create path2df() and utils.R

NAMESPACE

@@ -21,6 +21,7 @@ export(light2mat)
 export(pam_classify)
 export(pam_read)
 export(pam_sta)
+export(path2df)
 export(refracted)
 export(solar)
 export(trainset_read)

R/geopressure.R

@@ -721,6 +721,12 @@ geopressure_ts_path <- function(path,
 #' stationary period id (`sta_id`) as column. Optionally, if indexes were requested, it will be
 #' return. You will need to use `which.max(as.matrix(raster))` and not `which.max(raster)` to get
 #' the correct location.
+#' @examples
+#' # See `geopressure_prob_map()` for generating pressure_prob
+#' pressure_prob_1 <- readRDS(system.file("extdata/1_pressure/", "18LX_pressure_prob_1.rda",
+#'   package = "GeoPressureR"
+#' ))
+#' geopressure_map2path(list(pressure_prob_1))
 #' @seealso [`geopressure_prob_map()`], [`geopressure_ts_path()`], [GeoPressureManual | Pressure Map
 #' ](https://raphaelnussbaumer.com/GeoPressureManual/pressure-map.html#compute-altitude)
 #' @export

R/utils.R

@@ -0,0 +1,79 @@
+#' Progress bar function
+#' @param x value of the current status
+#' @param max maximum value that x will reach
+#' @param text text to display
+#' @noRd
+
+progress_bar <- function(x, max = 100, text = "") {
+  percent <- x / max * 100
+  cat(sprintf(
+    "\r[%-50s] %d / %d %s",
+    paste(rep("=", percent / 2), collapse = ""),
+    x, max, text
+  ))
+  if (x == max) {
+    cat("\n")
+  }
+}
+
+#' Path to data.frame
+#'
+#' This function convert a GeoPressureR path to a data.frame which can be read in [movevis](
+#' https://movevis.org/index.html) for instance.
+#'
+#' The function basically duplicate location position at the start and end time of each stationary
+#' period.
+#'
+#' @param pam pam logger dataset list with `pam$sta` computed (see `pam_sta`)
+#' @param path data.frame containtings the path(s) of the bird with column `lat`, `lon` and `sta_id`
+#' at least. Path can be generated with `geopressure_map2path`, `graph_simulation`, `geopressureviz`
+#' .
+#'
+#' @examples
+#' pam <- pam_read(
+#'   pathname = system.file("extdata/0_PAM/18LX", package = "GeoPressureR")
+#' )
+#' pam <- trainset_read(pam,
+#'   pathname = system.file("extdata/1_pressure/labels", package = "GeoPressureR")
+#' )
+#' pam <- pam_sta(pam)
+#' pressure_prob_1 <- readRDS(system.file("extdata/1_pressure/", "18LX_pressure_prob_1.rda",
+#'   package = "GeoPressureR"
+#' ))
+#' path <- geopressure_map2path(list(pressure_prob_1))
+#' path2df(pam, path)
+#' @seealso [`movevis::df2move`](https://movevis.org/reference/df2move.html),
+#' [`geopressure_map2path`], [`graph_simulation`], [`geopressureviz`]
+#' @export
+path2df <- function(pam, path) {
+
+  # Check input variable
+  assertthat::assert_that(is.list(pam))
+  assertthat::assert_that(assertthat::has_name(pam, "sta"))
+  assertthat::assert_that(is.data.frame(pam$sta))
+  assertthat::assert_that(assertthat::has_name(pam$sta, c("sta_id", "start", "end")))
+
+  assertthat::assert_that(is.list(path))
+  assertthat::assert_that(assertthat::has_name(path, c("lat", "lon", "sta_id")))
+
+  if (is.matrix(path$lat)) {
+    df0 <- data.frame(
+      lat = utils::stack(as.data.frame(t(path$lat)))$values,
+      lon = stack(as.data.frame(t(path$lon)))$values,
+      sta_id = rep(path$sta_id, dim(path$lat)[1]),
+      track_id = paste0(pam$id, "_", rep(seq(1, dim(path$lat)[1]), dim(path$lat)[2]))
+    )
+    df0 <- merge(df0, pam$sta, by = "sta_id")
+  } else {
+    df0 <- merge(as.data.frame(path), pam$sta, by = "sta_id")
+    df0$track_id <- pam$id
+  }
+
+  df1 <- df0
+  df1$time <- df1$start
+  df2 <- df0
+  df2$time <- df2$end
+
+  df <- rbind(df1, df2)
+  df[, names(df) %in% c("time", "track_id", "lat", "lon")]
+}

_pkgdown.yml

@@ -39,6 +39,10 @@ reference:
   desc: Vizualize trajectory with a shiny app
   contents:
   - geopressureviz
+- title: Utility
+  desc: Short functions
+  contents:
+  - path2df
 navbar:
   left:
     - text: "Reference"