[adegenet-commits] r756 - in pkg: R man

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2011-01-05 18:54:33 +0100 (Wed, 05 Jan 2011)
New Revision: 756

Modified:
   pkg/R/SNPbin.R
   pkg/man/SNPbin.Rd
   pkg/man/as.genind.Rd
   pkg/man/genlight.Rd
   pkg/man/inbreeding.ml.Rd
   pkg/man/virClasses.Rd
Log:
Various fixes to the doc, the package now passes the check


Modified: pkg/R/SNPbin.R
===================================================================
--- pkg/R/SNPbin.R	2011-01-05 16:55:18 UTC (rev 755)
+++ pkg/R/SNPbin.R	2011-01-05 17:54:33 UTC (rev 756)
@@ -570,6 +570,9 @@
 })
 
 
+## KLUDGE - needed for as.matrix.genlight to be dispatched correctly (R-2.12.1)
+setGeneric("as.matrix")
+
 as.matrix.genlight <- function(x, ...){
     return(as(x, "matrix"))
 }

Modified: pkg/man/SNPbin.Rd
===================================================================
--- pkg/man/SNPbin.Rd	2011-01-05 16:55:18 UTC (rev 755)
+++ pkg/man/SNPbin.Rd	2011-01-05 17:54:33 UTC (rev 756)
@@ -12,7 +12,8 @@
 \alias{names,SNPbin-method}
 \alias{ploidy,SNPbin-method}
 \alias{as,SNPbin,integer-method}
-\alias{as.integer,SNPbin-method}
+\alias{coerce,SNPbin,integer-method}
+\alias{as.integer.SNPbin}
 % \alias{,SNPbin-method}
 % \alias{,SNPbin-method}
 % \alias{,SNPbin-method}

Modified: pkg/man/as.genind.Rd
===================================================================
--- pkg/man/as.genind.Rd	2011-01-05 16:55:18 UTC (rev 755)
+++ pkg/man/as.genind.Rd	2011-01-05 17:54:33 UTC (rev 756)
@@ -56,7 +56,6 @@
 
   - \linkS4class{genlight} for an efficient storage of binary SNPs genotypes\cr
 }
-}
 \examples{
 data(nancycats)
 nancycats at loc.names

Modified: pkg/man/genlight.Rd
===================================================================
--- pkg/man/genlight.Rd	2011-01-05 16:55:18 UTC (rev 755)
+++ pkg/man/genlight.Rd	2011-01-05 17:54:33 UTC (rev 756)
@@ -15,11 +15,14 @@
 \alias{locNames,genlight-method}
 \alias{indNames,genlight-method}
 \alias{as,genlight,matrix-method}
-\alias{as.matrix,genlight-method}
+\alias{coerce,genlight,matrix-method}
+\alias{as.matrix.genlight}
 \alias{as,genlight,data.frame-method}
-\alias{as.data.frame,genlight-method}
+\alias{coerce,genlight,data.frame-method}
+\alias{as.data.frame.genlight}
 \alias{as,genlight,list-method}
-\alias{as.list,genlight-method}
+\alias{coerce,genlight,list-method}
+\alias{as.list.genlight}
 % \alias{,genlight-method}
 % \alias{,genlight-method}
 % \alias{,genlight-method}
@@ -170,7 +173,7 @@
 names(dat) <- paste("indiv", 1:length(dat))
 print(object.size(dat), unit="aut") # size of the original data
 
-x <- new("genlight", dat) # conversion + time taken
+x <- new("genlight", dat) # conversion
 x
 print(object.size(x), unit="au") # size of the genlight object
 object.size(dat)/object.size(x) # conversion efficiency

Modified: pkg/man/inbreeding.ml.Rd
===================================================================
--- pkg/man/inbreeding.ml.Rd	2011-01-05 16:55:18 UTC (rev 755)
+++ pkg/man/inbreeding.ml.Rd	2011-01-05 17:54:33 UTC (rev 756)
@@ -10,7 +10,7 @@
   individuals of a \linkS4class{genind} object.
 }
 \usage{
-inbreeding(x, pop = NULL, truenames = TRUE, res.type = c("sample", "function"), N = 200, M = N * 10)
+inbreeding.ml(x, pop = NULL, truenames = TRUE, res.type = c("sample", "function"), N = 200, M = N * 10)
 }
 \arguments{
   \item{x}{an object of class \linkS4class{genind}.}

Modified: pkg/man/virClasses.Rd
===================================================================
--- pkg/man/virClasses.Rd	2011-01-05 16:55:18 UTC (rev 755)
+++ pkg/man/virClasses.Rd	2011-01-05 17:54:33 UTC (rev 756)
@@ -8,6 +8,7 @@
 \alias{factorOrNULL-class}
 \alias{intOrNum-class}
 \alias{listOrNULL-class}
+\alias{intOrNULL-class}
 \title{Virtual classes for adegenet}
 \description{These virtual classes are only for internal use in adegenet}
 \section{Objects from the Class}{A virtual Class: No objects may be created from it.}