Package index • GeoPressureR

Tag

Core functions related to a tag object.

tag_create(): Create a tag object
tag_set_map(): Configure the spatial and temporal parameters of the map of a tag object

Visualize tag

Print and plot a tag object.

print(<tag>): Print a tag object
plot(<tag>): Plot a tag object
plot_tag_pressure(): Plot pressure data of a tag
plot_tag_light(): Plot light data of a tag
plot_tag_twilight(): Plot twilight data of a tag
plot_tag_acceleration(): Plot acceleration data of a tag
plot_tag_temperature(): Plot temperature data of a tag
plot_tag_actogram(): Plot Actogram data of a tag

Label tag

Core functions related to labelling a tag object.

tag_label(): Label a tag object
tag_label_auto(): Automatic labelling acceleration data of a tag
tag_label_write(): Write a tag label file
tag_label_read(): Read a tag label file
tag_label_stap(): Create stationary periods from a tag label

Tag utilities

Various utility functions related to a tag object.

tag_assert(): Assert the status of a tag
read_stap(): Read or validate stap data
tag_stap_daily(): Create stationary periods from twilight midpoints
tag2path(): Build a path from the likelihood maps of a tag

GeoPressure

Core functions of the GeoPressureAPI.

GeoPressure map

Geopositioning based on pressure data.

geopressure_map() geopressure_map_likelihood() geopressure_map_mismatch(): Compute likelihood map from pressure data
geopressure_map_preprocess(): Prepare pressure data for geopressure_map()

GeoPressure time series

Retrieving time series pressure at a given location.

geopressure_timeseries(): Request and download pressure time series at a given location

GeoLight

Geopositioning based on light data.

twilight_create(): Estimate twilights from light data
twilight_label_write(): Write a twilight label file
twilight_label_read(): Read a twilight label file
geolight_solar(): Solar zenith angle using NOAA / Meeus equations
geolight_map() geolight_map_aggregate() geolight_map_calibrate() geolight_map_likelihood(): Compute likelihood map from twilight
geolight_fit_location(): Estimate one location per stationary period from twilight times
plot_twl_calib() plot_twl_calib_path(): Plot twilight calibration diagnostics
ts2mat(): Format time series data frame into a matrix

Graph

Constructing the Hidden-Markov model with a graph and computing trajectory products.

graph_create(): Create a graph object

Graph movement

Defining the movement model, optionally using wind data and bird morphology.

graph_set_movement(): Define the movement model of a graph
tag_download_wind(): Download flight data
graph_add_wind(): Compute windspeed and airspeed on a graph
bird_create(): Create bird flight traits
print(<bird>): Print a bird object
speed2prob(): Compute probability of a bird speed
edge_add_wind(): Retrieve ERA5 variable along edge
plot_graph_movement(): Plot movement model of a graph

Graph products

Compute the three main products of the Hidden-Markov model.

graph_most_likely(): Compute the most likely trajectory
graph_marginal(): Compute marginal probability map
graph_simulation(): Simulate randomly multiple trajectories

Graph utilities

Utility functions for a graph object

graph_assert(): Assert the status of a graph
print(<graph>): Print a graph object

Map

Container for spatio-temporal (stationary periods) data.

map_create(): Create a map object
print(<map>): Print a map object
plot(<map>): Plot a map object
rast.map(): Construct a SpatRaster from a map
map_expand(): Construct grid from extent and scale
map_add_mask_water(): Create water mask for geolight map

Path

Data.frame of positions defining a bird trajectory.

path2edge(): Extract the edges of a path from a graph
plot_path(): Plot a path

Sampling path

Gibbs sampling from movement model.

tag2path(): Build a path from the likelihood maps of a tag

Pressurepath

Data.frame of pressure time series along a path.

pressurepath_create(): Create a pressurepath
plot_pressurepath(): Plot a pressurepath
path2elevation(): Download ground elevation along a path

GeoPressureTemplate

Wrapper functions for the full GeoPressureR worflow

geopressuretemplate() geopressuretemplate_config() geopressuretemplate_graph() geopressuretemplate_pressurepath() geopressuretemplate_tag(): Workflow for GeoPressureR
load_interim(): Load interim objects from an RData file

Shiny Apps

Web applications for labeling and visualizing data.

geopressureviz(): Start the GeoPressureViz shiny app
geolightviz(): Start the GeoLightViz shiny app
trainset(): Start the GeoPressure Trainset shiny app

Param

List of parameters used in tag and graph.

param_create(): Create a param list
print(<param>): Print a param list

Utilities

General utility functions of the package.

stap2flight(): Compute flights from stationary periods
stap2duration(): Compute duration of stationary periods
speed2bearing(): Compute the bearing of a speed vector
windsupport(): Compute wind support and drift from a wind and ground speed vectors
path2twilight(): Compute exact astronomical twilights from a path (positions and dates)
GeoPressureR: GeoPressureR: Global positioning by atmospheric pressure.