SpatialEpi: Methods and Data for Spatial Epidemiology

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Methods and data for cluster detection and disease mapping.

Author
Cici Chen [ctb], Albert Y. Kim [aut, cre], Michelle Ross [ctb], Jon Wakefield [aut]
Date of publication
2016-01-29 01:02:40
Maintainer
Albert Y. Kim <albert@stat.washington.edu>
License
GPL-2
Version
1.2.2

View on CRAN

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...

Files in this package

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