version 1.0-12

CHANGES

@@ -91,3 +91,6 @@ Version: 1.0-11
 add src/Makevars for BLAS usage
 
 ----------------------------------------
+
+Version: 1.0-12
+R_Ext/Mathlib.h is deprecated - change to Rmath.h

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bqtl
-Version: 1.0-11
-Date: 2003-25-03
+Version: 1.0-12
+Date: 2003-16-09
 Title: Bayesian QTL mapping toolkit 
 Author: Charles C. Berry <cberry@ucsd.edu>
 Maintainer: Charles C. Berry <cberry@ucsd.edu>

R/version.bqtl.R

@@ -1 +1 @@
-version.bqtl<-"Version:1.0-11"
+version.bqtl<-"Version:1.0-12"

man/bqtl-internal.Rd

@@ -10,7 +10,7 @@
  Internal bqtl functions and objects
 }
 \usage{
-x\%equiv\%y
+"%equiv%"( x, y )
 map.dx(lambda, theta, min.lambda)
 rhs.bqtl(reg.terms, ana.obj, bqtl.specials, local.covar, scope, 
     expand.specials = NULL, method, ...) 

man/little.bc.markers.Rd

@@ -21,18 +21,55 @@ a factor with levels
 \code{AA} 
 \code{Aa} 
 }
-\dots
-\item{m.49}{
-a factor with levels
-\code{AA} 
-\code{Aa} 
-}
-\item{m.50}{
-a factor with levels
-\code{AA} 
-\code{Aa} 
-}
-}
+\item{m.3}{ ditto }
+ \item{m.4}{ ditto }
+ \item{m.5}{ ditto }
+ \item{m.6}{ ditto }
+ \item{m.7}{ ditto }
+ \item{m.8}{ ditto }
+ \item{m.9}{ ditto }
+ \item{m.10}{ ditto }
+ \item{m.11}{ ditto }
+ \item{m.12}{ ditto }
+ \item{m.13}{ ditto }
+ \item{m.14}{ ditto }
+ \item{m.15}{ ditto }
+ \item{m.16}{ ditto }
+ \item{m.17}{ ditto }
+ \item{m.18}{ ditto }
+ \item{m.19}{ ditto }
+ \item{m.20}{ ditto }
+ \item{m.21}{ ditto }
+ \item{m.22}{ ditto }
+ \item{m.23}{ ditto }
+ \item{m.24}{ ditto }
+ \item{m.25}{ ditto }
+ \item{m.26}{ ditto }
+ \item{m.27}{ ditto }
+ \item{m.28}{ ditto }
+ \item{m.29}{ ditto }
+ \item{m.30}{ ditto }
+ \item{m.31}{ ditto }
+ \item{m.32}{ ditto }
+ \item{m.33}{ ditto }
+ \item{m.34}{ ditto }
+ \item{m.35}{ ditto }
+ \item{m.36}{ ditto }
+ \item{m.37}{ ditto }
+ \item{m.38}{ ditto }
+ \item{m.39}{ ditto }
+ \item{m.40}{ ditto }
+ \item{m.41}{ ditto }
+ \item{m.42}{ ditto }
+ \item{m.43}{ ditto }
+ \item{m.44}{ ditto }
+ \item{m.45}{ ditto }
+ \item{m.46}{ ditto }
+ \item{m.47}{ ditto }
+ \item{m.48}{ ditto }
+ \item{m.49}{ ditto }
+ \item{m.50}{ ditto }
+\item{row.names}{row names}}
 }
 
 \keyword{datasets}

man/little.dx.Rd

@@ -1,19 +1,19 @@
-\name{little.dx}
-\alias{little.dx}
+\name{little.map.dx}
+\alias{little.map.dx}
 \non_function{}
 \title{ Marker Map Description for Simulated Data }
 \description{
-The \code{little.dx} data frame has 50 rows and 2 columns that specify 
+The \code{little.map.dx} data frame has 50 rows and 2 columns that specify 
  the map locations of a simulated set of markers }
 
 \format{
 This data frame contains the following columns:
 \describe{
-\item{marker.name}{
+\item{marker.names}{
 a factor with levels
 \code{m.1} \dots \code{m.50} 
 }
-\item{dx}{
+\item{cM}{
 a numeric vector of map locations in centimorgans
 }
 }

man/little.f2.markers.Rd

@@ -22,18 +22,59 @@ a factor with levels
 \code{Aa}
 \code{aa}  
 }
-\dots
+\item{m.3}{ ditto }
+ \item{m.4}{ ditto }
+ \item{m.5}{ ditto }
+ \item{m.6}{ ditto }
+ \item{m.7}{ ditto }
+ \item{m.8}{ ditto }
+ \item{m.9}{ ditto }
+ \item{m.10}{ ditto }
+ \item{m.11}{ ditto }
+ \item{m.12}{ ditto }
+ \item{m.13}{ ditto }
+ \item{m.14}{ ditto }
+ \item{m.15}{ ditto }
+ \item{m.16}{ ditto }
+ \item{m.17}{ ditto }
+ \item{m.18}{ ditto }
+ \item{m.19}{ ditto }
+ \item{m.20}{ ditto }
+ \item{m.21}{ ditto }
+ \item{m.22}{ ditto }
+ \item{m.23}{ ditto }
+ \item{m.24}{ ditto }
 \item{m.25}{
 a factor with levels
 \code{A-} 
 \code{aa} 
 }
-\dots
+ \item{m.26}{ ditto }
+ \item{m.27}{ ditto }
+ \item{m.28}{ ditto }
+ \item{m.29}{ ditto }
+ \item{m.30}{ ditto }
+ \item{m.31}{ ditto }
+ \item{m.32}{ ditto }
+ \item{m.33}{ ditto }
+ \item{m.34}{ ditto }
+ \item{m.35}{ ditto }
+ \item{m.36}{ ditto }
+ \item{m.37}{ ditto }
+ \item{m.38}{ ditto }
+ \item{m.39}{ ditto }
+ \item{m.40}{ ditto }
+ \item{m.41}{ ditto }
+ \item{m.42}{ ditto }
+ \item{m.43}{ ditto }
+ \item{m.44}{ ditto }
 \item{m.45}{
 a factor with levels
 \code{a-} 
 }
-\dots
+\item{m.46}{ ditto }
+ \item{m.47}{ ditto }
+ \item{m.48}{ ditto }
 \item{m.49}{
 a factor with levels
 \code{AA} 
@@ -46,7 +87,7 @@ a factor with levels
 \code{Aa} 
 \code{aa}
 }
-}
+\item{row.names}{row names}}
 }
 
 \keyword{datasets}

man/little.map.frame.Rd

@@ -1,11 +1,10 @@
 \name{little.map.frame}
-\alias{little.map.dx}
 \alias{little.map.frame}
 \non_function{}
 \title{ Package of Simulated Marker Map Information }
 \description{
 The \code{little.map.frame} data frame has 50 rows and 9 columns that
-describe the marker map of \code{\link{little.dx}} in the format
+describe the marker map of \code{\link{little.map.dx}} in the format
 produced by \code{\link{make.map.frame}. \code{little.map.dx} has the
   minimal data needed to construct this.}
 }
@@ -19,7 +18,7 @@ a factor with levels
 \dots
 \code{m.50} 
 }
-\item{dx}{
+\item{cM}{
 a vector of locations
 }
 \item{prior}{

man/little.mf.5.Rd

@@ -13,7 +13,7 @@ This data frame contains the following columns:
 The marker names taken from \code{little.map.frame} and those created to
 fill virtual markers in between actual markers.
 }
-\item{dx}{
+\item{cM}{
 a vector of locations
 }
 \item{prior}{

man/locus.Rd

@@ -13,8 +13,7 @@ function.  It is used on the right hand side of a formula in the
 \synopsis{
 locus(x, ..., scope, method, chromo, cM, ana.obj)}
 \usage{
-locus(x)
-locus(chromo,cM)
+locus(x, ..., scope, method, chromo, cM, ana.obj)
 add(x)
 dom(x)
 }

man/map.index.Rd

@@ -10,20 +10,19 @@ its row (their rows). \code{map.index} performs a lookup in a specific
 two) map distance(s).
 }
 \usage{
-map.index(x, ...)
+map.index(x, ... )
 }
 %- maybe also `usage' for other objects documented here.
 \arguments{
   \item{x }{A \code{map.frame} or \code{analysis.object}}
   \item{...}{ For methods that look up a location in a \code{map.frame}
-    the following named arguments may be used}
-  \item{chromo }{A chromosome number or 2 ordered numbers }
-  \item{cM }{(Optional) map distance or two. If the same chromosome
+    the following named arguments may be used:
+  \code{chromo }{A chromosome number or 2 ordered numbers }
+  \code{cM }{(Optional) map distance or two. If the same chromosome
     number is used twice in \code{chromo}, \code{cM} must be
     ordered. If \code{cM} is omitted, all loci on the chromosome will
   be included.}
-
-}
+}}
 \details{
   It is often convenient to refer to genetic loci or regions by the
   numerical index(es) in a \code{map.frame}. \code{map.index} allows

man/map.location.Rd

@@ -10,24 +10,24 @@
  Report the chromosome number and location of loci in a genetic map.
 }
 \usage{
-map.location(x,\dots)
+map.location(x,\dots )
 map.loc(x, \dots )
 }
 
 \arguments{
   \item{x}{A object of class \code{map.frame},\code{analysis.object},
 \code{bqtl}, or \code{bqtl.list}}
-  \item{\dots}{Other arguments usage depend on the class of \code{x} }
-  \item{y}{A vector of row numbers or \code{map.names} specifying which
+  \item{\dots}{Other arguments usage depend on the class of \code{x} :
+  \code{y}{A vector of row numbers or \code{map.names} specifying which
     subset of the \code{map.frame} of \code{x} is to be returned}
-  \item{chromo}{A vector of chromosome numbers}
-  \item{cM }{(Optional) map distance vector. If the same chromosome
+  \code{chromo}{A vector of chromosome numbers}
+  \code{cM }{(Optional) map distance vector. If the same chromosome
     number is used twice in \code{chromo}, \code{cM} must be
     ordered. If \code{cM} is omitted, all loci on each chromosome listed
     in \code{chromo} will be included.}
 
-  \item{map.names}{A vector of \code{map.names}}
-}
+  \code{map.names}{A vector of \code{map.names}}
+}}
 \details{ It is often helpful to refer to genentic loci by their
 locations. The methods of \code{map.location} (alias \code{map.loc})
 will extract the row index, chromosome number and location, and the name

man/plot.map.frame.Rd

@@ -8,7 +8,7 @@
   of the sort created by \code{\link{make.map.frame}}
 }
 \usage{
-\method{plot}{map.frame}(x, ...)
+\method{plot}{map.frame}(x, y, ...)
 }
 \synopsis{
 plot.map.frame(x, y, fun, type, include.rug, rug.lwd,
@@ -22,16 +22,17 @@ plot.map.frame(x, y, fun, type, include.rug, rug.lwd,
    will be drawn in a single frame representing the chromosomes as
    horizontal bars and giving tic marks to show the locations markers
    and virtual markers (if any).  }
- \item{fun}{ A plotting function to be used \emph{after} the plot axes and
+ \item{\dots}{ more args:
+ \code{fun}{ A plotting function to be used \emph{after} the plot axes and
    labels have been drawn.  The current default \code{if (y.type ==
      "matrix") matlines else lines} usually is good enough.  But a
    fancier function could be used for a fancier plot. }
- \item{type}{ \code{"l"} for lines, "p" for points, et cetera.  see \code{\link{par}} }
- \item{include.rug}{ if \code{TRUE} place a tick on the x-axis at each marker location }
- \item{title.string}{(optional) label to prepend to each title }
- \item{ylab}{plot label for y-axis, see \code{\link{par}}  }
- \item{xlab}{plot label for x-axis, see \code{\link{par}}  }
- \item{\dots}{(optional args to pass to \code{fun}  }
+ \code{type}{ \code{"l"} for lines, "p" for points, et cetera.  see \code{\link{par}} }
+ \code{include.rug}{ if \code{TRUE} place a tick on the x-axis at each marker location }
+ \code{title.string}{(optional) label to prepend to each title }
+ \code{ylab}{plot label for y-axis, see \code{\link{par}}  }
+ \code{xlab}{plot label for x-axis, see \code{\link{par}}  }
+  }
 }
 \details{
   This function enables drawing graphs that depend on chromosome and

man/predict.linear.bayes.Rd

@@ -10,7 +10,7 @@
  the 'intercept' is lost; see `Details' below.
 }
 \usage{
-\method{residuals}{linear.bayes}(object)
+\method{residuals}{linear.bayes}(object, newdata, return.resids})
 
 \method{predict}{linear.bayes}(object)
 

man/twohk.Rd

@@ -17,19 +17,19 @@ twohk(varcov, ana.obj, ...)
  \item{ana.obj}{An \code{analysis.object} --- see \code{make.analysis.obj} }
  \item{\dots}{Additional arguments override the default choices of
     candidate loci (\code{locs}), prior for locus (\code{locs.prior}),
-    or method specified by \code{ana.obj}. See the next arguments.}
-\item{locs}{A vector indexing the loci to use.}
-  \item{locs.prior}{ 
+    or method specified by \code{ana.obj}:
+\code{locs}{A vector indexing the loci to use.}
+  \code{locs.prior}{ 
     The prior mass to  associate with each locus. Typically, these sum
     to one, but sometimes they might each be set to one (as in computing
     lod scores). }
-\item{combo.prior}{Only valid for \code{ana.obj$method=="F2"}. 
+\code{combo.prior}{Only valid for \code{ana.obj$method=="F2"}. 
     The prior probability for each term or combination of terms for the
     phenotypic effect at a locus. Typically, there will be three of
     these - one for the 'additive' term (linear in number of alleles
     from one parent strain), the 'dominance' term (quadratic in allele
     number), or both terms. The default sets them all to 1/3.}
-}
+}}
 \details{
   The marginal posterior (integrating over regression parameters and
   dispersion) is calculated for each one and two gene model under the

src/condreg.c

@@ -28,7 +28,7 @@
 #include "lapadj.h"
 #ifdef USING_R
 #include <R_ext/Applic.h>
-#include <R_ext/Mathlib.h>
+#include <Rmath.h>
 #else
 int F77_SYMBOL(dqrsl1)();
 int F77_SYMBOL(dqr)();

src/hkreg.c

@@ -6,7 +6,7 @@
 #include "lapadj.h"
 #ifdef USING_R
 #include <R_ext/Applic.h>
-#include <R_ext/Mathlib.h>
+#include <Rmath.h>
 #define lgamma(x) lgammafn(x)
 #else
 int F77_SYMBOL(dqrsl1)();