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SpatialEpi (version 1.2.1)
Methods and Data for Spatial Epidemiology
Description
Cluster Detection, Disease Mapping
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Install
install.packages('SpatialEpi')
Monthly Downloads
732
Version
1.2.1
License
GPL-2
Maintainer
Albert Kim
Last Published
June 5th, 2014
Functions in SpatialEpi (1.2.1)
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MCMC_simulation
MCMC simulation to sample configurations
NYleukemia
Upstate New York Leukemia Data
besag_newell_internal
Internal Besag Newell method
grid2latlong
Convert Coordinates from Grid to Latitude/Longitude
check_overlap
Check if proposed configurations overlap
return_birth_moves
Return all possible birth moves
mapvariable
Plot Levels of a Variable in a Colour-Coded Map
return_death_moves
Return all death moves
estimate_lambda
Estimate lambda values
clean_moves_matrix
Clean up proposed moves matrix
create_geo_objects
Create geographical objects to be used in Bayesian Cluster Detection Method
scotland
Lip Cancer in Scotland
polygon2spatial_polygon
Convert a Polygon to a Spatial Polygons Object
circle
Compute cartesian coordinates of a cluster center and radius
kulldorffMC
Compute permutation distribution for kulldorff method
EBpostdens
Produce plots of emprical 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.
NumericVectorEquality
Test if two numeric vectors are equal
plotmap
Plot Levels of a Variable in a Colour-Coded Map
return_local_moves
Return all possible local moves: growth, trim, recenter
EBpostthresh
Produce the probabilities of exceeding a threshold given a posterior gamma distribution.
binomialLogLkhd
Compute Binomial Likelihoods
ldnbinom
log Negative Binomial Density
coeff
Compute log Bayes Factors
kulldorff
Kulldorff Cluster Detection Method
LogNormalPriorCh
Compute Parameters to Calibrate a Log-normal Distribution
eBayes
Empirical Bayes Estimates of Relative Risk
normalize
Normalize vector to sum to 1.
poissonLogLkhd
Compute Poisson Likelihoods
ldmultinom
log multinomial Density
latlong2grid
Convert Coordinates from Latitude/Longitude to Grid
expected
Compute Expected Numbers of Disease
ProbSampleReplace
Draw a sample of size 1 given probabilities
bayes_cluster
Bayesian Cluster Detection Method
GammaPriorCh
Compute Parameters to Calibrate a Gamma Distribution
pennLC
Pennsylvania Lung Cancer
SpatialEpi-package
Methods and Data for Spatial Epidemiology
besag_newell
Besag-Newell Cluster Detection Method
computeAllLogLkhd
Compute log likelihood for all single zones
process_MCMC_sample
Process MCMC Sample
zones
Create set of all single zones and output geographical information
process.MCMC.chain
Process MCMC Chain
create.geo.objects
Create geographical objects to be used in
bayes.cluster
function.
ranking
Get rankings of non-overlapping elements
bayes.cluster
Bayesian Cluster Detection
besag.newell
Besag-Newell Cluster Detection Method
MCMC
MCMC Wrapper Function
polygon2spatial.polygon
Convert a Polygon to a Spatial Polygons Object
estimate.lambda
Internal Function to Estimate Lambda
estimate.q
Estimate q values for prior prob of j clusters/anti-clusters