[adegenet-commits] r259 - in pkg: R man

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

Author: jombart
Date: 2009-01-27 20:35:57 +0100 (Tue, 27 Jan 2009)
New Revision: 259

Modified:
   pkg/R/genind2genpop.R
   pkg/man/genind2genpop.Rd
Log:
genind2genpop can now proceed the other slot, and tapply it by pop (whatever action is requested).


Modified: pkg/R/genind2genpop.R
===================================================================
--- pkg/R/genind2genpop.R	2009-01-27 19:05:05 UTC (rev 258)
+++ pkg/R/genind2genpop.R	2009-01-27 19:35:57 UTC (rev 259)
@@ -1,7 +1,8 @@
 #########################
 # Function genind2genpop
 #########################
-genind2genpop <- function(x,pop=NULL,missing=c("NA","0","chi2"),quiet=FALSE){
+genind2genpop <- function(x,pop=NULL,missing=c("NA","0","chi2"),quiet=FALSE,
+                          proceed.other=FALSE, other.action=mean){
 
   if(!is.genind(x)) stop("x is not a valid genind object")
   checkType(x)
@@ -60,8 +61,29 @@
   prevcall <- match.call()
 
   res <- genpop(tab=tabcount, prevcall=prevcall, ploidy=x at ploidy, type=x at type)
+
+  ## handle @other here
   res at other <- x at other
+  if(proceed.other){
+      ## auxiliary function doing the job
+      f1 <- function(e){
+          N <- row(x at tab)
+          if(is.vector(e) & is.numeric(e) & length(e)==N){ # numeric vector
+              res <- tapply(e, pop, other.action)
+              return(res)
+          } else if(is.matrix(e) & is.numeric(e) & nrow(e)==N){ # numeric matrix
+              res <- apply(e, 2, function(vec) tapply(vec, pop, other.action))
+              return(res)
+          } else if(is.data.frame(e) & nrow(e)==N & all(sapply(e,is.numeric)) ){ # df of numeric vectors
+              res <- lapply(e, function(vec) tapply(vec, pop, other.action))
+              res <- data.frame(res)
+              return(res)
+          } else return(e)
+      } # end f1
 
+      res at other <- lapply(res at other, f1)
+  } # end if(proceed.other)
+
   if(missing != "NA"){
       res <- na.replace(res, method=missing, quiet=quiet)
   }

Modified: pkg/man/genind2genpop.Rd
===================================================================
--- pkg/man/genind2genpop.Rd	2009-01-27 19:05:05 UTC (rev 258)
+++ pkg/man/genind2genpop.Rd	2009-01-27 19:35:57 UTC (rev 259)
@@ -5,7 +5,8 @@
 \description{The function \code{genind2genpop} converts genotypes data
   (genind) into alleles counts per population (genpop).}
 \usage{
-genind2genpop(x,pop=NULL,missing=c("NA","0","chi2"),quiet=FALSE)
+genind2genpop(x,pop=NULL,missing=c("NA","0","chi2"),quiet=FALSE,
+              proceed.other=FALSE, other.action=mean)
 }
 \arguments{
   \item{x}{an object of class \code{genind}.}
@@ -15,9 +16,14 @@
   \item{missing}{can be "NA", "0", or "chi2". See details for more information.}
   \item{quiet}{logical stating whether a conversion message must be
     printed (TRUE,default) or not (FALSE).}
-    
+  \item{proceed.other}{a logical indicating whether the \code{@other}
+    slot should be proceeded (see details).}
+  \item{other.action}{a function to be used when proceeding the
+    \code{@other} slot. By default, 'mean' is used.}
 }
-\details{The values of the 'missing' argument in \code{genind2genpop}
+\details{
+  === 'missing' argument ===\cr
+  The values of the 'missing' argument in \code{genind2genpop}
   have the following effects:\cr
   - "NA": if all genotypes of a population for a given allele are
   missing, count value will be NA\cr
@@ -28,7 +34,17 @@
   - "chi2": if all genotypes of a population for a given allele are
   missing, count value will be that of a theoretical count in of a
   Chi-squared test. This is obtained by the product of the margins
-  sums divided by the total number of alleles.
+  sums divided by the total number of alleles.\cr
+  
+  === proceeding the \code{@other} slot ===\cr
+  Essentially, \code{genind2genpop} is about aggregating data per
+  population. The function can do the same for all numeric items in the
+  \code{@other} slot provided they have the same length (for vectors) or
+  the same number of rows (matrix-like objects) as the number of
+  genotypes. When the case is encountered and if \code{proceed.other} is
+  TRUE, then these objects are processed using the function defined in
+  \code{other.action} per population. For instance, spatial coordinates
+  of genotypes would be averaged to obtain population coordinates.
 }
 \value{
   A genpop object. The component @other in 'x' is passed to the created