PPV_heatmap {BayesianReasoning}

Plot PPV and NPV heatmaps

Description

Plot heatmaps showing the PPV for a given Sensitivity and a range of Prevalences and False Positive values or NPV values for a given Specificity and a range of Prevalences and True Positive values

Usage

PPV_heatmap(
  min_Prevalence = 1,
  max_Prevalence = 1000,
  Sensitivity = NULL,
  Specificity = NULL,
  limits_Sensitivity = NULL,
  limits_Specificity = NULL,
  one_out_of = FALSE,
  overlay = "no",
  overlay_labels = "",
  overlay_extra_info = FALSE,
  overlay_position_FP = NULL,
  overlay_position_FN = NULL,
  overlay_prevalence_1 = NULL,
  overlay_prevalence_2 = NULL,
  uncertainty_prevalence = "high",
  label_title = "",
  label_subtitle = "",
  Language = "en",
  folder = "",
  PPV_NPV = "PPV",
  steps_matrix = 100,
  DEBUG = FALSE,
  ...
)

Arguments

min_Prevalence

[x] out of y prevalence of disease: [1-Inf]

max_Prevalence

x out of [y] prevalence of disease: [1-Inf]

Sensitivity

Sensitivity of test: [0-100]

Specificity

Specificity of test: [0-100]

limits_Sensitivity

c(min Sensitivity, max Sensitivity)

limits_Specificity

c(min Specificity, max Specificity)

one_out_of

Show y scale as 1 out of x [TRUE, FALSE] FALSE by default

overlay

Type of overlay: ["line", "area"]

overlay_labels

Labels for each point in the overlay. For example: c("80", "70", "60", "50", "40", "30", "20 y.o.")

overlay_extra_info

show extra info in overlay? [TRUE/FALSE]

overlay_position_FP

FP value (position in the x-axis) for each point in the overlay. For example: c(7, 8, 9, 12, 14, 14)

overlay_position_FN

FN value (position in the x-axis) for each point in the overlay. For example: c(7, 8, 9, 12, 14, 14)

overlay_prevalence_1

Prevalence value (position in the y-axis) for each point in the overlay. For example: c(1, 1, 1, 2, 1, 1)

overlay_prevalence_2

Prevalence value (position in the y-axis) for each point in the overlay. For example: c(26, 29, 44, 69, 227, 1667)

uncertainty_prevalence

How much certainty we have about the prevalence ["high"/"low"]

label_title

Title for the plot

label_subtitle

Subtitle for the plot

Language

Language for the plot labels: ["sp", "en"]

folder

Where to save the plot (the filename would be automatically created using the plot parameters)

PPV_NPV

Should show PPV or NPV ["PPV", "NPV"]

steps_matrix

width of PPV/NPV matrix. 100 by default

DEBUG

Shows debug warnings [TRUE/FALSE]

...

Other parameters. Now used to pass dpi, height and width in the Show and Save plot section

Value

Shows a plot or, if given a folder argument, saves a .png version of the plot

Examples

PPV_heatmap(
  min_Prevalence = 1,
  max_Prevalence = 1000,
  Sensitivity = 100,
  Specificity = 98,
  Language = "en"
)