SpatialEpi: Methods and Data for Spatial Epidemiology

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 <>

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...


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


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/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

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