plot_tab {riskyr}R Documentation

Plot a 2 x 2 contingency table of population frequencies.

Description

plot_tab plots a 2 x 2 contingency table (aka. confusion table) of 4 classification cases (hi, mi, fa, cr) and corresponding row and column sums.

Usage

plot_tab(
  prev = num$prev,
  sens = num$sens,
  mirt = NA,
  spec = num$spec,
  fart = NA,
  N = num$N,
  by = "cddc",
  p_split = "v",
  area = "no",
  scale = "p",
  round = TRUE,
  sample = FALSE,
  f_lbl = "num",
  f_lbl_sep = NA,
  f_lbl_sum = f_lbl,
  f_lbl_hd = "nam",
  f_lwd = 0,
  gaps = c(NA, NA),
  brd_w = 0.1,
  p_lbl = NA,
  arr_c = -3,
  col_p = c(grey(0.15, 0.99), "yellow", "yellow"),
  brd_dis = 0.3,
  lbl_txt = txt,
  main = txt$scen_lbl,
  sub = "type",
  title_lbl = NULL,
  cex_lbl = 0.9,
  cex_p_lbl = NA,
  col_pal = pal,
  mar_notes = FALSE,
  ...
)

Arguments

prev

The condition's prevalence prev (i.e., the probability of condition being TRUE).

sens

The decision's sensitivity sens (i.e., the conditional probability of a positive decision provided that the condition is TRUE). sens is optional when its complement mirt is provided.

mirt

The decision's miss rate mirt (i.e., the conditional probability of a negative decision provided that the condition is TRUE). mirt is optional when its complement sens is provided.

spec

The decision's specificity value spec (i.e., the conditional probability of a negative decision provided that the condition is FALSE). spec is optional when its complement fart is provided.

fart

The decision's false alarm rate fart (i.e., the conditional probability of a positive decision provided that the condition is FALSE). fart is optional when its complement spec is provided.

N

The number of individuals in the population. A suitable value of N is computed, if not provided. Note: N is not represented in the plot, but used for computing frequency information freq from current probabilities prob.

by

A character code specifying 2 perspectives that split the population into subsets, with 6 options:

  1. "cddc": by condition (cd) and by decision (dc) (default);

  2. "cdac": by condition (cd) and by accuracy (ac);

  3. "dccd": by decision (dc) and by condition (cd);

  4. "dcac": by decision (dc) and by accuracy (ac);

  5. "accd": by accuracy (ac) and by condition (cd);

  6. "acdc": by accuracy (ac) and by decision (dc).

p_split

Primary perspective for population split, with 2 options:

  1. "v": vertical (default);

  2. "h": horizontal.

Note: In contrast to plot_area, this setting only determines which 3 probability links are shown (e.g., when p_link = "def").

area

A character code specifying the shape of the main area, with 4 options:

  1. "sq": main area is scaled to square;

  2. "no": no scaling (rectangular area fills plot size; default).

scale

Scale probabilities (but not table cell dimensions) either by exact probability or by (rounded or non-rounded) frequency, with 2 options:

  1. "p": scale main area dimensions by exact probability (default);

  2. "f": re-compute probabilities from (rounded or non-rounded) frequencies and scale main area dimensions by their frequency.

Note: scale setting matters for the display of probability values and for area plots with small population sizes N when round = TRUE.

round

A Boolean option specifying whether computed frequencies are rounded to integers. Default: round = TRUE.

sample

Boolean value that determines whether frequency values are sampled from N, given the probability values of prev, sens, and spec. Default: sample = FALSE.

f_lbl

Type of label for showing frequency values in 4 main areas, with 6 options:

  1. "def": abbreviated names and frequency values (default);

  2. "abb": abbreviated frequency names only (as specified in code);

  3. "nam": names only (as specified in lbl_txt = txt);

  4. "num": numeric frequency values only;

  5. "namnum": names (as specified in lbl_txt = txt) and numeric values;

  6. "no": no frequency labels (same for f_lbl = NA or NULL).

f_lbl_sep

Label separator for main frequencies (used for f_lbl = "def" OR "namnum"). Use f_lbl_sep = ":\n" to add a line break between name and numeric value. Default: f_lbl_sep = NA (set to " = " or ":\n" based on f_lbl).

f_lbl_sum

Type of label for showing frequency values in summary cells, with same 6 options as f_lbl (above). Default: f_lbl_sum = "def": abbreviated names and numeric values.

f_lbl_hd

Type of label for showing frequency values in header, with same 6 options as f_lbl (above). Default: f_lbl_hd = "nam": names only (as specified in lbl_txt = txt).

f_lwd

Line width of areas. Default: f_lwd = 1.

gaps

Size of gaps (as binary numeric vector) specifying the widths of vertical and horizontal gaps between 2 x 2 table and sums (in bottom row and right column). Default: gaps = c(.05, .06).

brd_w

Border width for showing 2 perspective summaries on top and left borders of main area (as a proportion of area size) in a range 0 <= brd_w <= 1. Default: brd_w = .10.

p_lbl

Type of label for showing 3 key probability links and values, with 7 options:

  1. "def": show links and abbreviated names and probability values;

  2. "abb": show links and abbreviated probability names;

  3. "nam": show links and probability names (as specified in code);

  4. "num": show links and numeric probability values;

  5. "namnum": show links with names and numeric probability values;

  6. "no": show links with no labels;

  7. NA: no link (same for p_lbl = NULL, default).

arr_c

Arrow code for symbols at ends of probability links (as a numeric value -3 <= arr_c <= +6), with the following options:

  • -1 to -3: points at one/other/both end/s;

  • 0: no symbols;

  • +1 to +3: V-arrow at one/other/both end/s;

  • +4 to +6: T-arrow at one/other/both end/s.

Default: arr_c = -3 (points at both ends).

col_p

Colors of probability links (as vector of 3 colors). Default: col_p = c(grey(.15, .99), "yellow", "yellow").

brd_dis

Distance of probability links from cell center (as a constant). Default: brd_dis = .30. Note: Adjust to avoid overlapping labels.

lbl_txt

Default label set for text elements. Default: lbl_txt = txt.

main

Text label for main plot title. Default: main = txt$scen_lbl.

sub

Text label for the subtitle of the plot (shown below the main title). Default: sub = "type" shows information on current plot type.

title_lbl

Deprecated text label for current plot title. Replaced by main.

cex_lbl

Scaling factor for text labels (frequencies and headers). Default: cex_lbl = .90.

cex_p_lbl

Scaling factor for text labels (probabilities). Default: cex_p_lbl = cex_lbl - .05.

col_pal

Color palette. Default: col_pal = pal.

mar_notes

Boolean option for showing margin notes. Default: mar_notes = FALSE.

...

Other (graphical) parameters.

Details

plot_tab computes its frequencies freq from a sufficient and valid set of 3 essential probabilities (prev, and sens or its complement mirt, and spec or its complement fart) or existing frequency information freq and a population size of N individuals.

plot_tab is derived from plot_area, but does not scale the dimensions of table cells.

Value

Nothing (NULL).

See Also

plot_area for plotting mosaic plot (scaling area dimensions); pal contains current color settings; txt contains current text settings.

Other visualization functions: plot.riskyr(), plot_area(), plot_bar(), plot_crisk(), plot_curve(), plot_fnet(), plot_icons(), plot_mosaic(), plot_plane(), plot_prism(), plot_tree()

Examples

## Basics:
# (1) Plotting global freq and prob values:
plot_tab()
plot_tab(area = "sq", f_lwd = 3, col_pal = pal_rgb)
plot_tab(f_lbl = "namnum", f_lbl_sep = " = ", brd_w = .10, f_lwd = .5)

# (2) Computing local freq and prob values:
plot_tab(prev = .5, sens = 4/5, spec = 3/5, N = 10, f_lwd = 1)

# (3) Rounding and sampling:
plot_tab(N = 100, prev = 1/3, sens = 2/3, spec = 6/7, round = FALSE)
plot_tab(N = 100, prev = 1/3, sens = 2/3, spec = 6/7, sample = TRUE)

## Plot versions:
# by x p_split [yields (3 x 2) x 2] = 12 versions]:
plot_tab(by = "cddc", p_split = "v", p_lbl = "def")  # v01 (see v07)
plot_tab(by = "cdac", p_split = "v", p_lbl = "def")  # v02 (see v11)
plot_tab(by = "cddc", p_split = "h", p_lbl = "def")  # v03 (see v05)
plot_tab(by = "cdac", p_split = "h", p_lbl = "def")  # v04 (see v09)

# plot_tab(by = "dccd", p_split = "h", p_lbl = "def")  # v07 (v01 rotated)
# plot_tab(by = "dccd", p_split = "v", p_lbl = "def")  # v05 (v03 rotated)
plot_tab(by = "dcac", p_split = "v", p_lbl = "def")    # v06 (see v12)
plot_tab(by = "dcac", p_split = "h", p_lbl = "def")    # v08 (see v10)

# plot_tab(by = "accd", p_split = "v", p_lbl = "def")  # v09 (v04 rotated)
# plot_tab(by = "acdc", p_split = "v", p_lbl = "def")  # v10 (v08 rotated)
# plot_tab(by = "accd", p_split = "h", p_lbl = "def")  # v11 (v02 rotated)
# plot_tab(by = "acdc", p_split = "h", p_lbl = "def")  # v12 (v06 rotated)

## Explore labels and links:
# plot_tab(f_lbl = "abb", p_lbl = NA)  # abbr. labels, no probability links
# plot_tab(f_lbl = "num", f_lbl_sum = "abb", p_lbl = "num", f_lbl_hd = "abb")
plot_tab(f_lbl = "def", f_lbl_sum = "def", p_lbl = "def", f_lbl_hd = "nam")
plot_tab(f_lbl = "namnum", f_lbl_sep = " = ",
         f_lbl_sum = "namnum", f_lbl_hd = "num", p_lbl = "namnum")

## Misc. options:
plot_tab(area = "sq")        # area: square
# plot_tab(main = "")     # no titles
# plot_tab(mar_notes = TRUE)   # show margin notes
plot_tab(by = "cddc", gaps = c(.08, .00), area = "sq")      # gaps
# plot_tab(by = "cddc", gaps = c(.02, .08), p_split = "h")  # gaps

# Showing prob as lines:
plot_tab(prev = 1/4, sens = 6/7, spec = 3/5, N = 100,
         by = "cddc", p_split = "v", col_pal = pal_rgb,
         p_lbl = "def", brd_dis = .25, arr_c = +3, lwd = 2)

# Custom text labels and colors:
plot_tab(prev = .5, sens = 4/5, spec = 3/5, N = 10,
         by = "cddc", p_split = "v", area = "no",
         main = "Main title", sub = "The subtitle", lbl_txt = txt_TF,  # custom text
         f_lbl = "namnum", f_lbl_sep = ":\n", f_lbl_sum = "num", f_lbl_hd  = "nam",
         col_pal = pal_vir, f_lwd = 3)  # custom colors
plot_tab(prev = .5, sens = 3/5, spec = 4/5, N = 10,
         by = "cddc", p_split = "h", area = "sq",
         main = NA, sub = NA, lbl_txt = txt_org,  # custom text
         f_lbl = "namnum", f_lbl_sep = ":\n", f_lbl_sum = "num", f_lbl_hd  = "nam",
         col_pal = pal_kn, f_lwd = 1)  # custom colors

## Note some differences to plot_area (i.e., area/mosaic plot):
# In plot_tab:
# (1) p_split does not matter (except for selecting different prob links):
plot_tab(by = "cddc", p_split = "v")  # v01 (see v07)
plot_tab(by = "cddc", p_split = "h")  # v03 (see v05)

# (2) scale does not matter for dimensions (which are constant),
#     BUT matters for values shown in prob links and on margins:
plot_tab(N = 5, prev = .3, sens = .9, spec = .5,
         by = "cddc", scale = "p", p_lbl = "def", round = TRUE)  # (a) exact prob values
plot_tab(N = 5, prev = .3, sens = .9, spec = .5,
         by = "cddc", scale = "f", p_lbl = "def", round = TRUE)  # (b) prob from rounded freq!
plot_tab(N = 5, prev = .3, sens = .9, spec = .5,
         by = "cddc", scale = "f", p_lbl = "def", round = FALSE) # (c) same values as (a)
[Package riskyr version 0.4.0 Index]