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, 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, 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 1 or 2 perspectives that split the population into 2 subsets. Specifying 1 perspective plots a frequency tree (single tree) with 3 options:
Specifying 2 perspectives plots a frequency prism (network, double tree) with 6 options:

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

scale  Scale probabilities and corresponding area dimensions either by exact probability or by (rounded or nonrounded) frequency, with 2 options:
Note: 
round  Boolean option specifying whether computed frequencies
are rounded to integers. Default: 
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_lwd  Line width of areas.
Default: 
p_lwd  Line width of probability links.
Default: 
p_scale  Boolean option for scaling current widths of probability links
(as set by 
p_lbl  Type of label for showing 3 key probability links and values, with many options:

arr_c  Arrow code for symbols at ends of probability links
(as a numeric value
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_prism
generalizes and replaces plot_fnet
by removing the dependency on the R package diagram
and providing many additional options.
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_curve
, plot_fnet
,
plot_icons
, plot_mosaic
,
plot_plane
, plot_tab
,
plot_tree
## 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 = 1/2, sens = 4/5, spec = 3/5)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)## Custom color and text settings: 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 labelsmy_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 colorsplot_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 colorsplot_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 decision (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") # v02plot_prism(by = "cdcd") # (+) Message#>plot_prism(by = "dccd") # v03plot_prism(by = "dcac") # v04plot_prism(by = "dcdc") # (+) Message#>plot_prism(by = "accd") # v05plot_prism(by = "acdc") # v06plot_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 probplot_prism(N = 5, prev = .3, sens = .8, spec = .6, area = "hr", scale = "f") # widths scaled by (rounded or nonrounded) freqplot_prism(N = 4, prev = .2, sens = .7, spec = .8, area = "sq", scale = "p") # areas scaled by probplot_prism(N = 4, prev = .2, sens = .7, spec = .8, area = "sq", scale = "f") # areas scaled by (rounded or nonrounded) freq## Frequency boxes: # f_lbl: plot_prism(f_lbl = "abb") # abbreviated freq names (variable names)plot_prism(f_lbl = "nam") # only freq namesplot_prism(f_lbl = "num") # only numeric freq values (default)plot_prism(f_lbl = "namnum") # names and numeric freq valuesplot_prism(f_lbl = "namnum", cex_lbl = .75) # smaller freq labelsplot_prism(f_lbl = NA) # no freq labelsplot_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 linesplot_prism(f_lwd = 3) # thicker linesplot_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)plot_prism(area = "hr", f_lbl = "num", f_lwd = .5, p_lbl = NA, arr_c = 0, col_pal = pal_mod, 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 namesplot_prism(p_lbl = "num") # only numeric prob valuesplot_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 arrowsplot_prism(arr_c = 3) # arr_c = 1 to 3: points at both endsplot_prism(arr_c = 2) # point at far endplot_prism(arr_c = +2) # crr_c = 13: Vshape arrows at far end# plot_prism(arr_c = +3) # Vshape arrows at both ends # plot_prism(arr_c = +6) # arr_c = 46: Tshape arrows ## Plain plot versions: plot_prism(area = "no", f_lbl = "def", p_lbl = "num", col_pal = pal_mod, f_lwd = 1, title_lbl = "", mar_notes = FALSE) # remove titles and margin notesplot_prism(area = "no", f_lbl = "nam", p_lbl = "min", col_pal = pal_rgb)plot_prism(area = "no", f_lbl = "num", p_lbl = "num", col_pal = pal_kn)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")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 plotplot_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&whiteplot_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)