SpatialEpi: Methods and Data for Spatial Epidemiology
Version 1.2.2

Methods and data for cluster detection and disease mapping.

AuthorCici Chen [ctb], Albert Y. Kim [aut, cre], Michelle Ross [ctb], Jon Wakefield [aut]
Date of publication2016-01-29 01:02:40
MaintainerAlbert Y. Kim <albert@stat.washington.edu>
LicenseGPL-2
Version1.2.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SpatialEpi")

Getting started

Package overview
README.md

Popular man pages

bayes_cluster: Bayesian Cluster Detection Method
besag_newell: Besag-Newell Cluster Detection Method
besag_newell_internal: Internal Besag Newell method
eBayes: Empirical Bayes Estimates of Relative Risk
grid2latlong: Convert Coordinates from Grid to Latitude/Longitude
kulldorff: Kulldorff Cluster Detection Method
ProbSampleReplace: Draw a sample of size 1 given probabilities
See all...

All man pages Function index File listing

Man pages

bayes_cluster: Bayesian Cluster Detection Method
besag_newell: Besag-Newell Cluster Detection Method
besag_newell_internal: Internal Besag Newell method
binomialLogLkhd: Compute Binomial Likelihoods
check_overlap: Check if proposed configurations overlap
circle: Compute cartesian coordinates of a cluster center and radius
clean_moves_matrix: Clean up proposed moves matrix
coeff: Compute log Bayes Factors
computeAllLogLkhd: Compute log likelihood for all single zones
create_geo_objects: Create geographical objects to be used in Bayesian Cluster...
eBayes: Empirical Bayes Estimates of Relative Risk
EBpostdens: Produce plots of emprical Bayes posterior densities when the...
EBpostthresh: Produce the probabilities of exceeding a threshold given a...
estimate_lambda: Estimate lambda values
expected: Compute Expected Numbers of Disease
GammaPriorCh: Compute Parameters to Calibrate a Gamma Distribution
grid2latlong: Convert Coordinates from Grid to Latitude/Longitude
kulldorff: Kulldorff Cluster Detection Method
kulldorffMC: Compute permutation distribution for kulldorff method
latlong2grid: Convert Coordinates from Latitude/Longitude to Grid
ldmultinom: log multinomial Density
ldnbinom: log Negative Binomial Density
LogNormalPriorCh: Compute Parameters to Calibrate a Log-normal Distribution
mapvariable: Plot Levels of a Variable in a Colour-Coded Map
MCMC_simulation: MCMC simulation to sample configurations
normalize: Normalize vector to sum to 1.
NumericVectorEquality: Test if two numeric vectors are equal
NYleukemia: Upstate New York Leukemia Data
pennLC: Pennsylvania Lung Cancer
plotmap: Plot Levels of a Variable in a Colour-Coded Map
poissonLogLkhd: Compute Poisson Likelihoods
polygon2spatial_polygon: Convert a Polygon to a Spatial Polygons Object
ProbSampleReplace: Draw a sample of size 1 given probabilities
process_MCMC_sample: Process MCMC Sample
return_birth_moves: Return all possible birth moves
return_death_moves: Return all death moves
return_local_moves: Return all possible local moves: growth, trim, recenter
scotland: Lip Cancer in Scotland
SpatialEpi-package: Methods and Data for Spatial Epidemiology
zones: Create set of all single zones and output geographical...

Functions

EBpostdens Man page Source code
EBpostthresh Man page Source code
GammaPriorCh Man page Source code
LogNormalPriorCh Man page Source code
MCMC_simulation Man page Source code
NYleukemia Man page
NumericVectorEquality Man page Source code
ProbSampleReplace Man page Source code
SpatialEpi Man page
bayes_cluster Man page Source code
besag_newell Man page Source code
besag_newell_internal Man page Source code
binomialLogLkhd Man page Source code
check_overlap Man page Source code
circle Man page Source code
clean_moves_matrix Man page Source code
coeff Man page Source code
computeAllLogLkhd Man page Source code
create_geo_objects Man page Source code
eBayes Man page Source code
estimate_lambda Man page Source code
expected Man page Source code
grid2latlong Man page Source code
kulldorff Man page Source code
kulldorffMC Man page Source code
latlong2grid Man page Source code
ldmultinom Man page Source code
ldnbinom Man page Source code
mapvariable Man page Source code
normalize Man page Source code
pennLC Man page
plotmap Man page Source code
poissonLogLkhd Man page Source code
polygon2spatial_polygon Man page Source code
process_MCMC_sample Man page Source code
return_birth_moves Man page Source code
return_death_moves Man page Source code
return_local_moves Man page Source code
scotland Man page
zones Man page Source code

Files

src
src/cluster_detection.cpp
src/RcppExports.cpp
src/bayes_cluster.cpp
NAMESPACE
data
data/pennLC.rda
data/scotland.rda
data/NYleukemia.rda
R
R/latlong2grid.R
R/bayes_cluster.R
R/create_geo_objects.R
R/LogNormalPriorCh.R
R/process_MCMC_sample.R
R/GammaPriorCh.R
R/circle.R
R/grid2latlong.R
R/polygon2spatial_polygon.R
R/besag_newell.R
R/zones.R
R/RcppExports.R
R/estimate_lambda.R
R/EBpostdens.R
R/EBpostthresh.R
R/mapvariable.R
R/eBayes.R
R/kulldorff.R
R/plotmap.R
R/expected.R
README.md
MD5
DESCRIPTION
man
man/clean_moves_matrix.Rd
man/besag_newell_internal.Rd
man/poissonLogLkhd.Rd
man/grid2latlong.Rd
man/polygon2spatial_polygon.Rd
man/bayes_cluster.Rd
man/estimate_lambda.Rd
man/coeff.Rd
man/ProbSampleReplace.Rd
man/kulldorff.Rd
man/SpatialEpi-package.Rd
man/mapvariable.Rd
man/return_birth_moves.Rd
man/zones.Rd
man/ldmultinom.Rd
man/NYleukemia.Rd
man/eBayes.Rd
man/besag_newell.Rd
man/NumericVectorEquality.Rd
man/process_MCMC_sample.Rd
man/kulldorffMC.Rd
man/check_overlap.Rd
man/LogNormalPriorCh.Rd
man/latlong2grid.Rd
man/EBpostthresh.Rd
man/create_geo_objects.Rd
man/EBpostdens.Rd
man/return_local_moves.Rd
man/computeAllLogLkhd.Rd
man/binomialLogLkhd.Rd
man/plotmap.Rd
man/ldnbinom.Rd
man/expected.Rd
man/MCMC_simulation.Rd
man/return_death_moves.Rd
man/normalize.Rd
man/GammaPriorCh.Rd
man/pennLC.Rd
man/circle.Rd
man/scotland.Rd
SpatialEpi documentation built on May 20, 2017, 3:11 a.m.

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