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SpatialEpi (version 1.2.1)

Methods and Data for Spatial Epidemiology

Description

Cluster Detection, Disease Mapping

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Version

Install

install.packages('SpatialEpi')

Monthly Downloads

691

Version

1.2.1

License

GPL-2

Maintainer

Albert Kim

Last Published

June 5th, 2014

Functions in SpatialEpi (1.2.1)

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