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melmasri / HPprediction

R code for a hierarchical Bayesian model for predicting ecological interactions using evolutionary relationships
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load_GMPD in example folder doesn't work #2

Closed melmasri closed 7 years ago

melmasri commented 7 years ago

I am trying the load_GMPD.R, this part causes lots of warnings can you check it?

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Removing parasites not reported to species

Sys.setlocale('LC_ALL','C')

dt <- dt[grep("sp[.]",dt$ParasiteCorrectedName, invert=TRUE),] dt <- dt[grep("ABOLISHED",dt$ParasiteCorrectedName, invert=TRUE),] dt <- dt[grep("no binomial name",dt$ParasiteCorrectedName, invert=TRUE),] dt <- dt[grep("not identified to genus",dt$ParasiteCorrectedName, invert=TRUE),] dt <- dt[grep("SPLITTED in ICTV",dt$ParasiteCorrectedName, invert=TRUE),] dt <- dt[grep("Diphyllobothrium sp",dt$ParasiteCorrectedName, invert=TRUE),] `

maxfarrell commented 7 years ago

I'm not sure why I had to do this, but I originally had the Sys.setlocale('LC_ALL','C') commented out. I'm not sure if setting this will affect your downstream code though. Try it now.

melmasri commented 7 years ago

Ok works, thanks.