riskyr (version 0.4.0)

comp_prob_prob: Compute probabilities from (3 essential) probabilities.

Description

comp_prob_prob computes current probability information from a sufficient and valid set of 3 essential probabilities (prev, and sens or its complement mirt, and spec or its complement fart). It returns a list of 13 key probabilities (prob) as its output.

Usage

comp_prob_prob(
  prev = prob$prev,
  sens = prob$sens,
  mirt = NA,
  spec = prob$spec,
  fart = NA,
  tol = 0.01
)

Value

A list prob containing 13 key probability values.

Arguments

prev

The condition's prevalence value prev (i.e., the probability of condition being TRUE).

sens

The decision's sensitivity value 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.

mirt

The decision's miss rate value 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.

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.

tol

A numeric tolerance value for is_complement. Default: tol = .01.

Details

comp_prob_prob is a wrapper function for the more basic function comp_prob.

Extreme probabilities (sets containing 2 or more probabilities of 0 or 1) may yield unexpected values (e.g., predictive values PPV or NPV turning NaN when is_extreme_prob_set evaluates to TRUE).

Key relationships between frequencies and probabilities (see documentation of comp_freq or comp_prob for details):

• Three perspectives on a population:

  by condition / by decision / by accuracy.

• Defining probabilities in terms of frequencies:

  Probabilities can be computed as ratios between frequencies, but beware of rounding issues.

Functions translating between representational formats:

1. comp_prob_prob (defined here) is a wrapper function for comp_prob and an analog to 3 other format conversion functions:

2. comp_prob_freq computes current probability information contained in prob from 4 essential frequencies (hi, mi, fa, cr).

3. comp_freq_prob computes current frequency information contained in freq from 3 essential probabilities (prev, sens, spec).

4. comp_freq_freq computes current frequency information contained in freq from 4 essential frequencies (hi, mi, fa, cr).

See Also

comp_freq_prob computes current frequency information from (3 essential) probabilities; comp_freq_freq computes current frequency information from (4 essential) frequencies; comp_prob_freq computes current probability information from (4 essential) frequencies; num contains basic numeric variables; init_num initializes basic numeric variables; freq contains current frequency information; comp_freq computes current frequency information; prob contains current probability information; comp_prob computes current probability information; comp_complement computes a probability's complement; comp_comp_pair computes pairs of complements; comp_complete_prob_set completes valid sets of probabilities; comp_min_N computes a suitable population size N (if missing).

Other functions computing frequencies: comp_freq_freq(), comp_freq_prob(), comp_freq(), comp_min_N()

Other format conversion functions: comp_freq_freq(), comp_freq_prob(), comp_prob_freq()

Examples

# Basics:
comp_prob_prob(prev = .11, sens = .88, spec = .77)                        # ok: PPV = 0.3210614
comp_prob_prob(prev = .11, sens = NA, mirt = .12, spec = NA, fart = .23)  # ok: PPV = 0.3210614
comp_prob_prob()          # ok, using current defaults
length(comp_prob_prob())  # 13 key probability values

# Ways to work:
comp_prob_prob(.99, sens = .99, spec = .99)              # ok: PPV = 0.999898
comp_prob_prob(.99, sens = .90, spec = NA, fart = .10)   # ok: PPV = 0.9988789

# Watch out for extreme cases:
comp_prob_prob(1, sens = 0, spec = 1)      # ok, but with warnings (as PPV & FDR are NaN)
comp_prob_prob(1, sens = 0, spec = 0)      # ok, but with warnings (as PPV & FDR are NaN)
comp_prob_prob(1, sens = 0, spec = NA, fart = 0)  # ok, but with warnings (as PPV & FDR are NaN)
comp_prob_prob(1, sens = 0, spec = NA, fart = 1)  # ok, but with warnings (as PPV & FDR are NaN)

comp_prob_prob(1, sens = 1, spec = 0)      # ok, but with warnings (as NPV & FOR are NaN)
comp_prob_prob(1, sens = 1, spec = 1)      # ok, but with warnings (as NPV & FOR are NaN)
comp_prob_prob(1, sens = 1, spec = NA, fart = 0)  # ok, but with warnings (as NPV & FOR are NaN)
comp_prob_prob(1, sens = 1, spec = NA, fart = 1)  # ok, but with warnings (as NPV & FOR are NaN)

# Ways to fail:
comp_prob_prob(NA, 1, 1, NA)  # only warning: invalid set (prev not numeric)
comp_prob_prob(8,  1, 1, NA)  # only warning: prev no probability
comp_prob_prob(1,  8, 1, NA)  # only warning: sens no probability
comp_prob_prob(1,  1, 1,  1)  # only warning: is_complement not in tolerated range