petersenlab (version 1.1.0)

nomogrammer: Create Nomogram.

Description

Create nomogram plot.

Usage

nomogrammer(
  TP = NULL,
  TN = NULL,
  FP = NULL,
  FN = NULL,
  pretestProb = NULL,
  selectionRate = NULL,
  SN = NULL,
  SP = NULL,
  FPR = NULL,
  PLR = NULL,
  NLR = NULL,
  Detail = FALSE,
  NullLine = FALSE,
  LabelSize = (14/5),
  Verbose = FALSE
)

Value

ggplot object of nomogram plot.

Arguments

TP

Number of true positive cases.

TN

Number of true negative cases.

FP

Number of false positive cases.

FN

Number of false negative cases.

pretestProb

Pretest probability (prevalence/base rate/prior probability) of characteristic, as a number between 0 and 1.

selectionRate

Selection rate (marginal probability of positive test), as a number between 0 and 1.

SN

Sensitivity of the test at a given cut point, as a number between 0 and 1.

SP

Specificity of the test at a given cut point, as a number between 0 and 1.

FPR

False positive rate of the test at a given cut point, as a number between 0 and 1.

PLR

Positive likelihood ratio of the test at a given cut point.

NLR

Positive likelihood ratio of the test at a given cut point.

Detail

If TRUE, overlay key statistics onto the plot.

NullLine

If TRUE, add a line from prior prob through LR = 1.

LabelSize

Label size.

Verbose

Print out relevant metrics in the console.

Details

Create nomogram plot from the following at a given cut point:

• 1) true positives (TP), true negatives (TN), false positives (FP), and false negatives (FN)

• 2) pretest probability (pretestProb), sensitivity (SN), and specificity (SP), OR

• 3) pretest probability (pretestProb), sensitivity (SN), and false positive rate (FPR), OR

• 4) pretest probability (pretestProb), sensitivity (SN), and selection rate (selectionRate), OR

• 5) pretest probability (pretestProb), positive likelihood ratio (PLR), and negative likelihood ratio (NLR)

See Also

https://github.com/achekroud/nomogrammer

Other accuracy: accuracyAtCutoff(), accuracyAtEachCutoff(), accuracyOverall(), optimalCutoff(), posttestOdds()

Examples

nomogrammer(
  TP = 253,
  TN = 386,
  FP = 14,
  FN = 347)

nomogrammer(
  pretestProb = .60,
  SN = 0.421,
  SP = 0.965)

nomogrammer(
  pretestProb = .60,
  SN = 0.421,
  FPR = 0.035)

nomogrammer(
  pretestProb = .60,
  SN = 0.421,
  selectionRate = 0.267)

nomogrammer(
  pretestProb = .60,
  PLR = 12,
  NLR = 0.6)