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utils-export.R
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utils-export.R
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# General exported utilities
#' @title Helpers for IPM construction
#' @inheritParams define_kernel
#' @param ... Named expressions. See Details for more information on their usage in
#' each \code{define_*} function.
#'
#' @param pop_vectors If the population vectors are already pre-defined (i.e. are
#' not defined by a function passed to \code{...}), then they can
#' be passed as a named list here.
#'
#' @details
#' These are helper functions to define IPMs. They are used after defining the kernels,
#' but before calling \code{make_ipm()} They are meant to be called in the
#' following order:
#'
#' \enumerate{
#'
#' \item \code{define_impl()}
#'
#' \item \code{define_domains()}
#'
#' \item \code{define_pop_state()}
#'
#' \item \code{define_env_state()}
#'
#' }
#'
#' The order requirement is so that information is correctly matched to each kernel.
#' Below are specific details on the way each works.
#'
#' \strong{\code{define_impl}}
#'
#' This has two arguments - \code{proto_ipm} (the model object you wish to work with),
#' and the \code{kernel_impl_list}. The format of the \code{kernel_impl_list} is:
#' names of the list should be kernel names, and each kernel should have 3 entries:
#' \code{int_rule}, \code{state_start}, and \code{state_end}. See examples.
#'
#' \strong{\code{define_domains}}
#'
#' If the \code{int_rule = "midpoint"}, the \code{...} entries are vectors of
#' length 3 where the name corresponds to the
#' state variable, the first entry is the lower bound of the domain, the second
#' is the upper bound of the domain, and the third entry is the number of
#' meshpoints. Other \code{int_rule}s are not yet implemented, so for now this is the
#' only format they can take. See examples.
#'
#' \strong{\code{define_pop_state}}
#'
#' This takes either calls to functions in the \code{...}, or a pre-generated
#' list of vectors in the \code{pop_vectors}. The names used
#' for each entry in \code{...} and/or for the \code{pop_vectors} should be
#' \code{n_<state_variable>}. See examples.
#'
#' \strong{\code{define_env_state}}
#'
#' Takes expressions that generate values for environmental covariates at each
#' iteration of the model in \code{...}. The \code{data_list} should contain any
#' parameters that the function uses, as well as the function itself. The
#' functions should return named lists. Names in that list can be referenced in
#' vital rate expressions and/or kernel formulas.
#'
#' \strong{\code{discretize_pop_vec}}
#'
#' This takes a numeric vector of a trait distribution and computes the relative
#' frequency of trait values. By default, it integrates the kernel density estimate
#' of the trait using the midpoint rule with \code{n_mesh} mesh points.
#' This is helpful for creating an initial population state vector that
#' corresponds to an observed trait distribution.
#'
#' @return All \code{define_*} functions return a proto_ipm. \code{make_impl_args_list}
#' returns a list, and so must be used within a call to \code{define_impl} or
#' before initiating the model creation procedure.
#'
#' @examples
#'
#' # Example with kernels named "P" and "F", and a domain "z"
#'
#' kernel_impl_list <- list(P = list(int_rule = "midpoint",
#' state_start = "z",
#' state_end = "z"),
#' F = list(int_rule = "midpoint",
#' state_start = "z",
#' state_end = "z"))
#'
#' # an equivalent version using make_impl_args_list
#'
#' kernel_impl_list <- make_impl_args_list(
#' kernel_names = c("P", "F"),
#' int_rule = c("midpoint", "midpoint"),
#' state_start = c("z", "z"),
#' state_end = c("z", "z")
#' )
#'
#' data(sim_di_det_ex)
#'
#' proto_ipm <- sim_di_det_ex$proto_ipm
#'
#' # define_domains
#'
#' lower_bound <- 1
#' upper_bound <- 100
#' n_meshpoints <- 50
#'
#'
#' define_domains(proto_ipm, c(lower_bound, upper_bound, n_meshpoints))
#'
#' # define_pop_state with a state variable named "z". Note that "n_" is prefixed
#' # to denote that it is a population state function!
#'
#' define_pop_state(proto_ipm, n_z = runif(100))
#'
#' # alternative, we can make a list before starting to make the IPM
#'
#' pop_vecs <- list(n_z = runif(100))
#'
#' define_pop_state(proto_ipm, pop_vectors = pop_vecs)
#'
#' # define_env_state. Generates a random draw from a known distribution
#' # of temperatures.
#'
#' env_sampler <- function(env_pars) {
#'
#' temp <- rnorm(1, env_pars$temp_mean, env_pars$temp_sd)
#'
#' return(list(temp = temp))
#'
#' }
#'
#' env_pars <- list(temp_mean = 12, temp_sd = 2)
#'
#' define_env_state(
#' proto_ipm,
#' env_values = env_sampler(env_pars),
#' data_list = list(env_sampler = env_sampler,
#' env_pars = env_pars)
#'
#' )
#'
#' data(iceplant_ex)
#'
#' z <- c(iceplant_ex$log_size, iceplant_ex$log_size_next)
#'
#' pop_vecs <- discretize_pop_vector(z,
#' n_mesh = 100,
#' pad_low = 1.2,
#' pad_high = 1.2)
#'
#' @rdname define_star
#' @importFrom rlang is_empty
#' @export
define_pop_state <- function(proto_ipm, ..., pop_vectors = list()) {
pop_quos <- rlang::enquos(...)
temp <- rlang::list2(!!! pop_quos, !!! pop_vectors)
out <- Filter(Negate(rlang::is_empty), temp)
# Catch a few cases where names me be defined incorrectly:
nm_test <- vapply(names(out), function(x) substr(x, 1, 1), character(1L))
if(any(nm_test != "n")) {
stop("All population state names must start with 'n_'",
" (e.g. 'n_<stateVariable>)'.",
call. = FALSE)
}
nm_test <- vapply(names(out),
function(x) grepl("*_t$", x) | grepl("*_t_1$", x),
logical(1L))
if(any(nm_test)) {
stop("Detected '_t' attached to end of name supplied in 'define_pop_state()'.",
"\nVariables in define_pop_state() automatically have '_t' and '_t_1'",
" appended to them.\nPlease remove these suffixes!.")
}
names(out) <- gsub('^n_', 'pop_state_', names(out))
proto_ipm$pop_state <- list(out)
return(proto_ipm)
}
#' @inheritParams define_pop_state
#' @param data_list A list of named values that contain data used in the expressions
#' in \code{...} in \code{define_env_state()}.
#'
#' @rdname define_star
#' @export
define_env_state <- function(proto_ipm, ..., data_list = list()) {
env_quos <- rlang::enquos(...)
data_list <- lapply(
data_list,
function(x) {
attr(x, "flat_protect") <- TRUE
na_test <- suppressWarnings(any(is.na(x)))
if(na_test) {
warning("'data_list' in 'define_env_state()' contains NAs. Is this correct?",
call. = FALSE)
}
return(x)
})
out <- list(env_quos = unlist(env_quos),
constants = data_list)
proto_ipm$env_state <- list(out)
return(proto_ipm)
}
#' @title Predict methods in ipmr
#' @rdname predict_methods
#'
#' @description This function is used when a \code{predict} method is incorporated
#' into the vital rate expressions of a kernel. Generally, ipmr can handle this
#' without any additional user effort, but some model classes will fail (often
#' with an obscure error message).
#' When this happens, \code{use_vr_model} can ensure that model object is
#' correctly represented in the \code{data_list}.
#'
#' @param model A fitted model object representing a vital rate. Primarily used to avoid
#' writing the mathematical expression for a vital rate, and using a \code{predict()}
#' method instead.
#'
#' @return A model object with a \code{"flat_protect"} attribute.
#'
#' @details ipmr usually recognizes model objects passed into the \code{data_list} argument
#' automatically. Unfortunately, sometimes it'll miss one, and the user will need
#' to manually protect it from the standard build process. This function
#' provides a wrapper around that process. Additionally, please file a bug
#' report here: \url{https://github.com/padrinoDB/ipmr/issues} describing what type
#' of model you are trying to use so it can be added to later versions of the
#' package.
#'
#' Wrap a model object in \code{use_vr_model} when building the \code{data_list}
#' to pass to \code{define_kernel}.
#'
#'
#' @examples
#'
#' data(iceplant_ex)
#'
#' grow_mod <- lm(log_size_next ~ log_size, data = iceplant_ex)
#' surv_mod <- glm(survival ~ log_size, data = iceplant_ex, family = binomial())
#'
#' data_list <- list(
#' grow_mod = use_vr_model(grow_mod),
#' surv_mod = use_vr_model(surv_mod),
#' recruit_mean = 20,
#' recruit_sd = 5
#' )
#'
#' @export
use_vr_model <- function(model) {
attr(model, "flat_protect") <- TRUE
attr(model, "na_ok") <- TRUE
return(model)
}
#' @title Right/left multiplication
#'
#' @description Performs right and left multiplication.
#'
#' @param kernel,vectr \code{kernel} should be a bivariate kernel, \code{vectr}
#' should be a univariate trait distribution.
#' @param family,start_end Used internally, do not touch.
#'
#' @return \code{left_mult} returns \code{t(kernel) \%*\% vectr}. \code{right_mult}
#' returns \code{kernel \%*\% vectr}.
#'
#'
#' @export
right_mult <- function(kernel, vectr, family = NULL, start_end = NULL) {
kernel %*% vectr
}
#' @rdname right_mult
#' @export
left_mult <- function(kernel, vectr) {
t(kernel) %*% vectr
}
#' @title Raise a matrix to a power
#' @rdname matrix-power
#'
#' @description Raises a matrix \code{x} to the \code{y}-th power. \code{x ^ y} computes
#' element wise powers, whereas this computes \emph{y - 1} matrix multiplications.
#' \code{mat_power(x, y)} is identical to \code{x \%^\% y}.
#'
#' @param x A numeric or integer matrix.
#' @param y An integer.
#'
#' @return A matrix.
#'
#' @export
#'
`%^%` <- function(x, y) {
if(!is_square(x)) {
stop('not implemented for non-square matrices')
}
if(!is.integer(y)) {
y <- as.integer(y)
}
init_dim <- dim(x)[1]
use_list <- lapply(seq_len(y), function(a, b) b, b = x)
init_i <- diag(init_dim)
out <- Reduce('%*%', use_list, init = init_i)
return(out)
}
#' @rdname matrix-power
#'
#' @export
mat_power <- function(x, y) {
return(x %^% y)
}
#' @rdname make_iter_kernel
#' @export
format_mega_kernel <- function(ipm, ...) {
UseMethod("format_mega_kernel")
}
#' @rdname make_iter_kernel
#' @export
format_mega_kernel.default <- function(ipm, mega_mat, ...) {
mega_mat <- rlang::enquo(mega_mat)
if(!rlang::quo_is_call(mega_mat)) {
text <- rlang::eval_tidy(mega_mat)
if(length(text) > 1) {
exprr <- syms(text)
exprr <- rlang::call2("c", !!! exprr)
} else{
exprr <- rlang::parse_expr(text)
}
mega_mat <- rlang::enquo(exprr)
}
if(any(ipm$proto_ipm$uses_par_sets)) {
levs <- ipm$proto_ipm$par_set_indices[ipm$proto_ipm$uses_par_sets] %>%
.flatten_to_depth(1L) %>%
.[!duplicated(names(.))]
if("drop_levels" %in% names(levs)) {
ind <- which(names(levs) != "drop_levels")
use_levs <- levs[ind]
} else {
use_levs <- levs
}
use_levs <- expand.grid(use_levs, stringsAsFactors = FALSE)
out_nms <- temp <- character(dim(use_levs)[1])
base_expr <- rlang::quo_text(mega_mat)
base_name <- names(use_levs) %>% paste(collapse = "_")
it <- 1
for(i in seq_len(dim(use_levs)[2])) {
nm <- names(use_levs)[i]
for(j in seq_len(dim(use_levs)[1])) {
if(i > 1) {
base_expr <- temp[it]
base_name <- out_nms[it]
}
temp[it] <- gsub(nm, use_levs[j, i], base_expr)
out_nms[it] <- gsub(nm, use_levs[j, i], base_name)
it <- it + 1
} # end single var substitution - reset counter to modify exprs w/ adtl par_sets if present
it <- 1
}
if("drop_levels" %in% names(levs)) {
# Need to use fuzzy matching for temp because the level is already
# appended to each kernel name. Don't have the same problem for
# out_nms, as that is just vector with the exact levels
for(i in seq_along(levs$drop_levels)) {
temp <- temp[!grepl(levs$drop_levels[i], temp)]
}
out_nms <- out_nms[!out_nms %in% levs$drop_levels]
}
mega_mat <- as.list(temp) %>%
lapply(function(x) {
y <- rlang::parse_expr(x)
rlang::enquo(y)
})
out_nms <- paste("mega_matrix", out_nms, sep = "_")
} else {
mega_mat <- list(mega_mat)
out_nms <- "mega_matrix"
}
out <- lapply(mega_mat,
function(x, ipm) {
.make_mega_mat(ipm, x)
},
ipm = ipm)
names(out) <- out_nms
return(out)
}
#' @rdname make_iter_kernel
#' @export
format_mega_kernel.age_x_size_ipm <- function(ipm,
name_ps,
f_forms,
...) {
kern_ids <- ipm$proto_ipm$kernel_id
# Remove the iteration procedure from the id list. We shouldn't need that
# to generate a block matrix from the sub kernels anyway.
fams <- vapply(ipm$proto_ipm$params,
function(x) x$family,
character(1L))
if(any(fams == "IPM")) {
k_ind <- which(fams == "IPM")
kern_ids <- kern_ids[-c(k_ind)]
}
clean_ids <- vapply(kern_ids,
function(x) strsplit(x, "_")[[1]][1],
character(1L))
clean_p <- strsplit(name_ps, "_")[[1]][1]
p_ind <- which(clean_ids == clean_p)
# Get all ages. If there's max age, we'll create an object with that
# info called add_p. if there isn't then add_p is just a column of 0s
ages <- ipm$proto_ipm$age_indices %>%
.flatten_to_depth(1L) %>%
.[!duplicated(names(.))]
all_ages <- unlist(ages)
tot_len <- length(all_ages)
add_p <- matrix("0", nrow = (tot_len - 1), ncol = 1)
Ps <- matrix(data = NA_character_,
nrow = (tot_len - 1),
ncol = (tot_len - 1))
Fs <- matrix(NA_character_,
nrow = 1,
ncol = tot_len)
# Next, get the base kernel name. We need this because we only want to modify
# age here, not any additional par_sets (if present). The ps are a bit easier
# because there really only should be 1 of those. However, the Fs may have a
# some additional terms (e.g. F + C), so we have to get both of those, then
# iterate over each one using the base expression and substituting as needed.
base_p <- kern_ids[p_ind]
f_terms <- .args_from_txt(f_forms)
clean_fs <- vapply(f_terms,
function(x) strsplit(x, "_")[[1]][1],
character(1L))
base_fs <- kern_ids[clean_ids %in% clean_fs]
# Now, modify the f_forms expression to use the actual kernel names
# as they appear in the kernel_ids column
for(i in seq_along(base_fs)) {
f_forms <- gsub(f_terms[i], base_fs[i], f_forms)
}
diag_ps <- character(tot_len - 1)
for(i in seq_along(all_ages)) {
diag_ps[i] <- gsub("age", all_ages[i], base_p)
Fs[ , i] <- gsub("age", all_ages[i], f_forms)
}
# now, handle the max_age case.
if("max_age" %in% names(ages)) {
max_p <- diag_ps[length(diag_ps)]
add_p[(tot_len - 1), ] <- max_p
diag_ps <- diag_ps[-c(tot_len)]
}
diag(Ps) <- diag_ps
mega_mat <- rbind(
Fs,
cbind(Ps, add_p)
)
# Insert 0s for impossible transitions. If only we could grow younger... ::sigh::
mega_mat[is.na(mega_mat)] <- "0"
# finally, convert back to vector that format_mega.default expects
mega_mat <- as.vector(t(mega_mat))
out <- format_mega_kernel.default(ipm, mega_mat = mega_mat)
return(out)
}
# Accessors functions ----------------------
#' @rdname accessors
#' @export
domains <- function(object) {
UseMethod("domains")
}
#' @title Accessor functions for (proto_)ipm objects
#' @rdname accessors
#'
#' @description Functions that access slots of a \code{*_ipm} (including
#' \code{proto_ipm}). \code{default} methods correspond to \code{*_ipm} objects.
#'
#' @param object A \code{proto_ipm} or object created by \code{make_ipm()}.
#'
#' @return Depending on the class of \code{object}, a list
#' with types numeric or character.
#'
#' @details The \code{*.default} method corresponds to output from \code{make_ipm()},
#' and the \code{*.proto_ipm} methods correspond to outputs from \code{define_*}.
#'
#' When using \code{kernel_formulae<-} and \code{vital_rates_exprs<-}, the right
#' hand side of the expression must be wrapped in \code{new_fun_form}. See
#' examples.
#'
#' Note that when using \code{vital_rate_funs}, unless the vital rate expression
#' explicitly contains an expression for integration, these functions
#' \strong{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.
#'
#' @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)
#'
#' @export
domains.proto_ipm <- function(object) {
out <- lapply(object$domain, function(x) x)
out <- lapply(out,
function(x) {
temp <- lapply(x, function(y) {
if(!all(is.na(y))) {
names(y) <- c("lower_bound",
"upper_bound",
"n_meshpoints")
}
return(y)
}
)
return(temp)
}
) %>%
.flatten_to_depth(1L) %>%
lapply(function(x) {
if(any(is.na(x))) {
return(NULL)
} else {
return(x)
}
}) %>%
Filter(f = Negate(is.null), x = .) %>%
.[!duplicated(names(.)) & !is.na(names(.))]
class(out) <- c("ipmr_domains", "list")
attr(out, "proto") <- object
return(out)
}
#' @rdname accessors
#' @export
domains.default <- function(object) {
domains(object$proto_ipm)
}
#' @rdname accessors
#' @export
vital_rate_exprs <- function(object) {
UseMethod("vital_rate_exprs")
}
#' @rdname accessors
#' @importFrom stats setNames
#' @export
vital_rate_exprs.proto_ipm <- function(object) {
out <- lapply(object$params, function(x) x$vr_text) %>%
stats::setNames(c("")) %>%
lapply(function(x)
if(any(is.na(x) | is.null(x) | rlang::is_empty(x))) {
return(NULL)
} else {
return(x)
}
) %>%
Filter(Negate(is.null), x = .) %>%
Filter(Negate(rlang::is_empty), x = .) %>%
.flatten_to_depth(1L) %>%
lapply(rlang::parse_expr)
out <- out[!duplicated(names(out))]
class(out) <- c("ipmr_vital_rate_exprs", "list")
attr(out, "proto") <- object
return(out)
}
#' @rdname accessors
#' @export
vital_rate_exprs.default <- function(object) {
vital_rate_exprs(object$proto_ipm)
}
#' @rdname accessors
#' @export
vital_rate_funs <- function(ipm) {
UseMethod("vital_rate_funs")
}
#' @rdname accessors
#' @export
vital_rate_funs.ipmr_ipm <- function(ipm) {
proto <- .initialize_kernels(ipm$proto_ipm, TRUE, "right")$others
env_list <- ipm$env_list
if(length(env_list) < 2) {
stop("Cannot find sub-kernel evaluation environments in 'ipm'.",
" Re-run 'make_ipm()' with 'return_all_envs = TRUE'.")
}
out <- switch(as.character(grepl("stoch_param|_dd_", class(ipm)[1])),
"TRUE" = .vr_funs_stoch_param(proto, env_list, ipm),
"FALSE" = .vr_funs_det_kerns(proto, env_list, ipm))
out <- lapply(out,
function(x) {
class(x) <- c("ipmr_vital_rate_funs",
class(x))
return(x)
})
return(out)
}
.vr_funs_stoch_param <- function(proto, env_list, ipm) {
kern_nms <- proto$kernel_id
if(any(proto$uses_par_sets)) {
kern_seq <- ipm$env_seq
if(inherits(kern_seq, "data.frame")) {
kern_seq <- as.character(kern_seq$kernel_seq)
}
} else {
kern_seq <- NULL
}
n_its <- ncol(ipm$pop_state[[1]]) - 1
out <- list()
for(i in seq_len(n_its)) {
use_it <- kern_seq[i]
kern_ind <- paste(kern_seq[i], "it", i, sep = "_")
kern_ind <- paste("*_", kern_ind, "$", sep = "")
if(all(is.null(kern_seq))) {
kern_ind <- gsub("__","_", kern_ind)
}
use_nm <- names(ipm$sub_kernels)[grepl(kern_ind, names(ipm$sub_kernels))]
use_env <- env_list[use_nm]
kern_ind <- gsub(paste("_it_", i, sep =""), "", use_nm)
pro_ind <- which(proto$kernel_id %in% kern_ind)
kern_vrs <- lapply(proto$params[pro_ind],
function(x) names(x$vr_text))
out[[i]] <- lapply(seq_along(pro_ind),
function(x, use_env, kern_vrs, proto, env_list, pro_ind)
.get_vr_fun(use_env[[x]],
kern_vrs[[x]], proto[pro_ind[x], ],
env_list),
use_env = use_env,
kern_vrs = kern_vrs,
proto = proto,
env_list = env_list,
pro_ind = pro_ind)
names(out[[i]]) <- use_nm
}
out <- .flatten_to_depth(out, 2L)
return(out)
}
.vr_funs_det_kerns <- function(proto, env_list, ipm) {
out <- list()
for(i in seq_len(nrow(proto))) {
kern_nm <- proto$kernel_id[i]
kern_vrs <- names(proto$params[[i]]$vr_text)
if(rlang::is_empty(kern_vrs)) {
out[[i]] <- "No vital rate functions specified"
names(out)[i] <- kern_nm
next
}
use_env <- env_list[[kern_nm]]
out[[i]] <- .get_vr_fun(use_env, kern_vrs, proto[i, ], env_list)
names(out)[i] <- kern_nm
}
return(out)
}
.get_vr_fun <- function(use_env, kern_vrs, proto, env_list) {
kern_nm <- proto$kernel_id
out <- rlang::env_get_list(env = use_env,
nms = kern_vrs,
inherit = FALSE)
out <- lapply(out,
function(x, kern_cls, start, end, main_env, nm) {
class(x) <- c(kern_cls, class(x))
.fun_to_iteration_mat(x, start, end, main_env, nm)
},
kern_cls = proto$params[[1]]$family,
start = names(proto$domain[[1]])[1],
end = names(proto$domain[[1]])[2],
main_env = env_list$main_env,
nm = kern_nm
)
return(out)
}
#' @rdname accessors
#'
#' @param kernel The name of the kernel to insert the new vital rate expression
#' into.
#' @param vital_rate The name of the vital rate to replace. If the vital rate
#' doesn't already exist in the \code{object}, a new one with this name will be
#' created.
#'
#' @export
`vital_rate_exprs<-` <- function(object, kernel, vital_rate, value) {
UseMethod("vital_rate_exprs<-")
}
#' @rdname accessors
#' @export
`vital_rate_exprs<-.proto_ipm` <- function(object, kernel, vital_rate, value) {
object$params[[kernel]]$vr_text[[vital_rate]] <- rlang::quo_text(value)
return(object)
}
#' @rdname accessors
#'
#' @param form An expression representing the new vital rate or kernel formula
#' to insert.
#'
#' @export
new_fun_form <- function(form) {
rlang::enquo(form)
}
#' @rdname accessors
#' @export
kernel_formulae <- function(object) {
UseMethod("kernel_formulae")
}
#' @rdname accessors
#' @export
kernel_formulae.proto_ipm <- function(object) {
out <- lapply(object$params, function(x) x$formula) %>%
.flatten_to_depth(1L) %>%
Filter(f = Negate(is.na), x = .) %>%
lapply(rlang::parse_expr)
class(out) <- c("ipmr_kernel_exprs", "list")
attr(out, "proto") <- object
return(out)
}