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Plot bar charts of population frequencies.

Source: R/plot_bar.R
plot_bar.Rd

plot_bar draws bar charts that represent the proportions of frequencies in the current population popu as relatives sizes of rectangular areas.

Usage

plot_bar(
  prev = num$prev,
  sens = num$sens,
  mirt = NA,
  spec = num$spec,
  fart = NA,
  N = num$N,
  by = "all",
  dir = 1,
  scale = "f",
  round = TRUE,
  sample = FALSE,
  f_lbl = "num",
  f_lwd = 1,
  lty = 0,
  lbl_txt = txt,
  main = txt$scen_lbl,
  sub = "type",
  title_lbl = NULL,
  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. (This value is not represented in the plot, but used when new frequency information freq and a new population table popu are computed from scratch from current probabilities.)

by

A character code specifying the perspective (or the dimension by which the population is split into 2 subsets) with the following options:

  1. by = "cd": by condition;

  2. by = "dc": by decision;

  3. by = "ac": by accuracy;

  4. by = "all" combines perspectives (5 bars, default).

dir

Number of directions in which bars are plotted. Options:

  1. dir = 1: uni-directional bars (all up, default);

  2. dir = 2: bi-directional bars (up vs. down).

scale

Scale the heights of bars either by current frequencies (scale = "f") or by exact probabilities (scale = "p"). Default: scale = "f". For large population sizes N and when round = FALSE, both settings yield the same bar heights.

round

Boolean option specifying whether computed frequencies are to be 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 frequency labels, as character code with the following options:

  1. f_lbl = "nam": names;

  2. f_lbl = "num": numeric values (default);

  3. f_lbl = "abb": abbreviated names;

  4. f_lbl = NA/NULL/"no": no labels;

  5. f_lbl = "any": abbreviated names and numeric values (abb = num).

f_lwd

Line width of frequency box (border). Values of NA/NULL/0 set lwd to invisible tiny_lwd <- .001 and lty <- 0 ("blank"). Default: f_lwd = 1.

lty

Line type of frequency box (border). Values of NA/NULL/0 set lty to lty <- 0. Default: lty = 0 (i.e., no line).

lbl_txt

Current text information (for labels, titles, etc.). Default: lbl_txt = txt (see init_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.

col_pal

Current color palette. Default: col_pal = pal (see init_pal).

mar_notes

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

...

Other (graphical) parameters (e.g., cex, font, lty, etc.).

Details

If a sufficient and valid set of 3 essential probabilities (prev, and sens or its complement mirt, and spec or its complement fart) is provided, new frequency information freq and a new population table popu are computed from scratch. Otherwise, the existing population popu is shown.

By default, plot_bar uses current frequencies (i.e., rounded or not rounded, depending on the value of round) as bar heights, rather than using exact probabilities to scale bar heights (i.e., default scaling is scale = "f"). Using the option scale = "p" scales bar heights by probabilities (e.g., showing bars for non-natural frequencies even when frequencies are rounded). When round = FALSE, bar heights for scale = "f" and for scale = "p" are identical.

The distinction between scale = "f" and scale = "p" matters mostly for small populations sizes N (e.g., when N < 100). For rounded and small frequency values (e.g., freq < 10) switching from scale = "f" to scale = "p" yields different plots.

plot_bar contrasts compound frequencies along 1 dimension (height). See plot_mosaic for 2-dimensional visualizations (as areas) and various box) options in plot_tree and plot_fnet for related functions.

See also

comp_popu computes the current population; popu contains the current population; comp_freq computes current frequency information; freq contains current frequency information; num for basic numeric parameters; txt for current text settings; pal for current color settings

Other visualization functions: plot.riskyr(), plot_area(), 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_bar()


# (2) Providing values:
plot_bar(prev = .33, sens = .75, spec = .66, main = "Test 1")

plot_bar(N = 1000, prev = .33, sens = .75, spec = .60, main = "Test 2")  # by "all" (default)


# (3) Rounding and sampling:
plot_bar(N = 100, prev = 1/3, sens = 2/3, spec = 6/7, area = "hr", round = FALSE)
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter

plot_bar(N = 100, prev = 1/3, sens = 2/3, spec = 6/7, area = "hr", sample = TRUE, scale = "freq")
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter
#> Warning: "area" is not a graphical parameter


# Perspectives (by):
# plot_bar(N = 1000, prev = .33, sens = .75, spec = .60, by = "cd",
#          main = "Test 3a")  # by condition
plot_bar(N = 1000, prev = .33, sens = .75, spec = .60, by = "cd", dir = 2,
         main = "Test 3b", f_lbl = "num")  # bi-directional


# plot_bar(N = 1000, prev = .33, sens = .75, spec = .60, by = "dc",
#          main = "Test 4a")  # by decision
plot_bar(N = 1000, prev = .33, sens = .75, spec = .60, by = "dc", dir = 2,
         main = "Test 4b", f_lbl = "num")  # bi-directional


# plot_bar(N = 1000, prev = .33, sens = .75, spec = .60, by = "ac",
#          main = "Test 5a")  # by accuracy
plot_bar(N = 1000, prev = .33, sens = .75, spec = .60, by = "ac", dir = 2,
         main = "Test 5b", f_lbl = "num")  # bi-directional


# Customize colors and text:
plot_bar(dir = 1, f_lbl = "num", col_pal = pal_org)

# plot_bar(dir = 2, f_lbl = "nam", col_pal = pal_bw)

# Frequency labels (f_lbl):
# plot_bar(f_lbl = "def")  # default labels: name = num
plot_bar(f_lbl = "nam")  # name only

plot_bar(f_lbl = "num")  # numeric value only

# plot_bar(f_lbl = "abb")  # abbreviated name
# plot_bar(f_lbl = NA)     # no labels (NA/NULL/"no")

# Scaling and rounding effects:
plot_bar(N = 3, prev = .1, sens = .7, spec = .6, dir = 2,
         scale = "f", round = TRUE,
         main = "Rounding (1)") # => Scale by freq and round freq.

plot_bar(N = 3, prev = .1, sens = .7, spec = .6, dir = 2,
         scale = "p", round = TRUE,
         main = "Rounding (2)") # => Scale by prob and round freq.

plot_bar(N = 3, prev = .1, sens = .7, spec = .6, dir = 2,
         scale = "f", round = FALSE,
         main = "Rounding (3)") # => Scale by freq and do NOT round freq.

plot_bar(N = 3, prev = .1, sens = .7, spec = .6, dir = 2,
         scale = "p", round = FALSE,
         main = "Rounding (4)") # => Scale by prob and do NOT round freq.