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 11 probabilities (prob) as its output.

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

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.

Value

A list prob containing 11 probability values.

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, comp_popu

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
#> $prev #> [1] 0.11 #> #> $sens #> [1] 0.88 #> #> $mirt #> [1] 0.12 #> #> $spec #> [1] 0.77 #> #> $fart #> [1] 0.23 #> #> $ppod #> [1] 0.3015 #> #> $PPV #> [1] 0.3210614 #> #> $FDR #> [1] 0.6789386 #> #> $NPV #> [1] 0.9811024 #> #> $FOR #> [1] 0.01889764 #> #> $acc #> [1] 0.7821 #> #> $p_acc_hi #> [1] 0.1237693 #> #> $p_err_fa #> [1] 0.9394218 #>
comp_prob_prob(prev = .11, sens = NA, mirt = .12, spec = NA, fart = .23) # => ok: PPV = 0.3210614
#> $prev #> [1] 0.11 #> #> $sens #> [1] 0.88 #> #> $mirt #> [1] 0.12 #> #> $spec #> [1] 0.77 #> #> $fart #> [1] 0.23 #> #> $ppod #> [1] 0.3015 #> #> $PPV #> [1] 0.3210614 #> #> $FDR #> [1] 0.6789386 #> #> $NPV #> [1] 0.9811024 #> #> $FOR #> [1] 0.01889764 #> #> $acc #> [1] 0.7821 #> #> $p_acc_hi #> [1] 0.1237693 #> #> $p_err_fa #> [1] 0.9394218 #>
comp_prob_prob() # => ok, using current defaults
#> $prev #> [1] 0.25 #> #> $sens #> [1] 0.85 #> #> $mirt #> [1] 0.15 #> #> $spec #> [1] 0.75 #> #> $fart #> [1] 0.25 #> #> $ppod #> [1] 0.4 #> #> $PPV #> [1] 0.53125 #> #> $FDR #> [1] 0.46875 #> #> $NPV #> [1] 0.9375 #> #> $FOR #> [1] 0.0625 #> #> $acc #> [1] 0.775 #> #> $p_acc_hi #> [1] 0.2741935 #> #> $p_err_fa #> [1] 0.8333333 #>
length(comp_prob_prob()) # => 11 probabilities
#> [1] 13
# Ways to work: comp_prob_prob(.99, sens = .99, spec = .99) # => ok: PPV = 0.999898
#> $prev #> [1] 0.99 #> #> $sens #> [1] 0.99 #> #> $mirt #> [1] 0.01 #> #> $spec #> [1] 0.99 #> #> $fart #> [1] 0.01 #> #> $ppod #> [1] 0.9802 #> #> $PPV #> [1] 0.999898 #> #> $FDR #> [1] 0.00010202 #> #> $NPV #> [1] 0.5 #> #> $FOR #> [1] 0.5 #> #> $acc #> [1] 0.99 #> #> $p_acc_hi #> [1] 0.99 #> #> $p_err_fa #> [1] 0.01 #>
comp_prob_prob(.99, sens = .90, spec = NA, fart = .10) # => ok: PPV = 0.9988789
#> $prev #> [1] 0.99 #> #> $sens #> [1] 0.9 #> #> $mirt #> [1] 0.1 #> #> $spec #> [1] 0.9 #> #> $fart #> [1] 0.1 #> #> $ppod #> [1] 0.892 #> #> $PPV #> [1] 0.9988789 #> #> $FDR #> [1] 0.001121076 #> #> $NPV #> [1] 0.08333333 #> #> $FOR #> [1] 0.9166667 #> #> $acc #> [1] 0.9 #> #> $p_acc_hi #> [1] 0.99 #> #> $p_err_fa #> [1] 0.01 #>
# Watch out for extreme cases: comp_prob_prob(1, sens = 0, spec = 1) # => ok, but with warnings (as PPV & FDR are NaN)
#> Warning: Extreme case (prev = 1 & sens = 0): #> N mi (FN) cases; 0 cond_false or dec_true cases; PPV = NaN.
#> Warning: PPV is NaN.
#> Warning: FDR is NaN.
#> Warning: Some derived prob values are peculiar. Check for extreme probabilities!
#> $prev #> [1] 1 #> #> $sens #> [1] 0 #> #> $mirt #> [1] 1 #> #> $spec #> [1] 1 #> #> $fart #> [1] 0 #> #> $ppod #> [1] 0 #> #> $PPV #> [1] NaN #> #> $FDR #> [1] NaN #> #> $NPV #> [1] 0 #> #> $FOR #> [1] 1 #> #> $acc #> [1] 0 #> #> $p_acc_hi #> [1] NaN #> #> $p_err_fa #> [1] 0 #>
comp_prob_prob(1, sens = 0, spec = 0) # => ok, but with warnings (as PPV & FDR are NaN)
#> Warning: Extreme case (prev = 1 & sens = 0): #> N mi (FN) cases; 0 cond_false or dec_true cases; PPV = NaN.
#> Warning: PPV is NaN.
#> Warning: FDR is NaN.
#> Warning: Some derived prob values are peculiar. Check for extreme probabilities!
#> $prev #> [1] 1 #> #> $sens #> [1] 0 #> #> $mirt #> [1] 1 #> #> $spec #> [1] 0 #> #> $fart #> [1] 1 #> #> $ppod #> [1] 0 #> #> $PPV #> [1] NaN #> #> $FDR #> [1] NaN #> #> $NPV #> [1] 0 #> #> $FOR #> [1] 1 #> #> $acc #> [1] 0 #> #> $p_acc_hi #> [1] NaN #> #> $p_err_fa #> [1] 0 #>
comp_prob_prob(1, sens = 0, spec = NA, fart = 0) # => ok, but with warnings (as PPV & FDR are NaN)
#> Warning: Extreme case (prev = 1 & sens = 0): #> N mi (FN) cases; 0 cond_false or dec_true cases; PPV = NaN.
#> Warning: PPV is NaN.
#> Warning: FDR is NaN.
#> Warning: Some derived prob values are peculiar. Check for extreme probabilities!
#> $prev #> [1] 1 #> #> $sens #> [1] 0 #> #> $mirt #> [1] 1 #> #> $spec #> [1] 1 #> #> $fart #> [1] 0 #> #> $ppod #> [1] 0 #> #> $PPV #> [1] NaN #> #> $FDR #> [1] NaN #> #> $NPV #> [1] 0 #> #> $FOR #> [1] 1 #> #> $acc #> [1] 0 #> #> $p_acc_hi #> [1] NaN #> #> $p_err_fa #> [1] 0 #>
comp_prob_prob(1, sens = 0, spec = NA, fart = 1) # => ok, but with warnings (as PPV & FDR are NaN)
#> Warning: Extreme case (prev = 1 & sens = 0): #> N mi (FN) cases; 0 cond_false or dec_true cases; PPV = NaN.
#> Warning: PPV is NaN.
#> Warning: FDR is NaN.
#> Warning: Some derived prob values are peculiar. Check for extreme probabilities!
#> $prev #> [1] 1 #> #> $sens #> [1] 0 #> #> $mirt #> [1] 1 #> #> $spec #> [1] 0 #> #> $fart #> [1] 1 #> #> $ppod #> [1] 0 #> #> $PPV #> [1] NaN #> #> $FDR #> [1] NaN #> #> $NPV #> [1] 0 #> #> $FOR #> [1] 1 #> #> $acc #> [1] 0 #> #> $p_acc_hi #> [1] NaN #> #> $p_err_fa #> [1] 0 #>
comp_prob_prob(1, sens = 1, spec = 0) # => ok, but with warnings (as NPV & FOR are NaN)
#> Warning: Extreme case (prev = 1 & sens = 1): #> N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> Warning: NPV is NaN.
#> Warning: FOR is NaN.
#> Warning: Some derived prob values are peculiar. Check for extreme probabilities!
#> $prev #> [1] 1 #> #> $sens #> [1] 1 #> #> $mirt #> [1] 0 #> #> $spec #> [1] 0 #> #> $fart #> [1] 1 #> #> $ppod #> [1] 1 #> #> $PPV #> [1] 1 #> #> $FDR #> [1] 0 #> #> $NPV #> [1] NaN #> #> $FOR #> [1] NaN #> #> $acc #> [1] 1 #> #> $p_acc_hi #> [1] 1 #> #> $p_err_fa #> [1] NaN #>
comp_prob_prob(1, sens = 1, spec = 1) # => ok, but with warnings (as NPV & FOR are NaN)
#> Warning: Extreme case (prev = 1 & sens = 1): #> N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> Warning: NPV is NaN.
#> Warning: FOR is NaN.
#> Warning: Some derived prob values are peculiar. Check for extreme probabilities!
#> $prev #> [1] 1 #> #> $sens #> [1] 1 #> #> $mirt #> [1] 0 #> #> $spec #> [1] 1 #> #> $fart #> [1] 0 #> #> $ppod #> [1] 1 #> #> $PPV #> [1] 1 #> #> $FDR #> [1] 0 #> #> $NPV #> [1] NaN #> #> $FOR #> [1] NaN #> #> $acc #> [1] 1 #> #> $p_acc_hi #> [1] 1 #> #> $p_err_fa #> [1] NaN #>
comp_prob_prob(1, sens = 1, spec = NA, fart = 0) # => ok, but with warnings (as NPV & FOR are NaN)
#> Warning: Extreme case (prev = 1 & sens = 1): #> N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> Warning: NPV is NaN.
#> Warning: FOR is NaN.
#> Warning: Some derived prob values are peculiar. Check for extreme probabilities!
#> $prev #> [1] 1 #> #> $sens #> [1] 1 #> #> $mirt #> [1] 0 #> #> $spec #> [1] 1 #> #> $fart #> [1] 0 #> #> $ppod #> [1] 1 #> #> $PPV #> [1] 1 #> #> $FDR #> [1] 0 #> #> $NPV #> [1] NaN #> #> $FOR #> [1] NaN #> #> $acc #> [1] 1 #> #> $p_acc_hi #> [1] 1 #> #> $p_err_fa #> [1] NaN #>
comp_prob_prob(1, sens = 1, spec = NA, fart = 1) # => ok, but with warnings (as NPV & FOR are NaN)
#> Warning: Extreme case (prev = 1 & sens = 1): #> N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> Warning: NPV is NaN.
#> Warning: FOR is NaN.
#> Warning: Some derived prob values are peculiar. Check for extreme probabilities!
#> $prev #> [1] 1 #> #> $sens #> [1] 1 #> #> $mirt #> [1] 0 #> #> $spec #> [1] 0 #> #> $fart #> [1] 1 #> #> $ppod #> [1] 1 #> #> $PPV #> [1] 1 #> #> $FDR #> [1] 0 #> #> $NPV #> [1] NaN #> #> $FOR #> [1] NaN #> #> $acc #> [1] 1 #> #> $p_acc_hi #> [1] 1 #> #> $p_err_fa #> [1] NaN #>
# Ways to fail: comp_prob_prob(NA, 1, 1, NA) # => only warning: invalid set (prev not numeric)
#> Warning: Invalid probabilities. Please enter a valid set of essential probabilities.
#> [1] "Invalid probabilities. Please enter a valid set of essential probabilities."
comp_prob_prob(8, 1, 1, NA) # => only warning: prev no probability
#> Warning: Invalid probabilities. Please enter a valid set of essential probabilities.
#> [1] "Invalid probabilities. Please enter a valid set of essential probabilities."
comp_prob_prob(1, 8, 1, NA) # => only warning: sens no probability
#> Warning: Invalid probabilities. Please enter a valid set of essential probabilities.
#> [1] "Invalid probabilities. Please enter a valid set of essential probabilities."
comp_prob_prob(1, 1, 1, 1) # => only warning: is_complement not in tolerated range
#> Warning: Probabilities (p1 and p2) are not complements (in tolerated range).
#> Warning: Invalid probabilities. Please enter a valid set of essential probabilities.
#> [1] "Invalid probabilities. Please enter a valid set of essential probabilities."