tinytable Output Method for "colldiag" Objects

This function uses the tinytable package to give a display of collinearity diagnostics with shaded backgrounds indicating the severity of collinearity in the dimensions of the data and the proportions of variance related to each variable in these dimensions. It gives a table version of the graphic shown by tableplot, but something that can be rendered in HTML, PDF and other formats.

Usage

# S3 method for class 'colldiag'
tt(
  x,
  digits = if (percent) 0 else 2,
  fuzz = NULL,
  descending = FALSE,
  percent = FALSE,
  prop.col = c("white", "pink", "red"),
  cond.col = c("#A8F48D", "#DDAB3E", "red"),
  prop.breaks = c(0, 0.2, 0.5, 1),
  cond.breaks = c(0, 5, 10, 1000),
  font.scale = 1,
  ...
)

Arguments

x: A "colldiag" object created from a linear model
digits: Number of digits to use when printing; set to 0 when percent = TRUE
fuzz: Variance decomposition proportions less than fuzz are printed as fuzzchar
descending: Logical; TRUE prints the values in descending order of condition indices
percent: Logical; if TRUE, the variance proportions are printed as percents, 0-100
prop.col: A vector of colors used for the variance proportions. The default is c("white", "pink", "red").
cond.col: A vector of colors used for the condition indices, according to cond.breaks
prop.breaks: Scale breaks for the variance proportions, a vector of length one more than the number of prop.col, whose values are between 0 and 1.
cond.breaks: Scale breaks for the condition indices a vector of length one more than the number of cond.col
font.scale: Controls font size scaling for variance proportions. Either a single numeric value (no scaling) or a vector of length 2 specifying the minimum and maximum font sizes in em units. Default is 1 (no scaling). Use c(1, 1.5) to scale font sizes from 1em to 1.5em based on variance proportion values, making larger proportions more visually prominent.
...: arguments to be passed on to or from other methods (unused)

Value

a "tinytable" object

Details

The "tinytable" object returned can be customized using other functions from the tinytable package. For example, for HTML output, you can change the font family used in the output via theme_html(), as in:


tt(cd) |>
  theme_html(css = "font-family: Arial, sans-serif;")

The present version, when run in an RStudio editor window, renders the graphic result in the Viewer panel. There is still some difficulty in producing this output in .Rmd and .qmd documents directy via the tinytable print() method. A work-around is to save the result to a graphic file and use knitr::include_graphics(). For example, in a code chunk you can use:


tt(cd) |>
  save_tt("myfig.png")
knitr::include_graphics("myfig.png")

Author

Michael Friendly

Examples

library(VisCollin)
library(tinytable)
#> Warning: package 'tinytable' was built under R version 4.5.2
data(cars, package = "VisCollin")
cars.mod <- lm (mpg ~ cylinder + engine + horse + weight + accel + year,
                data = cars)
cd <- colldiag(cars.mod, center=TRUE)
# show all values, in same order as `cd`
tt(cd)
#> 
#> +------------+----------+--------+-------+--------+-------+------+
#> | Cond
#> +------------+----------+--------+-------+--------+-------+------+
#> index | cylinder | engine | horse | weight | accel | year |
#> +============+==========+========+=======+========+=======+======+
#> | 1.00       | 0.00     | 0.00   | 0.01  | 0.00   | 0.01  | 0.01 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 2.25       | 0.00     | 0.00   | 0.00  | 0.01   | 0.02  | 0.79 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 2.52       | 0.00     | 0.00   | 0.00  | 0.01   | 0.42  | 0.14 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 5.66       | 0.31     | 0.01   | 0.31  | 0.09   | 0.06  | 0.01 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 8.34       | 0.12     | 0.00   | 0.65  | 0.72   | 0.47  | 0.05 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 10.82      | 0.56     | 0.98   | 0.03  | 0.18   | 0.01  | 0.00 |
#> +------------+----------+--------+-------+--------+-------+------+ 

# show results in percent
tt(cd, percent = TRUE)
#> 
#> +------------+----------+--------+-------+--------+-------+------+
#> | Cond
#> +------------+----------+--------+-------+--------+-------+------+
#> index | cylinder | engine | horse | weight | accel | year |
#> +============+==========+========+=======+========+=======+======+
#> | 1.00       | 0        | 0      | 1     | 0      | 1     | 1    |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 2.25       | 0        | 0      | 0     | 1      | 2     | 79   |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 2.52       | 0        | 0      | 0     | 1      | 42    | 14   |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 5.66       | 31       | 1      | 31    | 9      | 6     | 1    |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 8.34       | 12       | 0      | 65    | 72     | 47    | 5    |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 10.82      | 56       | 98     | 3     | 18     | 1     | 0    |
#> +------------+----------+--------+-------+--------+-------+------+ 

# try descending & fuzz
tt(cd, descending = TRUE, fuzz = 0.3)
#> 
#> +------------+----------+--------+-------+--------+-------+------+
#> | Cond
#> +------------+----------+--------+-------+--------+-------+------+
#> index | cylinder | engine | horse | weight | accel | year |
#> +============+==========+========+=======+========+=======+======+
#> | 10.82      | 0.56     | 0.98   |       |        |       |      |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 8.34       |          |        | 0.65  | 0.72   | 0.47  |      |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 5.66       | 0.31     |        | 0.31  |        |       |      |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 2.52       |          |        |       |        | 0.42  |      |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 2.25       |          |        |       |        |       | 0.79 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 1.00       |          |        |       |        |       |      |
#> +------------+----------+--------+-------+--------+-------+------+ 

# vary font size from 1em to 1.5em based on variance proportions
tt(cd, font.scale = c(1, 1.5))
#> 
#> +------------+----------+--------+-------+--------+-------+------+
#> | Cond
#> +------------+----------+--------+-------+--------+-------+------+
#> index | cylinder | engine | horse | weight | accel | year |
#> +============+==========+========+=======+========+=======+======+
#> | 1.00       | 0.00     | 0.00   | 0.01  | 0.00   | 0.01  | 0.01 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 2.25       | 0.00     | 0.00   | 0.00  | 0.01   | 0.02  | 0.79 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 2.52       | 0.00     | 0.00   | 0.00  | 0.01   | 0.42  | 0.14 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 5.66       | 0.31     | 0.01   | 0.31  | 0.09   | 0.06  | 0.01 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 8.34       | 0.12     | 0.00   | 0.65  | 0.72   | 0.47  | 0.05 |
#> +------------+----------+--------+-------+--------+-------+------+
#> | 10.82      | 0.56     | 0.98   | 0.03  | 0.18   | 0.01  | 0.00 |
#> +------------+----------+--------+-------+--------+-------+------+

`tinytable` Output Method for "colldiag" Objects