Make lists of constraint functions and their gradients when using a reference taxon

Make lists of constraint functions and their gradients when using a reference taxon

Usage

make_reference_constraints(p, j)

Arguments

p

The number of columns in the design matrix X. If you don't know the number of columns, you can find it with ncol(radEmu::make_design_matrix(formula = your_formula, data = your_data)). your_formula should be the expression you give to emuFit's formula argument.

j

A single value or a vector of length p - 1 where p is the number of columns in the design matrix X. If a single value, j will be used as the reference category for all covariates. If a vector of values, j[k] will be used as the reference category for the covariate in design matrix column k + 1.

Value

A list with elements constraints_list and constraints_grad_list. The constraints_list is a list of constraint functions for each column p of the design matrix. By default, the constraint for the intercept is the pseudo Huber median. The constraints for covariates are determined by reference categories given by the argument j. The constraints_grad_list is a list of gradients of each constraint function.

Examples

# two columns in design matrix, reference taxon is taxon 5
list1 <- make_reference_constraints(p = 2, j = 5)

# four columns in design matrix, reference taxon for all covariates is taxon 2
list2 <- make_reference_constraints(p = 4, j = 2)

# four columns in design matrix, reference taxon for covariates 1 and 2 is taxon 3 and
# reference taxon for covariate 3 is taxon 4
list3 <- make_reference_constraints(p = 4, j = c(3, 3, 4))