Description Usage Arguments Details Value Author(s) See Also Examples

Return something similar to a contrast matrix for a categorical covariate that we wish to be monotonically non-decreasing in a specified order.

1 2 3 | ```
contr.isotonic(n, perm, contrasts = TRUE, sparse = FALSE)
contr.opisotonic(n, perm, contrasts = TRUE, sparse = FALSE)
``` |

`n` |
a vector of levels for a factor, or the number of levels. |

`perm` |
a permutation of the levels of |

`contrasts` |
a logical indicating whether constrasts should be computed. |

`sparse` |
included for compatibility reasons. Has no effect. |

`contr.isotonic`

is used in creating the design matrix
for categorical covariates with a specified order under a
particular parameterisation. For Poisson and negative binomial models, this
occurs if a categorical covariate is defined as monotonic;
for binomial models, each parameterisation defines a
permutation of the levels that must be monotonically
increasing.

For overparameterised binomial models, the design matrix for
categorical covariates must include isotonic-style dummy
covariates for every possible permutation of the levels. This
is the function of `contr.opisotonic`

.

In the order specified by `perm`

, the coefficient
associated with each level is the sum of increments between
the preceding levels. That is, the first level is defined
as *0*, the second as *0 + d_2*, the third as *0 + d_2 + d_3*, and
so on. In fitting the model, these increments are
constrained to be non-negative.

Note that these are not ‘contrasts’ as defined in the
theory for linear models; rather this is used to define the
`contrasts`

attribute of each variable so that
`model.matrix`

produces the desired design
matrix.

A matrix with `n`

rows and `k`

columns, with
`k=n-1`

if `contrasts`

is `TRUE`

and
`k=n`

if `contrasts`

is `FALSE`

.

Mark W. Donoghoe markdonoghoe@gmail.com

`model.matrix`

, which uses
`contr.isotonic`

to create the design matrix.

`contr.treatment`

, `contrasts`

for
their usual use in regression models.

1 2 3 4 5 6 7 8 | ```
contr.isotonic(4,1:4)
contr.isotonic(4,c(1,3,2,4))
# Show how contr.isotonic applies within model.matrix
x <- factor(round(runif(20,0,2)))
mf <- model.frame(~x)
contrasts(x) <- contr.isotonic(levels(x), levels(x))
model.matrix(mf)
``` |

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