[adegenet-commits] r747 - pkg/R

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

Author: jombart
Date: 2010-12-25 01:58:28 +0100 (Sat, 25 Dec 2010)
New Revision: 747

Modified:
   pkg/R/SNPbin.R
Log:
Fixed examples commented at the end of the code.
Various levels of ploidy work.
Differences in compression efficiency came from using integers or numeric (doubles)  as inputs. 


Modified: pkg/R/SNPbin.R
===================================================================
--- pkg/R/SNPbin.R	2010-12-25 00:22:55 UTC (rev 746)
+++ pkg/R/SNPbin.R	2010-12-25 00:58:28 UTC (rev 747)
@@ -322,16 +322,22 @@
 ################################
 ## testing :
 ##
-## HAPLOID DATA
 ##
 ## library(adegenet)
 
-## dat <- sample(c(0L,1L,NA), 1e6, prob=c(.5, .495, .005), replace=TRUE)
+## HAPLOID DATA - NO NA
+## dat <- sample(c(0,1), 1e6, replace=TRUE)
 ## x <- new("SNPbin", dat)
+## identical(as(x, "integer"),dat) # SHOULD NORMALLY BE TRUE
+## all(as(x, "integer") == dat, na.rm=TRUE) # MUST BE TRUE
+## object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
 
+
+## HAPLOID DATA - WITH NAs
+## dat <- sample(c(0,1,NA), 1e6, prob=c(.5, .49, .01), replace=TRUE)
+## x <- new("SNPbin", dat)
 ## identical(as(x, "integer"),dat) # SHOULD NORMALLY BE TRUE
 ## all(as(x, "integer") == dat, na.rm=TRUE) # MUST BE TRUE
-
 ## object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION