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SpatialEpi (version 1.2.3)

Methods and Data for Spatial Epidemiology

Description

Methods and data for cluster detection and disease mapping.

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Version

Install

install.packages('SpatialEpi')

Monthly Downloads

965

Version

1.2.3

License

GPL-2

Issues

1

Pull Requests

0

Stars

30

Forks

8

Maintainer

Albert Kim

Last Published

June 2nd, 2018

Functions in SpatialEpi (1.2.3)

besag_newell_internal

Internal Besag Newell method
clean_moves_matrix

Clean up proposed moves matrix
kulldorffMC

Compute permutation distribution for kulldorff method
ldmultinom

log multinomial Density
polygon2spatial_polygon

Convert a Polygon to a Spatial Polygons Object
mapvariable

Plot Levels of a Variable in a Colour-Coded Map
zones

Create set of all single zones and output geographical information
scotland

Lip Cancer in Scotland
normalize

Normalize vector to sum to 1.
poissonLogLkhd

Compute Poisson Likelihoods
ldnbinom

log Negative Binomial Density
kulldorff

Kulldorff Cluster Detection Method
latlong2grid

Convert Coordinates from Latitude/Longitude to Grid
plotmap

Plot Levels of a Variable in a Colour-Coded Map
return_local_moves

Return all possible local moves: growth, trim, recenter
pennLC

Pennsylvania Lung Cancer
estimate_lambda

Estimate lambda values
grid2latlong

Convert Coordinates from Grid to Latitude/Longitude
return_death_moves

Return all death moves
expected

Compute Expected Numbers of Disease
process_MCMC_sample

Process MCMC Sample
return_birth_moves

Return all possible birth moves
ProbSampleReplace

Draw a sample of size 1 given probabilities
SpatialEpi-package

SpatialEpi
NYleukemia

Upstate New York Leukemia Data
NumericVectorEquality

Test if two numeric vectors are equal
MCMC_simulation

MCMC simulation to sample configurations
bayes_cluster

Bayesian Cluster Detection 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.
circle

Compute cartesian coordinates of a cluster center and radius
EBpostthresh

Produce the probabilities of exceeding a threshold given a posterior gamma distribution.
coeff

Compute log Bayes Factors
GammaPriorCh

Compute Parameters to Calibrate a Gamma Distribution
create_geo_objects

Create geographical objects to be used in Bayesian Cluster Detection Method
eBayes

Empirical Bayes Estimates of Relative Risk
LogNormalPriorCh

Compute Parameters to Calibrate a Log-normal Distribution
binomialLogLkhd

Compute Binomial Likelihoods
computeAllLogLkhd

Compute log likelihood for all single zones
check_overlap

Check if proposed configurations overlap
besag_newell

Besag-Newell Cluster Detection Method