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alexpiper / HemipteraMetabarcodingMS

Reproducable analyses for hemiptera metabarcoding MS
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object 'psmock' not found #5

Closed peterjc closed 2 years ago

peterjc commented 2 years ago

I've been trying to run a subset of the R code in hemiptera_metabarcoding.Rmd sufficient to regenerate Figure 3. This has required assorted library(...) calls and also running the "R Assign Taxonomy" section before getting to "r Figure 3 - merged figure".

The code is now failing here: subset_samples(sample_names(psmock)!=rm_c1) %>%

Searching the file this is the only occurrence of psmock, the variable is never setup. Older versions did, e.g.

# Plot Fig1b - all 3 loci merged
psmock <- ps_filtered

I thinks the error crept in during fea4f83ee281d2c50391548f7827ff60031af1d1 and the simplest fix is to replace psmock with ps_filtered?

alexpiper commented 2 years ago

Thanks for noticing it, yep its a holdover from a previous change. In https://github.com/alexpiper/HemipteraMetabarcodingMS/commit/e7b050a572afb80ff8fda5a52689c7777db994e0 ive replaced it with ps_filtered