Function reference • silverblaze

Main Main functions for running different models
`sim_data()`	Simulate data
`bind_data()`	Bind data to project
`new_set()`	Create new parameter set
`delete_set()`	Delete parameter set
`optimise_beta()`	Optimise beta values for MCMC rungs
`run_mcmc()`	Run main MCMC
`get_output()`	Get specified output from project
`get_hitscores()`	Get hitscores
`gini()`	Calculate Gini coefficient
Plotting Functions for visulaising model output
`plot_DIC_gelman()`	Plot DIC over all K
`plot_acf()`	Produce MCMC autocorrelation plot
`plot_alpha()`	Plot alpha 95% credible intervals
`plot_coupling()`	Plot acceptance rate between rungs
`plot_density()`	Produce MCMC density plot
`plot_expected_popsize()`	Plot expected population size 95% credible intervals
`plot_loglike()`	Plot loglikelihood 95% credible intervals
`plot_loglike_diagnostic()`	Produce diagnostic plots of log-likelihood
`plot_lorenz()`	Produce Lorenz plot of hitscores
`plot_map()`	Create dynamic map
`plot_sigma()`	Plot sigma 95% credible intervals
`plot_structure()`	Posterior allocation plot
`plot_trace()`	Produce MCMC trace plot
Mapping Functions for mapping model output
`overlay_geoprofile()`	Add geoprofile to dynamic map
`overlay_piecharts()`	Add pie charts to dynamic map
`overlay_points()`	Add points to dynamic map
`overlay_ringsearch()`	Add ring-search geoprofile to dynamic map
`overlay_risk_map()`	Add risk surface to dynamic map
`overlay_sentinels()`	Add sentinel sites to dynamic map
`overlay_sources()`	Add sources to dynamic map
`overlay_spatial_prior()`	Add spatial prior to dynamic map
`overlay_surface()`	Add posterior probability surface to dynamic map
`overlay_trial_sites()`	Add trial sites to dynamic map
Misc Miscellaneous functions
`raster_grid()`	Make raster grid
`raster_from_shapefile()`	Make raster from shapefile
`bearing_to_lonlat()`	Get spatial coordinate given an origin, a great circle distance and a bearing
`lonlat_to_bearing()`	Calculate great circle distance and bearing between coordinates
`lonlat_to_cartesian()`	Convert lon/lat to cartesian coordinates
`dist_gc()`	Calculate pairwise great circle distance between points
`dispersal_sphere()`	Draw from spherical distribution
`kernel_smooth()`	Produce a smooth surface using 2D kernel density smoothing
`more_colours()`	Expand series of colours by interpolation
`realised_sources()`	Calculate realised sources
`print_full()`	Ordinary print function for class rgeoprofile_project
`is.rgeoprofile_project()`	Determine if object is of class rgeoprofile_project
`check_silverblaze_loaded()`	Check that silverblaze package has loaded successfully
`rgeoprofile_file()`	Import file
`rgeoprofile_project()`	Create a new RgeoProfile project
`rgeoprofile_shapefile()`	Import shapefile
`silverblaze`	Bayesian Geographic Profiling from Presence-Absence Data

Reference

Main

Plotting

Mapping

Misc