[adegenet-commits] r228 - in pkg: R man

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

Author: jombart
Date: 2009-01-24 20:47:14 +0100 (Sat, 24 Jan 2009)
New Revision: 228

Modified:
   pkg/R/classes.R
   pkg/R/import.R
   pkg/man/as.genind.Rd
   pkg/man/as.genpop.Rd
   pkg/man/df2genind.Rd
Log:
PA -> domin


Modified: pkg/R/classes.R
===================================================================
--- pkg/R/classes.R	2009-01-24 19:36:43 UTC (rev 227)
+++ pkg/R/classes.R	2009-01-24 19:47:14 UTC (rev 228)
@@ -200,7 +200,7 @@
     }
 
     ## check type of marker
-    if(!object at type %in% c("codom","PA") ){
+    if(!object at type %in% c("codom","domin") ){
         cat("\nunknowon type of marker\n")
         return(FALSE)
     }
@@ -278,7 +278,7 @@
 # Function genind
 ##################
 ## constructor of a genind object
-genind <- function(tab,pop=NULL,prevcall=NULL,ploidy=2,type=c("codom","PA")){
+genind <- function(tab,pop=NULL,prevcall=NULL,ploidy=2,type=c("codom","domin")){
 
   X <- as.matrix(tab)
   if(is.null(colnames(X))) stop("tab columns have no name.")
@@ -394,7 +394,7 @@
 ##################
 # Function genpop
 ##################
-genpop <- function(tab,prevcall=NULL,ploidy=as.integer(2),type=c("codom","PA")){
+genpop <- function(tab,prevcall=NULL,ploidy=as.integer(2),type=c("codom","domin")){
 
   X <- as.matrix(tab)
   if(is.null(colnames(X))) stop("tab columns have no name.")

Modified: pkg/R/import.R
===================================================================
--- pkg/R/import.R	2009-01-24 19:36:43 UTC (rev 227)
+++ pkg/R/import.R	2009-01-24 19:47:14 UTC (rev 228)
@@ -40,7 +40,7 @@
 #####################
 # Function df2genind
 #####################
-df2genind <- function(X, sep=NULL, ncode=NULL, ind.names=NULL, loc.names=NULL, pop=NULL, missing=NA, ploidy=2, type=c("codom","PA")){
+df2genind <- function(X, sep=NULL, ncode=NULL, ind.names=NULL, loc.names=NULL, pop=NULL, missing=NA, ploidy=2, type=c("codom","domin")){
 
     if(is.data.frame(X)) X <- as.matrix(X)
     if (!inherits(X, "matrix")) stop ("X is not a matrix")

Modified: pkg/man/as.genind.Rd
===================================================================
--- pkg/man/as.genind.Rd	2009-01-24 19:36:43 UTC (rev 227)
+++ pkg/man/as.genind.Rd	2009-01-24 19:47:14 UTC (rev 228)
@@ -20,8 +20,8 @@
 }
 
 \usage{
-genind(tab,pop=NULL,prevcall=NULL, ploidy=2, type="codom")
-as.genind(tab,pop=NULL,prevcall=NULL, ploidy=2, type="codom")
+genind(tab,pop=NULL,prevcall=NULL, ploidy=2, type=c("codom","PA"))
+as.genind(tab,pop=NULL,prevcall=NULL, ploidy=2, type=c("codom","PA"))
 is.genind(x)
 }
 
@@ -31,7 +31,8 @@
     Its content depends on \code{type} (type of marker).\cr
     - 'codom': table contains allele frequencies (numeric values summing
   to 1).\cr
-    - 'PA': table contains presence/absences (0,1).
+    - 'domin': table contains binary values, which indicate
+  presence(1)/absence(0) of alleles.\cr
   }
   \item{pop}{a factor giving the population of each genotype in 'x'}
   \item{prevcall}{call of an object}

Modified: pkg/man/as.genpop.Rd
===================================================================
--- pkg/man/as.genpop.Rd	2009-01-24 19:36:43 UTC (rev 227)
+++ pkg/man/as.genpop.Rd	2009-01-24 19:47:14 UTC (rev 228)
@@ -19,8 +19,8 @@
   'class ? genpop'.
 }
 \usage{
-genpop(tab,prevcall=NULL, ploidy=as.integer(2), type="codom")
-as.genpop(tab,prevcall=NULL)
+genpop(tab,prevcall=NULL, ploidy=as.integer(2), type=c("codom","domin"))
+as.genpop(tab, type=c("codom","domin"), prevcall=NULL)
 is.genpop(x)
 }
 \arguments{
@@ -31,7 +31,7 @@
       the genotypes. Beware: 2 is not an integer, but as.integer(2) is.}
     \item{\code{type}:}{ a character string indicating the type of
       marker: 'codom' stands for 'codominant' (e.g. microstallites,
-      allozymes); 'PA' stands for 'presence/absence' (e.g. AFLP).}
+      allozymes); 'domin' stands for 'dominant' (e.g. AFLP, RAPD).}
     \item{x}{an object}
   }
 \value{

Modified: pkg/man/df2genind.Rd
===================================================================
--- pkg/man/df2genind.Rd	2009-01-24 19:36:43 UTC (rev 227)
+++ pkg/man/df2genind.Rd	2009-01-24 19:47:14 UTC (rev 228)
@@ -22,7 +22,7 @@
  }
 \usage{
 df2genind(X, sep=NULL, ncode=NULL, ind.names=NULL, loc.names=NULL,
- pop=NULL, missing=NA, ploidy=2, type=c("codom","PA"))
+ pop=NULL, missing=NA, ploidy=2, type=c("codom","domin"))
 genind2df(x,pop=NULL, sep="", usepop=TRUE)
 }
 \arguments{
@@ -37,9 +37,9 @@
   \item{pop}{an optional factor giving the population of each individual.}
   \item{missing}{can be NA, 0 or "mean". See details section.}
   \item{ploidy}{an integer indicating the degree of ploidy of the genotypes.}
- \item{\code{type}:}{ a character string indicating the type of
-      marker: 'codom' (default) stands for 'codominant' (e.g. microstallites,
-      allozymes); 'PA' stands for 'presence/absence' (e.g. SNP, AFLP).}
+  \item{\code{type}:}{ a character string indicating the type of
+      marker: 'codom' stands for 'codominant' (e.g. microstallites,
+      allozymes); 'domin' stands for 'dominant' (e.g. AFLP, RAPD).}
   \item{x}{a \linkS4class{genind} object}
   \item{usepop}{a logical stating whether the population (argument \code{pop}
     or \code{x at pop} should be used (TRUE, default) or not (FALSE).}