Package: SpatialEpi 1.2.8.9000

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]

SpatialEpi_1.2.8.9000.tar.gz
SpatialEpi_1.2.8.9000.zip(r-4.7)SpatialEpi_1.2.8.9000.zip(r-4.6)SpatialEpi_1.2.8.9000.zip(r-4.5)
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SpatialEpi_1.2.8.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SpatialEpi/json (API)
NEWS

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

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

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

On CRAN:

Conda:

cpp

6.89 score 34 stars 206 scripts 1.1k downloads 7 mentions 19 exports 19 dependencies

Last updated from:08e5da8bc8. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK173
linux-devel-x86_64OK188
source / vignettesOK229
linux-release-arm64OK166
linux-release-x86_64OK164
macos-release-arm64OK125
macos-release-x86_64OK268
macos-oldrel-arm64OK132
macos-oldrel-x86_64OK179
windows-develOK141
windows-releaseOK139
windows-oldrelOK113
wasm-releaseOK134

Exports:bayes_clusterbesag_newellcirclecreate_geo_objectseBayesEBpostdensEBpostthreshestimate_lambdaexpectedGammaPriorChgrid2latlongkulldorfflatlong2gridLogNormalPriorChmapvariableplotmappolygon2spatial_polygonprocess_MCMC_samplezones

Dependencies:bootclassclassIntDBIdeldire1071KernSmoothlatticeMASSproxyRcppRcppArmadillos2sfspspDataspdepunitswk

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