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shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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convert_phyloseq.R #19

Closed linsalrob closed 3 years ago

linsalrob commented 4 years ago

This block of code

# Sumamrise per taxon counts
merged_table <- stmerge %>%
  select(-id) %>%
  unite("lineage", c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"), sep = "_") %>%
  group_by(lineage) %>%
  summarise_if(is.numeric, funs(sum(as.numeric(.)))) %>%
  separate("lineage", c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"), sep = "_") %>%
  ungroup()

Generates the warning:

Warning messages:
1: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
2: Expected 7 pieces. Additional pieces discarded in 2 rows [137, 138].
shandley commented 4 years ago

This shouldn't cause any errors in the results. I know how to convert this to more modern dplyr conventions. I will update in a pull request. But for now this shouldn't cause any issues.