Levels of Independent Variable where a Bernoulli Dependent Variable is Neither All Success Nor All Failure

good_levels() identifies levels of an independent variable for which values of a Bernoulli dependent variable are neither all one (success) nor all zero (failure).

drop_zero() drops data with levels of an independent variable for which values of a Bernoulli dependent variable are either all one (success) or all zero (failure).

Usage

good_levels(object, ...)

# S3 method for class 'data.frame'
good_levels(object, .dep_var, .ind_var, ...)

# S3 method for class 'binom_contingency'
good_levels(object, .ind_var, ...)

drop_zero(object, ...)

# S3 method for class 'data.frame'
drop_zero(object, .dep_var, .ind_var, ...)

# S3 method for class 'binom_contingency'
drop_zero(object, ...)

drop_null(object, ...)

Arguments

object: a data frame, or a data frame extension (e.g. a tibble), or an object of class "binom_contingency".
...: further arguments passed to or from other methods.
.dep_var: <data-masking> quoted name of a Bernoulli dependent variable that should be numeric with values of 0 and 1.
.ind_var: <data-masking> quoted name of the independent variable, which may be a factor, or a character vector.

Value

good_levels(): returns a character vector comprising levels of .ind_var for which the corresponding values of .dep_var are neither all one (success) nor all zero (failure)
drop_zero(): returns an object of the same class as that provided by argument object: either a data frame (or a data frame extension e.g., a tibble) comprising only rows with levels of the independent variable for which values of the Bernoulli dependent variable are neither all zero nor all one; or a "binom_contingency" object excluding any rows for which values of the Bernoulli dependent variable are either all one (success) or all zero (failure).

Details

For a Bernoulli trial dataset with a numeric dependent variable coded as 0 or 1, the generic function good_levels() identifies levels of an independent variable for which values of the dependent variable are neither all zero nor all one i.e., \(0 < p < 1\).

For a similar Bernoulli trial dataset, the generic function drop_zero() drops all rows of data other than those with levels of the independent variable identified by good_levels(). Unused factor levels are dropped from the independent variable and from any other factors in the data.

The drop_zero() S3 method for objects of class "binom_contingency" returns a binomial contingency table equivalent to the original having been created using binom_contingency() with argument .drop_zero = TRUE.

drop_null() is deprecated, please use drop_zero().

Note

Dropping levels of explanatory factors for which values of a Bernoulli dependent variable are either all zero or all one, prevents warning messages that ‘fitted probabilities numerically 0 or 1 occurred’ when fitting generalized linear models using glm() or calculating odds ratios using odds_ratio(); see binom_contingency().

Examples

(d_bern <- bernoulli_data(probs = c(0.8, 0.4, 0, 0.3, 0.6 )))
#> ___________________________
#> Simulated Bernoulli Data: -
#> 
#> # A tibble: 330 × 2
#>    iv       dv
#>  * <fct> <int>
#>  1 a         1
#>  2 a         1
#>  3 a         0
#>  4 a         0
#>  5 a         1
#>  6 a         1
#>  7 a         1
#>  8 a         1
#>  9 a         1
#> 10 a         1
#> # ℹ 320 more rows
d_bern |> levels_data()
#> $iv
#> [1] "a" "b" "c" "d" "e"
#> 

## S3 methods for class 'data.frame' 
d_bern |> good_levels(dv, iv)
#> [1] "a" "b" "d" "e"
d_bern |> drop_zero(dv, iv)
#> ___________________________
#> Simulated Bernoulli Data: -
#> 
#> # A tibble: 264 × 2
#>    iv       dv
#>    <fct> <int>
#>  1 a         1
#>  2 a         1
#>  3 a         0
#>  4 a         0
#>  5 a         1
#>  6 a         1
#>  7 a         1
#>  8 a         1
#>  9 a         1
#> 10 a         1
#> # ℹ 254 more rows
d_bern |> drop_zero(dv, iv) |> levels_data()
#> $iv
#> [1] "a" "b" "d" "e"
#> 

(d_bin <- d_bern |> binom_contingency(dv, iv))
#> _____________________________
#> Binomial Contingency Table: -
#> 
#> # A tibble: 5 × 3
#>   iv       pn    qn
#> * <fct> <int> <int>
#> 1 a        51    15
#> 2 b        23    43
#> 3 c         0    66
#> 4 d        15    51
#> 5 e        36    30

## S3 methods for class 'binom_contingency' 
d_bin |> good_levels(iv)
#> [1] "a" "b" "d" "e"
d_bin |> drop_zero()
#> _____________________________
#> Binomial Contingency Table: -
#> 
#> # A tibble: 4 × 3
#>   iv       pn    qn
#>   <fct> <int> <int>
#> 1 a        51    15
#> 2 b        23    43
#> 3 d        15    51
#> 4 e        36    30

## Results identical whether drop_zero() used
## before or after binom_contingency()
identical(
  d_bern |> drop_zero(dv, iv) |> binom_contingency(dv, iv),
  d_bin |> drop_zero()
)
#> [1] TRUE

## Results identical whether drop_zero() used
## during or after binom_contingency()
identical(
  d_bern |> binom_contingency(dv, iv, .drop_zero = TRUE),
  d_bin |> drop_zero()
)
#> [1] TRUE

rm(d_bern, d_bin)