Switching R dependency to xml2 (#18)

* switching to xml2 dependency

* cleaning up get_trkseg_dist code

* incrementing minor version to 4.2.0

R/package/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: eddington
 Title: Compute a Cyclist's Eddington Number
-Version: 4.1.3
+Version: 4.2.0
 Authors@R: c(
     person('Paul', 'Egeler', email = 'paulegeler@gmail.com', role = c('aut','cre')),
     person('Tashi', 'Reigle', role = 'ctb'))
@@ -26,12 +26,12 @@ Imports:
     Rcpp,
     R6,
     methods,
-    stats,
-    XML
+    xml2
 Suggests: 
     testthat,
     knitr,
     rmarkdown,
+    stats,
     dplyr
 SystemRequirements: C++17
 VignetteBuilder: knitr

R/package/NEWS.md

@@ -1,3 +1,9 @@
+# eddington 4.2.0 (Release date: 2024-03-23)
+
+Changes:
+
+- Substituted `XML` package dependency for `xml2`.
+
 # eddington 4.1.2 (Release date: 2023-12-12)
 
 Changes:

R/package/R/RcppExports.R

@@ -32,7 +32,7 @@
 #' rides <- rgamma(15, shape = 2, scale = 10)
 #'
 #' # View the rides sorted in decreasing order
-#' setNames(sort(rides, decreasing = TRUE), seq_along(rides))
+#' stats::setNames(sort(rides, decreasing = TRUE), seq_along(rides))
 #'
 #' # Get the Eddington number
 #' E_num(rides)

R/package/R/eddington-R6.r

@@ -17,7 +17,7 @@
 #' rides <- rgamma(15, shape = 2, scale = 10)
 #'
 #' # View the rides sorted in decreasing order
-#' setNames(sort(rides, decreasing = TRUE), seq_along(rides))
+#' stats::setNames(sort(rides, decreasing = TRUE), seq_along(rides))
 #'
 #' # Create the Eddington object
 #' e <- Eddington$new(rides, store.cumulative = TRUE)

R/package/R/gpx.r

@@ -99,16 +99,15 @@ get_haversine_distance <- function(lat_1,
 #'  }
 #' @export
 read_gpx <- function(file, units = c("miles", "kilometers")) {
-  x <- XML::xmlInternalTreeParse(file)
-  on.exit(XML::free(x))
+  x <- xml2::read_xml(file)
 
   distances <- get_trkseg_dist(x, match.arg(units))
 
   if (!length(distances)) {
     # No trkseg nodes were found. Returning an empty data frame
     return(
       data.frame(
-        date = double(0L),
+        date = structure(double(0L), class = "Date"),
         distance = double(0L)
       )
     )
@@ -117,67 +116,45 @@ read_gpx <- function(file, units = c("miles", "kilometers")) {
   dates <- get_dates(x)
 
   data.frame(
-    # do.call preserves "Date" class
-    date = if (length(dates) == length(distances)) do.call(c, dates) else as.Date(NA),
+    date = if (length(dates) == length(distances)) dates else as.Date(NA),
     distance = unlist(distances)
   )
 }
 
 # XML parsing helper functions --------------------------------------------
 
 get_dates <- function(x) {
-  timestamps <- XML::xpathApply(
-    x,
-    "//d:trkseg/d:trkpt[1]/d:time",
-    XML::xmlValue,
-    namespaces = NAMESPACES
-  )
-  lapply(timestamps, as.Date, TIMESTAMP_FORMAT)
+  x |>
+    xml2::xml_find_all("//d:trkseg/d:trkpt[1]/d:time", ns = NAMESPACES) |>
+    xml2::xml_text() |>
+    as.Date.character(TIMESTAMP_FORMAT)
 }
 
 get_trkseg_dist <- function(x, units = c("miles", "kilometers")) {
   r <- switch(match.arg(units), miles = R_E_MI, kilometers = R_E_KM)
 
   lapply(
-    XML::getNodeSet(x, "//d:trkseg", namespaces = NAMESPACES),
-    \(trkseg) {
-      trkpts <- XML::xmlChildren(trkseg)
-      if (length(trkpts) < 2) return(0.)
-      Reduce(
-        `+`,
-        apply(
-          cbind(trkpts[-1], trkpts[-length(trkpts)]),
-          1,
-          \(pair) .Call(`_eddington_get_haversine_distance_`,
-            as.double(XML::xmlGetAttr(pair[[1]], "lat")),
-            as.double(XML::xmlGetAttr(pair[[1]], "lon")),
-            as.double(XML::xmlGetAttr(pair[[2]], "lat")),
-            as.double(XML::xmlGetAttr(pair[[2]], "lon")),
+    xml2::xml_find_all(x, "//d:trkseg", ns = NAMESPACES),
+    \(trkseg) {  # get sum of distances for a single trkseg
+      trkpts <- xml2::xml_children(trkseg)
+
+      if (length(trkpts) < 2L)
+        return(0)
+
+      sum(
+        vapply(
+          seq_along(trkpts[-1L]),
+          \(i) .Call(
+            `_eddington_get_haversine_distance_`,
+            as.double(xml2::xml_attr(trkpts[[i]], "lat")),
+            as.double(xml2::xml_attr(trkpts[[i]], "lon")),
+            as.double(xml2::xml_attr(trkpts[[i + 1L]], "lat")),
+            as.double(xml2::xml_attr(trkpts[[i + 1L]], "lon")),
             r
-          )
+          ),
+          double(1)
         )
       )
-    })
-}
-
-# Unused ------------------------------------------------------------------
-
-get_trkseg_coords <- function(x) {
-  trksegs <- lapply(
-    XML::getNodeSet(x, "//d:trkseg", namespaces = NAMESPACES),
-    \(trkseg) XML::xmlApply(
-      trkseg,
-      \(trkpt) as.double(c(XML::xmlGetAttr(trkpt, "lat"),
-                           XML::xmlGetAttr(trkpt, "lon")))
-    )
-  )
-  lapply(
-    trksegs,
-    \(trkseg) stats::setNames(
-      as.data.frame(
-        do.call(rbind, trkseg),
-        row.names = FALSE),
-      c("lat", "lon")
-    )
+    }
   )
 }

R/package/src/eddington.cpp

@@ -33,7 +33,7 @@
 //' rides <- rgamma(15, shape = 2, scale = 10)
 //'
 //' # View the rides sorted in decreasing order
-//' setNames(sort(rides, decreasing = TRUE), seq_along(rides))
+//' stats::setNames(sort(rides, decreasing = TRUE), seq_along(rides))
 //'
 //' # Get the Eddington number
 //' E_num(rides)