Remove deprecated functions

NAMESPACE

@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.phylo,slendr_phylo)
-S3method(plot,slendr)
 S3method(print,slendr_map)
 S3method(print,slendr_model)
 S3method(print,slendr_pop)
@@ -11,38 +10,28 @@ export("%>%")
 export(animate_model)
 export(area)
 export(as.phylo.slendr_phylo)
-export(boundary)
 export(check_env)
 export(clear_env)
-export(compile)
 export(compile_model)
-export(dispersal)
 export(distance)
-export(expand)
 export(expand_range)
-export(explore)
 export(explore_model)
 export(gene_flow)
-export(geneflow)
 export(join)
 export(move)
 export(msprime)
 export(overlap)
-export(plot_graph)
 export(plot_map)
 export(plot_model)
 export(population)
-export(read)
 export(read_model)
 export(region)
 export(reproject)
 export(resize)
-export(sampling)
 export(schedule_sampling)
 export(set_dispersal)
 export(set_range)
 export(setup_env)
-export(shrink)
 export(shrink_range)
 export(slim)
 export(subtract)

R/compilation.R

@@ -34,8 +34,6 @@
 #'   present? Useful for non-interactive uses. In an interactive mode, the user
 #'   is asked to confirm the deletion manually.
 #' @param description Optional short description of the model
-#' @param dir Deprecated. Use \code{path} instead.
-#' @param geneflow Deprecated. Use \code{gene_flow} instead.
 #'
 #' @return Compiled \code{slendr_model} model object
 #'
@@ -47,25 +45,9 @@ compile_model <- function(populations, generation_time, path = NULL, resolution
                           gene_flow = list(), overwrite = FALSE, force = FALSE,
                           sim_length = NULL, direction = NULL,
                           slim_script = system.file("scripts", "script.slim", package = "slendr"),
-                          description = "", dir = NULL, geneflow = list()) {
+                          description = "") {
   if (inherits(populations, "slendr_pop"))  populations <- list(populations)
 
-  if (!is.null(dir) && is.null(path)) {
-    warning("The `dir =` argument of `compile_model()` is now deprecated",
-            " as part\nof cleaning up and unifying the function interfaces across the\n",
-            "entire package. Please consider moving to `path = ` at some point.",
-            call. = FALSE)
-    path <- dir
-  }
-
-  if (length(geneflow) > 0) {
-    warning("The `geneflow =` argument of `compile_model()` is now deprecated",
-            " as part\nof cleaning up and unifying the function interfaces across the\n",
-            "entire package. Please consider moving to `gene_flow = ` at some point.",
-            call. = FALSE)
-    gene_flow <- geneflow
-  }
-
   if (is.null(path)) path <- tempfile()
 
   map <- get_map(populations[[1]])

R/deprecate.R

@@ -1,100 +0,0 @@
-#' Deprecated function
-#' @inheritParams expand_range
-#' @export
-expand <- function(pop, by, end, start, overlap = 0.8, snapshots = NULL,
-                   polygon = NULL, lock = FALSE, verbose = TRUE) {
-  .Deprecated("expand_range")
-  expand_range(pop, by, end, start, overlap, snapshots = NULL,
-               polygon = NULL, lock, verbose)
-}
-
-#' Deprecated function
-#' @inheritParams shrink_range
-#' @export
-shrink <- function(pop, by, end, start, overlap = 0.8, snapshots = NULL,
-                   lock = FALSE, verbose = TRUE) {
-  .Deprecated("shrink_range")
-  expand_range(pop, by, end, start, overlap, snapshots = NULL,
-               polygon = NULL, lock, verbose)
-}
-
-#' Deprecated function
-#' @inheritParams plot_model
-#' @export
-plot_graph <- function(model) .Deprecated("plot_model")
-
-#' Deprecated function
-#' @inheritParams explore_model
-#' @export
-explore <- function(model) {
-  .Deprecated("explore_model")
-  explore_model(model)
-}
-
-#' Deprecated function
-#' @inheritParams compile_model
-#' @export
-compile <- function(populations, generation_time, path = NULL, resolution = NULL,
-                    competition = NULL, mating = NULL, dispersal = NULL,
-                    geneflow = list(), overwrite = FALSE,
-                    sim_length = NULL, direction = NULL,
-                    slim_script = system.file("scripts", "script.slim", package = "slendr"),
-                    description = "", dir = NULL) {
-  .Deprecated("compile_model")
-  compile_model(
-    populations, generation_time, path, resolution, competition,
-    mating, dispersal, geneflow, overwrite, sim_length, direction,
-    slim_script, description, dir
-  )
-}
-
-#' Deprecated function
-#' @inheritParams schedule_sampling
-#' @export
-sampling <- function(model, times, ..., locations = NULL, strict = FALSE) {
-  .Deprecated("schedule_sampling")
-  schedule_sampling(model, times, ..., locations, strict)
-}
-
-#' Deprecated function
-#' @inheritParams read_model
-#' @export
-read <- function(path) {
-  .Deprecated("read_model")
-  read_model(path)
-}
-
-#' Deprecated function
-#' @inheritParams set_dispersal
-#' @export
-dispersal <- function(pop, time, competition = NA, mating = NA, dispersal = NA,
-                      dispersal_fun = NULL) {
-  .Deprecated("set_dispersal")
-  set_dispersal(pop, time, competition, mating, dispersal, dispersal_fun)
-}
-
-#' Deprecated function
-#' @inheritParams set_range
-#' @export
-boundary <- function(pop, time, center = NULL, radius = NULL, polygon = NULL, lock = FALSE) {
-  .Deprecated("set_range")
-  set_range(pop, time, center, radius, polygon, lock)
-}
-
-#' Deprecated function
-#' @inheritParams gene_flow
-#' @export
-geneflow <- function(from, to, rate, start, end, overlap = TRUE) {
-  .Deprecated("gene_flow")
-  gene_flow(from, to, rate, start, end, overlap)
-}
-
-#' Deprecated function
-#' @inheritParams plot_map
-#' @export
-plot.slendr <- function(..., time = NULL, geneflows = FALSE,
-                        graticules = "original",
-                        intersect = TRUE, show_map = TRUE,
-                        title = NULL, interpolated_maps = NULL) {
-  .Deprecated("plot_map")
-}