add trip import for prefiltering

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: aniMotum
 Title: Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement
-Version: 1.2-03
-Date: 2024-02-06
+Version: 1.2-03.9100
+Date: 2024-02-13
 Authors@R: 
     c(
       person(given = "Ian",
@@ -43,7 +43,8 @@ Imports:
     tmvtnorm,
     rnaturalearth,
     traipse,
-    terra
+    terra,
+    trip (>= 1.10.0)
 LinkingTo: TMB, RcppEigen
 Suggests: 
     testthat,

NAMESPACE

@@ -166,6 +166,9 @@ importFrom(traipse,track_angle)
 importFrom(traipse,track_bearing_to)
 importFrom(traipse,track_distance)
 importFrom(traipse,track_distance_to)
+importFrom(trip,sda)
+importFrom(trip,speedfilter)
+importFrom(trip,trip)
 importFrom(utils,data)
 importFrom(utils,flush.console)
 importFrom(utils,globalVariables)

R/pf_sda_filter.R

@@ -18,6 +18,7 @@
 ##' in favour of `speedfilter`. Either `ang = NA` or 
 ##' `distlim = NA` are sufficient.
 ##' @importFrom sf st_coordinates st_is_longlat st_crs st_transform 
+##' @importFrom trip trip sda speedfilter
 ##' @keywords internal
 ##' @md
 
@@ -52,13 +53,15 @@ if (spdf) {
   } else {
     filt <- "sda"
   }
-  
+
   if(any(is.na(ang))) ang <- c(0,0)
   if(any(is.na(distlim))) distlim <- c(0,0)
-
+  trip.dat <- suppressWarnings(with(x.tr, trip(data.frame(lon, lat, tms = date, id), 
+                                                     correct_all = FALSE)))
+
   if (filt == "sda") {
     tmp <-
-      suppressWarnings(try(sda(x.tr,
+      suppressWarnings(try(sda(trip.dat,
                                smax = vmax * 3.6,
                                # convert m/s to km/h
                                ang = ang,
@@ -76,7 +79,7 @@ if (spdf) {
                          )
 
                          tmp <-
-                           suppressWarnings(try(speedfilter(x.tr,
+                           suppressWarnings(try(speedfilter(trip.dat,
                                                             max.speed = vmax * 3.6),    # convert m/s to km/h
                                                             silent = TRUE))
 

R/utils.R

@@ -69,7 +69,7 @@ wrap_lon <- function(lon, lon_min = -180) {
 
 }
 
-##' @title sda: filter track for speed, distance and angle.
+##' @title sda_int: filter track for speed, distance and angle.
 ##'
 ##' @description Create a filter index of a track for "bad" points with a
 ##' combination of speed, distance and angle tests.
@@ -87,7 +87,7 @@ wrap_lon <- function(lon, lon_min = -180) {
 ##' @importFrom traipse track_distance track_angle
 ##' @keywords internal
 
-sda <- function(x, smax, ang = c(15, 25), distlim = c(2.5, 5.0)) {
+sda_int <- function(x, smax, ang = c(15, 25), distlim = c(2.5, 5.0)) {
 
   x$speed.ok <- speedfilter(x, max.speed = smax)
   if(all("lon" %in% names(x), "lat" %in% names(x))) {
@@ -154,7 +154,7 @@ sda <- function(x, smax, ang = c(15, 25), distlim = c(2.5, 5.0)) {
   x$ok
 }
 
-##' @title speedfilter: filter track for speed.
+##' @title speedfilter_int: filter track for speed.
 ##'
 ##' @description Create a filter index of a track for "bad" points based only on
 ##' speed. Called from `sda`
@@ -165,7 +165,7 @@ sda <- function(x, smax, ang = c(15, 25), distlim = c(2.5, 5.0)) {
 ##' @return logical vector, with \code{FALSE} values where the tests failed
 ##' @importFrom traipse track_distance_to
 ##' @keywords internal
-speedfilter <- function (x, max.speed = NULL, test = FALSE) 
+speedfilter_int <- function (x, max.speed = NULL, test = FALSE) 
 {
 
   if(all("lon" %in% names(x), "lat" %in% names(x))) {