R/internal-create_iteration.R

In ipmr: Integral Projection Models

#' @noRd

.init_iteration <- function(others, iterate, direction) {

  UseMethod(".init_iteration")

}

#' @noRd

.init_iteration.default <- function(others, iterate, direction) {

  if(!iterate) return(NA_character_)

  fun        <- .iter_fun(direction)

  all_states <- unique(unlist(others$state_var))

  start_end  <- .find_start_end(others)

  temp       <- .create_iter_exprs(others, start_end, all_states, fun)

  # if every state only has 1 expression operating on it, then we're done!
  # otherwise, we're going to have collapse the ones with a + to generate
  # a complete expression for it

  out <- .combine_iter_exprs(temp$out, temp$all_states)

  kernel_id <- paste(c("K", temp$all_names), collapse = "_")

  temp_proto <- .define_k(
    others,
    name = kernel_id,
    family = "IPM",
    !!! out,
    data_list = list(),
    states = list(unique(unlist(others$state_var))),
    uses_par_sets = !is.null(temp$all_names),
    par_set_indices = temp$all_levels,
    evict_cor = FALSE,
    evict_fun = NULL,
    integrate = FALSE
  )

  ret <- temp_proto[nrow(temp_proto), ]

  return(ret)


}

#' @noRd

.find_start_end <- function(others) {

  start_end        <- others$domain
  names(start_end) <- others$kernel_id

  start_end <- lapply(start_end,
                      function(x) names(x))

  return(start_end)

}

#' @noRd

.create_iter_exprs <- function(others, start_end, all_states, fun) {

  UseMethod(".create_iter_exprs")

}

#' @noRd

.create_iter_exprs.default <- function(others, start_end, all_states, fun) {

  # Need to generate a deterministic simulation across all levels of par_sets
  # if needed.

  out <- list()

  if(any(others$uses_par_sets)) {

    all_levels <- .flatten_to_depth(others$par_set_indices, 1L) %>%
      .[!duplicated(names(.))] %>%
      .[!is.na(.)]

    if("drop_levels" %in% names(all_levels)) {
      all_levels <- all_levels[names(all_levels) != "drop_levels"]
    }

    all_names <- paste(names(all_levels), collapse = "_")



    if(grepl("_det$", class(others)[1])) {

      start_end <- lapply(start_end,
                          function(x, nms) {
                            paste(x, nms, sep = '_')
                          }, nms = all_names)

      all_states <- paste(all_states, all_names, sep = "_")

    }

  } else {

    all_levels <- list()
    all_names <- NULL

  }

  for(i in seq_along(others$kernel_id)) {

    temp <- .make_iter_expr(others, start_end, fun, i)

    out[[i]]      <- temp$iter_expr
    names(out)[i] <- temp$end_state

  }

  return(list(out = out,
              all_names = all_names,
              all_levels = all_levels,
              all_states = all_states))

}


.combine_iter_exprs <- function(temp, ...) {

  UseMethod(".combine_iter_exprs")
}

#' @noRd

.combine_iter_exprs.default <- function(temp, all_states, ...) {

  out <- list()

  if(length(temp) == length(all_states)) {

    out <- temp

  } else {

    for(i in seq_along(all_states)) {

      target_nm <- paste("n_", all_states[i], "_t_1", sep = "")

      to_collapse <- temp[names(temp) %in% target_nm] %>%
        lapply(rlang::expr_text)

      out[[i]] <- do.call("paste", list(to_collapse, collapse = " + ")) %>%
        rlang::parse_expr()

      names(out)[i] <- target_nm

    }
  }

  return(out)

}

#' @noRd

.combine_iter_exprs.age_x_size_exprs <- function(temp, ...) {

  out  <- list()

  temp <- temp$out

  if(!anyDuplicated(names(temp))) {

    out <- temp

  } else {

    all_nms <- unique(names(temp))

    for(i in seq_along(all_nms)) {

      target_nm <- all_nms[i]

      to_collapse <- temp[names(temp) %in% target_nm] %>%
        lapply(rlang::expr_text)

      out[[i]] <- do.call("paste", list(to_collapse, collapse = " + ")) %>%
        rlang::parse_expr()

      names(out)[i] <- target_nm

    }
  }

  return(out)

}

#' @noRd

.iter_fun <- function(direction) {

  fun <- switch(direction,
                "left"  = "left_mult",
                "right" = "right_mult",
                stop("Can only perform left or right multiplication for model iteration!",
                     call. = FALSE)
                )

  return(fun)

}

.init_iteration.age_x_size <- function(others, iterate, direction) {

  if(!iterate) return(NA_character_)

  fun        <- .iter_fun(direction)

  all_states <- unique(unlist(others$state_var))

  start_end  <- .find_start_end(others)

  temp        <- .create_iter_exprs(others, start_end, all_states, fun)

  age_indices <- .flatten_to_depth(others$age_indices, 1L) %>%
    .[!duplicated(names(.))]

  temp        <- .handle_max_age(temp, age_indices, start_end, fun)
  class(temp) <- "age_x_size_exprs"

  # if every state only has 1 expression operating on it, then we're done!
  # otherwise, we're going to have collapse the ones with a + to generate
  # a complete expression for it

  out <- .combine_iter_exprs(temp)

  kernel_id <- paste(c("K", temp$all_names), collapse = "_")

  temp_proto <- .define_k(
    others,
    name = kernel_id,
    family = "IPM",
    !!! out,
    data_list = list(),
    states = list(unique(unlist(others$state_var))),
    uses_par_sets = !is.null(temp$all_names),
    par_set_indices = temp$all_levels,
    age_indices = age_indices,
    evict_cor = FALSE,
    evict_fun = NULL,
    integrate = FALSE
  )

  ret <- temp_proto[nrow(temp_proto), ]

  return(ret)

}

.handle_max_age <- function(expr_list, age_indices, start_end, fun) {

  switch(fun,
         "right_mult" = .handle_max_age_right(expr_list,
                                              age_indices,
                                              start_end,
                                              fun),
         "left_mult" = .handle_max_age_left(expr_list,
                                            age_indices,
                                            start_end,
                                            fun))

}

# Prevents age_plus_1 from going over the maximum age limit during left
# iteration (which has form n_age_t_1 = kernel_age %*% n_age_plus_1_t)
.handle_max_age_left <- function(expr_list, age_indices, start_end, fun) {

  if(!"max_age" %in% names(age_indices)) {

    max_age <- unlist(age_indices) %>% max()

  } else {

    max_age <- age_indices$max_age

  }

  kerns <- lapply(names(expr_list$out),
                  function(x) {
                    grepl("_age_", x)
                  }) %>%
    unlist() %>%
    expr_list$out[.] %>%
    lapply(function(y, start_end) {
      args <- rlang::call_args(y)
      kern <- rlang::expr_text(args$kernel)
      sv   <- rlang::expr_text(args$vectr)

      kern <- c(gsub("age", "max_age", kern)) # P_max_age %*% n_max_age_t
      sv   <- c(gsub("age_plus_1", "max_age", sv))

      out <- list(kern = kern,
                  sv   = sv)
      return(out)
    },
    start_end = start_end)

  end_states <- gsub("_age_", "_max_age_", names(kerns))

  out <- list()

  it <- 1
  for(i in seq_along(kerns)) {

    if(length(kerns[[i]]$kern) != length(kerns[[i]]$sv)) {
      stop("Error generating iteration format for max_age!")
    }

    for(j in seq_along(kerns[[i]]$kern)) {

      args <- list(kernel = rlang::sym(kerns[[i]]$kern[j]),
                   vectr  = rlang::sym(kerns[[i]]$sv[j]))

      out[[it]] <- rlang::call2(fun, !!!args)

      names(out)[it] <- end_states[i]

      it <- it + 1

    }

  }

  expr_list$out <- c(expr_list$out, out)

  return(expr_list)

}

.handle_max_age_right <- function(expr_list, age_indices, start_end, fun) {

  if(!"max_age" %in% names(age_indices)) return(expr_list)

  # Generate a kernel name for the max age slot. This is the survival/growth
  # kernel (arbitrarily named) with "max_age_minus_1" tacked on. However,
  # check to see if max_age kernel is defined separately.

  if(!any(grepl("max_age", names(expr_list$out)))) {

    kerns <- lapply(names(expr_list$out),
                    function(x) {
                      grepl("_age_", x)
                    }) %>%
      unlist() %>%
      expr_list$out[.] %>%
      lapply(function(y, start_end){
        args <- rlang::call_args(y)
        kern <- rlang::expr_text(args$kernel)
        sv   <- rlang::expr_text(args$vectr)

        kern <- c(gsub("age", "max_age", kern), # P_max_age_minus_1 %*% n_max_age_minus_1_t
                  gsub("age_minus_1", "max_age", kern)) # P_max_age %*% n_max_age_t
        sv   <- c(gsub("age", "max_age", sv),
                  gsub("age_minus_1", "max_age", sv))

        out <- list(kern = kern,
                    sv   = sv)
        return(out)
      },
      start_end = start_end)

    end_states <- gsub("_age_", "_max_age_", names(kerns))

  } else {

    kerns <- lapply(names(expr_list$out),
                    function(x) {
                      grepl("max_age_", x)
                    }) %>%
      unlist() %>%
      expr_list$out[.] %>%
      lapply(function(y, start_end) {
        args <- rlang::call_args(y)
        kern <- rlang::expr_text(args$kernel)
        sv   <- rlang::expr_text(args$vectr)

        kern <- c(gsub("age_minus_1", "age", kern)) # P_max_age %*% n_max_age_t
        sv   <- c(gsub("age_minus_1", "age", sv))

        out <- list(kern = kern,
                    sv   = sv)
        return(out)
      },
      start_end = start_end)

    end_states <- names(kerns)

  }


  out <- list()

  it <- 1
  for(i in seq_along(kerns)) {

    if(length(kerns[[i]]$kern) != length(kerns[[i]]$sv)) {
      stop("Error generating iteration format for max_age!")
    }

    for(j in seq_along(kerns[[i]]$kern)) {

      args <- list(kernel = rlang::sym(kerns[[i]]$kern[j]),
                   vectr  = rlang::sym(kerns[[i]]$sv[j]))

      out[[it]] <- rlang::call2(fun, !!!args)

      names(out)[it] <- end_states[i]

      it <- it + 1

    }

  }

  expr_list$out <- c(expr_list$out, out)

  return(expr_list)

}

.create_iter_exprs.age_x_size <- function(others, start_end, all_states, fun) {

  # Need to generate a deterministic simulation across all levels of par_sets
  # if needed.

  out <- list()

  if(any(others$uses_par_sets)) {

    all_levels <- .flatten_to_depth(others$par_set_indices, 1L) %>%
      .[!duplicated(names(.))] %>%
      .[!is.na(.)]

    if("drop_levels" %in% names(all_levels)) {
      all_levels <- all_levels[names(all_levels) != "drop_levels"]
    }

    all_names <- paste(names(all_levels), collapse = "_")

    if(grepl("_det$", class(others)[1])) {

      start_end <- lapply(start_end,
                          function(x, nms) {
                            paste(x, nms, sep = '_')
                          }, nms = all_names)

      all_states <- paste(all_states, all_names, sep = "_")

    }

  } else {

    all_levels <- list()
    all_names <- NULL

  }

  for(i in seq_along(others$kernel_id)) {

    temp <- .make_iter_expr(others, start_end, fun, i)

    out[[i]]      <- temp$iter_expr
    names(out)[i] <- temp$end_state

  }

  return(list(out = out,
              all_names = all_names,
              all_levels = all_levels,
              all_states = all_states))

}


# Things get a little hairy here. For any non-fecundity expression in right iteration,
# we want end_state_age_t_1 = P_age_minus_1 %*% start_state_minus_1_t.
# The fecundity expressions will always have end_state_0_t_1, so we do not lag
# those. The ones that do not have _0_ in the name require an age_minus_1 for
# start state and the kernel name. On the other hand, the left iteration needs
# age_plus_1 to start and ends on age, with v(M+1) == 0
#' @noRd
#'


.make_iter_expr <- function(others, start_end, fun, it) {

  switch(fun,
         "right_mult" = .make_iter_right(others, start_end, fun, it),
         "left_mult"  = .make_iter_left(others, start_end, fun, it))

}


.make_iter_left <- function(others, start_end, fun, it) {

  UseMethod(".make_iter_left")

}

.make_iter_left.age_x_size <- function(others, start_end, fun, it) {

  # Start by reversing the list. This corresponds to n_i(t + 1) = K_ij %*% n_j_t ->
  # n_j(t+1) = K^T_ij %*% n_i(t) (Ellner Rees Am Nat 2006 Sup A, p 426)

  start_end   <- lapply(start_end, function(x) rev(x))

  start_state   <- paste("n_", start_end[[it]][1], "_t", sep = "")

  if(!grepl("_0_", start_state)) {

    end_state <- paste("n_", start_end[[it]][2], "_t_1", sep = "")

    start_state <- gsub("age", "age_plus_1", start_state)

    use_kernel  <- others$kernel_id[it]

    args <- list(kernel = rlang::sym(use_kernel),
                 vectr  = rlang::sym(start_state))

    iter_expr <- rlang::call2(fun, !!! args)

  } else {

    end_state <- paste("n_", start_end[[it]][2], "_t_1", sep = "")
    use_kernel  <- others$kernel_id[it]

    args <- list(kernel = rlang::sym(use_kernel),
                 vectr  = rlang::sym(start_state))

    iter_expr <- rlang::call2(fun, !!! args)

  }

  out <- list(iter_expr = iter_expr,
              end_state = end_state)

  return(out)


}

.make_iter_left.default <- function(others, start_end, fun, it) {

  start_end   <- lapply(start_end, function(x) rev(x))

  end_state   <- paste("n_", start_end[[it]][2], "_t_1", sep = "")
  start_state <- paste("n_", start_end[[it]][1], "_t", sep = "")

  args <- list(kernel = rlang::sym(others$kernel_id[it]),
               vectr  = rlang::ensym(start_state))

  iter_expr <- rlang::call2(fun, !!! args)


  out <- list(iter_expr = iter_expr,
              end_state = end_state)

  return(out)

}

.make_iter_right <- function(others, start_end, fun, it) {

  UseMethod(".make_iter_right")

}


.make_iter_right.age_x_size <- function(others, start_end, fun, it) {

  end_state   <- paste("n_", start_end[[it]][2], "_t_1", sep = "")

  if(!grepl("_0_", end_state)) {

    start_state <- paste("n_", start_end[[it]][1], "_t", sep = "") %>%
      gsub(pattern = "age", replacement = "age_minus_1", x = .)

    use_kernel  <- gsub("age", "age_minus_1", others$kernel_id[it])

    args <- list(kernel = rlang::sym(use_kernel),
                 vectr  = rlang::sym(start_state))

    iter_expr <- rlang::call2(fun, !!! args)

  } else {

    start_state <- paste("n_", start_end[[it]][1], "_t", sep = "")
    use_kernel  <- others$kernel_id[it]

    args <- list(kernel = rlang::sym(use_kernel),
                 vectr  = rlang::sym(start_state))

    iter_expr <- rlang::call2(fun, !!! args)

    iter_expr <- rlang::call2("sum", iter_expr)

  }

  out <- list(iter_expr = iter_expr,
              end_state = end_state)

  return(out)

}

.make_iter_right.default <- function(others, start_end, fun, it) {

  end_state   <- paste("n_", start_end[[it]][2], "_t_1", sep = "")
  start_state <- paste("n_", start_end[[it]][1], "_t", sep = "")

  args <- list(kernel = rlang::sym(others$kernel_id[it]),
               vectr  = rlang::ensym(start_state))

  iter_expr <- rlang::call2(fun, !!! args)


  out <- list(iter_expr = iter_expr,
              end_state = end_state)

  return(out)

}