[adegenet-commits] r168 - in pkg: R man

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

Author: jombart
Date: 2008-08-13 18:55:19 +0200 (Wed, 13 Aug 2008)
New Revision: 168

Modified:
   pkg/R/chooseCN.R
   pkg/man/chooseCN.Rd
Log:
dmin/dmax in chooseCN now available


Modified: pkg/R/chooseCN.R
===================================================================
--- pkg/R/chooseCN.R	2008-08-12 17:04:49 UTC (rev 167)
+++ pkg/R/chooseCN.R	2008-08-13 16:55:19 UTC (rev 168)
@@ -12,6 +12,20 @@
   if(!require(spdep, quiet=TRUE)) stop("spdep library is required.")
 
   res <- list()
+  
+  if(!is.null(d2)){
+      if(d2=="dmin"){
+          tempmat <- as.matrix(dist(xy))
+          d2min <- max(apply(tempmat, 1, function(r) min(r[r>1e-12])))
+          d2min <- d2min * 1.0001 # to avoid exact number problem
+          d2 <- d2min
+      } else if(d2=="dmax"){
+          d2max <- max(dist(xy))
+          d2max <- d2max * 1.0001 # to avoid exact number problem
+          d2 <- d2max
+      }
+  } # end handle d2
+  
   d1.first <- d1
   d2.first <- d2
   k.first <- k
@@ -95,13 +109,24 @@
       if(is.null(d1) |is.null(d2)){
         tempmat <- as.matrix(dist(xy))
         d2min <- max(apply(tempmat, 1, function(r) min(r[r>1e-12])))
+        d2min <- d2min * 1.0001 # to avoid exact number problem
         d2max <- max(dist(xy))
+        d2max <- d2max * 1.0001 # to avoid exact number problem
         dig <- options("digits")
         options("digits=5")
         cat("\n Enter minimum distance: ")
         d1 <- as.numeric(readLines(n = 1))
         cat("\n Enter maximum distance \n(dmin=", d2min, ", dmax=", d2max, "): ")
-        d2 <- as.numeric(readLines(n = 1))
+        d2 <- readLines(n = 1)
+        ## handle character
+        if(d2=="dmin") {
+            d2 <- d2min
+        } else if(d2=="dmax") {
+            d2 <- d2max
+        } else {
+            d2 <- as.numeric(d2)
+        }
+        ## restore initial digit option
         options(dig)
       }
     # avoid that a point is its neighbour

Modified: pkg/man/chooseCN.Rd
===================================================================
--- pkg/man/chooseCN.Rd	2008-08-12 17:04:49 UTC (rev 167)
+++ pkg/man/chooseCN.Rd	2008-08-13 16:55:19 UTC (rev 168)
@@ -25,7 +25,9 @@
   \item{d1}{the minimum distance between any two neighbours. Used if
     \code{type=5.}}
   \item{d2}{the maximum distance between any two neighbours. Used if
-    \code{type=5}.}
+    \code{type=5}. Can also be a character: "dmin" for the minimum
+    distance so that each site has at least one connection, or "dmax" to
+  have all sites connected (despite the later has no sense).}
   \item{k}{the number of neighbours per point. Used if
     \code{type=6}.}
   \item{a}{the exponent of the inverse distance matrix. Used if