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, sum_w = 0.1, gaps = c(NA, NA), f_lbl = "num", f_lbl_sep = NA, f_lbl_sum = "num", f_lbl_hd = "abb", 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, title_lbl = txt$scen_lbl, cex_lbl = 0.9, cex_p_lbl = NA, col_pal = pal, mar_notes = TRUE, ...)
prev  The condition's prevalence 

sens  The decision's sensitivity 
mirt  The decision's miss rate 
spec  The decision's specificity value 
fart  The decision's false alarm rate 
N  The number of individuals in the population.
A suitable value of 
by  A character code specifying 2 perspectives that split the population into subsets, with 6 options:

p_split  Primary perspective for population split, with 2 options:

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

scale  Scale probabilities and corresponding area dimensions either by exact probability or by (rounded or nonrounded) frequency, with 2 options:
Note: 
round  A Boolean option specifying whether computed frequencies
are rounded to integers. Default: 
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 
gaps  Size of gaps (as binary numeric vector) specifying
the width of vertical and horizontal gaps as proportions of area size.
Defaults: 
f_lbl  Type of label for showing frequency values in 4 main areas, with 6 options:

f_lbl_sep  Label separator for main frequencies
(used for 
f_lbl_sum  Type of label for showing frequency values in summary cells,
with same 6 options as 
f_lbl_hd  Type of label for showing frequency values in header,
with same 6 options as 
f_lwd  Line width of areas.
Default: 
p_lbl  Type of label for showing 3 key probability links and values, with 7 options:

arr_c  Arrow code for symbols at ends of probability links
(as a numeric value
Default: 
col_p  Colors of probability links (as vector of 3 colors).
Default: 
brd_dis  Distance of probability links from area border
(as proportion of area width).
Default: 
lbl_txt  Default label set for text elements.
Default: 
title_lbl  Text label for current plot title.
Default: 
cex_lbl  Scaling factor for text labels (frequencies and headers).
Default: 
cex_p_lbl  Scaling factor for text labels (probabilities).
Default: 
col_pal  Color palette.
Default: 
mar_notes  Boolean option for showing margin notes.
Default: 
...  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_curve
,
plot_fnet
, plot_icons
,
plot_mosaic
, plot_plane
,
plot_prism
, plot_tab
,
plot_tree
## Basics: plot_area() # default area plot,# same as: # plot_area(by = "cddc", p_split = "v", area = "sq", scale = "p") # Local freq and prob values: plot_area(prev = .5, sens = 4/5, spec = 3/5, N = 10)# Customizing text and color: plot_area(prev = .2, sens = 4/5, spec = 3/5, N = 10, by = "cddc", p_split = "v", scale = "p", title_lbl = "Custom text and color:", lbl_txt = txt_org, f_lbl = "namnum", f_lwd = 2, col_pal = pal_rgb)plot_area(prev = .4, sens = 6/7, spec = 4/7, N = 5, by = "cdac", p_split = "h", scale = "f", title_lbl = "Custom text and color:", lbl_txt = txt_org, f_lbl = "namnum", f_lbl_sep = ":\n", f_lwd = 1, col_pal = pal_kn)## 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 xvalues)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) # use default gaps (based on p_split)# freq labels: plot_area(f_lbl = "def", f_lbl_sep = " = ") # defaultplot_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 nameplot_area(f_lbl = "num") # only freq numberplot_area(f_lbl = "namnum", f_lbl_sep = ":\n", cex_lbl = .75) # explicit & smaller# prob labels: plot_area(p_lbl = NA) # no prob labels, no linksplot_area(p_lbl = "no") # show links, but no labelsplot_area(p_lbl = "namnum", cex_lbl = .70) # explicit & smaller labels# prob arrows: plot_area(arr_c = +3, f_lbl = NA) # Vshape arrowsplot_area(arr_c = +6, f_lbl = NA) # Tshape arrows plot_area(arr_c = +6, f_lbl = NA, brd_dis = .02, col_p = c("black")) # adjust arrow type/position # f_lwd: plot_area(f_lwd = 3) # thicker linesplot_area(f_lwd = .5) # thinner linesplot_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 panelsplot_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(f_lbl = "nam", p_lbl = NA, col_pal = pal_mod) # plot with freq labelsplot_area(f_lbl = "num", p_lbl = NA, col_pal = pal_rgb) # no borders around boxes