Learn R Programming
⚠️There's a newer version (1.2.8) of this package.Take me there.

SpatialEpi

Methods and Data for Spatial Epidemiology

Copy Link

Version

Install

install.packages('SpatialEpi')

Monthly Downloads

1,149

Version

1.2.2

License

GPL-2

Maintainer

Albert Kim

Last Published

January 29th, 2016

Functions in SpatialEpi (1.2.2)

EBpostthresh

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

Test if two numeric vectors are equal
besag_newell

Besag-Newell Cluster Detection Method
coeff

Compute log Bayes Factors
bayes_cluster

Bayesian Cluster Detection Method
check_overlap

Check if proposed configurations overlap
LogNormalPriorCh

Compute Parameters to Calibrate a Log-normal Distribution
besag_newell_internal

Internal Besag Newell method
eBayes

Empirical Bayes Estimates of Relative Risk
estimate_lambda

Estimate lambda values
ldmultinom

log multinomial Density
kulldorffMC

Compute permutation distribution for kulldorff method
normalize

Normalize vector to sum to 1.
return_birth_moves

Return all possible birth moves
mapvariable

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

Kulldorff Cluster Detection Method
return_death_moves

Return all death moves
pennLC

Pennsylvania Lung Cancer
zones

Create set of all single zones and output geographical information
GammaPriorCh

Compute Parameters to Calibrate a Gamma Distribution
return_local_moves

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

Clean up proposed moves matrix
plotmap

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

MCMC simulation to sample configurations
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.
binomialLogLkhd

Compute Binomial Likelihoods
latlong2grid

Convert Coordinates from Latitude/Longitude to Grid
create_geo_objects

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

Compute Expected Numbers of Disease
process_MCMC_sample

Process MCMC Sample
computeAllLogLkhd

Compute log likelihood for all single zones
ldnbinom

log Negative Binomial Density
scotland

Lip Cancer in Scotland
SpatialEpi-package

Methods and Data for Spatial Epidemiology
NYleukemia

Upstate New York Leukemia Data
ProbSampleReplace

Draw a sample of size 1 given probabilities
polygon2spatial_polygon

Convert a Polygon to a Spatial Polygons Object
poissonLogLkhd

Compute Poisson Likelihoods
grid2latlong

Convert Coordinates from Grid to Latitude/Longitude
circle

Compute cartesian coordinates of a cluster center and radius