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--- tau [2008/01/28 11:40] – created heidi
+++ tau [2008/07/22 13:31] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== mismatch distribution ======
+====== Divergence times allowing for unequal population sizes (tau) ======
-  * file: lines_Mismatch.r
+  * file: matrix_tau.r
-  * document page: 1
+  * document page: 31
 \\
 **code:**
 <code>
+#----read data------------------------------------------------------------------
+Data <- read.table("D:/Heidi/Master/R_Daten/SummaryStatistics/tau.txt", skip=5, fill=TRUE)
+Columns <- ncol(Data)+1
+Row <- nrow(Data)
+x <- 6
+n <- 2
+#----read data line by line-----------------------------------------------------
+tauMatrix <- as.matrix(scan("D:/Heidi/Master/R_Daten/SummaryStatistics/tau.txt",
+                             what=double(0), skip=x, nlines=1, nmax=n))
+tauMatrix <- cbind(t(tauMatrix), matrix(NA, ncol=(Columns-n), nrow=1))
+tauMatrix <- tauMatrix[,2:Columns]
+n <- n + 1
+x <- x + 1
+while(n<(Row+1)){
+  nextrow <- as.matrix(scan("D:/Heidi/Master/R_Daten/SummaryStatistics/tau.txt",
+                       what=double(0), skip=x, nlines=1, nmax=n))
+  nextrow <- cbind(t(nextrow), matrix(NA, ncol=(Columns-n), nrow=1))
+  nextrow <- nextrow[,2:Columns]
+  tauMatrix <- rbind(tauMatrix, nextrow)
+  n <- n + 1
+  x <- x + 1
+}
+a <- ncol(tauMatrix)
+b <- nrow(tauMatrix)
+x <- c(1:a)
+y <- c(1:b)
+#----draw plot------------------------------------------------------------------
+library(fields)
+ColorRamp <- rgb( seq(1,0,length=256),  # Red
+                  seq(1,0,length=256),  # Green
+                  seq(1,1,length=256))  # Blue
+#----Mirror matrix (left-right)----
+mirror.matrix <- function(x) {
+  xx <- as.data.frame(x);
+  xx <- rev(xx);
+  xx <- as.matrix(xx);
+  xx;
+}
+#----Rotate matrix 270 clockworks----
+rotate270.matrix <- function(x) {
+  mirror.matrix(t(x))
+}
+tauMatrix <- rotate270.matrix(tauMatrix)
+#----draw matrix plot----
+image.plot(x,y, tauMatrix, col=ColorRamp, main="Divergence times allowing for unequal
+              population sizes (tau)", xlab="Population", ylab="Population",
+              legend.args=list( text="tau", cex=1.0, side=4, line=2.2), axes = FALSE)
+       contour(tauMatrix, add = TRUE)
+       axis(1, at = c(1:a))
+       axis(2, at = c(1:b), labels=c(b:1))
+       box()
+</code>