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gps.R
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gps.R
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# vim:textwidth=80:expandtab:shiftwidth=4:softtabstop=4
#' Class to Store GPS Data
#'
#' This class stores GPS data. These objects may be read with
#' [read.gps()] or assembled with [as.gps()].
#'
#' @templateVar class gps
#'
#' @templateVar dataExample {}
#'
#' @templateVar metadataExample {}
#'
#' @template slot_summary
#'
#' @template slot_put
#'
#' @template slot_get
#'
#' @name gps-class
#' @docType class
#' @author Dan Kelley
#'
#' @family things related to gps data
setClass("gps", contains = "oce")
setMethod(
f = "initialize",
signature = "gps",
definition = function(.Object, longitude, latitude, filename = "", ...) {
.Object <- callNextMethod(.Object, ...)
if (!missing(longitude)) .Object@data$longitude <- as.numeric(longitude)
if (!missing(latitude)) .Object@data$latitude <- as.numeric(latitude)
.Object@metadata$filename <- filename
.Object@processingLog$time <- presentTime()
.Object@processingLog$value <- "create 'gps' object"
return(.Object)
}
)
#' Summarize a gps Object
#'
#' Summarize a [gps-class] object.
#'
#' @param object an object of class `"gps"`
#'
#' @param \dots further arguments passed to or from other methods.
#'
#' @author Dan Kelley
#'
#' @family things related to gps data
setMethod(
f = "summary",
signature = "gps",
definition = function(object, ...) {
cat("GPS Summary\n-----------------\n\n")
invisible(callNextMethod()) # summary
}
)
#' Extract Something From a gps Object
#'
#' @param x a [gps-class] object.
#'
#' @section Details of the Specialized Method:
#'
#' * If `i` is `"?"`, then the return value is a list
#' containing four items, each of which is a character vector
#' holding the names of things that can be accessed with `[[`.
#' The `data` and `metadata` items hold the names of
#' entries in the object's data and metadata
#' slots, respectively. The `dataDerived`
#' and `metadataDerived` items are each NULL, because
#' no derived values are defined by `gps` objects.
#'
#' * If `i` is `"longitude"` or `"latitude"`, then the corresponding
#' vector is returned.
#'
#' * If `i` is `"filename"` then a filename is returned, if
#' known (i.e. if the object was created with [read.gps()] or
#' with [as.gps()] with the `filename` argument specified).
#'
#' @template sub_subTemplate
#'
#' @author Dan Kelley
#'
#' @family things related to gps data
setMethod(
f = "[[",
signature(x = "gps", i = "ANY", j = "ANY"),
definition = function(x, i, j, ...) {
if (i == "?") {
return(list(
metadata = sort(names(x@metadata)),
metadataDerived = NULL,
data = sort(names(x@data)),
dataDerived = NULL
))
}
callNextMethod() # [[
}
)
#' Replace Parts of a gps Object
#'
#' @param x a [gps-class] object.
#'
#' @template sub_subsetTemplate
#'
#' @family things related to gps data
setMethod(
f = "[[<-",
signature(x = "gps", i = "ANY", j = "ANY"),
definition = function(x, i, j, ..., value) {
callNextMethod(x = x, i = i, j = j, ... = ..., value = value) # [[<-
}
)
#' Plot a gps Object
#'
#' This function plots a gps object. An attempt is made to use the whole space
#' of the plot, and this is done by limiting either the longitude range or the
#' latitude range, as appropriate, by modifying the eastern or northern limit,
#' as appropriate.
#' To get an inset map inside another map, draw the first map, do
#' `par(new=TRUE)`, and then call `plot.gps` with a value of
#' `mar` that moves the inset plot to a desired location on the existing
#' plot, and with `bg="white"`.
#'
#' @param x a [gps-class] object.
#'
#' @param xlab label for x axis
#'
#' @param ylab label for y axis
#'
#' @param asp Aspect ratio for plot. The default is for `plot.gps` to set
#' the aspect ratio to give natural latitude-longitude scaling somewhere near
#' the centre latitude on the plot. Often, it makes sense to set `asp`
#' yourself, e.g. to get correct shapes at 45N, use
#' `asp=1/cos(45*pi/180)`. Note that the land mass is not symmetric about
#' the equator, so to get good world views you should set `asp=1` or set
#' `ylim` to be symmetric about zero. Any given value of `asp` is
#' ignored, if `clongitude` and `clatitude` are given.
#'
#' @param clongitude,clatitude optional center latitude of map, in decimal
#' degrees. If both `clongitude` and `clatitude` are provided, then
#' any provided value of `asp` is ignored, and instead the plot aspect
#' ratio is computed based on the center latitude. If `clongitude` and
#' `clatitude` are provided, then `span` must also be provided.
#'
#' @param span optional suggested span of plot, in kilometers. The suggestion
#' is an upper limit on the scale; depending on the aspect ratio of the
#' plotting device, the radius may be smaller than `span`. A value for
#' `span` must be supplied, if `clongitude` and `clatitude` are
#' supplied.
#'
#' @param projection optional map projection to use (see
#' [mapPlot()]); if not given, a cartesian frame is used, scaled so
#' that gps shapes near the centre of the plot are preserved. If a projection
#' is provided, the coordinate system will bear an indirect relationship to
#' longitude and longitude, and further adornment of the plot must be done with
#' e.g. [mapPoints()] instead of [points()].
#'
# These archaic arguments have not worked for a long time, if ever.
# A pkg::build_site() run on April 1, 2020 flagged them as
# problematic, so they were removed then. (In plot,ctd-method,
# these were deprecated in 2016.)
# @param parameters optional parameters to map projection (see
# [mapPlot()] for details).
#
# @param orientation optional orientation of map projection (see
# [mapPlot()] for details).
#'
#' @param expand numerical factor for the expansion of plot limits, showing
#' area outside the plot, e.g. if showing a ship track as a gps, and then an
#' actual gps to show the ocean boundary. The value of `expand` is
#' ignored if either `xlim` or `ylim` is given.
#'
#' @param mgp 3-element numerical vector to use for `par(mgp)`, and also
#' for `par(mar)`, computed from this. The default is tighter than the R
#' default, in order to use more space for the data and less for the axes.
#'
#' @param mar value to be used with [`par`]`("mar")`.
#'
#' @param bg optional color to be used for the background of the map. This
#' comes in handy for drawing insets (see \dQuote{details}).
#'
#' @param axes boolean, set to `TRUE` to plot axes.
#'
#' @param cex.axis value for axis font size factor.
#'
#' @param add boolean, set to `TRUE` to draw the gps on an existing plot.
#' Note that this retains the aspect ratio of that existing plot, so it is
#' important to set that correctly, e.g. with `asp=1/cos(lat * pi / 180)`,
#' where `clat` is the central latitude of the plot.
#'
#' @param inset set to `TRUE` for use within [plotInset()]. The
#' effect is to prevent the present function from adjusting margins, which is
#' necessary because margin adjustment is the basis for the method used by
#' [plotInset()].
#'
#' @param geographical flag indicating the style of axes. If
#' `geographical=0`, the axes are conventional, with decimal degrees as
#' the unit, and negative signs indicating the southern and western
#' hemispheres. If `geographical=1`, the signs are dropped, with axis
#' values being in decreasing order within the southern and western
#' hemispheres. If `geographical=2`, the signs are dropped and the axes
#' are labelled with degrees, minutes and seconds, as appropriate.
#'
#' @param debug set to `TRUE` to get debugging information during
#' processing.
#'
#' @param \dots optional arguments passed to plotting functions. For example,
#' set `yaxp=c(-90,90,4)` for a plot extending from pole to pole.
#'
#' @author Dan Kelley
#'
#' @family functions that plot oce data
#' @family things related to gps data
#'
#' @aliases plot.gps
setMethod(
f = "plot",
signature = signature("gps"),
definition = function(x, xlab = "", ylab = "", asp, clongitude, clatitude, span, projection,
expand = 1, mgp = getOption("oceMgp"), mar = c(mgp[1] + 1, mgp[1] + 1, 1, 1), bg,
axes = TRUE, cex.axis = par("cex.axis"), add = FALSE, inset = FALSE, geographical = 0,
debug = getOption("oceDebug"), ...) {
oceDebug(debug, "plot.gps(...",
", clongitude=", if (missing(clongitude)) "(missing)" else clongitude,
", clatitude=", if (missing(clatitude)) "(missing)" else clatitude,
", span=", if (missing(span)) "(missing)" else span,
", geographical=", geographical,
", cex.axis=", cex.axis,
", inset=", inset,
", ...) START\n",
sep = "", unindent = 1
)
if (!missing(projection)) {
if (missing(span)) {
span <- 1000
}
longitudelim <- if (missing(clongitude)) {
c(-180, 180)
} else {
clongitude + c(-1, 1) * span / 111
}
latitudelim <- if (missing(clatitude)) {
c(-90, 90)
} else {
clatitude + c(-1, 1) * span / 111
}
return(mapPlot(x[["longitude"]], x[["latitude"]], longitudelim, latitudelim,
mgp = mgp, mar = mar,
bg = "white", type = "l", axes = TRUE,
projection = projection,
debug = debug, ...
))
}
geographical <- round(geographical)
if (geographical < 0 || geographical > 2) {
stop("argument geographical must be 0, 1, or 2")
}
if (is.list(x) && "latitude" %in% names(x)) {
if (!("longitude" %in% names(x))) {
stop("list must contain item named 'longitude'")
}
x <- as.gps(longitude = x$longitude, latitude = x$latitude)
} else {
if (!inherits(x, "gps")) {
stop("method is only for gps objects, or lists that contain 'latitude' and 'longitude'")
}
}
longitude <- x[["longitude"]]
latitude <- x[["latitude"]]
dots <- list(...)
dotsNames <- names(dots)
# gave.center <- !missing(clongitude) && !missing(clatitude)
if ("center" %in% dotsNames) {
stop("use 'clongitude' and 'clatitude' instead of 'center'")
}
if ("xlim" %in% dotsNames) {
stop("cannot supply 'xlim'; use 'clongitude' and 'span' instead")
}
if ("ylim" %in% dotsNames) {
stop("cannot supply 'ylim'; use 'clatitude' and 'span' instead")
}
if (!inset) {
par(mar = mar)
}
par(mgp = mgp)
if (add) {
lines(longitude, latitude, ...)
} else {
# gaveSpan <- !missing(span)
if (!missing(clatitude) && !missing(clongitude)) {
if (!missing(asp)) {
warning("argument 'asp' being ignored, because argument 'clatitude' and 'clongitude' were given")
}
asp <- 1 / cos(clatitude * atan2(1, 1) / 45) # ignore any provided asp, because lat from center over-rides it
xr <- clongitude + span * c(-1 / 2, 1 / 2) / 111.11 / asp
yr <- clatitude + span * c(-1 / 2, 1 / 2) / 111.11
xr0 <- xr
yr0 <- yr
oceDebug(debug, "xr=", xr, " yr=", yr, " asp=", asp, "\n")
} else {
xr0 <- range(longitude, na.rm = TRUE)
yr0 <- range(latitude, na.rm = TRUE)
oceDebug(debug, "xr0=", xr0, " yr0=", yr0, "\n")
if (missing(asp)) {
if ("ylim" %in% dotsNames) {
asp <- 1 / cos(mean(range(dots$ylim, na.rm = TRUE)) * atan2(1, 1) / 45) # dy/dx
} else {
asp <- 1 / cos(mean(yr0) * atan2(1, 1) / 45) # dy/dx
}
}
# Expand
if (missing(span)) {
if (expand >= 0 && max(abs(xr0)) < 100 && max(abs(yr0) < 70)) {
# don't expand if full map
xr <- mean(xr0) + expand * diff(xr0) * c(-1 / 2, 1 / 2)
yr <- mean(yr0) + expand * diff(yr0) * c(-1 / 2, 1 / 2)
} else {
xr <- xr0
yr <- yr0
}
} else {
xr <- mean(xr0) + span * c(-1 / 2, 1 / 2) / 111.11 / asp
yr <- mean(yr0) + span * c(-1 / 2, 1 / 2) / 111.11
}
oceDebug(debug, "xr=", xr, " yr=", yr, "\n")
}
# Trim lat or lon, to avoid empty margin space
asp.page <- par("fin")[2] / par("fin")[1] # dy / dx
oceDebug(debug, "par(\"pin\")=", par("pin"), "\n")
oceDebug(debug, "par(\"fin\")=", par("fin"), "\n")
oceDebug(debug, "asp=", asp, "\n")
oceDebug(debug, "asp.page=", asp.page, "\n")
if (!is.finite(asp)) {
asp <- 1 / cos(clatitude * atan2(1, 1) / 45)
}
if (asp < asp.page) {
oceDebug(debug, "type 1 (will narrow x range)\n")
d <- asp.page / asp * diff(xr)
oceDebug(debug, " xr original:", xr, "\n")
xr <- mean(xr) + d * c(-1 / 2, 1 / 2)
oceDebug(debug, " xr narrowed:", xr, "\n")
} else {
oceDebug(debug, "type 2 (will narrow y range)\n")
d <- asp.page / asp * diff(yr)
oceDebug(debug, " yr original:", yr, "\n")
yr <- mean(yr) + d * c(-1 / 2, 1 / 2)
oceDebug(debug, " yr narrowed:", yr, "\n")
}
# Avoid looking beyond the poles, or the dateline
if (xr[1] < (-180)) {
xr[1] <- (-180)
}
if (xr[2] > 180) {
xr[2] <- 180
}
if (yr[1] < (-90)) {
yr[1] <- (-90)
}
if (yr[2] > 90) {
yr[2] <- 90
}
oceDebug(debug, "after range trimming, xr=", xr, " yr=", yr, "\n")
# Draw underlay, if desired
plot(xr, yr, asp = asp, xlab = xlab, ylab = ylab, type = "n", xaxs = "i", yaxs = "i", axes = FALSE, ...)
if (!missing(bg)) {
plot.window(xr, yr, asp = asp, xlab = xlab, ylab = ylab, xaxs = "i", yaxs = "i", log = "", ...)
usr <- par("usr")
oceDebug(debug, "drawing background; usr=", par("usr"), "bg=", bg, "\n")
rect(usr[1], usr[3], usr[2], usr[4], col = bg)
par(new = TRUE)
}
# Ranges
usrTrimmed <- par("usr")
# Construct axes "manually" because axis() does not know the physical range
if (axes) {
prettyLat <- function(yr, ...) {
res <- pretty(yr, ...)
if (diff(yr) > 100) {
res <- seq(-90, 90, 45)
}
res
}
prettyLon <- function(xr, ...) {
res <- pretty(xr, ...)
if (diff(xr) > 100) {
res <- seq(-180, 180, 45)
}
res
}
oceDebug(debug, "xr:", xr, ", yr:", yr, ", xr0:", xr0, ", yr0:", yr0, "\n")
xr.pretty <- prettyLon(par("usr")[1:2], n = if (geographical) 3 else 5, high.u.bias = 20)
yr.pretty <- prettyLat(par("usr")[3:4], n = if (geographical) 3 else 5, high.u.bias = 20)
oceDebug(debug, "xr.pretty=", xr.pretty, "\n")
oceDebug(debug, "yr.pretty=", yr.pretty, "\n")
oceDebug(debug, "usrTrimmed", usrTrimmed, "(original)\n")
usrTrimmed[1] <- max(-180, usrTrimmed[1])
usrTrimmed[2] <- min(180, usrTrimmed[2])
usrTrimmed[3] <- max(-90, usrTrimmed[3])
usrTrimmed[4] <- min(90, usrTrimmed[4])
oceDebug(debug, "usrTrimmed", usrTrimmed, "\n")
oceDebug(debug, "par(\"usr\")", par("usr"), "\n")
xlabels <- format(xr.pretty)
ylabels <- format(yr.pretty)
if (geographical >= 1) {
xlabels <- sub("-", "", xlabels)
ylabels <- sub("-", "", ylabels)
} else if (geographical == 2) {
xr.pretty <- prettyPosition(xr.pretty, debug = debug - 1)
yr.pretty <- prettyPosition(yr.pretty, debug = debug - 1)
xlabels <- formatPosition(xr.pretty, type = "expression")
ylabels <- formatPosition(yr.pretty, type = "expression")
}
axis(1, at = xr.pretty, labels = xlabels, pos = usrTrimmed[3], cex.axis = cex.axis)
oceDebug(debug, "putting bottom x axis at", usrTrimmed[3], "with labels:", xlabels, "\n")
axis(2, at = yr.pretty, labels = ylabels, pos = usrTrimmed[1], cex.axis = cex.axis, cex = cex.axis)
oceDebug(debug, "putting left y axis at", usrTrimmed[1], "\n")
axis(3, at = xr.pretty, labels = rep("", length.out = length(xr.pretty)), pos = usrTrimmed[4], cex.axis = cex.axis)
axis(4, at = yr.pretty, pos = usrTrimmed[2], labels = FALSE, cex.axis = cex.axis)
oceDebug(debug, "putting right y axis at", usrTrimmed[2], "\n")
}
yaxp <- par("yaxp")
oceDebug(debug, "par(\"yaxp\")", par("yaxp"), "\n")
oceDebug(debug, "par(\"pin\")", par("pin"), "\n")
if (yaxp[1] < -90 || yaxp[2] > 90) {
oceDebug(debug, "trimming latitude; pin=", par("pin"), "FIXME: not working\n")
oceDebug(debug, "trimming latitdue; yaxp=", yaxp, "FIXME: not working\n")
# FIXME: should allow type as an arg
points(x[["longitude"]], x[["latitude"]], ...)
} else {
points(longitude, latitude, ...)
if (axes) {
rect(usrTrimmed[1], usrTrimmed[3], usrTrimmed[2], usrTrimmed[4])
}
}
}
# box()
oceDebug(debug, "par(\"usr\")=", par("usr"), "\n")
oceDebug(debug, "END plot.gps()\n", unindent = 1)
invisible(NULL)
}
)
#' Coerce Data Into a gps Object
#'
#' Coerces a sequence of longitudes and latitudes into a GPS dataset.
#' This may be used when [read.gps()] cannot read a file, or when the
#' data have been manipulated.
#'
#' @param longitude the longitude in decimal degrees, positive east of
#' Greenwich, or a data frame with columns named `latitude` and
#' `longitude`, in which case these values are extracted from the data
#' frame and the second argument is ignored.
#'
#' @param latitude the latitude in decimal degrees, positive north of the
#' Equator.
#'
#' @param filename name of file containing data (if applicable).
#'
#' @return A [gps-class] object.
#'
#' @examples
#' # Location of the Tower Tank at Dalhousie University
#' towerTank <- as.gps(-63.59428, 44.63572)
#'
#' @author Dan Kelley
#'
#' @family things related to gps data
as.gps <- function(longitude, latitude, filename = "") {
names <- names(longitude)
if ("longitude" %in% names && "latitude" %in% names) {
latitude <- longitude[["latitude"]]
longitude <- longitude[["longitude"]]
}
new("gps", longitude = longitude, latitude = latitude, filename = filename)
}
#' Read a gps File
#'
#' Reads GPX format files by simply finding all longitudes and latitudes; in
#' other words, information on separate tracks, or waypoints, etc., is lost.
#'
#' @param file name of file containing gps data.
#'
#' @param type type of file, which will be inferred from examination of the
#' data if not supplied. In the present version, the only choice for
#' `type` is `"gpx"`.
#'
#' @template encodingTemplate
#'
#' @param debug set to TRUE to print information about the header, etc.
#'
#' @param processingLog ignored.
#'
#' @return A [gps-class] object.
#'
#' @author Dan Kelley
#'
#' @family things related to gps data
read.gps <- function(file, type = NULL, encoding = "latin1", debug = getOption("oceDebug"), processingLog) {
oceDebug(debug, "read.gps(...) START\n", sep = "", unindent = 1)
if (missing(file)) {
stop("must supply 'file'")
}
if (is.character(file)) {
if (!file.exists(file)) {
stop("cannot find file \"", file, "\"")
}
if (0L == file.info(file)$size) {
stop("empty file \"", file, "\"")
}
}
filename <- NULL
if (is.character(file)) {
filename <- fullFilename(file)
file <- file(file, "r", encoding = encoding)
on.exit(close(file))
}
if (!inherits(file, "connection")) {
stop("\"file\" must be a character string or connection")
}
if (!isOpen(file)) {
open(file, "r", encoding = encoding)
on.exit(close(file))
}
if (is.null(type)) {
tokens <- scan(file, "character", n = 5)
found <- grep("gpx", tokens)
if (length(found) > 0) {
type <- "gpx"
} else {
warning("cannot determine file type; assuming \"gpx\"")
}
}
type <- match.arg(type, c("gpx"))
oceDebug(debug, "file type:", type, "\n")
lines <- readLines(file)
look <- grep("^<.* lat=", lines)
latlon <- lines[look]
latlonCleaned <- gsub("[a-zA-Z<>=\"/]*", "", latlon)
latlon <- read.table(text = latlonCleaned, encoding = encoding)
res <- new("gps", longitude = latlon[, 2], latitude = latlon[, 1], file = filename)
oceDebug(debug, "END read.gps()\n", sep = "", unindent = 1)
res
}