[Picante-commits] r120 - branches/gsoc/R

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

Author: mrhelmus
Date: 2008-06-25 06:26:29 +0200 (Wed, 25 Jun 2008)
New Revision: 120

Added:
   branches/gsoc/R/phylostruct.R
Removed:
   branches/gsoc/R/significance.r
Log:
Changed name from significance.r to phylostruct.R

Added: branches/gsoc/R/phylostruct.R
===================================================================
--- branches/gsoc/R/phylostruct.R	                        (rev 0)
+++ branches/gsoc/R/phylostruct.R	2008-06-25 04:26:29 UTC (rev 120)
@@ -0,0 +1,40 @@
+phylostruct<-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))
+  }
+}

Deleted: branches/gsoc/R/significance.r
===================================================================
--- branches/gsoc/R/significance.r	2008-06-23 03:58:21 UTC (rev 119)
+++ branches/gsoc/R/significance.r	2008-06-25 04:26:29 UTC (rev 120)
@@ -1,40 +0,0 @@
-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))
-  }
-}