[adegenet-commits] r613 - pkg/R pkg/man www

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

Author: jombart
Date: 2010-05-05 17:25:33 +0200 (Wed, 05 May 2010)
New Revision: 613

Modified:
   pkg/R/chooseCN.R
   pkg/man/chooseCN.Rd
   www/download.html
Log:
Patch to chooseCN.


Modified: pkg/R/chooseCN.R
===================================================================
--- pkg/R/chooseCN.R	2010-05-04 12:40:24 UTC (rev 612)
+++ pkg/R/chooseCN.R	2010-05-05 15:25:33 UTC (rev 613)
@@ -8,6 +8,7 @@
   if(ncol(xy) != 2) stop("xy does not have two columns.")
   if(any(is.na(xy))) stop("NA entries in xy.")
   result.type <- tolower(result.type)
+   if(is.null(type) & !ask) stop("Non-interactive mode but no graph chosen; please provide a value for 'type' argument.")
 
   if(!require(spdep, quiet=TRUE)) stop("spdep library is required.")
 
@@ -38,16 +39,14 @@
   }
 
   ## check for uniqueness of coordinates
-  x <- xy[,1]
-  y <- xy[,2]
-  temp <- table(x,y)
-  if(any(temp>1) & (!is.null(type) && !type %in% c(5,7))){ # coords need not be unique if type==5 or 7
-      xy <- jitter(xy)
-      warning("Random noise was added to xy as duplicated coordinates existed.")
+  if(any(xyTable(xy)$number>1)){ # if duplicate coords
+      DUPLICATE.XY <- TRUE
+  } else {
+      DUPLICATE.XY <- FALSE
   }
 
 
-  if(is.null(type) & !ask) { type <- 1 }
+  ## if(is.null(type) & !ask) { type <- 1 }
 
   ### begin large while ###
   chooseAgain <- TRUE
@@ -74,10 +73,22 @@
         type <- as.integer(readLines(n = 1))
         temp <- type < 1 |type > 7
         if(temp) cat("\nWrong answer\n")
+
+        if(type %in% 1:4 & DUPLICATE.XY){
+            cat("\n\n== PROBLEM DETECTED ==")
+            cat("\nDuplicate locations detected\nPlease choose another graph (5-7) or add random noise to locations (see ?jitter).\n")
+            temp <- TRUE
+        }
+
       } # end while
     }
     ##
 
+    ## warning about duplicate xy coords
+    if(type %in% 1:4 & DUPLICATE.XY){
+        stop("Duplicate locations detected and incompatible with graph type 1-4.\nPlease choose another graph (5-7) or add random noise to locations (see ?jitter).")
+    }
+
     ## graph types
     ## type 1: Delaunay
     if(type==1){

Modified: pkg/man/chooseCN.Rd
===================================================================
--- pkg/man/chooseCN.Rd	2010-05-04 12:40:24 UTC (rev 612)
+++ pkg/man/chooseCN.Rd	2010-05-05 15:25:33 UTC (rev 613)
@@ -7,7 +7,8 @@
   from 6 types of graph and one additional weighting scheme.
   \code{chooseCN} calls functions from appropriate packages, handles
   non-unique coordinates and returns a connection network either with
-  classe \code{nb} or \code{listw}.
+  classe \code{nb} or \code{listw}. For graph types 1-4, duplicated
+  locations are not accepted and will issue an error.
 }
 \usage{
 chooseCN(xy, ask = TRUE, type = NULL, result.type = "nb", d1 = NULL, 
@@ -53,7 +54,11 @@
   neighbours, but the spatial weights are directly proportional to the
   inversed spatial distances.\cr
   Also not that in this case, the output of the function is always a
-  \code{listw} object, even if \code{nb} was requested. 
+  \code{listw} object, even if \code{nb} was requested.\cr
+
+  The choice of the connection network has been discuted on the adegenet
+  forum. Please search the archives from adegenet website (section
+  'contact') using 'graph' as keyword. 
 }
 \value{Returns a connection network having the class \code{nb} or
   \code{listw}. The xy coordinates are passed as attribute to the

Modified: www/download.html
===================================================================
--- www/download.html	2010-05-04 12:40:24 UTC (rev 612)
+++ www/download.html	2010-05-05 15:25:33 UTC (rev 613)
@@ -45,11 +45,20 @@
 type <span style="font-family: monospace;">source("[your-patch-file.R]")</span>&nbsp;
 to
 use
-a patch.<br>
+a
+patch.<br>
 - <a href="files/patches/loadingplot.R"><span
  style="font-family: monospace;">loadingplot.R</span></a>: a few checks
 added when the 'at' argument the specified<br>
+- <a href="files/patches/chooseCN.R"><span
+ style="font-family: monospace;"><span
+ style="text-decoration: underline;">chooseCN</span></span></a><a
+ href="files/patches/chooseCN.R"><span style="font-family: monospace;">.R</span></a>:
+new checks
+about duplicated locations, which are problematic with some types of
+graph<br>
 <br>
+<br>
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 <span style="font-weight: bold;">Older
 versions</span>:<br>