fungioutline -- a tiny R package that integrates up-to-date taxonomic studies

Installitation and Update

library(devtools)
devtools::install_github("ypchan/fungioutline") # To update, just redo installitation

Usage

Load and take a look at the outline

library(fungioutline)
head(outline)

Update outline

Update data/outline..xlsx

Summary

• Count all taxonomic levels

  outline %>%
    summarise(across(c(Kingdom, Subkingdoms, Phyla, Subphyla,Classes,Subclasses,Orders,Families,Genera), ~length(unique(.))))
  

• Count by group names

  outline %>%
    filter(Classes == "Sordariomycetes") %>%
    summarise(across(c(Subclasses,Orders,Families,Genera), ~length(unique(.))))
  

• List by group names

  outline %>%
    filter(Classes == "Sordariomycetes") %>%
    select(Subclasses, Orders, Familes, Genera)
  

• Validate taxonomic names

  # first check the suffixes, for most taxon
  # family - aceae
  # order - ales
  # class - mycetes
  # subclass - mycetidae
  # subphyla - mycotina
  # phyla - mycota
  ## to validate a family name: Septochytriaceae
  outline %>% filter(Families == "Septochytriaceae")
  ## To validate a genus name: Periconia
  outline %>% filter(Genera == "Periconia")
  

• Assign lineage information to a table by taxa name at different levels.

  # Assign lineage information from family to phyla
  outline %>%
    select(Kingdom, Subkingdoms, Phyla, Subphyla,Classes,Subclasses,Orders,Families,Genera) -> lineage_tbl
  
  tbl_to_assign_by_genera_name %>%
    left_join(lineage_tbl, by = c("Genus" = "Genera")) -> assigned_tbl
  write_xlsx(assigned_tbl, "assigned_tbl.xlsx")
  

Updates

2025-3 Updated Phylum and Classes doi