Plot frequency net diagram of frequencies and probabilities.

Source: R/plot_fnet.R

plot_fnet plots a frequency net 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_fnet(
  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,
  joint_p = TRUE,
  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,
  ...
)

Source

Binder, K., Krauss, S., and Wiesner, P. (2020). A new visualization for probabilistic situations containing two binary events: The frequency net. Frontiers in Psychology, 11, 750. doi: 10.3389/fpsyg.2020.00750

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 2 options:

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

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

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

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;

  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_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 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.

joint_p

Boolean options for showing links to joint probabilities (i.e., diagonals from N in center to joint frequencies in 4 corners). Default: joint_p = TRUE.

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_fnet shows frequencies as nodes and probabilities as links (like trees and double trees generated by plot_prism), but combines elements from 2x2 tables (see plot_tab) and tree diagrams.

Similar to other 2D-visualizations (e.g., , plot_area, plot_prism and plot_tab), the frequency net selects and combines two perspectives (e.g., by = "cddc"). However, the frequency net is similar to a 2x2 table insofar as its perspectives (shown by arranging marginal frequencies in a vertical vs. horizontal fashion) do not suggest an order or dependency (in contrast to trees or mosaic plots). Additionally, the frequency net allows showing 3 kinds of (marginal, conditional, and joint) probabilities.

See the article by Binder K, Krauss S and Wiesner P (2020). A new visualization for probabilistic situations containing two binary events: The frequency net. Frontiers in Psychology, 11, 750. doi: 10.3389/fpsyg.2020.00750 for analysis and details.

See also

plot_prism for plotting prism plot (double tree); 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_icons(), plot_mosaic(), plot_plane(), plot_prism(), plot_tab(), plot_tree()

Examples

# (1) Basics: ----
# A. Using global prob and freq values:
plot_fnet()  # default frequency net, same as:

# plot_fnet(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)

# B. Providing values:
plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9)  # Binder et al. (2020, Fig. 3)


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

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


# Variants:
plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9, by = "cdac")

plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9, by = "dccd")

# plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9, by = "dcac")
# plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9, by = "accd")
# plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9, by = "acdc")

# Trees (only 1 dimension):
plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9, by = "cd")

# plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9, by = "dc")
# plot_fnet(N = 10000, prev = .02, sens = .8, spec = .9, by = "ac")

# Area and margin notes:
plot_fnet(N = 10, prev = 1/4, sens = 3/5, spec = 2/5, area = "sq", mar_notes = TRUE)



# (2) Use case (highlight horizontal vs. vertical perspectives: ----
# Define scenario:
mammo <- riskyr(N = 10000, prev = .01, sens = .80, fart = .096,
                scen_lbl = "Mammography screening", N_lbl = "Women",
                cond_lbl = "Breast cancer", dec_lbl = "Test result",
                cond_true_lbl = "Cancer (C+)", cond_false_lbl = "no Cancer (C-)",
                dec_pos_lbl = "positive (T+)", dec_neg_lbl = "negative (T-)",
                hi_lbl = "C+ and T+", mi_lbl = "C+ and T-",
                fa_lbl = "C- and T+", cr_lbl = "C- and T-")
# Colors:
my_non <- "grey95"
my_red <- "orange1"
my_blu <- "skyblue1"

# A. Emphasize condition perspective (rows):
my_col_1 <- init_pal(N_col = my_non,
                     cond_true_col = my_blu, cond_false_col = my_red,
                     dec_pos_col = my_non, dec_neg_col = my_non,
                     hi_col = my_blu, mi_col = my_blu,
                     fa_col = my_red, cr_col = my_red)
plot(mammo, type = "fnet", col_pal = my_col_1,
     f_lbl = "namnum", f_lwd = 2, p_lbl = "no", arr_c = 0)


# B. Emphasize decision perspective (columns):
my_col_2 <- init_pal(N_col = my_non,
                     cond_true_col = my_non, cond_false_col = my_non,
                     dec_pos_col = my_red, dec_neg_col = my_blu,
                     hi_col = my_red, mi_col = my_blu,
                     fa_col = my_red, cr_col = my_blu)
plot(mammo, type = "fnet", col_pal = my_col_2,
     f_lbl = "namnum", f_lwd = 2, p_lbl = "no", arr_c = 0)



# (3) Custom color and text settings: ----
plot_fnet(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


plot_fnet(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_fnet(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_fnet(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


# (4) Other options: ----
plot_fnet(N = 4, prev = .2, sens = .7, spec = .8,
          area = "sq", scale = "p")  # areas scaled by prob (matters for small N)

# plot_fnet(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_fnet(f_lbl = NA)       # no freq labels
# plot_fnet(f_lbl = "abb")    # abbreviated freq names (variable names)
plot_fnet(f_lbl = "nam")      # only freq names

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

# plot_fnet(f_lbl = "namnum") # names and numeric freq values
plot_fnet(f_lbl = "namnum", cex_lbl = .75)  # smaller freq labels

# plot_fnet(f_lbl = "def")    # informative default: short name and numeric value (abb = num)

# f_lwd:
# plot_fnet(f_lwd =  1)  # basic lines
# plot_fnet(f_lwd =  0)  # no lines (default), set to tiny_lwd = .001, lty = 0 (same if NA/NULL)
# plot_fnet(f_lwd = .5)  # thinner lines
plot_fnet(f_lwd =  3)    # thicker lines


## Probability links (p_lbl, p_lwd, p_scale):
# plot_fnet(p_lbl = NA)       # no prob labels (NA/NULL/"none")
plot_fnet(p_lbl = "mix")      # abbreviated names with numeric values (abb = num)

# plot_fnet(p_lbl = "min")    # minimal names (of key probabilities)
# plot_fnet(p_lbl = "nam")    # only prob names
plot_fnet(p_lbl = "num")      # only numeric prob values

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

plot_fnet(p_lwd = 6, p_scale = TRUE)

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


# arr_c:
# plot_fnet(arr_c =  0)  # acc_c = 0: no arrows
# plot_fnet(arr_c = -3)  # arr_c = -1 to -3: points at both ends
# plot_fnet(arr_c = -2)  # point at far end
plot_fnet(arr_c = +2)    # crr_c = 1-3: V-shape arrows at far end


plot_fnet(by = "cd", joint_p = FALSE)      # tree without joint probability links

# plot_fnet(by = "cddc", joint_p = FALSE)  # fnet ...

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

plot_fnet(area = "no", f_lbl = "nam", p_lbl = "min", col_pal = pal_rgb)


plot_fnet(area = "sq", f_lbl = "nam", p_lbl = "num", col_pal = pal_rgb)

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

## Suggested combinations:
# plot_fnet(f_lbl = "nam", p_lbl = "mix")  # basic plot
plot_fnet(f_lbl = "namnum", p_lbl = "num", cex_lbl = .80, cex_p_lbl = .75)

# plot_fnet(area = "no", f_lbl = "def", p_lbl = "abb",           # def/abb labels
#           f_lwd = .8, p_lwd = .8, lty = 2, col_pal = pal_bwp)  # black-&-white

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

plot_fnet(area = "sq", f_lbl = "nam", p_lbl = "num", f_lwd = .5, col_pal = pal_rgb)