accessors: Accessor functions for (proto_)ipm objects

In levisc8/ipmr: Integral Projection Models

Accessor functions for (proto_)ipm objects

Description

Functions that access slots of a *_ipm (including proto_ipm). default methods correspond to *_ipm objects.

Usage

domains(object)

## S3 method for class 'proto_ipm'
domains(object)

## Default S3 method:
domains(object)

vital_rate_exprs(object)

## S3 method for class 'proto_ipm'
vital_rate_exprs(object)

## Default S3 method:
vital_rate_exprs(object)

vital_rate_funs(ipm)

## S3 method for class 'ipmr_ipm'
vital_rate_funs(ipm)

vital_rate_exprs(object, kernel, vital_rate) <- value

## S3 replacement method for class 'proto_ipm'
vital_rate_exprs(object, kernel, vital_rate) <- value

new_fun_form(form)

kernel_formulae(object)

## S3 method for class 'proto_ipm'
kernel_formulae(object)

## Default S3 method:
kernel_formulae(object)

kernel_formulae(object, kernel) <- value

## S3 replacement method for class 'proto_ipm'
kernel_formulae(object, kernel) <- value

parameters(object)

## S3 method for class 'proto_ipm'
parameters(object)

## Default S3 method:
parameters(object)

parameters(object, ...) <- value

## S3 replacement method for class 'proto_ipm'
parameters(object, ...) <- value

int_mesh(ipm, full_mesh = TRUE)

## S3 method for class 'ipmr_ipm'
int_mesh(ipm, full_mesh = TRUE)

pop_state(object)

## S3 method for class 'proto_ipm'
pop_state(object)

## Default S3 method:
pop_state(object)

Arguments

object	A proto_ipm or object created by make_ipm().
ipm	An object created by make_ipm(). This argument only applies to int_mesh() and vital_rate_funs() (because these quantities don't exist until make_ipm() is called).
kernel	The name of the kernel to insert the new vital rate expression into.
vital_rate	The name of the vital rate to replace. If the vital rate doesn't already exist in the object, a new one with this name will be created.
value	For parameters<-, a named list of new parameters. The new list does not need to contain all of the parameters, just the ones to update/append. For vital_rate_exprs<- and kernel_formulae<-, a new functional form. The new functional form must be wrapped in a call to new_fun_form.
form	An expression representing the new vital rate or kernel formula to insert.
...	Additional arguments used in RPadrino methods.
full_mesh	Return the full integration mesh? Default is TRUE. FALSE returns only unique values for each state variable.

Details

The *.default method corresponds to output from make_ipm(), and the *.proto_ipm methods correspond to outputs from define_*.

When using kernel_formulae<- and vital_rates_exprs<-, the right hand side of the expression must be wrapped in new_fun_form. See examples.

Note that when using vital_rate_funs, unless the vital rate expression explicitly contains an expression for integration, these functions are not yet integrated! This is useful for things like sensitivity and elasticity analysis, but care must be taken to not use these values incorrectly.

Value

Depending on the class of object, a list with types numeric or character.

Examples

data(gen_di_det_ex)

proto <- gen_di_det_ex$proto_ipm

# Create a new, iterated IPM
new_ipm <- make_ipm(proto, iterate = TRUE,
                    iterations = 100, return_all_envs = TRUE)

vital_rate_exprs(new_ipm)
kernel_formulae(new_ipm)
vital_rate_funs(new_ipm)

domains(new_ipm)
parameters(new_ipm)

# Usage is the same for proto_ipm's as *_ipm's

vital_rate_exprs(proto)
kernel_formulae(proto)

domains(proto)
parameters(proto)

int_mesh(new_ipm)

# Setting new parameters, vital rate expressions, and kernel formulae
# only works on proto_ipm's.

# This replaces the "g_int" parameter and leaves the rest untouched

parameters(proto) <- list(g_int = 1.5)

# This creates a new g_z parameter and leaves the rest of parameters untouched
parameters(proto) <- list(g_z = 2.2)

# setting a new vital rate or kernel expression requires wrapping the
# right-hand side in a call to new_fun_form(). new_fun_form uses expressions
# with the same format as ... in define_kernel()

vital_rate_exprs(proto,
                 kernel = "P",
                 vital_rate = "g_mu") <- new_fun_form(g_int + g_z + g_slope * ht_1)

kernel_formulae(proto, kernel = "stay_discrete") <- new_fun_form(g_z * d_ht)

levisc8/ipmr documentation built on Feb. 22, 2023, 9:15 p.m.