Function reference • fdmr

Plotting

Create simple figures

plot_barchart(): Plot a bar chart using ggplot2

plot_boxplot(): Plot a boxplot using ggplot2

plot_dic(): Plot Deviance Information Criterion (DIC) values

plot_line_average(): Create a line plot with a confidence interval.

plot_line_comparison(): Plot line comparison for stdev etc

plot_map(): Create a simple map from data using either the leaflet or mapview packages

plot_mesh(): Plot a mesh on a Leaflet map

plot_priors_boxplot(): Create boxplots from priors run data

plot_priors_density(): Plot density function

plot_timeseries(): Plot timeseries data

Shiny apps

Interactive tools for building meshes, plotting maps and investigating priors

mesh_builder(): Mesh building shiny app. Creates and visualises a mesh from some spatial data.

model_builder(): Interactively set and see the result of different priors

model_viewer(): Mesh building shiny app. Creates and visualises a mesh from some spatial data.

Parsing model output

Functions to help parse model output and extract useful information

parse_model_output(): Parse model output to create a list of model parameters

create_prediction_field(): Create a prediction field from the parsed model output and the mesh

Mesh tools

Functions to help with creation and investigation of meshes

mesh_to_spatial(): Convert an INLA mesh to a SpatialPolygonsDataFrame

mesh_checker()

Check a mesh for errors:

A greater number of mesh nodes than observations
A greater number of mesh triangles than observations
Isolated triangles in mesh

Geospatial helpers

Functions to help convert coordinates and units

latlong_to_utm(): Convert latitude and longitude to UTM coordinates

antimeridian_wrapping(): Split polygons into two if crossing the dateline (antimeridian)

convert_from_lon_360(): Convert longitudes from 0 to 360 degrees to -180 to 180 degrees

Utility functions

These help us handle paths, retrieve data etc

to_dates(): Convert vector of date strings to Date objects

retrieve_tutorial_data(): Retrieve a tutorial dataset and unpacks it to ~/fdmr/tutorial_data

get_tutorial_datapath(): Return the filepath for a tutorial data file.

load_tutorial_data(): Load data from the tutorial data store

clear_caches(): Clear both tutorial data and downloaded archive caches

numbers_only(): Removes any character that isn't a letter