[Picante-commits] r119 - branches/gsoc/R

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

Author: mrhelmus
Date: 2008-06-23 05:58:21 +0200 (Mon, 23 Jun 2008)
New Revision: 119

Added:
   branches/gsoc/R/significance.r
Log:
Working function to calculate p-values and structure for the psd metrics and the sppregs function

Added: branches/gsoc/R/significance.r
===================================================================
--- branches/gsoc/R/significance.r	                        (rev 0)
+++ branches/gsoc/R/significance.r	2008-06-23 03:58:21 UTC (rev 119)
@@ -0,0 +1,40 @@
+phylo.struct<-function(samp,tree,env=NULL,metric=c("psv","psr","pse","psc","sppregs"),null.model=c("frequency","richness","both"),runs=10,alpha=0.05,fam="binomial"){
+
+  metric<-match.arg(metric)
+  null.model<-match.arg(null.model)
+  if(metric=="sppregs")
+  {
+  nulls<-t(replicate(runs,sppregs(randomizeSample(samp,null.model=null.model),env,tree,fam=fam)$correlations))
+  obs<-sppregs(samp,env,tree,fam=fam)$correlations
+  mean.null<-apply(nulls,2,mean)
+  quantiles.null<-t(apply(nulls,2,quantile,probs=c(alpha/2,1-(alpha/2))))
+  
+  return(list(metric=metric,null.model=null.model,runs=runs,obs=obs,mean.null=mean.null
+                ,quantiles.null=quantiles.null,phylo.structure=NULL,nulls=nulls))
+
+
+  } else {
+
+    nulls<-switch(metric,
+                       psv = replicate(runs,mean(psv(randomizeSample(samp,null.model=null.model),tree,compute.var=FALSE)[,1])),
+                       psr = replicate(runs,mean(psr(randomizeSample(samp,null.model=null.model),tree,compute.var=FALSE)[,1])),
+                       pse = replicate(runs,mean(pse(randomizeSample(samp,null.model=null.model),tree)[,1])),
+                       psc = replicate(runs,mean(psc(randomizeSample(samp,null.model=null.model),tree)[,1])))
+    quantiles.null<-quantile(nulls,probs=c(alpha/2,1-(alpha/2)))
+    mean.null<-mean(nulls)
+    obs<-switch(metric,
+                       psv = mean(psv(samp,tree,compute.var=FALSE)[,1]),
+                       psr = mean(psr(samp,tree,compute.var=FALSE)[,1]),
+                       pse = mean(pse(samp,tree)[,1]),
+                       psc = mean(psc(samp,tree)[,1]))
+
+    if(mean.obs<=quantiles.null[1])
+    {phylo.structure="underdispersed"
+    } else {if(mean.obs>=quantiles.null[2]){
+    phylo.structure="overdispersed"} else {phylo.structure="random"}
+    }
+    
+    return(list(metric=metric,null.model=null.model,runs=runs,obs=obs,mean.null=mean.null
+                ,quantiles.null=quantiles.null,phylo.structure=phylo.structure,null.means=null.means))
+  }
+}