Merge branch 'prunePhylogeny_switch' into 'master'

TheoreticalEcology · Oct 2, 2017 · 73ebaa3 · 73ebaa3
2 parents 3fae5e4 + ae6a44d
commit 73ebaa3
Show file tree

Hide file tree

Showing 16 changed files with 143 additions and 32 deletions.
diff --git a/.gitignore b/.gitignore
@@ -78,3 +78,7 @@ PhyloSim/inst/doc/PhyloSimManual.Rnw
 PhyloSim/inst/doc/PhyloSimManual.R
 
 PhyloSim/inst/doc/PhyloSimManual.pdf
+*.aux
+*.idea
+CMakeFiles
+cmake-build-debug
diff --git a/PhyloSim/DESCRIPTION b/PhyloSim/DESCRIPTION
@@ -27,7 +27,10 @@ Imports:
     adephylo,
     fields,
     shape,
-    foreach
+    foreach,
+    MESS,
+    apTreeshape,
+    PhyloMeasures
 Suggests:
     knitr
 LinkingTo: Rcpp

diff --git a/PhyloSim/R/RcppExports.R b/PhyloSim/R/RcppExports.R
@@ -3,7 +3,7 @@
 
 #' Core phylosim model
 #' @export
-callModel <- function(x, y, dispersal, runs, specRate, dens, env, neutral, mort, mortStrength, repro, dispersalCutoff, densityCutoff, seed, envStrength, compStrength, fission, redQueen, redQueenStrength, protracted, airmatR, soilmatR) {
-    .Call(`_PhyloSim_callModel`, x, y, dispersal, runs, specRate, dens, env, neutral, mort, mortStrength, repro, dispersalCutoff, densityCutoff, seed, envStrength, compStrength, fission, redQueen, redQueenStrength, protracted, airmatR, soilmatR)
+callModel <- function(x, y, dispersal, runs, specRate, dens, env, neutral, mort, mortStrength, repro, dispersalCutoff, densityCutoff, seed, envStrength, compStrength, fission, redQueen, redQueenStrength, protracted, airmatR, soilmatR, prunePhylogeny) {
+    .Call(`_PhyloSim_callModel`, x, y, dispersal, runs, specRate, dens, env, neutral, mort, mortStrength, repro, dispersalCutoff, densityCutoff, seed, envStrength, compStrength, fission, redQueen, redQueenStrength, protracted, airmatR, soilmatR, prunePhylogeny)
 }
 
diff --git a/PhyloSim/R/localPlots.R b/PhyloSim/R/localPlots.R
@@ -4,9 +4,9 @@
 #' @param which.result Integer, determines which result should be used. This argument is only usefull if your 'runs' argument in \code{\link{createCompletePar}} contains more than one element. By default, the last result is used.
 #' @param size A single value (or a vector) determining the edge length(s) of the generated subplots
 #' @param n The number of subplots to be generated
-#' @param community Logical, determining whether to generate a communiy table or not. default is FALSE
+#' @param community Logical, determining whether to generate a community table or not. default is FALSE
 #' @param plot Logical, determining whether the results should be shown graphically. Default is FALSE.
-#' @param nested Logical, determinig whether the subplots should be nested (see Details).
+#' @param nested Logical, determining whether the subplots should be nested (see Details).
 #' @return A list of subplots and (if coomunity = T) a community table with plots in rows and species in collumns
 #' @details If nested == TRUE the subplots are poduced in a sequential order. That means if your 'size' argument has the length 5 and your 'n' argument has the size 2 you will get ten subplots. The first five will be one group of nested plots and the last five the second group of nested plots.
 #' @example inst/examples/localPlots.R
@@ -29,11 +29,16 @@ localPlots <- function(simu, which.result=NULL,size, n, community = FALSE, plot
 
   matrix <- simu$specMat
   env <- simu$envMat
+  comp <- simu$compMat
+
   if(plot == T) plotmat <-matrix(0, ncol(matrix), nrow(matrix))
 
 
   subPlots <- list()
   envPlots <- list()
+  compPlots <- list()
+  positions <- list()
+
   communityTable <- data.frame("species"= numeric())
   count <-0
 
@@ -75,7 +80,13 @@ localPlots <- function(simu, which.result=NULL,size, n, community = FALSE, plot
 
 
       subPlots[[count]]  <- matrix[rsel, csel]
-      envPlots[[count]] <- env[rsel, csel]    
+      envPlots[[count]] <- env[rsel, csel]
+      compPlots[[count]] <- comp[rsel, csel]
+
+      # TODO: Is this the correct way to calculate the center of a rectangle in a matrix?
+      position <- c(rsel[1] + size[k] / 2 - 0.5, csel[1] + size[k] / 2 - 0.5)
+      positions[[count]] <- c(wrap_coordinates(position[1], limit=length(matrix[1,])),
+                              wrap_coordinates(position[2], limit=length(matrix[,1])))
 
 
       if(plot == T){
@@ -121,7 +132,9 @@ localPlots <- function(simu, which.result=NULL,size, n, community = FALSE, plot
   } 
 
   if(community == T){
-    return(list(subPlots=subPlots, communityTable=communityTable, envPlots=envPlots))
-  } else return(list(subPlots=subPlots, envPlots=envPlots))
+    return(list(subPlots=subPlots, communityTable=communityTable, envPlots=envPlots, compPlots=compPlots, positions=positions))
+  } else return(list(subPlots=subPlots, envPlots=envPlots, compPlots=compPlots, positions=positions))
 
-}
+}
+
+wrap_coordinates <- function(x, limit) if (x > limit) x - limit else if (x <= 0) limit + x else x
diff --git a/PhyloSim/R/parCreator.R b/PhyloSim/R/parCreator.R
@@ -20,6 +20,7 @@
 #' @param scenario String, further information you want to add to the parameter set in order to refer to a model run more conveniently. 
 #' @param calculateSummaries Logical, determining wheter summary statistics should be calculated
 #' @param convertToBinaryTree Logical, determining if the phylogeny should be converted into a binary tree
+#' @param prunePhylogeny Logical, determining whether the phylogeny should be prune by the internal pruning function
 #' @details If runs is a sequence of generations the intermediate and end results are saved in the output of \code{runSimulation}. \cr\cr If type = "Rneutral" the model will run entirely in R. This model is to be seen only for test and teaching purpose. To be used in practice it is far too slow. Also the output is reduced. Only the species landscape and the parameter settings will be displayed in the output.
 #' @return A List with parameters
 #' @examples 
@@ -32,7 +33,7 @@
 #' 
 #' @export
 
-createCompletePar <- function(x = 50, y = 50, dispersal = "global", runs = 100, specRate = 1.0, density = 0, environment = 0, fitnessActsOn = "mortality" , fitnessBaseMortalityRatio = 10, densityCut = 1, seed=NULL,  type = "base", fission = 0, redQueen = 0, redQueenStrength = 0, protracted = 0, airmat = 1, scenario = NULL, calculateSummaries = FALSE, convertToBinaryTree = TRUE){
+createCompletePar <- function(x = 50, y = 50, dispersal = "global", runs = 100, specRate = 1.0, density = 0, environment = 0, fitnessActsOn = "mortality" , fitnessBaseMortalityRatio = 10, densityCut = 1, seed=NULL,  type = "base", fission = 0, redQueen = 0, redQueenStrength = 0, protracted = 0, airmat = 1, scenario = NULL, calculateSummaries = FALSE, convertToBinaryTree = TRUE, prunePhylogeny = TRUE){
 
   soilmat <- 1 # Needs to be defined here as long as it is not
                # implemented in the model
@@ -62,7 +63,7 @@ createCompletePar <- function(x = 50, y = 50, dispersal = "global", runs = 100,
              seed = seed, type = type, scenario = scenario, fission = fission, 
              redQueen = redQueen, redQueenStrength = redQueenStrength, protracted = protracted,
              airmatR = airmat, soilmatR=soilmat, calculateSummaries=calculateSummaries,
-             convertToBinaryTree = convertToBinaryTree)
+             convertToBinaryTree = convertToBinaryTree, prunePhylogeny = prunePhylogeny)
 
 
 

diff --git a/PhyloSim/R/runSimulation.R b/PhyloSim/R/runSimulation.R
@@ -109,7 +109,8 @@ runSimulation <- function(par)
                       redQueenStrength = par$redQueenStrength, 
                       protracted = par$protracted, 
                       airmatR = par$airmat, 
-                      soilmatR = par$soilmat)  
+                      soilmatR = par$soilmat,
+                      prunePhylogeny = par$prunePhylogeny)  
 
     runtime <- as.numeric((proc.time() - ptm)[3])
 
@@ -132,6 +133,8 @@ runSimulation <- function(par)
         phyloi <- 0
         warning("Cannot build Phylogeny")
       }else{
+        # TODO: ape can not read the tree if it is not pruned by prunePhylogenyR:
+        # Error in if (tp[3] != "") obj$node.label <- tp[3] : missing value where TRUE/FALSE needed 
         phyloi <- ape::read.tree(text= out[[i]]$Phylogeny)
       }
 

diff --git a/PhyloSim/R/runSimulationBatch.R b/PhyloSim/R/runSimulationBatch.R
@@ -14,7 +14,7 @@
 #' par2 <- createCompletePar(x = 50, y = 50, dispersal = 0 , runs = c(500,1000),
 #'         density = 1, environment = 0.5, specRate = 1)
 #' 
-#' ## Merge the parameter sets. It is important to note, that the funktion
+#' ## Merge the parameter sets. It is important to note, that the function
 #' ## needs a list of parameter sets.
 #' par <- list(par1,par2)
 #' 

diff --git a/PhyloSim/R/summaryStatistics.R b/PhyloSim/R/summaryStatistics.R
@@ -18,8 +18,13 @@ calculateSummaryStatistics <- function(simulation) {
                             sacAuc=NA,
                             alphaDiversity = NA,
                             betaDiversity = NA,
+                            gammaDiversity = NA,
                             imbalance = NA,
-                            dispersion = NA)
+                            dispersion = NA,
+                            gammaStatistics = NA,
+                            meanNodeAge = NA,
+                            varPart_1 = NA,
+                            varPart_2 = NA)
 
   # TODO: implement special case: only 1 species
   if (is.double(simulation$Output[[1]]$phylogeny)) {
@@ -62,6 +67,8 @@ calculateSummaryStatistics <- function(simulation) {
   summaryStatistics$betaDiversity <- mean(vegan::betadiver(plots$communityTable,
                                                            method=method))
 
+  # gamma diversity
+  summaryStatistics$gammaDiversity <- gammaDiversity(simulation)
 
   # phylogenetic imbalance
   # uses apTreeshape's colless function
@@ -103,13 +110,71 @@ calculateSummaryStatistics <- function(simulation) {
   # phylogenetic dispersion
   # uses PhyloMeasures' implementation of the NRI
 
-  # Causes error. Drop fossil seems to drop clades that are no real fossils?!
+  # Commented code below causes error. Drop fossil seems to drop clades that are no real fossils?!
   #summaryStatistics$dispersion <- mean(PhyloMeasures::mpd.query(ape::drop.fossil(simulation$Output[[1]]$phylogeny),
   #                                                              plots$communityTable,
   #                                                              standardize = TRUE))
+
   summaryStatistics$dispersion <- mean(PhyloMeasures::mpd.query(simulation$Output[[1]]$phylogeny,
                                                                 plots$communityTable,
                                                                 standardize = TRUE))
 
+  # gamma statistics
+  # uses ape's implementation of the gammaStatistics
+  # attention: only works on ultrametric trees
+  summaryStatistics$gammaStatistics <- ape::gammaStat(ape::drop.fossil(simulation$Output[[1]]$phylogeny))
+
+  # mean node age
+  #summaryStatistics$meanNodeAge <- ape::chronoMPL(simulation$Output[[1]]$phylogeny)
+  summaryStatistics$meanNodeAge <- mean(ape::drop.fossil(simulation$Output[[1]]$phylogeny)$edge.length)
+
+
+  # variation partitioning
+  #distance_matrix <- distances(plots$positions, limits=c(nrow(simulation$Output[[1]]$specMat), ncol(simulation$Output[[1]]$specMat)))
+  env <- data.frame(unlist(lapply(plots$envPlots, mean)))
+  comp <- data.frame(unlist(lapply(plots$compPlots, mean)))
+
+  #mod <- vegan::varpart(plots$communityTable, as.dist(distance_matrix), env, comp)
+  mod <- vegan::varpart(plots$communityTable, env, comp)
+
+  summaryStatistics$varPart_1 <- mod$part$fract$Adj.R.squared[1]
+  summaryStatistics$varPart_2 <- mod$part$fract$Adj.R.squared[1]
+
   return(summaryStatistics)
 }
+
+gammaDiversity <- function(simulation, q=0){
+  spec_vector <- c(simulation$Output[[1]]$specMat)
+  specs <- unique(spec_vector)
+  n_specs <- length(specs)
+
+  if (q == 0) return(n_specs)
+
+  n_individuals <- length(spec_vector)
+
+  prop_abundances <- rep(NA, length(specs))
+
+  for(i in 1:length(specs)){
+    prop_abundances[i] <- sum(spec_vector == specs[i]) / n_individuals
+  }
+
+  gamma <- prop_abundances * prop_abundances^(q-1)
+  gamma <- sum(gamma)^(1/(q-1))
+  gamma <- 1/gamma
+  return(gamma)
+}
+
+distances <- function(positions, limits){
+  distance <- function(a, b, limits){
+    # sqrt(min(|x1 - x2|, w - |x1 - x2|)^2 + min(|y1 - y2|, h - |y1-y2|)^2)
+    return(sqrt(min(abs(a[1]-b[1]), limits[1] - abs(a[1]-b[1]))^2 + min(abs(a[2]-b[2]), limits[2] - abs(a[2]-b[2]))^2))
+  }
+  dist_mat <- matrix(0, ncol=length(positions), nrow=length(positions))
+  # TODO: maybe there is a better way to implement this instead of a for loop
+  for(i in 1:nrow(dist_mat)){
+    for(j in 1:ncol(dist_mat)){
+      dist_mat[i,j] <- distance(positions[[i]], positions[[j]], limits=limits)
+    }
+  }
+  return(dist_mat)
+}
diff --git a/PhyloSim/man/callModel.Rd b/PhyloSim/man/callModel.Rd
diff --git a/PhyloSim/man/createCompletePar.Rd b/PhyloSim/man/createCompletePar.Rd
diff --git a/PhyloSim/man/localPlots.Rd b/PhyloSim/man/localPlots.Rd
diff --git a/PhyloSim/man/runSimulationBatch.Rd b/PhyloSim/man/runSimulationBatch.Rd
diff --git a/PhyloSim/src/Main.cpp b/PhyloSim/src/Main.cpp
@@ -72,6 +72,7 @@ int main() {
     int protracted = 0;
     std::vector<double> airmat(1);
     std::vector<double> soilmat(1);
+    bool prunePhylogeny = 1;
 
     RandomGen ran;
     ran.seedrand(seed); // seed is int while seedrand expects unsigned int
@@ -89,8 +90,12 @@ int main() {
                        redQueen, redQueenStrength, protracted, airmat, soilmat);
     Model.update(runs);
 
-    Model.m_Global->m_Phylogeny.prunePhylogeny(runs);
-    Model.m_Global->m_Phylogeny.writePhylogenyR(1, Model.m_Global->m_Phylogeny.m_PrunedPhylo);
+    if(prunePhylogeny){
+        Model.m_Global->m_Phylogeny.prunePhylogeny(runs);
+        Model.m_Global->m_Phylogeny.writePhylogenyR(1, Model.m_Global->m_Phylogeny.m_PrunedPhylo);
+    }
+
+    Model.m_Global->m_Phylogeny.writePhylogenyR(1, Model.m_Global->m_Phylogeny.m_FullPhylogeny);
 
 //	Model.get_data();
 //	Model.getclimate();

diff --git a/PhyloSim/src/PhylSimModelInterface.cpp b/PhyloSim/src/PhylSimModelInterface.cpp
@@ -29,7 +29,7 @@ using namespace Rcpp;
 List callModel(int x, int y, int dispersal, IntegerVector runs, double specRate, bool dens, bool env, bool neutral,
                bool mort, int mortStrength, bool repro, int dispersalCutoff, int densityCutoff, int seed,
                double envStrength, double compStrength, int fission, double redQueen, double redQueenStrength,
-               int protracted, NumericVector airmatR, NumericVector soilmatR) {
+               int protracted, NumericVector airmatR, NumericVector soilmatR, bool prunePhylogeny) {
     #ifdef DEBUG
     std::ofstream debugFile;
     debugFile.open("debug.txt");
@@ -113,10 +113,16 @@ List callModel(int x, int y, int dispersal, IntegerVector runs, double specRate,
 
             #ifdef DEBUG
             std::cout << "before writePhylogenyR" << std::endl;
+            std::cout << prunePhylogeny << std::endl;
             // consistency checks -> length, etc
             #endif
-            phyloPass = phylSimModel.m_Global->m_Phylogeny.writePhylogenyR(1,
-                                                                           phylSimModel.m_Global->m_Phylogeny.m_PrunedPhylo);
+            if(prunePhylogeny){
+                phyloPass = phylSimModel.m_Global->m_Phylogeny.writePhylogenyR(1,
+                                                                               phylSimModel.m_Global->m_Phylogeny.m_PrunedPhylo);
+            }else{
+                phyloPass = phylSimModel.m_Global->m_Phylogeny.writePhylogenyR(1,
+                                                                               phylSimModel.m_Global->m_Phylogeny.m_FullPhylogeny);
+            }
             #ifdef DEBUG
             std::cout << "after writePhylogenyR" << std::endl;
             #endif
@@ -138,9 +144,15 @@ List callModel(int x, int y, int dispersal, IntegerVector runs, double specRate,
             }
             phylSimModel.m_Local->m_Phylogeny.prunePhylogeny(runcount);
 
-            std::string phyloPass = phylSimModel.m_Local->m_Phylogeny.writePhylogenyR(1,
-                                                                                      phylSimModel.m_Local->m_Phylogeny.m_PrunedPhylo);
+            std::string phyloPass("\0");
 
+            if(prunePhylogeny){
+                phyloPass = phylSimModel.m_Local->m_Phylogeny.writePhylogenyR(1,
+                                                                               phylSimModel.m_Local->m_Phylogeny.m_PrunedPhylo);
+            }else{
+                phyloPass = phylSimModel.m_Local->m_Phylogeny.writePhylogenyR(1,
+                                                                               phylSimModel.m_Local->m_Phylogeny.m_FullPhylogeny);
+            }
 
             char *cstr = new char[phyloPass.length() + 1];
             std::strcpy(cstr, phyloPass.c_str());

diff --git a/PhyloSim/src/RcppExportsIni.c b/PhyloSim/src/RcppExportsIni.c
@@ -10,13 +10,15 @@ See also comments here https://github.com/florianhartig/BayesianTools/issues/31
 */
 
 /* .Call calls */
+// every parameter passed to callModel must be represented as SEXP here
+// the number of parameters must be passed to CallEntries
 extern SEXP _PhyloSim_callModel(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP,
                                SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP,
                                SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP,
-                               SEXP, SEXP, SEXP, SEXP, SEXP);
+                               SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
 
 static const R_CallMethodDef CallEntries[] = {
-  {"_PhyloSim_callModel", (DL_FUNC) &_PhyloSim_callModel, 22},
+  {"_PhyloSim_callModel", (DL_FUNC) &_PhyloSim_callModel, 23},
   {NULL, NULL, 0}
 };
 

diff --git a/PhyloSim/src/debug.h b/PhyloSim/src/debug.h
@@ -5,6 +5,6 @@
  *      Author: Florian Hartig
  */
 
-//#ifndef DEBUG
-//#define DEBUG
-//#endif
+// #ifndef DEBUG
+// #define DEBUG
+// #endif