shadings {vcd} | R Documentation

## Shading-generating Functions for Residual-based Shadings

### Description

Shading-generating functions for computing residual-based shadings for mosaic and association plots.

### Usage

    shading_hcl(observed, residuals = NULL, expected = NULL, df = NULL,
      h = NULL, c = NULL, l = NULL, interpolate = c(2, 4), lty = 1,
      eps = NULL, line_col = "black", p.value = NULL, level = 0.95, ...)

    shading_hsv(observed, residuals = NULL, expected = NULL, df = NULL,
      h = c(2/3, 0), s = c(1, 0), v = c(1, 0.5),
      interpolate = c(2, 4), lty = 1, eps = NULL, line_col = "black",
      p.value = NULL, level = 0.95, ...)

    shading_max(observed = NULL, residuals = NULL, expected = NULL, df = NULL,
      h = NULL, c = NULL, l = NULL, lty = 1, eps = NULL, line_col = "black",
      level = c(0.9, 0.99), n = 1000, ...)

    shading_Friendly(observed = NULL, residuals = NULL, expected = NULL, df = NULL,
      h = c(2/3, 0), lty = 1:2, interpolate = c(2, 4),
      eps = 0.01, line_col = "black", ...)

    shading_binary(observed = NULL, residuals = NULL, expected = NULL, df = NULL,
      col = hcl(c(260, 0), 50, 70))

### Arguments

`observed` | contingecy table of observed values
`residuals` | contingecy table of residuals
`expected` | contingecy table of expected values
`df` | degrees of freedom of the associated independence model.
`h` | hue value in the HCL or HSV color description, has to be in [0, 360] for HCL and in [0, 1] for HSV colors. The default is to use blue and red for positive and negative residuals respectively. In the HCL specification it is `c(260, 0)` by default and for HSV `c(2/3, 0)`.
`c` | chroma value in the HCL color description. This controls the maximum chroma for significant and non-significant results respectively and defaults to `c(100, 20)`.
`l` | luminance value in the HCL color description. Defaults to `c(90, 50)` for small and large residuals respectively.
`s` | saturation value in the HSV color description. Defaults to `c(1, 0)` for large and small residuals respectively.
`v` | saturation value in the HSV color description. Defaults to `c(1, 0.5)` for significant and non-significant results respectively.
`interpolate` | a specification for mapping the absolute size of the residuals to a value in [0, 1]. This can be either a function or a numeric vector. In the latter case, a step function with steps of equal size going from 0 to 1 is used.
`lty` | a vector of two line types for positive and negative residuals respectively. Recycled if necessary.
`eps` | numeric tolerance value below which absolute residuals are considered to be zero, which is used for coding the border color. If set to `NULL` (default), all borders have the default color specified by `line\_col`. If set to a numeric value, all border colors corresponding to residuals with a larger absolute value are set to the full positive or negative color, respectively.
`line_col` | default border color.
`p.value` | the p value associated with the independence model. By default, this is computed from a Chi-squared distribution with `df` degrees of freedom. `p.value` can be either a scalar or a `function(observed, residuals, expected, df)` that computes the p value from the data. If set to `NA` no inference is performed.
`level` | confidence level of the test used. If `p.value` is smaller than `1 - level`, bright colors are used, otherwise dark colors are employed. For `shading_max` a vector of levels can be supplied. The corresponding critical values are then used as `interpolate` cut-offs.
`n` | number of permutations used in the call to `coindep_test`.
`col` | a vector of two colors for positive and negative residuals respectively.
`...` | Other arguments passed to `hcl` or `hsv`, respectively.

### Details

These shading-generating functions can be passed to `strucplot` to generate residual-based shadings for contingency tables. `strucplot` calls these functions with the arguments `observed`, `residuals`, `expected`, `df` which give the observed values, residuals, expected values and associated degrees of freedom for a particular contingency table and associated independence model.

The shadings `shading_hcl` and `shading_hsv` do the same thing conceptually, but use HCL or HSV colors respectively. The former is usually preferred because they are perceptually uniform. Both shadings visualize the sign of the residuals of an independence model using two hues (by default: blue and red). The absolute size of the residuals is visualized by the colorfulness and the amount of grey, by default in three categories: very colorful for large residuals (> 4), less colorful for medium sized residuals (< 4 and > 2), grey/white for small residuals (< 2). More categories or a continuous scale can be specified by setting `interpolate`. Furthermore, the result of a significance test can be visualized by the amount of grey in the colors. If significant, a colorful palette is used, if not, the amount of color is reduced. See Zeileis, Meyer, and Hornik (2005) and `diverge_hcl` for more details.

The shading `shading_max` is applicable in 2-way contingency tables and uses a similar strategy as `shading_hcl`. But instead of using the cut-offs 2 and 4, it employs the critical values for the maximum statistic (by default at 90% and 99%). Consequently, color in the plot signals a significant result at 90% or 99% significance level, respectively. The test is carried out by calling `coindep_test`.

The shading `shading_Friendly` is very similar to `shading_hsv`, but additionally codes the sign of the residuals by different line types. See Friendly (1994) for more details.

The shading `shading_binary` just visualizes the sign of the residuals by using two different colors.

### Value

A shading function which takes only a single argument, interpreted as a vector/table of residuals, and returns a `"gpar"` object with the corresponding vector(s)/table(s) of graphical parameter(s).

### Author(s)

Achim Zeileis Achim.Zeileis@R-project.org

### References

Friendly, M. (1994) Mosaic displays for multi-way contingency tables. Journal of the American Statistical Association, 89, 190–200.

Zeileis A., Meyer D., Hornik K. (2005), Residual-based Shadings for Visualizing (Conditional) Independence. Report 20, Department of Statistics and Mathematics, Wirtschaftsuniversität Wien, Research Report Series, http://epub.wu-wien.ac.at/.

### See Also

`hcl`, `hsv`, `mosaic`, `assoc`, `strucplot`, `diverge_hcl`

### Examples

    ## load Arthritis data
    data(Arthritis)
    art <- xtabs(~Treatment + Improved, data = Arthritis)

    ## plain mosaic display without shading
    mosaic(art)

    ## with shading for independence model
    mosaic(art, shade = TRUE)
    ## which uses the HCL shading
    mosaic(art, gp = shading_hcl)
    ## the residuals are two small to have color,
    ## hence the cut-offs can be modified
    mosaic(art, gp = shading_hcl, gp_args = list(interpolate = c(1, 1.8)))
    ## the same with the Friendly palette
    ## (without significance testing)
    mosaic(art, gp = shading_Friendly, gp_args = list(interpolate = c(1, 1.8)))

    ## assess independence using the maximum statistic
    ## cut-offs are now critical values for the test statistic
    mosaic(art, gp = shading_max)

    ## association plot with shading as in base R
    assoc(art, gp = shading_binary(col = c(1, 2)))

[Package vcd version 0.9-6 Index]