Fix typo in documentation for pf_simplify()

R/pf_simplify.R

@@ -11,8 +11,8 @@
 #' @param calc_distance A character that defines the method used to calculate distances between sequential combinations of particles (see \code{\link[flapper]{pf}}). Currently supported options are Euclidean distances (\code{"euclid"}) or shortest (least-cost) distances ("lcp"). In practice, Euclidean distances are calculated and then, for the subset of connections that meet specified criteria (see \code{calc_distance_limit}, \code{calc_distance_barrier}, \code{mobility_from_origin} and \code{mobility}), Euclidean distances are updated to shortest distances, if specified. Note that \code{calc_distance} does not need to be the same method as used for \code{\link[flapper]{pf}}: it is often computationally beneficial to implement \code{\link[flapper]{pf}} using Euclidean distances and then, for the subset of sampled particles, implement \code{\link[flapper]{pf_simplify}} with \code{calc_distance = "lcp"} to re-compute distances using the shortest-distances algorithm, along with the adjusted probabilities. However, for large paths, the quickest option is to implement both functions using \code{calc_distance = "euclid"} and then interpolate shortest paths only for the set of returned paths (see \code{\link[flapper]{lcp_interp}}). If \code{calc_distance = NULL}, the method saved in \code{archive} is used.
 #' @param calc_distance_lcp_fast (optional) If \code{calc_distance = "lcp"}, \code{calc_distance_lcp_fast} is a function that predicts the shortest distance. This function must accept two arguments (even if they are ignored): (a) a numeric vector of Euclidean distances and (b) an integer vector of barrier overlaps that defines whether (1) or not (1) each transect crosses a barrier (see \code{\link[flapper]{lcp_comp}}). This option avoids the need to implement shortest-distance algorithms.
 #' @param calc_distance_graph (optional) If \code{calc_distance = "lcp"} and \code{calc_distance_lcp_fast = NULL}, \code{calc_distance_graph} is a graph object that defines the distances between connected cells in \code{bathy}. If unsupplied, this is taken from \code{archive$args$calc_distance_graph}, if available, or computed via \code{\link[flapper]{lcp_graph_surface}}.
-#' @param calc_distance_limit (optional) If \code{calc_distance = "lcp"} and \code{calc_distance_lcp_fast = NULL}, \code{calc_distance_limit} is a number that defines the lower Euclidean distance limit for shortest-distances calculations. If supplied, shortest distances are only calculated for cell connections that are more than a Euclidean distance of \code{calc_distance_limit} apart. In other words, if supplied, it is assumed that there exists a valid shortest path (shorter than the maximum distance imposed by the animal's mobility constraints) if the Euclidean distance between two points is less than \code{calc_distance_limit} (unless that segment crosses a barrier: see \code{calc_distance_barrier}). This option can improve the speed of distance calculations. However, if supplied, note that Euclidean and shortest distances (and resultant probabilities) may be mixed in function outputs. This argument is currently only implemented for \code{\link[flapper]{pf_archive-class}} objects derived with \code{calc_distance = TRUE} and \code{calc_distance_euclid_fast = TRUE} via \code{\link[flapper]{pf}} for which connected cell pairs need to be derived (i.e., not following a previous implementation of \code{\link[flapper]{pf_simplify}}).
-#' @param calc_distance_barrier (optional) If \code{calc_distance = "lcp"}, \code{calc_distance_barrier} is a simple feature geometry that defines a barrier, such as the coastline, to movement (see \code{\link[flapper]{segments_cross_barrier}}). The coordinate reference system for this object must match \code{bathy}. If supplied, shortest distances are only calculated for segments that cross a barrier (or exceed \code{calc_distance_limit}). This option can improve the speed of distance calculations. However, if supplied, note that Euclidean and shortest distances (and resultant probabilities) may be mixed in function outputs. All \code{calc_distance_barrier*} arguments are currently only implemented for \code{\link[flapper]{pf_archive-class}} objects derived with \code{calc_distance = TRUE} and \code{calc_distance_euclid_fast = TRUE} via \code{\link[flapper]{pf}} for which connected cell pairs need to be derived (i.e., not following a previous implementation of \code{\link[flapper]{pf_simplify}}).
+#' @param calc_distance_limit (optional) If \code{calc_distance = "lcp"} and \code{calc_distance_lcp_fast = NULL}, \code{calc_distance_limit} is a number that defines the lower Euclidean distance limit for shortest-distances calculations. If supplied, shortest distances are only calculated for cell connections that are more than a Euclidean distance of \code{calc_distance_limit} apart. In other words, if supplied, it is assumed that there exists a valid shortest path (shorter than the maximum distance imposed by the animal's mobility constraints) if the Euclidean distance between two points is less than \code{calc_distance_limit} (unless that segment crosses a barrier: see \code{calc_distance_barrier}). This option can improve the speed of distance calculations. However, if supplied, note that Euclidean and shortest distances (and resultant probabilities) may be mixed in function outputs. This argument is currently only implemented for \code{\link[flapper]{pf_archive-class}} objects derived with \code{calc_distance = "euclid"} and \code{calc_distance_euclid_fast = TRUE} via \code{\link[flapper]{pf}} for which connected cell pairs need to be derived (i.e., not following a previous implementation of \code{\link[flapper]{pf_simplify}}).
+#' @param calc_distance_barrier (optional) If \code{calc_distance = "lcp"}, \code{calc_distance_barrier} is a simple feature geometry that defines a barrier, such as the coastline, to movement (see \code{\link[flapper]{segments_cross_barrier}}). The coordinate reference system for this object must match \code{bathy}. If supplied, shortest distances are only calculated for segments that cross a barrier (or exceed \code{calc_distance_limit}). This option can improve the speed of distance calculations. However, if supplied, note that Euclidean and shortest distances (and resultant probabilities) may be mixed in function outputs. All \code{calc_distance_barrier*} arguments are currently only implemented for \code{\link[flapper]{pf_archive-class}} objects derived with \code{calc_distance = "euclid"} and \code{calc_distance_euclid_fast = TRUE} via \code{\link[flapper]{pf}} for which connected cell pairs need to be derived (i.e., not following a previous implementation of \code{\link[flapper]{pf_simplify}}).
 #' @param calc_distance_barrier_limit (optional) If \code{calc_distance_barrier} is supplied, \code{calc_distance_barrier_limit} is the lower Euclidean limit for determining barrier overlaps. If supplied, barrier overlaps are only determined for cell connections that are more than \code{calc_distance_barrier_limit} apart. This option can reduce the number of cell connections for which barrier overlaps need to be determined (and ultimately the speed of distance calculations).
 #' @param calc_distance_barrier_grid (optional) If \code{calc_distance_barrier} is supplied, \code{calc_distance_barrier_grid} is a \code{\link[raster]{raster}} that defines the distance to the barrier (see \code{\link[flapper]{segments_cross_barrier}}). The coordinate reference system must match \code{bathy}. If supplied, \code{mobility_from_origin} and \code{mobility} are also required. \code{calc_distance_barrier_grid} is used to reduce the wall time of the barrier-overlap routine (see \code{\link[flapper]{segments_cross_barrier}}).
 #' @param calc_distance_restrict (optional) If and \code{calc_distance_lcp_fast = NULL} and \code{calc_distance_limit} and/or \code{calc_distance_barrier} are supplied, \code{calc_distance_restrict} is a logical variable that defines whether (\code{TRUE}) or not (\code{FALSE}) to restrict further the particle pairs for which shortest distances are calculated. If \code{TRUE}, the subset of particles flagged by \code{calc_distance_limit} and \code{calc_distance_barrier} for shortest-distance calculations is further restricted to consider only those pairs of particles for which there is not a valid connection to or from those particles under the Euclidean distance metric. Either way, there is no reduction in the set of particles, only in the number of connections evaluated between those particles. This can improve the speed of distance calculations.