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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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install.packages('SpatialEpi')
Monthly Downloads
732
Version
1.2.3
License
GPL-2
Issues
1
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0
Stars
26
Forks
8
Repository
https://github.com/rudeboybert/SpatialEpi
Maintainer
Albert Kim
Last Published
June 2nd, 2018
Functions in SpatialEpi (1.2.3)
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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