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.
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,
...
)
The condition's prevalence prev
(i.e., the probability of condition being TRUE
).
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.
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.
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.
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.
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
.
A character code specifying 2 perspectives that split the population into subsets, with 6 options:
"cddc"
: by condition (cd) and by decision (dc) (default);
"cdac"
: by condition (cd) and by accuracy (ac);
"dccd"
: by decision (dc) and by condition (cd);
"dcac"
: by decision (dc) and by accuracy (ac);
"accd"
: by accuracy (ac) and by condition (cd);
"acdc"
: by accuracy (ac) and by decision (dc).
Primary perspective for population split, with 2 options:
"v"
: vertical (default);
"h"
: horizontal.
A character code specifying the shape of the main area, with 2 options:
"sq"
: main area is scaled to a square (default);
"no"
: no scaling (rectangular area fills plot size).
Scale probabilities and corresponding area dimensions either by exact probability or by (rounded or non-rounded) frequency, with 2 options:
"p"
: scale main area dimensions by exact probability (default);
"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
.
A Boolean option specifying whether computed frequencies
are rounded to integers. Default: round = TRUE
.
Boolean value that determines whether frequency values
are sampled from N
, given the probability values of
prev
, sens
, and spec
.
Default: sample = FALSE
.
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.
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"
.
Type of label for showing frequency values in 4 main areas, with 6 options:
"def"
: abbreviated names and frequency values;
"abb"
: abbreviated frequency names only (as specified in code);
"nam"
: names only (as specified in lbl_txt = txt
);
"num"
: numeric frequency values only (default);
"namnum"
: names (as specified in lbl_txt = txt
) and numeric values;
"no"
: no frequency labels (same for f_lbl = NA
or NULL
).
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
).
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.
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
).
Line width of areas.
Default: f_lwd = 0
.
Type of label for showing 3 key probability links and values, with 7 options:
"def"
: show links and abbreviated names and probability values;
"abb"
: show links and abbreviated probability names;
"nam"
: show links and probability names (as specified in code);
"num"
: show links and numeric probability values;
"namnum"
: show links with names and numeric probability values;
"no"
: show links with no labels;
NA
: show no labels or links (same for p_lbl = NULL
, default).
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).
Colors of probability links (as vector of 3 colors).
Default: col_p = c(grey(.15, .99), "yellow", "yellow")
.
(Also consider: "black", "cornsilk", "whitesmoke").
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.
Default label set for text elements.
Default: lbl_txt = txt
.
Text label for main plot title.
Default: main = txt$scen_lbl
.
Text label for plot subtitle (on 2nd line).
Default: sub = "type"
shows information on current plot type.
Deprecated text label for current plot title.
Replaced by main
.
Scaling factor for text labels (frequencies and headers).
Default: cex_lbl = .90
.
Scaling factor for text labels (probabilities).
Default: cex_p_lbl = cex_lbl - .05
.
Color palette.
Default: col_pal = pal
.
Boolean option for showing margin notes.
Default: mar_notes = FALSE
.
Other (graphical) parameters.
Nothing (NULL).
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.
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()
## 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