minor doc update

DESCRIPTION

@@ -51,5 +51,5 @@ biocViews:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Language: en-GB

R/geopressure_map_likelihood.R

@@ -90,7 +90,7 @@ geopressure_map_likelihood <- function(tag,
 
   # remove mse maps computed by geopressure_map_mismatch()
   if (!keep_mse) {
-    tag[names(tag) %in% c("map_pressure_mse", "map_pressure_mask")] <- NULL
+    tag[names(tag) == "map_pressure_mse"] <- NULL
     tag$stap <- tag$stap[names(tag$stap) != "nb_sample"]
   }
 

R/geopressure_map_preprocess.R

@@ -32,7 +32,7 @@ geopressure_map_preprocess <- function(tag, compute_known = FALSE) {
     ))
     id <- pressure$stap_id == 0
     sequence <- seq_len(nrow(pressure))
-    pressure$stap_id[id] <- approx(sequence[!id], pressure$stap_id[!id], sequence[id])$y
+    pressure$stap_id[id] <- stats::approx(sequence[!id], pressure$stap_id[!id], sequence[id])$y
   }
 
   if (nrow(pressure) < 3) {

R/pressurepath_create.R

@@ -48,7 +48,7 @@
 #' ](https://doi.org/10.24381/cds.adbb2d47), `"land"` [doc](https://doi.org/10.24381/cds.e2161bac)
 #' or `"both"`. LAND has greater precision but is not available on water. Using a single one makes
 #' the query faster.
-#' @param preprocess logical to use `geopressure_map_preprocess`.
+#' @param preprocess logical to pre-process pressure data with `geopressure_map_preprocess()`.
 #' @param quiet logical to hide messages about the progress
 #' @param workers number of parallel requests on GEE. Integer between 1 and 99.
 #' @param debug logical to display additional information to debug a request

R/print.tag.R

@@ -76,21 +76,25 @@ print.tag <- function(x, ...) {
           "*" = "Dimensions (lat x lon): {.val {geo$dim[1]}} x {.val {geo$dim[2]}} (res. \\
           {.val {1/tag$param$scale}}\u00b0)"
         ))
-        fun_map <- "geopressure_map"
-        if ("map_pressure_mse" %in% status) {
-          map_pressure_mismatch <- c("map_pressure_mse", "map_pressure_mask")
-          map_pressure_mismatch <- map_pressure_mismatch[map_pressure_mismatch %in% names(tag)]
+
+        map_pressure_mismatch <- c("map_pressure_mse", "map_pressure_mask")
+        map_pressure_mismatch <- map_pressure_mismatch[map_pressure_mismatch %in% names(tag)]
+        if (length(map_pressure_mismatch) > 0) {
           cli::cli_bullets(c(
-            "v" = "Pressure mismatch {.field {map_pressure_mismatch}} computed."
+            "v" = "Pressure mismatch {.field {map_pressure_mismatch}} available."
           ))
-          fun_map <- "geopressure_map_likelihood"
         }
         # nolint end
         if ("map_pressure" %in% status) {
           cli::cli_bullets(c(
             "v" = "Pressure likelihood {.field map_pressure} computed!"
           ))
         } else {
+          if ("map_pressure_mse" %in% names(tag)){
+            fun_map <- "geopressure_map_likelihood"
+          } else {
+            fun_map <- "geopressure_map"
+          }
           cli::cli_bullets(c(
             "x" = "No pressure likelihood computed yet. Use {.fun {fun_map}}."
           ))

R/tag_label_stap.R

@@ -2,14 +2,17 @@
 #'
 #' @description
 #' This function computes the stationary periods from the pressure and/or acceleration label data.
+#' In most case, this function should be run directly after `tag_label_read()` in order to update
+#' `tag` to correspond to the new label file.
+#'
+#' A stationary period is a period during which the bird is considered static relative to the
+#' spatial resolution of interest (~10-50km). They are defined by being separated by a flight of any
+#' duration (label `"flight"`). The `stap_id` is an integer value for stationary periods and decimal
+#' value for flight. The `stap_id` is added as a new column to each sensor data.
 #'
 #' If an acceleration data.frame is present and contains a column `label`, the stationary period
 #' will be computed from it, otherwise, it uses the pressure data.frame.
 #'
-#' Stationary periods are defined by being separated by a flight (label `"flight"`). Flights of any
-#' duration will be considered.
-#'
-#' The function also adds the corresponding `stap_id` column to each sensor data.
 #'
 #' @inheritParams tag_label
 #' @param warning_flight_duration Threshold of flight duration to display warning for (hours)