Package: SpatialEpi 1.2.8.9000

Albert Y. Kim

SpatialEpi: Methods and Data for Spatial Epidemiology

Methods and data for cluster detection and disease mapping.

Authors:Cici Chen [ctb], Albert Y. Kim [aut, cre], Michelle Ross [ctb], Jon Wakefield [aut], Mikael Moise [aut]

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SpatialEpi.pdf |SpatialEpi.html✨
SpatialEpi/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/rudeboybert/spatialepi/issues

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

On CRAN:

6.67 score 30 stars 147 scripts 978 downloads 7 mentions 19 exports 20 dependencies

Last updated 2 years agofrom:08e5da8bc8. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-win-x86_64OKNov 09 2024
R-4.5-linux-x86_64OKNov 09 2024
R-4.4-win-x86_64OKNov 09 2024
R-4.4-mac-x86_64OKNov 09 2024
R-4.4-mac-aarch64OKNov 09 2024
R-4.3-win-x86_64OKNov 09 2024
R-4.3-mac-x86_64OKNov 09 2024
R-4.3-mac-aarch64OKNov 09 2024

Exports:bayes_clusterbesag_newellcirclecreate_geo_objectseBayesEBpostdensEBpostthreshestimate_lambdaexpectedGammaPriorChgrid2latlongkulldorfflatlong2gridLogNormalPriorChmapvariableplotmappolygon2spatial_polygonprocess_MCMC_samplezones

Dependencies:bootclassclassIntDBIdeldire1071KernSmoothlatticemagrittrMASSproxyRcppRcppArmadillos2sfspspDataspdepunitswk

Readme and manuals

Help Manual

Help pageTopics
Bayesian Cluster Detection Methodbayes_cluster
Besag-Newell Cluster Detection Methodbesag_newell
Compute cartesian coordinates of a cluster center and radiuscircle
Create geographical objects to be used in Bayesian Cluster Detection Methodcreate_geo_objects
Empirical Bayes Estimates of Relative RiskeBayes
Produce plots of empirical Bayes posterior densities when the data Y are Poisson with expected number E and relative risk theta, with the latter having a gamma distribution with known values alpha and beta, which are estimated using empirical Bayes.EBpostdens
Produce the probabilities of exceeding a threshold given a posterior gamma distribution.EBpostthresh
Estimate lambda valuesestimate_lambda
Compute Expected Numbers of Diseaseexpected
Compute Parameters to Calibrate a Gamma DistributionGammaPriorCh
Convert Coordinates from Grid to Latitude/Longitudegrid2latlong
Kulldorff Cluster Detection Methodkulldorff
Convert Coordinates from Latitude/Longitude to Gridlatlong2grid
Make legend labelsleglabs
Compute Parameters to Calibrate a Log-normal DistributionLogNormalPriorCh
Plot Levels of a Variable in a Colour-Coded Mapmapvariable
Upstate New York Leukemia DataNYleukemia
Upstate New York LeukemiaNYleukemia_sf
Pennsylvania Lung CancerpennLC
Pennsylvania Lung CancerpennLC_sf
Plot Levels of a Variable in a Colour-Coded Mapplotmap
Convert a Polygon to a Spatial Polygons Objectpolygon2spatial_polygon
Process MCMC Sampleprocess_MCMC_sample
Lip Cancer in Scotlandscotland
Lip Cancer in Scotlandscotland_sf
Create set of all single zones and output geographical informationzones