small updates

PhyloSim/R/localPlots.R

@@ -9,38 +9,54 @@
 #' @export
 localPlots <- function(simu,which.result=NULL,size, n, community=F){
 
-  if(n ==1){n <- 2 
-            single = T}else{single=F}
+  if(n ==1){
+    n <- 2 
+    single = T
+  }else{
+    single=F
+  }
 
   #if("PhyloSim" %in% class(simu)==T){
     if (is.null(which.result)) which.result = length(simu$Output) 
-    simu <- simu$Output[[which.result]]#}
+    simu <- simu$Output[[which.result]]
+  #}
 
   matrix <- simu$specMat
+  env <- simu$envMat
+
 
   edge <- round(sqrt(size))-1
   subPlots <- list()
+  envPlots <- list()
   communityTable <- data.frame("species"= numeric())
+
   for(i in 1:n)
   {                                                                          
     x = sample(x=1:length(matrix[1,]),size=1)
     y = sample(x=1:length(matrix[,1]),size=1)
 
     # Check for boundary issues and implemant warped bounaries if necessary
-    if(x+edge > length(matrix[1,]) && y+edge <= length(matrix[,1]))
-      subPlot <- matrix[c(seq(x,length(matrix[1,])),
-                          seq(1,(edge-length(seq(x,length(matrix[1,])))))),seq(y,y+edge)-1]
+    if(x+edge > length(matrix[1,]) && y+edge <= length(matrix[,1])){
+      rsel = c(seq(x,length(matrix[1,])), seq(1,(edge-length(seq(x,length(matrix[1,]))))))
+      csel = seq(y,y+edge)-1
+    }
+    else if(x+edge <= length(matrix[1,]) && y+edge > length(matrix[,1])){
+      rsel = seq(x,x+edge)-1
+      csel = c(seq(y,length(matrix[,1])),seq(1,(edge-length(seq(y,length(matrix[,1]))))))
+    }
+    else if(x+edge > length(matrix[1,]) && y+edge > length(matrix[,1])){
+      rsel = c(seq(x,length(matrix[1,])), seq(1,(edge-length(seq(x,length(matrix[1,]))))))
+      csel = c(seq(y,length(matrix[,1])),seq(1,(edge-length(seq(y,length(matrix[,1]))))))
+    }
+    else{
+      rsel = seq(x,x+edge)
+      csel = seq(y,y+edge)
+    }
 
-    else if(x+edge <= length(matrix[1,]) && y+edge > length(matrix[,1]))
-      subPlot <- matrix[seq(x,x+edge)-1, c(seq(y,length(matrix[,1])),seq(1,(edge-length(seq(y,length(matrix[,1]))))))] 
 
-    else if(x+edge > length(matrix[1,]) && y+edge > length(matrix[,1]))
-      subPlot <- matrix[c(seq(x,length(matrix[1,])), seq(1,(edge-length(seq(x,length(matrix[1,])))))), 
-                        c(seq(y,length(matrix[,1])),seq(1,(edge-length(seq(y,length(matrix[,1]))))))]    
-    else
-      subPlot <- matrix[seq(x,x+edge),seq(y,y+edge)]
+    subPlots[[i]] <- matrix[rsel, csel]
+    envPlots[[i]] <- env[rsel, csel]    
 
-    subPlots[[i]] <- subPlot
     if(community == T)
     {
       dataTable <- as.data.frame(table(subPlot))
@@ -66,6 +82,6 @@ localPlots <- function(simu,which.result=NULL,size, n, community=F){
   }
 
   if(single ==T){communityTable <- communityTable[-2,]}
-  return(list(subPlots=subPlots, communityTable=communityTable))
+  return(list(subPlots=subPlots, communityTable=communityTable, envPlots=envPlots))
 
   }

PhyloSim/examples/SAC/SAC.Rmd

@@ -0,0 +1,29 @@
+---
+title: "U"
+author: "Florian Hartig"
+date: "14 Jan 2016"
+output: html_document
+---
+
+```{r}
+
+
+library(PhyloSim)
+
+par <- createCompletePar(x = 50, y = 50, dispersal = 1, runs = 5000, density = 0, environment = 0.5, specRate = 1)
+
+system.time(simu <- runSimulation(par))
+
+plotSpatialPhylo(simu, plot = "both")
+
+plots <- localPlots(simu, size = 25, n = 100)
+
+
+library(fields)
+image.plot(simu$Output[[1]]$envMat)
+simu$Output[[1]]$specMat
+
+
+
+```
+

PhyloSim/vignettes/PhyloSimManual.Rnw

@@ -80,8 +80,7 @@ Tutorial for the PhyloSim package. Comments and contact: \href{https://florianha
 library(devtools)
 library(Rcpp)
 
-install_github("biometry/phylosim", subdir = "PhyloSim", auth_token ="fb17360869e0bb3518677936611776687b48e17a", dependencies = TRUE,
-build_vignettes = TRUE)
+install_url("https://dl.dropboxusercontent.com/s/zkdof0b5b523qxt/PhyloSim_0.3.tar.gz")
 
 ?PhyloSim
 browseVignettes("PhyloSim")

README.md

@@ -10,9 +10,9 @@ You can install directly from gh, using the 'devtools' package:
 
 ```{r}
 # install.packages(c("devtools","Rcpp")) # I case you don't have them installed
-library(devtools)
-library(Rcpp)
 
+library(Rcpp)
+library(devtools)
 install_url("https://dl.dropboxusercontent.com/s/zkdof0b5b523qxt/PhyloSim_0.3.tar.gz")
 
 ?PhyloSim

copyDropbox.command

@@ -1,5 +1,7 @@
 rsync -avz --delete /Users/Florian/Home/Projekte/Papers_in_Progress/15-PhylogeneticRpackage/phylosim/PhyloSim/vignettes/PhyloSimManual.pdf /Users/Florian/Dropbox/Projects/PhyloSim/Deploy
 
+rsync -avz --delete /Users/Florian/Home/Projekte/Papers_in_Progress/15-PhylogeneticRpackage/phylosim/PhyloSim_0.3.tar.gz /Users/Florian/Dropbox/Projects/PhyloSim/Deploy
+