Plot prism diagram of frequencies and probabilities.

Source: R/plot_prism.R

plot_prism plots a network diagram of 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_prism(
  prev = num$prev,
  sens = num$sens,
  mirt = NA,
  spec = num$spec,
  fart = NA,
  N = num$N,
  by = "cddc",
  area = "no",
  scale = "p",
  round = TRUE,
  sample = FALSE,
  f_lbl = "num",
  f_lbl_sep = NA,
  f_lwd = 0,
  p_lwd = 1,
  p_scale = FALSE,
  p_lbl = "mix",
  arr_c = NA,
  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 that a population size N is not needed for computing current probability information prob, but is needed for computing frequency information freq from current probabilities prob.

by

A character code specifying 1 or 2 perspective(s) that split(s) the population into 2 subsets. Specifying 1 perspective plots a frequency tree (single tree) with 3 options:

  1. "cd": by condition only;

  2. "dc": by decision only;

  3. "ac": by accuracy only.

Specifying 2 perspectives plots a frequency prism (double tree) 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).

area

A character code specifying the shapes of the frequency boxes, with 3 options:

  1. "no": rectangular frequency boxes, not scaled (default);

  2. "hr": frequency boxes are horizontal rectangles (scaled relative to N).

  3. "sq": frequency boxes are squares (scaled relative to N).

scale

Scale probabilities and corresponding node dimensions either by exact probability or by (rounded or non-rounded) frequency, with 2 options:

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

  2. "f": re-compute probabilities from (rounded or non-rounded) frequencies and scale node 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

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 nodes, 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

Separator for frequency labels (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_lwd

Line width of areas. Default: f_lwd = 0.

p_lwd

Line width of probability links. Default: p_lwd = 1, but consider increasing when setting p_scale = TRUE.

p_scale

Boolean option for scaling current widths of probability links (as set by p_lwd) by the current probability values. Default: p_scale = FALSE.

p_lbl

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

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

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

  3. "min": show links and minimum (prominent) probability names;

  4. "mix": show links and prominent probability names and all values (default);

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

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

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

  8. "no": show links with no labels (same for p_lbl = NA or NULL).

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 = NA, but adjusted by 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_prism generalizes and replaces plot_fnet by removing the dependency on the R package diagram and providing many additional options.

See also

plot_fnet for older (obsolete) version; plot_area for plotting mosaic plot (scaling area dimensions); plot_bar for plotting frequencies as vertical bars; 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_area(), plot_bar(), plot_crisk(), plot_curve(), plot_fnet(), plot_icons(), plot_mosaic(), plot_plane(), plot_tab(), plot_tree()

Examples

## Basics:
# (1) Using global prob and freq values:
plot_prism()  # default prism plot,

# same as:
# plot_prism(by = "cddc", area = "no", scale = "p",
#            f_lbl = "num", f_lwd = 0, cex_lbl = .90,
#            p_lbl = "mix", arr_c = -2, cex_p_lbl = NA)

# (2) Providing values:
plot_prism(N = 10, prev = 1/3, sens = 3/5, spec = 4/5, area = "hr")

plot_prism(N = 10, prev = 1/4, sens = 3/5, spec = 2/5, area = "sq", mar_notes = TRUE)


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

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


# (4) Custom colors and text:
plot_prism(col_pal = pal_bw, f_lwd = .5, p_lwd = .5, lty = 2, # custom fbox color, prob links,
           font = 3, cex_p_lbl = .75)                         # and text labels


my_txt <- init_txt(cond_lbl = "The Truth", cond_true_lbl = "so true", cond_false_lbl = "so false",
                   hi_lbl = "TP", mi_lbl = "FN", fa_lbl = "FP", cr_lbl = "TN")
my_col <- init_pal(N_col = rgb(0, 169, 224, max = 255),  # seeblau
                   hi_col = "gold", mi_col = "firebrick1", fa_col = "firebrick2", cr_col = "orange")
plot_prism(f_lbl = "nam", lbl_txt = my_txt,
           col_pal = my_col, f_lwd = .5)


## Local values and custom color/txt settings:
plot_prism(N = 7, prev = 1/2, sens = 3/5, spec = 4/5, round = FALSE,
           by = "cdac", lbl_txt = txt_org, f_lbl = "namnum", f_lbl_sep = ":\n",
           f_lwd = 1, col_pal = pal_rgb)  # custom colors


plot_prism(N = 5, prev = 1/2, sens = .8, spec = .5, scale = "p",  # note scale!
           by = "cddc", area = "hr", col_pal = pal_bw, f_lwd = 1) # custom colors


plot_prism(N = 3, prev = .50, sens = .50, spec = .50, scale = "p",              # note scale!
           area = "sq", lbl_txt = txt_org, f_lbl = "namnum", f_lbl_sep = ":\n", # custom text
           col_pal = pal_kn, f_lwd = .5)                                        # custom colors


## Plot versions:
# (A) tree/single tree (nchar(by) == 2):
#     3 versions:
plot_prism(by = "cd", f_lbl = "def", col_pal = pal_mod) # by condition (freq boxes: hi mi fa cr)

plot_prism(by = "dc", f_lbl = "def", col_pal = pal_mod) # by decision  (freq boxes: hi fa mi cr)

plot_prism(by = "ac", f_lbl = "def", col_pal = pal_mod) # by accuracy  (freq boxes: hi cr mi fa)


# (B) prism/double tree (nchar(by) == 4):
#     6 (3 x 2) versions (+ 3 redundant ones):
plot_prism(by = "cddc")    # v01 (default)

plot_prism(by = "cdac")    # v02

# plot_prism(by = "cdcd")  # (+) Message

plot_prism(by = "dccd")    # v03

plot_prism(by = "dcac")    # v04

# plot_prism(by = "dcdc")  # (+) Message

plot_prism(by = "accd")    # v05

plot_prism(by = "acdc")    # v06

# plot_prism(by = "acac")  # (+) Message

## Other options:

# area:
# plot_prism(area = "no")  # rectangular boxes (default): (same if area = NA/NULL)
plot_prism(area = "hr")  # horizontal rectangles (widths on each level sum to N)

plot_prism(area = "sq")  # squares (areas on each level sum to N)


# scale (matters for scaled areas and small N):
plot_prism(N = 5, prev = .3, sens = .8, spec = .6,
           area = "hr", scale = "p")  # widths scaled by prob

plot_prism(N = 5, prev = .3, sens = .8, spec = .6,
           area = "hr", scale = "f")  # widths scaled by (rounded or non-rounded) freq

plot_prism(N = 4, prev = .2, sens = .7, spec = .8,
           area = "sq", scale = "p")  # areas scaled by prob

plot_prism(N = 4, prev = .2, sens = .7, spec = .8,
           area = "sq", scale = "f")  # areas scaled by (rounded or non-rounded) freq


## Frequency boxes:
# f_lbl:
plot_prism(f_lbl = "abb")      # abbreviated freq names (variable names)

plot_prism(f_lbl = "nam")      # only freq names

plot_prism(f_lbl = "num")      # only numeric freq values (default)

plot_prism(f_lbl = "namnum")   # names and numeric freq values

# plot_prism(f_lbl = "namnum", cex_lbl = .75)  # smaller freq labels
# plot_prism(f_lbl = NA)       # no freq labels
# plot_prism(f_lbl = "def")    # informative default: short name and numeric value (abb = num)

# f_lwd:
# plot_prism(f_lwd =  0)  # no lines (default), set to tiny_lwd = .001, lty = 0 (same if NA/NULL)
plot_prism(f_lwd =  1)  # basic lines

plot_prism(f_lwd =  3)  # thicker lines

# plot_prism(f_lwd = .5)  # thinner lines

## Probability links:
# Scale link widths (p_lwd & p_scale):
plot_prism(p_lwd = 6, p_scale = TRUE)

plot_prism(area = "sq", f_lbl = "num", p_lbl = NA, col_pal = pal_bw, p_lwd = 6, p_scale = TRUE)


# p_lbl:
plot_prism(p_lbl = "mix")     # abbreviated names with numeric values (abb = num)

plot_prism(p_lbl = "min")     # minimal names (of key probabilities)

# plot_prism(p_lbl = NA)      # no prob labels (NA/NULL/"none")
plot_prism(p_lbl = "nam")     # only prob names

plot_prism(p_lbl = "num")     # only numeric prob values

plot_prism(p_lbl = "namnum")  # names and numeric prob values

# plot_prism(p_lbl = "namnum", cex_p_lbl = .70)  # smaller prob labels
# plot_prism(by = "cddc", p_lbl = "min")  # minimal labels
# plot_prism(by = "cdac", p_lbl = "min")
# plot_prism(by = "cddc", p_lbl = "mix")  # mix abbreviated names and numeric values
# plot_prism(by = "cdac", p_lbl = "mix")
# plot_prism(by = "cddc", p_lbl = "abb")  # abbreviated names
# plot_prism(by = "cdac", p_lbl = "abb")
# plot_prism(p_lbl = "any") # short name and value (abb = num)

# arr_c:
plot_prism(arr_c =  0)  # acc_c = 0: no arrows

plot_prism(arr_c = -3)  # arr_c = -1 to -3: points at both ends

plot_prism(arr_c = -2)  # point at far end

plot_prism(arr_c = +2)  # crr_c = 1-3: V-shape arrows at far end

# plot_prism(arr_c = +3)  # V-shape arrows at both ends
# plot_prism(arr_c = +6)  # arr_c = 4-6: T-shape arrows

## Plain plot versions:
plot_prism(area = "no", f_lbl = "def", p_lbl = "num", col_pal = pal_mod, f_lwd = 1,
           main = NA, sub = NA, mar_notes = FALSE)  # remove titles and margin notes

plot_prism(area = "no", f_lbl = "nam", p_lbl = "min",
           main = NA, sub = "My subtitle", col_pal = pal_rgb)  # only subtitle

plot_prism(area = "no", f_lbl = "num", p_lbl = "num", col_pal = pal_kn)  # default title & subtitle


plot_prism(area = "hr", f_lbl = "nam", f_lwd = .5, p_lwd = .5, col_pal = pal_bwp)

plot_prism(area = "hr", f_lbl = "nam", f_lwd = .5, p_lbl = "num", main = NA, sub = NA)


# plot_prism(area = "sq", f_lbl = "nam", p_lbl = NA, col_pal = pal_rgb)
plot_prism(area = "sq", f_lbl = "def", f_lbl_sep = ":\n", p_lbl = NA, f_lwd = 1, col_pal = pal_kn)


## Suggested combinations:
plot_prism(f_lbl = "nam", p_lbl = "mix", col_pal = pal_mod)  # basic plot

plot_prism(f_lbl = "namnum", p_lbl = "num", cex_lbl = .80, cex_p_lbl = .75)

# plot_prism(area = "no", f_lbl = "def", p_lbl = "abb",           # def/abb labels
#            f_lwd = .8, p_lwd = .8, lty = 3, col_pal = pal_bwp)  # black-&-white

plot_prism(area = "hr", f_lbl = "num", p_lbl = "mix", f_lwd = 1, cex_p_lbl = .75)

plot_prism(area = "hr", f_lbl = "nam", p_lbl = "num", p_lwd = 6, p_scale = TRUE)

plot_prism(area = "hr", f_lbl = "abb", p_lbl = "abb", f_lwd = 1, col_pal = pal_kn)


# plot_prism(area = "sq", f_lbl = "nam", p_lbl = "abb", lbl_txt = txt_TF)
plot_prism(area = "sq", f_lbl = "num", p_lbl = "num", f_lwd = 1, col_pal = pal_rgb)

plot_prism(area = "sq", f_lbl = "namnum", p_lbl = "mix", f_lwd = .5, col_pal = pal_kn)