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Plot an area diagram of probabilities or frequencies.

Source: R/plot_area.R
plot_area.Rd

plot_area assigns the total probability or population frequency to an area (square or rectangle) and shows the probability or frequency of 4 classification cases (hi, mi, fa, cr) as relative proportions of this area.

Usage

plot_area(
  prev = num$prev,
  sens = num$sens,
  mirt = NA,
  spec = num$spec,
  fart = NA,
  N = num$N,
  by = "cddc",
  p_split = "v",
  area = "sq",
  scale = "p",
  round = TRUE,
  sample = FALSE,
  sum_w = 0.1,
  gaps = c(NA, NA),
  f_lbl = "num",
  f_lbl_sep = NA,
  f_lbl_sum = "num",
  f_lbl_hd = "nam",
  f_lwd = 0,
  p_lbl = NA,
  arr_c = -3,
  col_p = c(grey(0.15, 0.99), "yellow", "yellow"),
  brd_dis = 0.06,
  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.

area

A character code specifying the shape of the main area, with 2 options:

  1. "sq": main area is scaled to a square (default);

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

scale

Scale probabilities and corresponding area 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.

sum_w

Border width of 2 perspective summaries (on top and left borders) of main area as a proportion of area size (i.e., in range 0 <= sum_w <= 1). Default: sum_w = .10. Setting sum_w = 0, NA, or NULL removes summaries; setting sum_w = 1 scales summaries to same size as main areas.

gaps

Size of gaps (as binary numeric vector) specifying the width of vertical and horizontal gaps as proportions of area size. Defaults: gaps = c(.02, .00) for p_split = "v" and gaps = c(.00, .02) for p_split = "h".

f_lbl

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

  1. "def": abbreviated names and frequency values;

  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 (default);

  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 = "num": numeric values only.

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 = 0.

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: show no labels or links (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"). (Also consider: "black", "cornsilk", "whitesmoke").

brd_dis

Distance of probability links from area border (as proportion of area width). Default: brd_dis = .06. Note: Adjust to avoid overlapping labels. Negative values show links outside of main area.

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 plot subtitle (on 2nd line). 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.

Value

Nothing (NULL).

Details

plot_area computes probabilities prob and 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_area generalizes and replaces plot_mosaic. by removing the dependency on the R packages vcd and grid and providing many additional options.

See also

plot_mosaic for older (obsolete) version; plot_tab for plotting table (without scaling area dimensions); pal contains current color settings; txt contains current text settings.

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

Examples

## Basics:
# (1) Using global prob and freq values:
plot_area()  # default area plot,

# same as:
# plot_area(by = "cddc", p_split = "v", area = "sq", scale = "p")

# (2) Providing values:
plot_area(prev = .5, sens = 4/5, spec = 3/5, N = 10)


# (3) Rounding and sampling:
plot_area(N = 100, prev = 1/3, sens = 2/3, spec = 6/7, area = "hr", round = FALSE)

plot_area(N = 100, prev = 1/3, sens = 2/3, spec = 6/7, area = "hr", sample = TRUE, scale = "freq")


# (4) Custom colors and text:
plot_area(prev = .2, sens = 4/5, spec = 3/5, N = 10,
          by = "cddc", p_split = "v", scale = "p",
          main = "Custom text and color:",
          lbl_txt = txt_org, f_lbl = "namnum",
          f_lbl_sep = ":\n", f_lwd = 2, col_pal = pal_rgb)


## Versions:
## by x p_split (= [3 x 2 x 2] = 12 versions):
plot_area(by = "cddc", p_split = "v")  # v01 (see v07)

plot_area(by = "cdac", p_split = "v")  # v02 (see v11)

# plot_area(by = "cddc", p_split = "h")  # v03 (see v05)
# plot_area(by = "cdac", p_split = "h")  # v04 (see v09)

# plot_area(by = "dccd", p_split = "v")  # v05 (is v03 rotated)
plot_area(by = "dcac", p_split = "v")  # v06 (see v12)

# plot_area(by = "dccd", p_split = "h")  # v07 (is v01 rotated)
# plot_area(by = "dcac", p_split = "h")  # v08 (see v10)

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

## Options:
# area:
plot_area(area = "sq")  # main area as square (by scaling x-values)

plot_area(area = "no")  # rectangular main area (using full plotting region)


# scale (matters for small N):
plot_area(N = 5, prev = .5, sens = .8, spec = .6,
          by = "cddc", p_split = "v", scale = "p", p_lbl = "def")  # scaled by prob (default)

plot_area(N = 5, prev = .5, sens = .8, spec = .6,
          by = "cddc", p_split = "v", scale = "f", p_lbl = "def")  # scaled by freq (for small N)

plot_area(N = 4, prev = .4, sens = .8, spec = .6,
          by = "cdac", p_split = "h", scale = "p", p_lbl = "def")  # scaled by prob (default)

plot_area(N = 4, prev = .4, sens = .8, spec = .6,
          by = "cdac", p_split = "h", scale = "f", p_lbl = "def")  # scaled by freq (for small N)


# gaps (sensible range: 0--.10):
plot_area(gaps = NA)             # default gaps (based on p_split)

plot_area(gaps = c(0, 0))        # no gaps

# plot_area(gaps = c(.05, .01))  # v_gap > h_gap

# freq labels:
plot_area(f_lbl = "def", f_lbl_sep = " = ")  # default

plot_area(f_lbl = NA)       # NA/NULL: no freq labels (in main area & top/left boxes)

plot_area(f_lbl = "abb")    # abbreviated name (i.e., variable name)

# plot_area(f_lbl = "nam")  # only freq name
# plot_area(f_lbl = "num")  # only freq number
plot_area(f_lbl = "namnum", f_lbl_sep = ":\n", cex_lbl = .75)  # explicit & smaller


# prob labels:
plot_area(p_lbl = NA)      # default: no prob labels, no links

# plot_area(p_lbl = "no")  # show links, but no labels
plot_area(p_lbl = "namnum", cex_lbl = .70)  # explicit & smaller labels


# prob arrows:
plot_area(arr_c = +3, p_lbl = "def", f_lbl = NA)  # V-shape arrows

# plot_area(arr_c = +6, p_lbl = "def", f_lbl = NA)  # T-shape arrows
# plot_area(arr_c = +6, p_lbl = "def", f_lbl = NA,
#           brd_dis = -.02, col_p = c("black")) # adjust arrow type/position

# f_lwd:
plot_area(f_lwd =  3)    # thicker lines

plot_area(f_lwd = .5)    # thinner lines

# plot_area(f_lwd =  0)  # no lines (if f_lwd = 0/NULL/NA: lty = 0)

# sum_w:
# plot_area(sum_w = .10)  # default (showing top and left freq panels & labels)
plot_area(sum_w =  0)   # remove top and left freq panels

plot_area(sum_w =  1,         # top and left freq panels scaled to size of main areas
          col_pal = pal_org)  # custom colors


## Plain and suggested plot versions:
plot_area(sum_w = 0, f_lbl = "abb", p_lbl = NA)  # no compound indicators (on top/left)

plot_area(gap = c(0, 0), sum_w = 0, f_lbl = "num", p_lbl = "num",  # no gaps, numeric labels
          f_lwd = .5, col_pal = pal_bw, main = "Black-and-white")  # b+w print version

# plot_area(f_lbl = "nam", p_lbl = NA, col_pal = pal_mod)  # plot with freq labels
plot_area(f_lbl = "num", p_lbl = NA, col_pal = pal_rgb)  # no borders around boxes