Accessor functions for (proto_)ipm objects
Functions that access slots of a *_ipm (including
proto_ipm). default methods correspond to *_ipm objects.
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) 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) pop_state(object) ## S3 method for class 'proto_ipm' pop_state(object) ## Default S3 method: pop_state(object)
object |
A |
ipm |
An object created by |
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 |
value |
A named list of new parameters. The new list does not need to contain all of the parameters, just the ones to update/append. |
form |
An expression representing the new vital rate or kernel formula to insert. |
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.
Depending on the class of object, a list
with types numeric or character.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.