Addressing "avgdist silently drops observations" #251
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jarioksa
requested changes
Sep 5, 2017
| @@ -11,7 +11,10 @@ | |||
| transf <- match.fun(transf) | |||
| # Get the list of iteration matrices | |||
| distlist <- lapply(seq_len(iterations), function(i) { | |||
| inputcast <- rrarefy(x, sample = sample) | |||
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This fails examples: no inputcast found. You removed it from this line, and reference it later.
R/avgdist.R
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| # Print any samples that were removed, if they were removed | ||
| if(nrow(x) != nrow(output)) { | ||
| dropsamples <- setdiff(row.names(inputcast), row.names(output)) | ||
| write( |
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canonical way of printing warnings is to use warning().
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Thanks for the comments. I went back and fixed the typos that were losing the data frames, and used |
jarioksa
approved these changes
Sep 16, 2017
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As described in issue #246, samples were being dropped silently if they failed to meet the subsampling threshold. I fixed that by including printed text identifying the removed samples.