Get and Set Contrasts Matrix for an Independent Variable in Data

get_contrasts() returns the "contrasts" attribute a selected factor within a data frame.

set_contrasts() sets the "contrasts" attribute for a selected factor within a data frame;

set_contrasts()<- is the replacement function form.

Usage

get_contrasts(data, .f)

set_contrasts(data, .f, how.many = NULL, ..., contr)

set_contrasts(data, .f, how.many = NULL, ...) <- value

Arguments

data

a data frame, or a data frame extension (e.g. a tibble).

.f

<data-masking> quoted name of a factor in data.

how.many

the number of contrasts to set, by default one less than nlevels(object).

...

additional arguments for the function contr.

contr

which contrasts to use. Can be a matrix with one row for each level of the factor or a suitable function like contr.poly or a character string giving the name of the function

value

either a numeric matrix (or a sparse or dense matrix of a class extending dMatrix from package Matrix) whose columns give coefficients for contrasts in the levels of x, or (the quoted name of) a function which computes such matrices.

Value

A dataframe or tibble with the "contrasts" attribute set for .f.

Details

The "contrasts" attribute of .f may be set using either a numeric matrix or (the quoted name of) a function which computes such matrices, supplied to set_contrasts() using the contr argument or the value argument in the case of the replacement function form set_contrasts()<-. A suitable contrast matrix may be obtained using a contrast function such as contr.helmert, contr.poly, contr.sum, contr.treatment or contr.SAS, or the (quoted) name of the function itself may be supplied. Additional arguments, such as base = x, may be supplied to a contrast function using the ... argument of set_contrasts() or set_contrasts()<-.

If a base argument is supplied when contr = contr.treatment, its value is capped to be no greater than nlevels(.f), hence it can be specified as a large integer (e.g., 99L) to ensure the last level is the reference level. This may be convenient when using set_contrasts() programmatically.

If NULL is supplied as the contr or value argument, any existing "contrasts" attribute will be removed from .f.

See also

contrast, contrasts, C, contr.helmert, contr.poly, contr.sum, contr.treatment or contr.SAS.

Other get-contrasts: get_contr_data()

Examples

## Create data frame with a factor iv
(d <- binom_data())
#> __________________________
#> Simulated Binomial Data: -
#> 
#> # A tibble: 5 × 3
#>   iv       pn    qn
#> * <fct> <int> <int>
#> 1 a        37    29
#> 2 b        24    42
#> 3 c        21    45
#> 4 d        13    53
#> 5 e         5    61

## set_contrasts()
d |> set_contrasts(iv, contr = contr.helmert) |> get_contrasts(iv)
#>   [,1] [,2] [,3] [,4]
#> a   -1   -1   -1   -1
#> b    1   -1   -1   -1
#> c    0    2   -1   -1
#> d    0    0    3   -1
#> e    0    0    0    4

d |> set_contrasts(iv, contr = contr.poly) |> get_contrasts(iv)
#>           .L         .Q         .C         ^4
#> a -0.6324555  0.5345225 -0.3162278  0.1195229
#> b -0.3162278 -0.2672612  0.6324555 -0.4780914
#> c  0.0000000 -0.5345225  0.0000000  0.7171372
#> d  0.3162278 -0.2672612 -0.6324555 -0.4780914
#> e  0.6324555  0.5345225  0.3162278  0.1195229

d |> set_contrasts(iv, contr = contr.sum) |> get_contrasts(iv)
#>   [,1] [,2] [,3] [,4]
#> a    1    0    0    0
#> b    0    1    0    0
#> c    0    0    1    0
#> d    0    0    0    1
#> e   -1   -1   -1   -1

d |> set_contrasts(iv, contr = contr.treatment) |> get_contrasts(iv)
#>   b c d e
#> a 0 0 0 0
#> b 1 0 0 0
#> c 0 1 0 0
#> d 0 0 1 0
#> e 0 0 0 1

d |> set_contrasts(iv, contr = contr.SAS) |> get_contrasts(iv)
#>   a b c d
#> a 1 0 0 0
#> b 0 1 0 0
#> c 0 0 1 0
#> d 0 0 0 1
#> e 0 0 0 0

## how.many argument
d |> set_contrasts(iv, 3, contr = contr.poly) |> get_contrasts(iv)
#>           .L         .Q         .C
#> a -0.6324555  0.5345225 -0.3162278
#> b -0.3162278 -0.2672612  0.6324555
#> c  0.0000000 -0.5345225  0.0000000
#> d  0.3162278 -0.2672612 -0.6324555
#> e  0.6324555  0.5345225  0.3162278

## base argument of contr.treatment
d |> set_contrasts(iv, base = 1, contr = contr.treatment) |> get_contrasts(iv)
#>   b c d e
#> a 0 0 0 0
#> b 1 0 0 0
#> c 0 1 0 0
#> d 0 0 1 0
#> e 0 0 0 1

d |> set_contrasts(iv, base = 3, contr = contr.treatment) |> get_contrasts(iv)
#>   a b d e
#> a 1 0 0 0
#> b 0 1 0 0
#> c 0 0 0 0
#> d 0 0 1 0
#> e 0 0 0 1

## base argument of contr.treatment limited to nlevels(d$iv) 
d |> set_contrasts(iv, base = 99L, contr = contr.treatment) |> get_contrasts(iv)
#>   a b c d
#> a 1 0 0 0
#> b 0 1 0 0
#> c 0 0 1 0
#> d 0 0 0 1
#> e 0 0 0 0

## Remove "contrasts" attribute using NULL
d |> set_contrasts(iv, contr = NULL) |> get_contrasts(iv)
#> NULL

## set_contrasts()<- replacement form
set_contrasts(d, iv) <- contr.helmert
d |> get_contrasts(iv)
#>   [,1] [,2] [,3] [,4]
#> a   -1   -1   -1   -1
#> b    1   -1   -1   -1
#> c    0    2   -1   -1
#> d    0    0    3   -1
#> e    0    0    0    4

set_contrasts(d, iv) <- contr.poly
d |> get_contrasts(iv)
#>           .L         .Q         .C         ^4
#> a -0.6324555  0.5345225 -0.3162278  0.1195229
#> b -0.3162278 -0.2672612  0.6324555 -0.4780914
#> c  0.0000000 -0.5345225  0.0000000  0.7171372
#> d  0.3162278 -0.2672612 -0.6324555 -0.4780914
#> e  0.6324555  0.5345225  0.3162278  0.1195229

set_contrasts(d, iv) <- contr.sum
d |> get_contrasts(iv)
#>   [,1] [,2] [,3] [,4]
#> a    1    0    0    0
#> b    0    1    0    0
#> c    0    0    1    0
#> d    0    0    0    1
#> e   -1   -1   -1   -1

set_contrasts(d, iv) <- contr.treatment
d |> get_contrasts(iv)
#>   b c d e
#> a 0 0 0 0
#> b 1 0 0 0
#> c 0 1 0 0
#> d 0 0 1 0
#> e 0 0 0 1

set_contrasts(d, iv) <- contr.SAS
d |> get_contrasts(iv)
#>   a b c d
#> a 1 0 0 0
#> b 0 1 0 0
#> c 0 0 1 0
#> d 0 0 0 1
#> e 0 0 0 0

## how.many argument
set_contrasts(d, iv, 3) <- contr.poly
d |> get_contrasts(iv)
#>           .L         .Q         .C
#> a -0.6324555  0.5345225 -0.3162278
#> b -0.3162278 -0.2672612  0.6324555
#> c  0.0000000 -0.5345225  0.0000000
#> d  0.3162278 -0.2672612 -0.6324555
#> e  0.6324555  0.5345225  0.3162278

## base argument of contr.treatment
set_contrasts(d, iv, base = 2) <- contr.treatment
d |> get_contrasts(iv)
#>   a c d e
#> a 1 0 0 0
#> b 0 0 0 0
#> c 0 1 0 0
#> d 0 0 1 0
#> e 0 0 0 1

set_contrasts(d, iv, base = 4) <- contr.treatment
d |> get_contrasts(iv)
#>   a b c e
#> a 1 0 0 0
#> b 0 1 0 0
#> c 0 0 1 0
#> d 0 0 0 0
#> e 0 0 0 1

## base argument of contr.treatment limited to nlevels(d$iv) 
set_contrasts(d, iv, base = 99L) <- contr.treatment
d |> get_contrasts(iv)
#>   a b c d
#> a 1 0 0 0
#> b 0 1 0 0
#> c 0 0 1 0
#> d 0 0 0 1
#> e 0 0 0 0

rm(d)