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grunwaldlab / metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
http://grunwaldlab.github.io/metacoder_documentation
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Phyloseq parser error #228

Closed amusheg closed 6 years ago

amusheg commented 6 years ago

Hello, I installed version 0.2.0.9012 of metacoder because I'd like to use the calc_group_medians function. However, this version seems to have a problem with the phyloseq parser. 

devtools::install_github("grunwaldlab/taxa")
devtools::install_github("grunwaldlab/metacoder")
library(metacoder)
obj<-parse_phyloseq(adata)
Error: 'parse_tax_data' is not an exported object from 'namespace:taxa'

Please let me know if you need more details.

Thank you!

zachary-foster commented 6 years ago

Hello @amusheg, it looks like you are using the wrong taxa repo. It should be "ropensci", not "grunwaldlab". The one on grunwaldlab is probably an old fork.

devtools::install_github("ropensci/taxa")
devtools::install_github("grunwaldlab/metacoder")
library(metacoder)
obj<-parse_phyloseq(adata)
amusheg commented 6 years ago

That works. Thank you!