[adegenet-commits] r869 - pkg/R www

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

Author: jombart
Date: 2011-05-09 11:14:04 +0200 (Mon, 09 May 2011)
New Revision: 869

Modified:
   pkg/R/glPlot.R
   pkg/R/glSim.R
   www/literature.html
Log:
Added one ref.


Modified: pkg/R/glPlot.R
===================================================================
--- pkg/R/glPlot.R	2011-05-05 17:00:19 UTC (rev 868)
+++ pkg/R/glPlot.R	2011-05-09 09:14:04 UTC (rev 869)
@@ -20,7 +20,7 @@
           col=myCol, ...)
 
     ## add y axis
-    axis(side=2, at=nInd(x)-ylabpos, lab=ylabpos)
+    axis(side=2, at=nInd(x)-ylabpos+1, lab=ylabpos)
 
     ## add legend
     if(legend){

Modified: pkg/R/glSim.R
===================================================================
--- pkg/R/glSim.R	2011-05-05 17:00:19 UTC (rev 868)
+++ pkg/R/glSim.R	2011-05-09 09:14:04 UTC (rev 869)
@@ -3,7 +3,7 @@
 ## glSim
 ##########
 glSim <- function(n.ind, n.snp.nonstruc, n.snp.struc=0, grp.size=round(n.ind/2), ploidy=1, alpha=0,
-                  block.size=NULL){
+                  block.size=NULL, LD=FALSE){
 
     ## BASIC CHECKS ##
     if( any(c(n.ind, n.snp.nonstruc+n.snp.struc) <1)) stop("null numbers of individuals and/or SNPs requested")
@@ -29,26 +29,50 @@
 
 
     ## AUXIL FUNCTIONS ##
-    ## draw p snp for i indiv and convert into a genlight - no structure
-    f1 <- function(n,p){
-        temp <- sapply(1:p, function(i) rbinom(n, ploidy, runif(1)))
-        if(n==1) {temp <- matrix(temp,nrow=1)}
-        return(new("genlight", temp, ploidy=ploidy))
-    }
+    if(LD) { # LD - use mvrnorm
+        if(!require(MASS)) stop("MASS package is missing.")
+        QUANT <- qnorm(seq(0,1, le=ploidy+2), 0,1) # quantiles needed for continuous->discrete
 
-    ## draw p snp for i indiv and convert into a genlight - differences between 2 groups
-    if(n.snp.struc > 0){
-        f2 <- function(n,p){
-            probA <- runif(p, min=0, max=0.5-alpha)
-            probB <- 1-probA
-            tempA <- sapply(probA, function(i) rbinom(grpA.size, ploidy, i) )
-            if(grpA.size==1) {tempA <- matrix(tempA,nrow=1)}
-            tempB <- sapply(probB, function(i) rbinom(grpB.size, ploidy, i) )
-            if(grpB.size==1) {tempB <- matrix(tempB,nrow=1)}
-            return(new("genlight", rbind(tempA,tempB), ploidy=ploidy))
+        f1 <- function(n,p){
+            Sig <- matrix(runif(p^2), p, p)
+            Sig <- t(Sig) %*% Sig/2 # get the covariance matrix
+            temp <- mvrnorm(n, rep(0,p), Sig) # continuous data
+            temp <- matrix(as.integer(cut(temp, breaks=QUANT))-1, nrow=n, ncol=p)
+            return(new("genlight", temp, ploidy=ploidy))
         }
+
+        if(n.snp.struc > 0){
+            if(alpha>1e-10) warning("assymetry parameter alpha ignored when LD used")
+            f2 <- function(n,p){
+                temp <-rbind(f1(grpA.size,p), f1(grpB.size,p))
+                ploidy(temp) <- ploidy
+                return(temp)
+            }
+        }
+    } else { # no LD - use rbinom
+        ## draw p snp for i indiv and convert into a genlight - no structure
+        f1 <- function(n,p){
+            temp <- sapply(1:p, function(i) rbinom(n, ploidy, runif(1)))
+            if(n==1) {temp <- matrix(temp,nrow=1)}
+            return(new("genlight", temp, ploidy=ploidy))
+        }
+
+        ## draw p snp for i indiv and convert into a genlight - differences between 2 groups
+        if(n.snp.struc > 0){
+            f2 <- function(n,p){
+                probA <- runif(p, min=0, max=0.5-alpha)
+                probB <- 1-probA
+                tempA <- sapply(probA, function(i) rbinom(grpA.size, ploidy, i) )
+                if(grpA.size==1) {tempA <- matrix(tempA,nrow=1)}
+                tempB <- sapply(probB, function(i) rbinom(grpB.size, ploidy, i) )
+                if(grpB.size==1) {tempB <- matrix(tempB,nrow=1)}
+                return(new("genlight", rbind(tempA,tempB), ploidy=ploidy))
+            }
+        }
     }
 
+
+
     ## NON-STRUCTURED DATA ##
     ## generate data
     if(n.snp.nonstruc <= block.size){ # no need to use blocks

Modified: www/literature.html
===================================================================
--- www/literature.html	2011-05-05 17:00:19 UTC (rev 868)
+++ www/literature.html	2011-05-09 09:14:04 UTC (rev 869)
@@ -442,7 +442,13 @@
 <span class="citation_journal_title">PLoS Pathog</span><span
  class="citation_issue"> 7(4):</span>
 <span class="citation_start_page">e1001343.</span>
-<span class="citation_doi">doi:10.1371/journal.ppat.1001343</span> </p>
+<span class="citation_doi">doi:10.1371/journal.ppat.1001343<br>
+</span></p>
+<p class="intro">[37] CRISCIONE, C. D., VILAS, R., PANIAGUA, E. and
+BLOUIN, M. S. (2011), More than meets the eye: detecting cryptic
+microgeographic population structure in a parasite with a complex life
+cycle. Molecular Ecology, 20:&nbsp;no.
+doi:&nbsp;10.1111/j.1365-294X.2011.05113.x </p>
 <p class="intro"></p>
 <p class="auth_list"></p>
 <br>