R: Histograms and Kernel Density Plots

B_03_histogram {lattice} | R Documentation

## Histograms and Kernel Density Plots

### Description

Draw Histograms and Kernel Density Plots, possibly conditioned on other variables.

### Usage

    histogram(x, data, ...)
    densityplot(x, data, ...)
    ## S3 method for class 'formula'
    histogram(x,
              data,
              allow.multiple, outer = TRUE,
              auto.key = FALSE,
              aspect = "fill",
              panel = lattice.getOption("panel.histogram"),
              prepanel, scales, strip, groups,
              xlab, xlim, ylab, ylim,
              type = c("percent", "count", "density"),
              nint = if (is.factor(x)) nlevels(x)
              else round(log2(length(x)) + 1),
              endpoints = extend.limits(range(as.numeric(x),
                              finite = TRUE), prop = 0.04),
              breaks,
              equal.widths = TRUE,
              drop.unused.levels =
                  lattice.getOption("drop.unused.levels"),
              ...,
              lattice.options = NULL,
              default.scales = list(),
              default.prepanel =
                  lattice.getOption("prepanel.default.histogram"),
              subscripts,
              subset)

    ## S3 method for class 'numeric'
    histogram(x, data = NULL, xlab, ...)
    ## S3 method for class 'factor'
    histogram(x, data = NULL, xlab, ...)

    ## S3 method for class 'formula'
    densityplot(x,
                data,
                allow.multiple = is.null(groups) || outer,
                outer = !is.null(groups),
                auto.key = FALSE,
                aspect = "fill",
                panel = lattice.getOption("panel.densityplot"),
                prepanel, scales, strip, groups, weights,
                xlab, xlim, ylab, ylim,
                bw, adjust, kernel, window, width, give.Rkern,
                n = 50, from, to, cut, na.rm,
                drop.unused.levels =
                    lattice.getOption("drop.unused.levels"),
                ...,
                lattice.options = NULL,
                default.scales = list(),
                default.prepanel =
                    lattice.getOption("prepanel.default.densityplot"),
                subscripts,
                subset)
    ## S3 method for class 'numeric'
    densityplot(x, data = NULL, xlab, ...)

    do.breaks(endpoints, nint)

### Arguments

`x` | The object on which method dispatch is carried out. For the `formula` method, `x` can be a formula of the form `~ x | g1 * g2 * ...`, indicating that histograms or kernel density estimates of the `x` variable should be produced conditioned on the levels of the (optional) variables `g1`, `g2`, .... `x` should be numeric (or possibly a factor in the case of `histogram`), and each of `g1`, `g2`, ... should be either factors or shingles. As a special case, the right hand side of the formula can contain more than one term separated by ‘+’ signs (e.g., `~ x1 + x2 | g1 * g2`). What happens in this case is described in the documentation for `xyplot`. Note that in either form, all the terms in the formula must have the same length after evaluation. For the `numeric` and `factor` methods, `x` is the variable whose histogram or Kernel density estimate is drawn. Conditioning is not allowed in these cases.
`data` | For the `formula` method, an optional data source (usually a data frame) in which variables are to be evaluated (see `xyplot` for details). `data` should not be specified for the other methods, and is ignored with a warning if it is.
`type` | A character string indicating the type of histogram that is to be drawn. `"percent"` and `"count"` give relative frequency and frequency histograms respectively, and can be misleading when breakpoints are not equally spaced. `"density"` produces a density histogram. `type` defaults to `"density"` when the breakpoints are unequally spaced or `breaks = NULL`, and to `"percent"` otherwise.
`nint` | An integer specifying the number of histogram bins, applicable only when `breaks` is unspecified or `NULL` in the call. Ignored when the variable being plotted is a factor.
`endpoints` | A numeric vector of length 2 indicating the range of x-values that is to be covered by the histogram. This applies only when `breaks` is unspecified and the variable being plotted is not a factor. In `do.breaks`, this specifies the interval that is to be divided up.
`breaks` | Usually a numeric vector of length (number of bins + 1) defining the breakpoints of the bins. Note that when breakpoints are not equally spaced, the only value of `type` that makes sense is density. When unspecified, the default is to use
          breaks = seq_len(1 + nlevels(x)) - 0.5
when `x` is a factor, and
          breaks = do.breaks(endpoints, nint)
otherwise. Breakpoints calculated in such a manner are used in all panels. Other values of `breaks` are possible, in which case they affect the display in each panel differently. A special value of `breaks` is `NULL`, in which case the number of bins is determined by `nint` and then breakpoints are chosen according to the value of `equal.widths`. Other valid values of `breaks` are those of the `breaks` argument in `hist`. This allows specification of `breaks` as an integer giving the number of bins (similar to `nint`), as a character string denoting a method, or as a function.
`equal.widths` | A logical flag, relevant only when `breaks=NULL`. If `TRUE`, equally spaced bins will be selected, otherwise, approximately equal area bins will be selected (typically producing unequally spaced breakpoints).
`n` | Integer, giving the number of points at which the kernel density is to be evaluated. Passed on as an argument to `density`.
`panel` | A function, called once for each panel, that uses the packet (subset of panel variables) corresponding to the panel to create a display. The default panel functions `panel.histogram` and `panel.densityplot` are documented separately, and have arguments that can be used to customize its output in various ways. Such arguments can usually be directly supplied to the high-level function.
`allow.multiple, outer` | See `xyplot`.
`auto.key` | See `xyplot`.
`aspect` | See `xyplot`.
`prepanel` | See `xyplot`.
`scales` | See `xyplot`.
`strip` | See `xyplot`.
`groups` | See `xyplot`. Note that the default panel function for `histogram` does not support grouped displays, whereas the one for `densityplot` does.
`xlab, ylab` | See `xyplot`.
`xlim, ylim` | See `xyplot`.
`drop.unused.levels` | See `xyplot`.
`lattice.options` | See `xyplot`.
`default.scales` | See `xyplot`.
`subscripts` | See `xyplot`.
`subset` | See `xyplot`.
`default.prepanel` | Fallback prepanel function. See `xyplot`.
`weights` | numeric vector of weights for the density calculations, evaluated in the non-standard manner used for `groups` and terms in the formula, if any. If this is specified, it is subsetted using `subscripts` inside the panel function to match it to the corresponding `x` values. At the time of writing, `weights` do not work in conjunction with an extended formula specification (this is not too hard to fix, so just bug the maintainer if you need this feature).
`bw, adjust, width` | Arguments controlling bandwidth. Passed on as arguments to `density`.
`kernel, window` | The choice of kernel. Passed on as arguments to `density`.
`give.Rkern` | Logical flag, passed on as argument to `density`. This argument is made available only for ease of implementation, and will produce an error if `TRUE`.
`from, to, cut` | Controls range over which density is evaluated. Passed on as arguments to `density`.
`na.rm` | Logical flag specifying whether `NA` values should be ignored. Passed on as argument to `density`, but unlike in `density`, the default is `TRUE`.
`...` | Further arguments. See corresponding entry in `xyplot` for non-trivial details.

### Details

`histogram` draws Conditional Histograms, and `densityplot` draws Conditional Kernel Density Plots. The default panel function uses the `density` function to compute the density estimate, and all arguments accepted by `density` can be specified in the call to `densityplot` to control the output. See documentation of `density` for details. Note that the default value of the argument `n` of `density` is changed to 50.

These and all other high level Trellis functions have several arguments in common. These are extensively documented only in the help page for `xyplot`, which should be consulted to learn more detailed usage.

`do.breaks` is an utility function that calculates breakpoints given an interval and the number of pieces to break it into.

### Value

An object of class `"trellis"`. The `update` method can be used to update components of the object and the `print` method (usually called by default) will plot it on an appropriate plotting device.

### Note

The form of the arguments accepted by the default panel function `panel.histogram` is different from that in S-PLUS. Whereas S-PLUS calculates the heights inside `histogram` and passes only the breakpoints and the heights to the panel function, lattice simply passes along the original variable `x` along with the breakpoints. This approach is more flexible; see the example below with an estimated density superimposed over the histogram.

### Author(s)

Deepayan Sarkar Deepayan.Sarkar@R-project.org

### References

Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R, Springer. http://lmdvr.r-forge.r-project.org/

### See Also

`xyplot`, `panel.histogram`, `density`, `panel.densityplot`, `panel.mathdensity`, `Lattice`

### Examples

    require(stats)
    histogram( ~ height | voice.part, data = singer, nint = 17,
              endpoints = c(59.5, 76.5), layout = c(2,4), aspect = 1,
              xlab = "Height (inches)")

    histogram( ~ height | voice.part, data = singer,
              xlab = "Height (inches)", type = "density",
              panel = function(x, ...) {
                  panel.histogram(x, ...)
                  panel.mathdensity(dmath = dnorm, col = "black",
                                    args = list(mean=mean(x),sd=sd(x)))
              } )

    densityplot( ~ height | voice.part, data = singer, layout = c(2, 4),
                xlab = "Height (inches)", bw = 5)

[Package lattice version 0.20-6 Index]