riskyr (version 0.4.0)

plot_plane: Plot a plane of selected values (e.g., PPV or NPV) as a function of sensitivity and specificity.

Description

plot_plane draws a 3D-plane of selected values (e.g., predictive values PPV or NPV) as a function of a decision's sensitivity sens and specificity value spec for a given prevalence (prev).

Usage

plot_plane(
  prev = num$prev,
  sens = num$sens,
  mirt = NA,
  spec = num$spec,
  fart = NA,
  what = "PPV",
  what_col = pal,
  line_col = "grey85",
  sens_range = c(0, 1),
  spec_range = c(0, 1),
  step_size = 0.05,
  show_points = TRUE,
  point_col = "yellow",
  theta = -45,
  phi = 0,
  p_lbl = "def",
  lbl_txt = txt,
  main = txt$scen_lbl,
  sub = "type",
  title_lbl = NULL,
  cex_lbl = 0.85,
  col_pal = pal,
  mar_notes = FALSE,
  ...
)

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. If sens = NA, then show_points = FALSE.

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. If spec = NA, then show_points = FALSE.

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.

what

A character code that specifies one metric to be plotted as a plane. Currently available options are c("PPV", "NPV", "ppod", "acc"). Default: what = "PPV".

what_col

Color for surface facets corresponding to the metric specified in what. Default: what_col uses color corresponding to what in current col_pal.

line_col

Color for lines between surface facets. Default: line_col = "grey85".

sens_range

Range (minimum and maximum) of sens values on x-axis (i.e., values in c(0, 1) range). Default: sens_range = c(0, 1).

spec_range

Range (minimum and maximum) of spec values on y-axis (i.e., values in c(0, 1) range). Default: spec_range = c(0, 1).

step_size

Sets the granularity of the sens-by-spec grid. (in range .01 <= step_size <= 1). Default: step_size = .05.

show_points

Boolean option for showing the current value of the selected metric for the current conditions (prev, sens, spec) as a point on the plane. Default: show_points = TRUE.

point_col

Fill color for showing current value on plane. Default: point_col = "yellow".

theta

Horizontal rotation angle (used by persp). Default: theta = -45.

phi

Vertical rotation angle (used by persp). Default: phi = 0.

p_lbl

Type of label for shown probability values, with the following options:

1. "abb": show abbreviated probability names;

2. "def": show abbreviated probability names and values (default);

3. "nam": show only probability names (as specified in code);

4. "num": show only numeric probability values;

5. "namnum": show names and numeric probability values;

6. "no": hide labels (same for p_lbl = NA or NULL).

lbl_txt

Labels and 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 the size of text labels (e.g., on axes, legend, margin text). Default: cex_lbl = .85.

col_pal

Color palette (if what_col is unspecified). Default: col_pal = pal.

mar_notes

Boolean value for showing margin notes. Default: mar_notes = FALSE.

...

Other (graphical) parameters.

Details

plot_plane is a generalization of plot_PV3d (see legacy code) that allows for additional dependent values.

See Also

comp_popu computes the current population; popu contains the current population; comp_freq computes current frequency information; freq contains current frequency information; num for basic numeric parameters; txt for current text settings; pal for current color settings

Other visualization functions: plot.riskyr(), plot_area(), plot_bar(), plot_crisk(), plot_curve(), plot_fnet(), plot_icons(), plot_mosaic(), plot_prism(), plot_tab(), plot_tree()

Examples

# Basics:
plot_plane()              # => default plot (what = "PPV")
# same as:
# plot_plane(what = "PPV")  # => plane of PPV

plot_plane(what = "NPV")  # => plane of NPV
plot_plane(what = "ppod") # => plane of ppod
plot_plane(what = "acc")  # => plane of acc

# Plane with/out points:
# plot_plane(prev = .5, sens = NA, spec = NA, what = "ppv")           # plane with 0 points
plot_plane(prev = .5, sens = c(.2, .5, .8), spec = .6, what = "npv")  # plane with 3 points

# Zooming into sens and spec ranges:
# plot_plane(prev = .02, sens = c(.8, .9), spec = c(.8, .8, .9, .9))  # default ranges
plot_plane(prev = .02, sens = c(.8, .9), spec = c(.8, .8, .9, .9),
           sens_range = c(.7, 1), spec_range = c(.7, 1), step_size = .02)  # zooming in

# Options:
# plot_plane(main = "No point and smaller labels", show_points = FALSE, cex_lbl = .60)

plot_plane(main = "Testing plot colors", what_col = "royalblue4", line_col = "sienna2")
plot_plane(main = "Testing b/w plot", what = "npv", what_col = "white", line_col = "black")
plot_plane(main = "Testing color pal_bwp", col_pal = pal_bwp)

plot_plane(step_size = .333, what_col = "firebrick")    # => coarser granularity + color
plot_plane(step_size = .025, what_col = "chartreuse4")  # => finer granularity + color
plot_plane(what_col = "steelblue4", theta = -90, phi = 50)  # => rotated, from above