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track.R
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track.R
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#' Create a `track_*`
#'
#' Constructor to crate a track, the basic building block of the `amt` package. A
#' `track` is usually created from a set of `x` and `y` coordinates, possibly
#' time stamps, and any number of optional columns, such as id, sex, age, etc.
#'
#' @param tbl [data.frame] \cr The `data.frame` from which a track should be
#' created.
#' @param .x,.y,.t `[expression(1)]` \cr Unquoted variable names of columns
#' containing the x and y coordinates, and optionally a time stamp.
#' @param ... `[expression]` \cr Additional columns from `tbl` to be used in a
#' track. Columns should be provided in the form of `key = val` (e.g., for ids
#' this may look like this `id = c(1, 1, 1, 2, 2, 2` for three points for ids
#' 1 and 2 each).
#' @param crs `[crs]` \cr An optional coordinate reference system of the
#' points. Usually just the `epsg` code is sufficient.
#' @param order_by_ts `[logical(1)]` \cr Should relocations be ordered by time
#' stamp, default is `TRUE`.
#' @param check_duplicates `[logical(1)=FALSE]` \cr Should it be checked if there are
#' duplicated time stamp, default is `FALSE`.
#' @param all_cols `[logical(1)=FALSE]` \cr Should all columns be carried over to the track object, default is `FALSE`.
#' @param x,y `[numeric]` \cr The x and y coordinates.
#' @param t `[POSIXct]` \cr The time stamp.
#' @return If `t` was provided an object of class `track_xyt` is returned
#' otherwise a `track_xy`.
#' @export
#' @name track
mk_track <- function(tbl, .x, .y, .t, ..., crs = NA_crs_, order_by_ts = TRUE,
check_duplicates = FALSE, all_cols = FALSE) {
if (missing(.x) | missing(.y)) {
stop(".x and .y are required.")
}
if (!is_tibble(tbl)) {
tbl <- as_tibble(tbl)
}
.x <- enquo(.x)
.y <- enquo(.y)
vars <- if (all_cols) {
xx <- setdiff(
names(tbl),
c(quo_name(.x), quo_name(.y), if (!missing(.t)) quo_name(enquo(.t))))
} else {
quos(...)
}
if (!all(sub("~", "", as.character(vars)) %in% names(tbl))) {
stop("Non existent columns from tbl were requested.")
}
if (missing(.t)) {
message(".t missing, creating `track_xy`.")
out <- tbl %>%
dplyr::select(x_ = !!.x,
y_ = !!.y,
!!!vars)
class(out) <- c("track_xy", class(out))
} else {
message(".t found, creating `track_xyt`.")
.t <- enquo(.t)
if (order_by_ts) {
tbl <- arrange(tbl, !!(.t))
}
tt <- dplyr::select(tbl, t = !!.t) %>% pull(t)
if (check_duplicates & any(duplicated(tt))) {
stop("duplicated time stamps.")
}
if (any(is.na(tt))) {
stop("NA in time stamps.")
}
if (any(diff(tt) < 0)) {
stop("negative time diffs.")
}
out <- tbl %>%
dplyr::select(x_ = !!.x,
y_ = !!.y,
t_ = !!.t,
!!!vars)
class(out) <- c("track_xyt", "track_xy", class(out))
}
if (!is.na(crs)) {
if (is(crs, "CRS")) {
.Deprecated("It looks like you used `CRS()` to create the crs,
please use the ESPG directly.")
crs <- sf::st_crs(crs)
} else {
crs <- sf::st_crs(crs)
if (is.na(crs)) {
warning("`crs` invalid.")
}
}
}
attributes(out)$crs_ <- crs
out
}
#' @export
#' @rdname track
make_track <- mk_track
#' @rdname track
#' @export
track <- function(x, y, t, ..., crs = NULL) {
# .Deprecated("mk_track", msg = "Use mk_track instead")
if (missing(x) | missing(y)) {
stop("x and y are required")
}
if (missing(t)) {
out <- tibble(
x_ = x,
y_ = y,
...
)
class(out) <- c("track_xy", class(out))
} else {
out <- tibble(
x_ = x,
y_ = y,
t_ = t,
...
)
class(out) <- c("track_xyt", "track_xy", class(out))
}
attributes(out)$crs_ <- crs
out
}
# S3 Methods --------------------------------------------------------------
# track_transfer_attr <- function(from, to) {
# from <- attributes(from)
# attributes(to)$class <- from$class
# attributes(to)$crs_ <- from$crs_
# to
# }
track_transfer_attr <- function(from, to) {
from <- attributes(from)
attributes(to)$class <- c(setdiff(from$class, class(to)), class(to))
attributes(to)$crs_ <- from$crs_
to
}
# tibble methods
#' @export
`[.track_xy` <- function(x, i, j, drop = FALSE) {
xx <- NextMethod()
track_transfer_attr(x, xx)
}
#' @export
`[.track_xyt` <- function(x, i, j, drop = FALSE) {
xx <- NextMethod()
track_transfer_attr(x, xx)
}
# dplyr methods -----------------------------------------------------------
#' @export
arrange.track_xy <- function(.data, ..., .dots) {
x <- NextMethod()
track_transfer_attr(.data, x)
}
#' @export
arrange.track_xyt <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
filter.track_xy <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
filter.track_xyt <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
group_by.track_xy <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
group_by.track_xyt <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
nest.track_xy <- function(.data, ..., .dots) {
x <- NextMethod()
class(x) <- c("nested_track", "tbl_df", "tbl", "data.frame")
x
}
#' @export
unnest.nested_track <- function(
data, cols, ...
#keep_empty = FALSE, ptype = NULL, names_sep = NULL,
####names_repair = "check_unique",
############.drop = NULL, .id = NULL, .sep = NULL, .preserve = NULL
) {
col <- rlang::as_label(rlang::enquo(cols))
if (length(col) > 1) {
stop("amt currently only supports unnesting one column")
}
dd <- data[[col]]
# check length > 1
class_col_entries <- if (length(dd) > 1) {
class(dd[[1]])
} else {
all_classes_equal <- all(
sapply(dd[-1],
function(x) all(class(x) == class(dd[[1]]))))
if (all_classes_equal) {
class(dd[[1]])
} else {
stop("Not all elments are of the same class.")
}
}
# check they are all of the same class
class(data) <- c("tbl_df", "tbl", "data.frame")
x <- unnest(data, cols = !!rlang::enquo(cols))
# keep_empty = keep_empty, ptype = ptype,
#### names_sep = names_sep, names_repair = names_repair,
# .drop = .drop, .id = .id, .sep = .sep,
#### .preserve = .preserve)
class(x) <- class_col_entries
track_transfer_attr(dd[[1]], x)
}
#' @export
ungroup.track_xy <- function(x, ..., .dots) {
x <- track_transfer_attr(x, NextMethod())
class(x) <- class(x)[class(x) != "grouped_df"]
x
}
#' @export
ungroup.track_xyt <- function(x, ..., .dots) {
x <- track_transfer_attr(x, NextMethod())
class(x) <- class(x)[class(x) != "grouped_df"]
x
}
#' @export
mutate.track_xy <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
mutate.track_xyt <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
select.track_xy <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
select.track_xyt <- function(.data, ..., .dots) {
track_transfer_attr(.data, NextMethod())
}
#' @export
summarise.track_xy <- function(.data, ..., .dots) {
NextMethod()
# track_transfer_attr(.data, NextMethod())
}
#' @export
summarise.track_xyt <- function(.data, ..., .dots) {
NextMethod()
# track_transfer_attr(.data, NextMethod())
}
#' @export
summarize.track_xy <- function(.data, ..., .dots) {
NextMethod()
# track_transfer_attr(.data, NextMethod())
}
#' @export
summarize.track_xyt <- function(.data, ..., .dots) {
NextMethod()
# track_transfer_attr(.data, NextMethod())
}