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Error in PCC.disagreement: Input is not a numeric matrix. #51
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Hi, thanks for your interest in the package ! I did not succeed in replicating this bug for now. Did you install from CRAN ? Perhaps you are still on a version < 3 ? For k-medoïds, I will correct that. It is because you can't have more clusters than individuals. |
PS: as a side note, the handling of |
@Jean-Baptiste-Camps Since you cannot reproduce the problem, I tried to use the steps in the example from the readme instead of the interactive PCC function. On my minimal example above, I used a threshold of 0.1 and skipped the step with "myNewData = PCC.equipollent" So basically:
and I find alternateReadings interesting, because I deal with ancient data sets where it is very likely that a word or part is only partially readable. So imho this looks like a way to say something like "this is either (one of) the word(s) in other witnesses at this position or something different". At least it would be something worth comparing to always using '?' for damaged words. And very fragmentary and therefor uncertain/fuzzy data is a problem for a lot of (phylogenetic) approaches anyway. |
Ok, many thanks on your very clear message. |
I see, thanks for the clarification. I am aware of the NA feature and I find it very useful. In fact I wanted to compare a matrix with NA readings with an alternative encoding which tries to assign multiple readings to fragmented words. That is where I encountered the issue. My data set right now is already quite sparse, so every reading would help, I guess. But atm it is just on-the-side playing around out of curiosity. I'll watch the project with interest for sure. |
Thank you for this R package, it looks like an interesting project.
I have started playing around with it (without much insight into the stemma creation method yet and with no experience in R at all)
I have tried to use data with multiple readings the parameter
alternateReadings=TRUE
In the interactive mode the first few steps work fine but then the error
is thrown.
I have tried with a real data set first but then used the example matrix from the documentation as test data.
I had to duplicate the matrix a few times, otherwise I got the error
So my minimal data example for the error would be:
I have loaded it from a txt file with
mydata = read.table("filename.txt")
andmydata = as.matrix(mydata)
and then usedPCC(mydata,alternateReadings=TRUE)
.The text was updated successfully, but these errors were encountered: