ipmr (version 0.0.7)

format_mega_kernel: Create iteration kernels from an IPM object

Description

Creates iteration kernels for IPMs. ipmr does not create these to iterate models, but they may be useful for further analyses.

Usage

format_mega_kernel(ipm, ...)
# S3 method for default
format_mega_kernel(ipm, mega_mat, ...)
# S3 method for age_x_size_ipm
format_mega_kernel(ipm, name_ps, f_forms, ...)
make_iter_kernel(ipm, ..., name_ps, f_forms)

Value

A list containing a large matrix or many large matrices (when used with suffix syntax). The names in the former case will be "mega_matrix"

and in the latter case, "mega_matrix_<par_sets>" with the levels of the grouping effects substituted in.

Arguments

ipm

Output from make_ipm.

...

Other arguments passed to methods.

mega_mat

A vector with symbols, I's, and/or 0s representing the matrix blocks. They should be specified in ROW MAJOR order! Can also be a character string specifying the call. Parameter set index syntax is supported. When used, format_mega_kernel will produce as many mega-matrices as there are combinations of par_set_indices in the proto_ipm.

name_ps

The prefix(es) for the kernel name that correspond to survival and growth/maturation of existing individuals. For the model K = P_age + F_age, this would be "P". Only applies to age X size models. The "_age" suffix is appended automatically, so does not need to be supplied.

f_forms

The names of the kernels that correspond to production of new individuals, and possibly, how they are combined. For example, a model that includes sexual (with an "F" kernel) and asexual reproduction (with a "C" kernel), this would be "F + C". If data come from multiple sites or years, then this information is supplied using the index syntax (i.e. f_forms = "F_yr + C_yr"). Only applies to age X size models. The "_age" index is appended automatically, so does not need to be supplied.

Details

ipmr does not generate complete iteration kernels, and uses sub-kernels to iterate models. However, some further analyses are just easier to code with a complete iteration kernel. This handles constructing those for simple and general models of all forms. format_mega_kernel is used internally by make_iter_kernel for general IPMs. The difference between these two functions is that make_iter_kernel always returns a list of objects with c(ipmr_matrix, array, matrix) classes, whereas format_mega_kernel always returns a list of objects with c(array, matrix) classes. The former has plot() methods while the latter does not.

I and 0 represent identity matrices and 0 matrices, respectively. They can be used to fill in blocks that represent either, without having to create those separately and append them to the model object. The function will work out the correct dimensions for both internally, and there is no restriction on the number that may be used in a given call.

For age_size_ipms, the correct form of mega_mat is generated internally by creating sub-diagonal matrices for the name_ps kernels, and a top row using the f_forms. If parameter set indices are part of the model, the indices should be attached to the name_ps, f_forms in the function arguments, and the correct block matrices will be generated internally.

Examples

data(gen_di_det_ex)

big_k <- make_iter_kernel(gen_di_det_ex,
                            mega_mat = c(0, go_discrete,
                                         leave_discrete, P))

char_call <- c(0, "go_discrete", "leave_discrete", "P")

big_k_c <- make_iter_kernel(gen_di_det_ex, mega_mat = char_call)

# Now, with an Identity matrix instead of a 0

big_k <- make_iter_kernel(gen_di_det_ex,
                            mega_mat = c(I, go_discrete,
                                         leave_discrete, P))

# For simple IPMs with no grouping effects, this computes the sum of
# the sub-kernels (i.e. K = P + F)

data(sim_di_det_ex)

simple_k <- make_iter_kernel(sim_di_det_ex)