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Normalize Incertae sedis and fill missing taxonomy ranks

Source: R/taxonomy_cleaning.r
replace_incertae_sedis_NAs.Rd

Cleans hierarchical taxonomy columns by standardizing common "Incertae sedis" variants, filling missing child ranks from stable parent ranks, and replacing empty/uninformative entries with "unknown".

Usage

replace_incertae_sedis_NAs(
  df,
  hierarchy = c("Domain", "Phylum", "Class", "Order", "Family", "Genus"),
  clean_levels = c("Phylum", "Class", "Order", "Family", "Genus")
)

Arguments

df

A data.frame or tibble containing taxonomy columns.

hierarchy

Character vector of column names in rank order from highest (parent) to lowest (child). Only columns present in df are used.

clean_levels

Character vector of ranks to normalize and fill. Only ranks present in both df and hierarchy are used.

Value

An object of the same class as df (tibble in, tibble out) with cleaned taxonomy columns.

Details

The function is designed for rank-ordered taxonomy (e.g., Domain → Phylum → Class → ...), and performs a downward pass through the hierarchy to propagate parent information.

The following rules are applied:

  • "Incertae sedis" variants (case-insensitive; underscores/spaces tolerated) are converted to "inc. sed.".

  • Empty strings ("") in clean_levels are treated as missing (NA).

  • A parent is considered unstable if it is missing (NA) or matches "unknown", "unclassified", or "inc. sed." (case-insensitive).

  • If a child is "inc. sed." and the parent is stable, the child becomes "<parent> inc. sed."; otherwise it becomes "unknown".

  • If a child is missing and the parent is stable, the child becomes "<parent>, unclassified"; otherwise it becomes "unknown".

  • Underscores are converted to spaces and values are trimmed.

Examples

tax_df <- data.frame(
  Domain = c("Bacteria", "Bacteria", NA),
  Phylum = c("Proteobacteria", "IncertaE_Sedis", "Actinobacteriota"),
  Class  = c(NA, "Alphaproteobacteria", ""),
  Order  = c("", "Rhizobiales", "inc. sed."),
  Family = c("Rhizobiaceae", NA, "unknown"),
  Genus  = c("", "inc. sed.", NA)
)

replace_incertae_sedis_NAs(
  df = tax_df,
  hierarchy = c("Domain", "Phylum", "Class", "Order", "Family", "Genus"),
  clean_levels = c("Phylum", "Class", "Order", "Family", "Genus")
)
#>     Domain             Phylum                          Class       Order
#> 1 Bacteria     Proteobacteria   Proteobacteria, unclassified     unknown
#> 2 Bacteria Bacteria inc. sed.            Alphaproteobacteria Rhizobiales
#> 3     <NA>   Actinobacteriota Actinobacteriota, unclassified     unknown
#>                      Family                      Genus
#> 1              Rhizobiaceae Rhizobiaceae, unclassified
#> 2 Rhizobiales, unclassified                    unknown
#> 3                   unknown                    unknown