R version 4.5.0 RC (2025-04-04 r88113 ucrt) -- "How About a Twenty-Six"
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Platform: x86_64-w64-mingw32/x64

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> library(Thresher)
Loading required package: ClassDiscovery
Loading required package: cluster
Loading required package: oompaBase
Loading required package: PCDimension
> 
> # unstructured matrix
> suppressWarnings( RNGversion("3.5.0") )
> set.seed(9948489)
> dumb <- matrix(rnorm(100*12), ncol=12)
> colnames(dumb) <- paste("G", 1:12, sep='')
> thresh <- Thresher(dumb)
> # test 'failure' version of constructor
> r <- new("Reaper", thresh,
+          useLoadings=FALSE,
+          keep=FALSE,
+          nGroups=NA,
+          fit=NA,
+          bic=NA,
+          allfits=list(),
+          metric='pearson')
> r@nGroups
[1] NA
> # now construct it for real
> reap <- Reaper(thresh)
> reap@nGroups
[1] 2
> screeplot(reap)
> plot(reap)
> scatter(reap)
> heat(reap)
> 
> # matrices with structure
> set.seed(250264)
> load(system.file("Examples/thresh.Rda", package="Thresher"))
> thresh@nSample # 300
[1] 300
> thresh@rho     # 0.5
[1] 0.5
> thresh@pcdim   # 2
[1] 2
> min(thresh@delta) > 0.5 # TRUE
[1] TRUE
> round(det(thresh@covariance), 5) # 0.00117
[1] 0.00117
> # create Reaper
> reap <- Reaper(thresh)
> reap@pcdim   # two real components
[1] 2
> reap@nGroups # and two clusters
[1] 2
> reap@bic     # check the BIC levels
     NC=2      NC=3      NC=4      NC=5 
-2563.702  2476.929  3308.706  4140.482 
> screeplot(reap, col='gold', lcol='black')
> plot(reap)
> scatter(reap)
> heat(reap)
> 
> colsch <- Thresher:::.makeColorScheme(4)
> bin.hc  <- reap@signalSet@binaryClusters
> bin.csc <- colsch[cutree(bin.hc, k=4)]
> con.hc  <- reap@signalSet@continuousClusters
> con.csc <- colsch[cutree(con.hc, k=4)]
> heat(reap, Colv=as.dendrogram(bin.hc), ColSideColors=con.csc,
+        main=paste(reap@name, "binary signals, cont. colors"))
> heat(reap, Colv=as.dendrogram(con.hc), ColSideColors=bin.csc,
+        main=paste(reap@name, "cont. signals, binary colors"))
> 
> if(FALSE) {
+   makeFigures(reap)
+ }
> 
> proc.time()
   user  system elapsed 
   1.90    0.18    2.03