Package: RiskMap 0.1.0

Emanuele Giorgi

RiskMap: Geo-Statistical Modeling of Spatially Referenced Data

Provides functions for geo-statistical analysis of both continuous and count data using maximum likelihood methods. The models implemented in the package use stationary Gaussian processes with Matern correlation function to carry out spatial prediction in a geographical area of interest. The underpinning theory of the methods implemented in the package are found in Diggle and Giorgi (2019, ISBN: 978-1-138-06102-7).

Authors:Emanuele Giorgi [aut, cre], Claudio Fronterre [ctb]

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RiskMap.pdf |RiskMap.html✨
RiskMap/json (API)

# Install 'RiskMap' in R:
install.packages('RiskMap', repos = c('https://claudiofronterre.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/claudiofronterre/riskmap/issues

Pkgdown site:https://claudiofronterre.github.io

Datasets:
  • anopheles - Anopheles mosquitoes in Southern Cameroon
  • galicia - Heavy metal biomonitoring in Galicia
  • 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

On CRAN:

3.18 score 5 scripts 525 downloads 21 exports 51 dependencies

Last updated 5 months agofrom:578e61c5d1. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 15 2025
R-4.5-winNOTEFeb 15 2025
R-4.5-macNOTEFeb 15 2025
R-4.5-linuxNOTEFeb 15 2025
R-4.4-winNOTEFeb 15 2025
R-4.4-macNOTEFeb 15 2025
R-4.3-winNOTEFeb 15 2025
R-4.3-macNOTEFeb 15 2025

Exports:check_mcmccreate_griddist_summariesglgpmglgpm_simgpLaplace_sampling_MCMCmatern_cormatern.grad.phimatern.hessian.phimaxim.integrandplot_s_variogrampred_over_gridpred_target_gridpred_target_shppropose_utmres_variogramset_control_simto_tableupdate_predictors

Dependencies:classclassIntclicodacolorspaceDBIdigeste1071fansifarvergenericsggplot2gluegtableisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmaxLikmgcvmiscToolsmunsellmvtnormnlmenumDerivpillarpkgconfigproxyR6RColorBrewerRcpprlangs2sandwichscalessfsnsterratibbleunitsutf8vctrsviridisLitewithrwkxtablezoo

Readme and manuals

Help Manual

Help pageTopics
Anopheles mosquitoes in Southern Cameroonanopheles
Check MCMC Convergence for Spatial Random Effectscheck_mcmc
Extract Parameter Estimates from a "RiskMap" Model Fitcoef.RiskMap
Create Grid of Points Within Shapefilecreate_grid
Summaries of the distancesdist_summaries
Heavy metal biomonitoring in Galiciagalicia
Estimation of Generalized Linear Gaussian Process Modelsglgpm
Simulation from Generalized Linear Gaussian Process Modelsglgpm_sim
Gaussian Process Model Specificationgp
Simulated data-set on the Italian peninsulaitaly_sim
Laplace Sampling Markov Chain Monte Carlo (MCMC) for Generalized Linear Gaussian Process ModelsLaplace_sampling_MCMC
River-blindness in Liberialiberia
Loa loa prevalence data from 197 village surveysloaloa
Malaria Transmission in the Western Kenyan Highlandsmalkenya
Malnutrition in Ghanamalnutrition
Matern Correlation Functionmatern_cor
First Derivative with Respect to phimatern.grad.phi
Second Derivative with Respect to phimatern.hessian.phi
Maximization of the Integrand for Generalized Linear Gaussian Process Modelsmaxim.integrand
Plotting the empirical variogramplot_s_variogram
Plot Method for RiskMap_pred_target_grid Objectsplot.RiskMap_pred_target_grid
Plot Method for RiskMap_pred_target_shp Objectsplot.RiskMap_pred_target_shp
Prediction of the random effects components and covariates effects over a spatial grid using a fitted generalized linear Gaussian process modelpred_over_grid
Predictive Target Over a Regular Spatial Gridpred_target_grid
Predictive Target over a Shapefilepred_target_shp
Print Summary of RiskMap Modelprint.summary.RiskMap
EPSG of the UTM Zonepropose_utm
Random Effect Model Specificationre
Empirical variograms_variogram
Set Control Parameters for Simulationset_control_sim
Summarize Model Fitssummary.RiskMap
Create LaTeX Table from Model Fitto_table
Covariates Dataset for Malaria Prediction in Tanzaniatz_covariates
Malaria Dataset from Tanzania Demographic Health Surveys 2015tz_malaria
Update Predictors for a RiskMap Prediction Objectupdate_predictors