Initialize basic numeric variables.

init_num initializes basic numeric variables to define num as a list of named elements containing four basic probabilities (prev, sens, spec, and fart) and one frequency parameter (the population size N).

Usage

init_num(
  prev = num.def$prev,
  sens = num.def$sens,
  spec = num.def$spec,
  fart = num.def$fart,
  N = num.def$N
)

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).

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 is 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.

N

The population size N.

Value

A list containing a valid quadruple of probabilities (prev, sens, spec, and fart) and one frequency (population size N).

Details

If spec is provided, its complement fart is optional. If fart is provided, its complement spec is optional. If no N is provided, a suitable minimum value is computed by comp_min_N.

See also

num contains basic numeric parameters; pal contains current color settings; txt contains current text settings; freq contains current frequency information; comp_freq computes frequencies from probabilities; prob contains current probability information; comp_prob computes current probability information; is_valid_prob_set verifies sets of probability inputs; is_extreme_prob_set verifies sets of extreme probabilities; comp_min_N computes a suitable minimum population size N.

Other functions initializing scenario information: init_pal(), init_txt(), riskyr()

Examples

# ways to succeed:
init_num(1, 1, 1, 0, 100)  # => succeeds
#> Warning: Extreme case (prev = 1 & sens = 1):
#>   N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> $prev
#> [1] 1
#> 
#> $sens
#> [1] 1
#> 
#> $spec
#> [1] 1
#> 
#> $fart
#> [1] 0
#> 
#> $N
#> [1] 100
#> 
init_num(1, 1, 0, 1, 100)  # => succeeds
#> Warning: Extreme case (prev = 1 & sens = 1):
#>   N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> $prev
#> [1] 1
#> 
#> $sens
#> [1] 1
#> 
#> $spec
#> [1] 0
#> 
#> $fart
#> [1] 1
#> 
#> $N
#> [1] 100
#> 

# watch out for:
init_num(1, 1, 0, 1)           # => succeeds (with N computed)
#> Warning: Extreme case (prev = 1 & sens = 1):
#>   N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> $prev
#> [1] 1
#> 
#> $sens
#> [1] 1
#> 
#> $spec
#> [1] 0
#> 
#> $fart
#> [1] 1
#> 
#> $N
#> [1] 1000
#> 
init_num(1, 1, NA, 1, 100)     # => succeeds (with spec computed)
#> Warning: Extreme case (prev = 1 & sens = 1):
#>   N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> $prev
#> [1] 1
#> 
#> $sens
#> [1] 1
#> 
#> $spec
#> [1] 0
#> 
#> $fart
#> [1] 1
#> 
#> $N
#> [1] 100
#> 
init_num(1, 1, 0, NA, 100)     # => succeeds (with fart computed)
#> Warning: Extreme case (prev = 1 & sens = 1):
#>   N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> $prev
#> [1] 1
#> 
#> $sens
#> [1] 1
#> 
#> $spec
#> [1] 0
#> 
#> $fart
#> [1] 1
#> 
#> $N
#> [1] 100
#> 
init_num(1, 1, NA, 1)          # => succeeds (with spec and N computed)
#> Warning: Extreme case (prev = 1 & sens = 1):
#>   N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> $prev
#> [1] 1
#> 
#> $sens
#> [1] 1
#> 
#> $spec
#> [1] 0
#> 
#> $fart
#> [1] 1
#> 
#> $N
#> [1] 1000
#> 
init_num(1, 1, 0, NA)          # => succeeds (with fart and N computed)
#> Warning: Extreme case (prev = 1 & sens = 1):
#>   N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> $prev
#> [1] 1
#> 
#> $sens
#> [1] 1
#> 
#> $spec
#> [1] 0
#> 
#> $fart
#> [1] 1
#> 
#> $N
#> [1] 1000
#> 
init_num(1, 1, .51, .50, 100)  # => succeeds (as spec and fart are within tolarated range)
#> Warning: Extreme case (prev = 1 & sens = 1):
#>   N hi (TP) cases; 0 cond_false or dec_false cases; NPV = NaN.
#> $prev
#> [1] 1
#> 
#> $sens
#> [1] 1
#> 
#> $spec
#> [1] 0.51
#> 
#> $fart
#> [1] 0.5
#> 
#> $N
#> [1] 100
#> 

# ways to fail:
init_num(prev = NA)                                  # => NAs + warning (NA)
#> $prev
#> [1] NA
#> 
#> $sens
#> [1] NA
#> 
#> $spec
#> [1] NA
#> 
#> $fart
#> [1] NA
#> 
#> $N
#> [1] NA
#> 
init_num(prev = 88)                                  # => NAs + warning (beyond range)
#> $prev
#> [1] NA
#> 
#> $sens
#> [1] NA
#> 
#> $spec
#> [1] NA
#> 
#> $fart
#> [1] NA
#> 
#> $N
#> [1] NA
#> 
init_num(prev =  1, sens = NA)                       # => NAs + warning (NA)
#> $prev
#> [1] NA
#> 
#> $sens
#> [1] NA
#> 
#> $spec
#> [1] NA
#> 
#> $fart
#> [1] NA
#> 
#> $N
#> [1] NA
#> 
init_num(prev =  1, sens = 1, spec = NA, fart = NA)  # => NAs + warning (NAs)
#> $prev
#> [1] NA
#> 
#> $sens
#> [1] NA
#> 
#> $spec
#> [1] NA
#> 
#> $fart
#> [1] NA
#> 
#> $N
#> [1] NA
#> 
init_num(1, 1, .52, .50, 100)   # => NAs + warning (complements beyond range)
#> Warning: Probabilities (p1 and p2) are not complements (in tolerated range).
#> $prev
#> [1] NA
#> 
#> $sens
#> [1] NA
#> 
#> $spec
#> [1] NA
#> 
#> $fart
#> [1] NA
#> 
#> $N
#> [1] NA
#>