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Hey,
I was wondering what the status of predict() function is. Are you going to add it in the near future?
There is a StackOverflow answer that gives the basics of predict, but I don't know if there is more to it than that.

Regards,
Damir

Hi, I am using apcluster and found this error, it's probably because the matrix is too large, is there a way to deal with big matrix when using apcluster? Thank you so much.

s2 <- corSimMat(Placenta_betaNorm_sig, sel=NA, r=1, signed=TRUE, method="pearson")

apres1a <- apcluster(s2)

Error in which(s > -Inf) : 
  long vectors not supported yet: ../../src/include/Rinlinedfuns.h:519

I am using apcluster for clustering 21k items for which I already have a precomputed similarity matrix.

The issue:

changing apcluster() parameters even to convits=1000, lam=0.75 maxits=5000 does not get rid of the "algorithm did not converge" warnings. Increasing lam to 0.9 also did not made any change.

clust_result <- apcluster(matrix_sim, details=TRUE, maxits=5000, lam=0.9)

Question

Is this something to seriously worry about, so I should try to tweak parameters even more, or it is something not crucial?
In the plot(clust_result) the lines go flat rather fast (after 100 iterations or so).

Thank yo for your help

Darek Kedra