Uploading CRAN version 1.2.2

DESCRIPTION

@@ -1,8 +1,9 @@
 Package: SpatialEpi
 Title: Methods and Data for Spatial Epidemiology
-Version: 1.2.3
+Version: 1.2.2
 Depends: R (>= 3.0.2), sp
-Imports: Rcpp, MASS, maptools, spdep, methods, grDevices, graphics, stats
+Imports: Rcpp, MASS, maptools, spdep, methods, grDevices, graphics,
+        stats
 LinkingTo: Rcpp, RcppArmadillo
 Authors@R: c(
     person("Cici", "Chen", email = "[email protected]", role = "ctb"),
@@ -15,3 +16,11 @@ Description:
     Methods and data for cluster detection and disease mapping.
 License: GPL-2
 LazyData: true
+NeedsCompilation: yes
+Packaged: 2016-01-28 20:33:39 UTC; rudeboybert
+Author: Cici Chen [ctb],
+  Albert Y. Kim [aut, cre],
+  Michelle Ross [ctb],
+  Jon Wakefield [aut]
+Repository: CRAN
+Date/Publication: 2016-01-29 01:02:40

R/kulldorff.R

@@ -46,14 +46,6 @@ cluster <- cluster[1:which(cluster == end)]
 # Simulate cases under null hypothesis of no area effects i.e. conditioned on E
 perm <- rmultinom(n.simulations, round(sum(cases)), prob=denominator)
 
-# Ensure that # of cases is less than population size of each area. If not,
-# resample
-for(i in 1:ncol(perm)){
-  while(any(perm[,i] > population))
-    perm[,i] <- rmultinom(1, round(sum(cases)), prob=denominator)
-}
-
-
 # Compute simulated lambda's:  max log-lkhd in region
 sim.lambda <- kulldorffMC(perm, denominator, nearest.neighbors, n.zones, type)
 

R/plotmap.R

@@ -1,6 +1,6 @@
 plotmap <-
 function(values, map, log=FALSE, nclr=7, include.legend=TRUE, lwd=0.5, round=3,
-         brks=NULL, legend=NULL, location='topright', rev=FALSE, leg.cex=1){
+         brks=NULL, legend=NULL, location='topright', rev=FALSE){
 
 # create colors, each based on quantiles of data
 plotclr <- grey(1-seq(0, 1, by=1/(nclr-1)))
@@ -44,7 +44,7 @@ if(is.null(legend)){
 
 plot(map, axes=TRUE, col=colcode, lwd=lwd)
 if(include.legend) {
-  legend(location, legend=legend, fill=plotclr, bty="n", cex=leg.cex)
+  legend(location, legend=legend, fill=plotclr, bty="n")
 }
 
 }

SpatialEpi.Rproj

@@ -15,4 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace,vignette
+PackageRoxygenize: vignette

man/plotmap.Rd

@@ -4,7 +4,7 @@
 \description{Plot levels of a variable in a colour-coded map.}
 \usage{
 plotmap(values, map, log = FALSE, nclr = 7, include.legend = TRUE, lwd = 0.5, 
-round = 3, brks = NULL, legend = NULL, location = "topright", rev = FALSE, leg.cex = 1)
+round = 3, brks = NULL, legend = NULL, location = "topright", rev = FALSE)
 }
 \arguments{
   \item{values}{variable to plot}
@@ -18,7 +18,6 @@ round = 3, brks = NULL, legend = NULL, location = "topright", rev = FALSE, leg.c
   \item{legend}{if desired, a pre-specified legend}
   \item{location}{location of legend}
   \item{rev}{boolean of whether to reverse colour scheme (darker colours for smaller values)}
-  \item{leg.cex}{factor for legend font size}
 }
 \value{A map colour-coded to indicate the different levels of \code{values}.}
 \seealso{ 

src/cluster_detection.cpp

@@ -1,38 +1,22 @@
 #include <Rcpp.h>
-using namespace Rcpp; 
+using namespace Rcpp;
 
 
 // [[Rcpp::export]]
 double binomialLogLkhd(double cz, double nz, double N, double C) {
-  double logLkhd = 0;
-
-  if(cz / nz <= (C - cz)/(N - nz)) {
-    logLkhd = 0;
-  } else if (cz == nz){
-    // Special case: log(0)*0 should = 0, so remove last term
-    logLkhd = 
-      log(N-nz-C+cz) * (N-nz-C+cz) + 
-      log(N-C) * (C-N) +
-      log(N-nz) * (nz-N) + 
-      log(C) * (-C) +
-      log( nz ) *(-nz) +
-      log(N) * N +
-      log(cz) * cz +
-      log(C-cz) *(C-cz);
-  } else {
-    logLkhd  =	
-      log(N-nz-C+cz) * (N-nz-C+cz) + 
-      log(N-C) * (C-N) +
-      log(N-nz) * (nz-N) + 
-      log(C) * (-C) +
-      log( nz ) *(-nz) +
-      log(N) * N +
-      log(cz) * cz +
-      log(C-cz) *(C-cz) +
-      log(nz-cz)*(nz-cz);
-  }
-
-  return logLkhd;
+	double logLkhd = 0;
+
+	if(cz / nz <= (C - cz)/(N - nz)) {
+		logLkhd = 0;
+	} else {
+		logLkhd  =	
+		N * ( log( N-nz-C+cz ) - log( N-C )  + log( N ) - log( N-nz ) ) +
+		nz * ( log( nz-cz ) - log( N-nz-C+cz )  + log( N-nz ) - log( nz ) )+
+		cz * ( log( cz ) - log( nz-cz ) + log( N-nz-C+cz ) - log( C-cz ) )+
+		C * ( log( C-cz ) - log( C ) + log( N-C ) - log( N-nz-C+cz ) );
+	}
+
+	return logLkhd;
 }