version 1.0-10

CHANGES

@@ -80,5 +80,10 @@ cleanup of Rd files to conform to R-1.6.0
 Version: 1.0-9
 bugfix - not.r computation was off in make.marker.map
 
+----------------------------------------
+
+Version: 1.0-10
+bugfix - new classes for unique() broke summary.swap
 
+----------------------------------------
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bqtl
-Version: 1.0-9
-Date: 2002-11-04
+Version: 1.0-10
+Date: 2002-11-08
 Title: Bayesian QTL mapping toolkit 
 Author: Charles C. Berry <cberry@ucsd.edu>
 Maintainer: Charles C. Berry <cberry@ucsd.edu>

R/make.state.matrix.s

@@ -23,7 +23,7 @@
 ### marker. frame is assumed to be all numeric
 ###
     sum.or.one <- function(x)  {y <- sum(x);if (y>0) y else 1.0}
-    md.unique <- unique(marker.distances)
+    md.unique <- unique( c( marker.distances ) )
     md.ind <- factor(marker.distances, md.unique)
     n.ind <- length(md.unique)
 ###

R/summary.swap.s

@@ -3,6 +3,7 @@ function(object, method=NULL, ncoef=length(object$alt.coef),nloc=object$nloc,...
 {
 ### summarize a swap.cycle object
   this.call <- sys.call()
+  if (exists("unique.default")) unique <- unique.default
   if (missing(method))
     method <-
       if(diff(dim(object$config))[1] < 0 )
@@ -29,10 +30,10 @@ function(object, method=NULL, ncoef=length(object$alt.coef),nloc=object$nloc,...
                                                               )))
   cp <- object$coefs * rep.post
   tap.coef <- tapply(cp, object$conf, sum)
-  coefs[sort(unique(object$config))] <- if (method=="F2") tap.coef[-1] else tap.coef
+  coefs[sort(unique(c( object$config )))] <- if (method=="F2") tap.coef[-1] else tap.coef
   coefs <- coefs/sum(object$post)
   if (method=="F2") {
-    locs <- apply((object$config - 1) %/% 2 + 1, 2:3, function(x) {unique(x[x > 0])})
+    locs <- apply((object$config - 1) %/% 2 + 1, 2:3, function(x) {unique(c( x[x > 0]) )})
   }
   else
     locs <- object$config
@@ -41,7 +42,7 @@ function(object, method=NULL, ncoef=length(object$alt.coef),nloc=object$nloc,...
     diml <- c(1, diml)
   loc.post <- rep(0, nloc)
   rep.marg <- rep(object$marg, rep(diml[1], diml[2] * diml[3]))
-  loc.post[sort(unique(locs))] <-
+  loc.post[sort(unique(c( locs )))] <-
     tapply(rep.marg, locs, sum)/sum(rep.marg)*diml[2]
   ## note assumption that second subscript tells size of model
   blk.ratio <- apply(object$cond/object$marg, 2, mean)

R/swapbc1.c.s

@@ -34,7 +34,7 @@
     nlocs <- length(in.locs)
     nstep <- nlocs
 
-    len.locs <- length(unique(locs))
+    len.locs <- length(unique(c( locs ) ))
 
     nopt <- len.locs
     optmax <- 1

R/swapf2.c.s

@@ -37,7 +37,7 @@
     mode.offset <- mode.offset[ match( uniq.locs, in.locs ) ]
     nlocs <- length(uniq.locs)
     nstep <- nlocs
-    len.locs <- length(unique(locs))
+    len.locs <- length(unique(c( locs) ))
 
     nopt <- len.locs*3
     optmax <- 2
@@ -53,7 +53,7 @@
         stop("length(locs.prior)!=length(unique(locs))")
     if (length(nreps)>1) stop("nreps should be an integer")
     optpri <- c(locs.prior)%o%c(combo.prior)
-    optvars <- matrix(c(rbind(unique(locs)*2-2,-1),rbind(unique(locs)*2-1,-1),
+    optvars <- matrix(c(rbind(unique(c(locs))*2-2,-1),rbind(unique(c(locs))*2-1,-1),
                         locs*2-rep(2:1,nopt/3)),nrow=2)
 
     optcur <- uniq.locs + mode.offset*len.locs

R/twohkf2.s

@@ -26,7 +26,7 @@
     if (missing(locs))
         locs <- rep(seq(ncol(varcov$var.x)/2), rep(2, ncol(varcov$var.x)/2))
 
-    uniq.locs <- unique(locs)
+    uniq.locs <- unique(c( locs ))
     nlocs <- length(uniq.locs)
     nin <- 2
     nopt <-  nlocs*3

R/version.bqtl.R

@@ -1 +1 @@
-version.bqtl<-"Version:1.0-9"
+version.bqtl<-"Version:1.0-10"