spelling check + typo + doc

Author: Rafnuss

NEWS.md

@@ -28,7 +28,7 @@
 - Update to GeoPressureAPI v2 for `geopressure_timeseries()` https://github.com/Rafnuss/GeoPressureR/pull/103/commits/732d1a02cc241dc7d2dde3401c8747fa860650c6
 - Fix major bug https://github.com/Rafnuss/GeoPressureR/pull/103/commits/05c3203ef1588bbc1f769050377cadf5f1aadcbd
 - Migrate from `httr`to `httr2`
-- Fix major bug with saving enviremnt variable in param https://github.com/Rafnuss/GeoPressureR/commit/9bcbf790a7de133448c738db272bf136dc831f8f
+- Fix major bug with saving environment variable in param https://github.com/Rafnuss/GeoPressureR/commit/9bcbf790a7de133448c738db272bf136dc831f8f
 - Add functions `speed2bearing()` and `windsupport()` https://github.com/Rafnuss/GeoPressureR/commit/fe244f6057db14b6a286c0a77aaaef4c5ec0152c
 - Use interpolated `stap_id` for flight instead of `0` https://github.com/Rafnuss/GeoPressureR/commit/d7491c2a5580c9eeafe598935933727489590a75
 - Create `edge_add_wind()` https://github.com/Rafnuss/GeoPressureR/commit/36412dc8f0fd061798a701ca632766dbe6f069c8

R/bird_create.R

@@ -5,16 +5,16 @@
 #' power curve: mass, wing span, wing aspect ratio, and body frontal area.
 #'
 #' When any of these variables are missing, we query the
-#' \href{https://doi.org/10.6084/m9.figshare.16586228.v5}{AVONET database} using the scientific
-#' name from \href{https://www.birds.cornell.edu/clementschecklist/}{the Clements Checklist}.
+#' [AVONET database](https://doi.org/10.6084/m9.figshare.16586228.v5) using the scientific
+#' name from [the Clements Checklist](https://www.birds.cornell.edu/clementschecklist/).
 #'
 #'
 #' @param scientific_name Scientific name of the species
-#' @param mass Mass of the bird in kilograms.
-#' @param wing_span Wing span in meters.
-#' @param wing_aspect Wing aspect ratio (no unit).
-#' @param wing_area Wing area in meter square.
-#' @param body_frontal_area Body frontal area in meter square.
+#' @param mass Mass of the bird in kilograms
+#' @param wing_span Wing span in meters
+#' @param wing_aspect Wing aspect ratio (no unit)
+#' @param wing_area Wing area in meter square
+#' @param body_frontal_area Body frontal area in meter square
 #' @param species_name `r lifecycle::badge("deprecated")` Use `scientific_name` instead
 #' @importFrom lifecycle deprecated
 #' @return List containing mass, wing span, wing aspect ratio, and body frontal area.
@@ -27,7 +27,7 @@
 #'
 #' # Import your own bird. You will need mass, and at least two of wing_span,
 #' # wing_aspect or wing_area.
-#' bird_create("custum_bird", mass = 1, wing_span = 1, wing_aspect = 4)
+#' bird_create("Madynuss nutshell", mass = 8, wing_span = 0.2, wing_aspect = 4)
 #'
 #' @family bird
 #' @family movement

R/edge_add_wind.R

@@ -4,7 +4,7 @@
 #' Reads the NetCDF files and extract the variable requested along each flight defined by the edges.
 #'
 #' - Time: linear interpolation using the resolution requested with `rounding_interval`
-#' - Space: nearet neighbor interpolation by default or bi-linear with `pracma::interp2` if
+#' - Space: nearest neighbour interpolation by default or bi-linear with `pracma::interp2` if
 #' `interp_spatial_linear=TRUE`
 #' - Pressure/altitude: linear interpolation using the exact `pressure` values
 #'
@@ -20,7 +20,7 @@
 #' ](https://bit.ly/3BrwLBM) using the `shortName` notation: `"u"`, `"v"`,  `"t"`, `"cc"`, `"r"`,
 #' `"w"`, `"ciwc"`, `"clwc"`, `"q"`, `"cswc"`, `"d"`, `"z"`, `"o3"`, `"pv"`, `'vo"`.
 #' @param rounding_interval temporal resolution on which to query the variable (min). Default is to
-#' macth ERA5 native resolution (1hr).
+#' match ERA5 native resolution (1hr).
 #' @param interp_spatial_linear logical to interpolate the variable linearly over space, if `FALSE`
 #' takes the nearest neighbour. ERA5 native resolution is 0.25°
 #' @param return_averaged_variable logical to return the variable for each timestep or average for
@@ -213,7 +213,7 @@ edge_add_wind <- function(
       # We assume that the bird is moving with a constant groundspeed between `flight$start` and
       # `flight$end`. Using a linear interpolation, we extract the position (lat, lon) at every hour
       # on `t_q`. Extrapolation outside (before the bird departure or after he arrived) is with a
-      # nearest neighbor.
+      # nearest neighbour.
 
       dlat_se <- (lat_e - lat_s) / fl_s$duration[i_fl]
       dlon_se <- (lon_e - lon_s) / fl_s$duration[i_fl]

R/geolight_map.R

@@ -18,7 +18,7 @@
 #'
 #' Instead of calibrating the twilight errors in terms of duration, we directly model the zenith
 #' angle error. We use a kernel distribution to fit the zenith angle during the known stationary
-#' period(s). The `twl_calib_adjust` parameter allows to mararnually adjust how smooth you want the
+#' period(s). The `twl_calib_adjust` parameter allows to manually adjust how smooth you want the
 #' fit of the zenith angle to be. Because the zenith angle error model is fitted with data from the
 #' calibration site only, and we are using it for all locations of the bird’s journey, it is safer
 #' to assume a broader/smoother distribution.

R/geopressuretemplate.R

@@ -1,29 +1,22 @@
 #' Workflow for GeoPressureR
 #'
 #' @description
-#' The `geopressuretemplate` function manages the complete workflow for modeling bird trajectories
-#' using geospatial pressure and light data. It includes the creation of tag data, likelihood map
-#' computation (pressure and/or light), graph model construction, trajectory estimation, and
-#' pressure path computation. The function follows a standard structure as defined by the GitHub
-#' repository [geopressuretemplate](https://github.com/Rafnuss/GeoPressureTemplate), which
-#' separates data and analysis for improved readability, sharability, and reproducibility.
-#'
-#' @param id A unique identifier for the tag being processed.
-#' @param config A configuration object specifying workflow parameters, which is loaded by default
-#' using `config::get(config = id)`.
-#' @param quiet Logical. If `TRUE`, suppresses informational messages during execution. The default
-#' value is `FALSE`.
-#' @param file A file path to save the intermediate results (e.g., tag, graph, and pressure paths).
-#' Default is `./data/interim/{id}.RData`.
-#' @param assert_graph Logical. If `TRUE`, check that the config is compatible for the creation of
-#' a graph. The default value is `TRUE`. Set to `FALSE` only if you don't want to create a graph
-#' model
-#' @param ... Additional parameters to overwrite default or config values. Always prefer to modify
-#' `config.yml` if possible.
+#' The `geopressuretemplate()` function manages the complete workflow for modelling bird
+#' trajectories using geolocator data. It includes the creation `tag` object, the construction of
+#' the likelihood maps (pressure and/or light), the creation of the graph model construction, and,
+#' finally, the estimation of the trajectory products and the pressure path computation. Read the
+#' [Workflow chapter in the GeoPressureManual
+#' ](https://raphaelnussbaumer.com/GeoPressureManual/geopressuretemplate-workflow.html) for more
+#' information.
+#'
+#' To be able to run successfully these function, you will need to have correctly set-up the data
+#' and configuration files according following the [GeoPressureTemplate standard
+#' ](https://raphaelnussbaumer.com/GeoPressureManual/geopressuretemplate-project.html).
+#'
 #'
 #' @details
 #' The `geopressuretemplate` function is a high-level entry point that coordinates multiple
-#' steps for processing geospatial animal movement data. It relies on underlying child
+#' steps for processing the geolocator data and produce trajectories. It relies on underlying child
 #' functions for each step:
 #'
 #' * **Tag Creation [`geopressuretemplate_tag()`]**: Initializes and labels the `tag` object. It
@@ -67,6 +60,19 @@
 #' Each of these child functions can be called individually or automatically as part of
 #' the `geopressuretemplate` workflow.
 #'
+#' @param id unique identifier of a tag.
+#' @param config configuration object specifying workflow parameters, which is loaded by default
+#' using `config::get(config = id)`.
+#' @param quiet Logical. If `TRUE`, suppresses informational messages during execution. The default
+#' value is `FALSE`.
+#' @param file A file path to save the intermediate results (e.g., tag, graph, and pressure paths).
+#' Default is `./data/interim/{id}.RData`.
+#' @param assert_graph Logical. If `TRUE`, check that the config is compatible for the creation of
+#' a graph. The default value is `TRUE`. Set to `FALSE` only if you don't want to create a graph
+#' model
+#' @param ... Additional parameters to overwrite default or config values. Always prefer to modify
+#' `config.yml` if possible.
+#'
 #'
 #' @return
 #' The function returns nothing. Instead, it saves the processed outputs (tag, graph,
@@ -75,10 +81,22 @@
 #' @examples
 #' \dontrun{
 #' # Run the complete geopressuretemplate workflow
-#' geopressuretemplate("18LX", quiet = TRUE)
+#' geopressuretemplate("18LX")
+#'
+#' # Or run step-by-step
+#' # you can check that all the parameters are correctly set in the config file
+#' geopressuretemplate_config(id)
+#' # 1. creation of the tag
+#' tag <- geopressuretemplate_tag("18LX")
+#' # 2. creation of the graph
+#' geopressuretemplate_graph("18LX")
+#' # 3. Computation of the pressurepath
+#' geopressuretemplate_pressurepath("18LX")
 #' }
 #'
 #' @family geopressuretemplate
+#' @seealso [GeoPressureManual
+#' ](https://raphaelnussbaumer.com/GeoPressureManual/geopressuretemplate-workflow.html)
 #' @export
 geopressuretemplate <- function(
     id,

R/geopressureviz.R

@@ -118,7 +118,7 @@ geopressureviz <- function(x,
 
   names(maps) <- names(maps_choices[maps_is_available])
 
-  # Set color of each stationary period
+  # Set colour of each stationary period
   col <- rep(RColorBrewer::brewer.pal(8, "Dark2"), times = ceiling(nrow(tag$stap) / 8))
   tag$stap$col <- col[tag$stap$stap_id]
   tag$stap$duration <- stap2duration(tag$stap)

R/map_create.R

@@ -11,7 +11,7 @@
 #' @param stap a data.frame of stationary periods.
 #' @inheritParams tag_create
 #' @param type type of data one of `"unknown"`,`"pressure"`, `"light"`, `"pressure_mse"`,
-#' `"water_mask"`, `"pressure_mask"`, `"marginal"`. Allows for custom color palette on plot.
+#' `"water_mask"`, `"pressure_mask"`, `"marginal"`. Allows for custom colour palette on plot.
 #'
 #' @return A GeoPressure `map` object is returned
 #'

R/plot.tag.R

@@ -531,7 +531,7 @@ plot_tag_twilight <- function(tag,
       twl$discard <- FALSE
     }
 
-    # plotly doesn't like much changing color...
+    # plotly doesn't like much changing colour...
     if (plot_plotly) {
       p <- p +
         ggplot2::geom_point(

R/speed2bearing.R

@@ -2,11 +2,11 @@
 #'
 #' @description
 #' This function convert a speed vector represented in complex number into a bearing angle (0°=N ;
-#' 90°=E...). This conversion is needed because trigonomtric angle are different than bearing.
+#' 90°=E...). This conversion is needed because trigonometric angle are different than bearing.
 #'
 #' @param speed speed as complex value
 #' @param speed_ref reference vector of the angle. Default is the North in order to return bearing.
-#' Normal trigonometriy should be `speed_ref = 1`
+#' Use `speed_ref = 1` for trigonometric orientation (clockwise from East).
 #' @param positive logical to ensure the bearing is positive between 0-360 degree.
 #'
 #' @return bearing angle in degree

R/tag_create.R

@@ -2,7 +2,7 @@
 #'
 #' @description
 #' Create a GeoPressureR `tag` object from the data collected by a tracking device. The function
-#' can read data formatted according to three manufacturers SOI, Migratetech or Lun CAnMove, as
+#' can read data formatted according to three manufacturers SOI, Migratetech or Lund CAnMove, as
 #' well as according to the GeoLocator Data package standard and also accept manual data.frame as
 #' input. Pressure data is required for the GeoPressureR workflow but can be allowed to be missing
 #' with `assert_pressure = FALSE`.
@@ -85,7 +85,8 @@
 #'    (i.e. jiggle). In the SOI sensor, it is summarised from 32 measurements at 10Hz
 #'    - `pitch` is the relative position of the bird’s body relative to the z axis. In the SOI
 #'    sensor, it is an average over 32 measurements at 10Hz.
-#' - `magnetic` (optional) data.frame with columns: `date`, `mX`, `mY`, `mZ`, `gX`, `gY` and `gZ`
+#' - `magnetic` (optional) data.frame with columns: `date`, `magnetic_x`, `magnetic_y`, `magnetic_z`
+#'    , `acceleration_x`, `acceleration_y` and `acceleration_z`
 #'
 #' @examples
 #' withr::with_dir(system.file("extdata", package = "GeoPressureR"), {