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SpatialEpi
Methods and Data for Spatial Epidemiology
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Install
install.packages('SpatialEpi')
Monthly Downloads
732
Version
1.2.2
License
GPL-2
Maintainer
Albert Kim
Last Published
January 29th, 2016
Functions in SpatialEpi (1.2.2)
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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