output from being produced. In one dimensions, the default setting `"line"` will produce the estimate. (For compatibility with earlier versions of the package, the setting `"se"` will produce a variability band to show the variability, but not the bias, of the estimate. This should now be controlled by setting the separate parameter `se` to `TRUE`.) In two dimensions, the default setting `"persp"` will produce a perspective plot of the estimate, while the settings `"slice"`, `"image"` and `"rgl"` will produce slice (contour), image or `rgl` plots.

eval.grid

  logical flag which controls how the options `eval.points` are used fow two-dimensional data. If `eval.grid=TRUE` (default), evaluation is perfomed at points obtained by the cross-product of the two columns of `eval.points`. If `eval.grid=FALSE` then evaluation is performed at points with coordinates specified by the coordinates in `eval.points`

eval.points

  the points at which the density or the regression curve or surface estimate should be evaluated, for the values returned in the result of the function. This should be a vector for one-dimensional data and a two-column matrix for two-dimensional data. This argument does not apply with three-dimensional data.

h.weights

  a vector of weights which multiply the smoothing parameter used in the kernel function at each observation. This argument does not apply with three-dimensional data. Default value: 1.

hmult

  a factor which can be used to multiply the normal smoothing parameter before construction of the density estimate. Default value: 1.

hull

  a logical value which controls whether the estimate is evaluated and plotted only on grid points which fall within the convex hull of the data. When this argument is set to `FALSE`, evaluation and plotting take place at all grid points where the contribution from at least one kernel function is non-negligible. Both of these settings ensure that the estimate is not evaluated at points where there are no observations nearby. This argument applies only to `sm.regression` and `sm.discontinuity` in the case of two covariates.

lty

  the line type used to plot the estimate. This argument applies only when the estimate is displayed as a curve or a countour. Default value: 1.

method

  the method used to select smoothing parameters. In density estimation the default is `"normal"` which uses a value which is asymptotically optimal for the normal distribution. Other possibilities are `"cv"` for cross-validation and `"sj"` for the Sheather-Jones method. In nonparametric regression, the deault is `"df"` which selects a smoothing parameters associated with the approximate degrees of freedom given in the `df` option. Other possibilities are `"cv"` for cross-validation and `"aicc"` for an AIC-based method proposed by Hurvich, Simonoff and Tsai.

nbins

  the number of bins used in one-dimensional binning operations; in two-dimensional cases, `nbins` refers to the number of bins formed along each axis. Bins with 0 observed frequencies are ignored. If `nbins=0`, binning is not performed; if `nbins=NA` (default), binning is switched on when the number of observations exceeds a certain threshold, which depends on the function.

nboot

  number of samples generated in bootstraps. Default value: 100.

ngrid

  the number of points in the regular grid used to plot the estimate. For two- and three-dimensional data, `ngrid` refers to the number of points along the axis in each dimension. The same parameter is also used by a few other functions which perform some form of search (e.g. `hcv`). Default value for `sm.regression`: 50 and 20 for 1-, 2-dimensional data, respectively. Default value for `sm.density`: 100, 50 and 20 for 1-, 2- and 3-dimensional data, respectively.

panel

  a logical value which, when set to true, creates a panel which allows interactive control of `sm.regression` or `sm.density` plots for one- or two-dimensional data. The panel can be used to alter the value of the smoothing parameter and control a variety of other settings.

panel.plot

  a logical value which, when set to true (the default), places the plot inside the control panel (see the `panel` argument above), This creates a neater screen arrangement.

pch

  the standard plotting charater identified for data plotting. Default value: 1.

period

  a vector of length one or two identifying the period for covariates which are on a periodic scale. Periodic smoothing is implemented by local mean estimation, using a von Mises kernel function. Non-periodic covariates are identified by NA. Default value: NA.

phi

  the vertical rotation (in degrees) of perspective plots of estimate in the form of surfaces. Default value: 40.

poly.index

  an integer defining local constant (0) or local linear (1) smoothing. Default value: 1.

positive

  a logical value which indicates whether the data should be assumed to take positive values only, in `sm.density`. When this argument is set to `TRUE`, a log transformation is applied to the data before construction of a density estimate. The result is transformed back to the original scale. This argument does not apply with three-dimensional data. Default value: `FALSE`.

props

  a vector defining the proportions of the data to be included within each contour in a slice plot, from two-dimensional data, or a contour surface plot, from three-dimensional data. In the three-dimensional case only the first element of the vector will be used. This argument does not apply to one-dimensional data. Default value: `c(75,50,25)`.

rugplot

  logical flag which regulates whether a rugplot is superimposed to the density estimate, in the univariate case. Default value: `TRUE`.

se

  logical flag which regulates whether a standard error information is added to the plot produced by `sm.regression`. If a `model` is specified, then these standard errors refer to the difference between this fitted model and the nonparametric regression estimate. Default value: `TRUE`.

se.breaks

  a numerical vector which defines the cut-points, on a standard error scale, for the assignment of colours when painting a regression surface with standard error information. Default value: `c(-3, -2, 3, 3)`.

show.script

  logical flag which affects the behaviour of `sm.script` when this is called with non-empty argument. If `show.script=TRUE` (default) a window is opened to display the source code of the script.

size

  an integer which defines the size of plotted points in `rgl` displays. The default value is `2`.

structure.2d

  the structure of the smoothing parameter in two-dimensional settings. The default is `"scaled"`, which uses the structure (h*sd(x[,1]), h*sd(x[,2])). Other possibilities are `"separate"`, which uses (h1, h2), and `"common"` which uses (h, h). The `"common"` option may be particularly appropriate when the data have a spatial origin, where distances in each variable havae the same meaning. Note that the `"separate"` option is not available when `"method"` is set to `"df"`.

test

  a logical flag controlling the production of a formal test, using the reference model as the null hypothesis. Default value: `TRUE`.

theta

  the horizontal rotation (in degrees) of perspective plots of estimates in the form of surfaces. Default value: -30.

verbose

  regulates the amount of messages and other output printed out. If `verbose=0` only errors produce messages; if `verbose=1` (default value) warnings and the more relevant numerical output are printed ; if `verbose=2` more messages and more numerical output are printed.

xlab

  the label attached to the x-axis.

xlim

  the range of the horizontal axis of the plot. This argument does not apply with three-dimensional data.

yht

  the upper limit of the vertical axis in a plot of a one-dimensional density estimate. The lower limit is always set to 0. This argument does not apply with two- or three-dimensional data.

ylab

  the label attached to the y-axis.

ylim

  the range of the vertical axis of the plot. This argument does not apply with three-dimensional data.

zlab

  the label attached to the z-axis (three-dimensional plots only).

zlim

  the range of the vertical axis when estimates are displayed as perspective plots.

### Details

Arguments which are set by a function call will remain in effect until the end of the current S-plus session, unless overwritten by a subsequent call. In addition, they can be added as optional parameters of calls to specific functions of the `sm` package; in this case, their effect is limited to that function call.

See the documentation of specific functions for the list of options which are recognised by that function. Notice that some options are relevant only to some functions.

### Value

a list with the updated values of the parameters. If the argument list is not empty, the returned list is invisible.

### Examples

    ## Not run: sm.options(poly.index = 0)
    # subsequent regression estimations will be performed using local means
    # instead of local regression
    #
    sm.options(describe = FALSE)
    # turns off typing documentation files of data loaded by `sm.script'
    # (works from command-line)
    #

    ## End(Not run)

[Package sm version 2.2-5.4 Index]