SpatialEpi v1.2.3

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Methods and Data for Spatial Epidemiology

Methods and data for cluster detection and disease mapping.

Functions in SpatialEpi

Name Description
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
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Details

Type Package
License GPL-2
LazyData true
URL https://github.com/rudeboybert/SpatialEpi
BugReports https://github.com/rudeboybert/SpatialEpi/issues
LinkingTo Rcpp, RcppArmadillo
NeedsCompilation yes
RoxygenNote 6.0.1
Packaged 2018-06-02 04:06:51 UTC; aykim
Repository CRAN
Date/Publication 2018-06-02 04:58:39 UTC

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