Package index • RiskMap

Model Fitting

set_control_sim(): Set Control Parameters for Simulation
Laplace_sampling_MCMC(): Laplace-sampling MCMC for Generalized Linear Gaussian Process Models
glgpm_sim(): Simulation from Generalized Linear Gaussian Process Models
dast_sim(): Simulation from Decay-adjusted Spatio-temporal (DAST) models
surf_sim(): Simulate surface data based on a spatial model

pred_over_grid(): Prediction of the random effects components and covariates effects over a spatial grid using a fitted generalized linear Gaussian process model
pred_target_grid(): Predictive Target Over a Regular Spatial Grid
pred_target_shp(): Predictive Targets over a Shapefile (grid-aggregated)
update_predictors(): Update Predictors for a RiskMap Prediction Object

check_mcmc(): Check MCMC Convergence for Spatial Random Effects
assess_pp(): Assess Predictive Performance via Spatial Cross-Validation
assess_sim(): Assess Simulations
plot_AnPIT(): Plot Calibration Curves (AnPIT / PIT) from Spatial Cross-Validation
plot_score(): Plot Spatial Scores for a Specific Model and Metric
dist_summaries(): Summaries of the distances
s_variogram(): Empirical variogram
plot_s_variogram(): Plotting the empirical variogram
plot_sim_surf(): Plot simulated surface data for a given simulation
plot_mda(): Plot the estimated MDA impact function

summary(<RiskMap>): Summarize Model Fits
summary(<RiskMap.sim.res>): Summarize Simulation Results
summary(<RiskMap.spatial.cv>): Summarize Cross-Validation Scores for Spatial RiskMap Models
print(<summary.RiskMap>): Print Summary of RiskMap Model
print(<summary.RiskMap.sim.res>): Print Simulation Results
print(<summary.RiskMap.spatial.cv>): Print Summary of RiskMap Spatial Cross-Validation Scores
plot(<RiskMap_pred_target_grid>): Plot Method for RiskMap_pred_target_grid Objects
plot(<RiskMap_pred_target_shp>): Plot Method for RiskMap_pred_target_shp Objects

create_grid(): Create Grid of Points Within Shapefile
compute_ID_coords(): Compute Unique Coordinate Identifiers
convex_hull_sf(): Convex Hull of an sf Object
propose_utm(): EPSG of the UTM Zone
matern_cor(): Matern Correlation Function
matern.grad.phi(): First Derivative with Respect to \(\phi\)
matern.hessian.phi(): Second Derivative with Respect to \(\phi\)
maxim.integrand(): Maximization of the Integrand for Generalized Linear Gaussian Process Models
to_table(): Generate LaTeX Tables from RiskMap Model Fits and Validation
coef(<RiskMap>): Extract Parameter Estimates from a "RiskMap" Model Fit

abund_sma: Female Culex pipiens abundance (collections) in the Sacramento Metropolitan Area
anopheles: Anopheles mosquitoes in Southern Cameroon
galicia: Heavy metal biomonitoring in Galicia
infect_sma: West Nile virus pool tests for female *Culex pipiens* in the Sacramento Metropolitan Area
italy_sim: Simulated data-set on the Italian peninsula
liberia: River-blindness in Liberia
loaloa: Loa loa prevalence data from 197 village surveys
malkenya: Malaria Transmission in the Western Kenyan Highlands
malnutrition: Malnutrition in Ghana
tz_covariates: Covariates Dataset for Malaria Prediction in Tanzania
tz_malaria: Malaria Dataset from Tanzania Demographic Health Surveys 2015