Package: RiskMap 1.0.0

Emanuele Giorgi

RiskMap: Geostatistical Modeling of Spatially Referenced Data

Geostatistical analysis of continuous and count data. Implements stationary Gaussian processes with Matérn correlation for spatial prediction, as described in Diggle and Giorgi (2019, ISBN: 978-1-138-06102-7).

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

RiskMap_1.0.0.tar.gz

RiskMap_1.0.0.tgz(r-4.6-x86_64)RiskMap_1.0.0.tgz(r-4.6-arm64)RiskMap_1.0.0.tgz(r-4.5-x86_64)RiskMap_1.0.0.tgz(r-4.5-arm64)
RiskMap_1.0.0.tar.gz(r-4.7-arm64)RiskMap_1.0.0.tar.gz(r-4.7-x86_64)RiskMap_1.0.0.tar.gz(r-4.6-arm64)RiskMap_1.0.0.tar.gz(r-4.6-x86_64)
RiskMap_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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/docs site:https://claudiofronterre.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • 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

On CRAN:

Conda:

cpp

4.83 score 41 scripts 265 downloads 34 exports 67 dependencies

Last updated from:385ee2a832. Checks:8 WARNING, 2 OK, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING331
linux-devel-x86_64WARNING358
source / vignettesOK283
linux-release-arm64WARNING331
linux-release-x86_64WARNING353
macos-release-arm64WARNING237
macos-release-x86_64WARNING448
macos-oldrel-arm64WARNING259
macos-oldrel-x86_64WARNING414
windows-develFAIL87
windows-releaseFAIL149
windows-oldrelFAIL91
wasm-releaseOK230

Exports:assess_ppassess_simcheck_mcmccompute_ID_coordsconvex_hull_sfcreate_griddastdast_simdist_summariesdsgmelogitglgpmglgpm_simgpLaplace_sampling_MCMCmatern_cormatern.grad.phimatern.hessian.phimaxim.integrandplot_AnPITplot_mdaplot_s_variogramplot_scoreplot_sim_surfpred_over_gridpred_target_gridpred_target_shppropose_utmres_variogramset_control_simsurf_simto_tableupdate_predictors

Dependencies:abindclassclassIntclicodacodetoolscpp11DBIDerivdigestdplyre1071farverfurrrfuturegenericsggplot2globalsgluegridExtragtableisobandKernSmoothlabelinglatticelifecyclelistenvmagrittrMASSMatrixmvtnormnumDerivparallellypillarpkgconfigproxypurrrR6RColorBrewerRcppRcppEigenrlangrsamples2S7scalessfslidersnsspatialEcospatialsamplestarsstringistringrterratibbletidyrtidyselectTMBunitsutf8vctrsviridisLitewarpwithrwkxtable

Readme and manuals

Help Manual

Help pageTopics
Female Culex pipiens abundance (collections) in the Sacramento Metropolitan Areaabund_sma
Anopheles mosquitoes in Southern Cameroonanopheles
Assess Predictive Performance via Spatial Cross-Validationassess_pp
Assess Simulationsassess_sim
Check MCMC Convergence for Spatial Random Effectscheck_mcmc
Extract Parameter Estimates from a "RiskMap" Model Fitcoef.RiskMap
Compute Unique Coordinate Identifierscompute_ID_coords
Convex Hull of an sf Objectconvex_hull_sf
Create Grid of Points Within Shapefilecreate_grid
Fitting of decay-adjusted spatio-temporal (DAST) modeldast
Simulation from Decay-adjusted Spatio-temporal (DAST) modelsdast_sim
Summaries of the distancesdist_summaries
Fit a Doubly Stochastic Geostatistical Model (DSGM)dsgm
Empirical Logit Transformation for Binomial Dataelogit
Heavy metal biomonitoring in Galiciagalicia
Estimation of Generalized Linear Gaussian Process Modelsglgpm
Simulation from Generalized Linear Gaussian Process Modelsglgpm_sim
Gaussian Process Model Specificationgp
West Nile virus pool tests for female *Culex pipiens* in the Sacramento Metropolitan Areainfect_sma
Simulated data-set on the Italian peninsulaitaly_sim
Laplace-sampling 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
Plot Calibration Curves (AnPIT / PIT) from Spatial Cross-Validationplot_AnPIT
Plot the estimated MDA impact functionplot_mda
Plotting the empirical variogramplot_s_variogram
Plot Spatial Scores for a Specific Model and Metricplot_score
Plot simulated surface data for a given simulationplot_sim_surf
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 gridpred_over_grid
Predictive Target Over a Regular Spatial Gridpred_target_grid
Predictive Targets over a Shapefile (grid-aggregated)pred_target_shp
Print Summary of RiskMap Modelprint.summary.RiskMap
Print Simulation Resultsprint.summary.RiskMap.sim.res
Print Summary of RiskMap Spatial Cross-Validation Scoresprint.summary.RiskMap.spatial.cv
EPSG of the UTM Zonepropose_utm
Random Effect Model Specificationre
Empirical variograms_variogram
Set Control Parameters for Simulationset_control_sim
Summarize Model Fitssummary.RiskMap
Summarize Simulation Resultssummary.RiskMap.sim.res
Summarize Cross-Validation Scores for Spatial RiskMap Modelssummary.RiskMap.spatial.cv
Simulate surface data based on a spatial modelsurf_sim
Generate LaTeX Tables from RiskMap Model Fits and Validationto_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