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

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

scale 
Scale probabilities and corresponding node 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: 
sample 
Boolean value that determines whether frequency values
are sampled from 
f_lbl 
Type of label for showing frequency values in nodes, with 6 options:

f_lbl_sep 
Separator for frequency labels
(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: 
main 
Text label for main plot title.
Default: 
sub 
Text label for plot subtitle (on 2nd line).
Default: 
title_lbl 
Deprecated text label for current plot title.
Replaced by 
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. 
plot_prism
generalizes and replaces plot_fnet
by removing the dependency on the R package diagram
and providing many additional options.
Nothing (NULL).
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()
## 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 nonrounded) 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 nonrounded) 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 = 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, 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)
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