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Sort columns into standard taxonomic rank order

Source: R/taxon_sort.R
taxon_sort.Rd

Reorders data frame columns so that detected taxonomic rank columns appear in standard hierarchical order, with non-taxonomic columns preserved in their original relative positions. Taxonomic columns are detected automatically via taxon_column, or a custom column order can be specified manually via manual.

Usage

taxon_sort(data, manual = FALSE)

Arguments

data

A data frame.

manual

Optional. A numeric vector of at least two column indices specifying a custom sort order for those columns. The selected columns are moved to the position of the lowest index in manual, in the order supplied. If FALSE (default), standard taxonomic rank order is used via automatic detection.

Value

The input data frame with taxonomic columns reordered, all other columns retained in their original relative positions. A console message reports the number of columns sorted, the insertion position, and the resulting column order. If duplicate rank assignments are detected, a warning is issued and the data frame is returned unchanged.

Details

The standard rank hierarchy used for automatic sorting is, from broadest to most specific: kingdom, subkingdom, infrakingdom, superphylum, phylum, subphylum, infraphylum, superclass, class, subclass, infraclass, superorder, order, suborder, infraorder, superfamily, family, subfamily, tribe, subtribe, genus, subgenus, species, subspecies, variety.

Taxonomic columns not matching a rank in the hierarchy are appended after the sorted known-rank columns. If multiple columns are detected for the same rank, a warning is issued and the data frame is returned unsorted – use taxon_column with output = "list" to inspect assignments and either rename columns or use manual to specify the desired order explicitly.

If no taxonomic columns are detected, a message is printed and the original data frame is returned unchanged.

See also

taxon_column for detecting taxonomic columns and inspecting rank assignments before sorting,

taxon_add for appending higher taxonomic rank columns before sorting,

taxon_validate for validating taxonomic names before sorting.

Examples

df <- data.frame(
  id      = 1:3,
  species = c("Homo sapiens", "Panthera leo", "Canis lupus"),
  kingdom = c("Animalia", "Animalia", "Animalia"),
  family  = c("Hominidae", "Felidae", "Canidae"),
  order   = c("Primates", "Carnivora", "Carnivora")
)

# Automatic sort into standard rank order
taxon_sort(df)
#> [taxon_sort] 4 taxonomic column(s) sorted from position 2: kingdom -> order -> family -> species
#>   id  kingdom     order    family      species
#> 1  1 Animalia  Primates Hominidae Homo sapiens
#> 2  2 Animalia Carnivora   Felidae Panthera leo
#> 3  3 Animalia Carnivora   Canidae  Canis lupus

# Manual sort by column index
taxon_sort(df, manual = c(3, 5, 4, 2))
#> [taxon_sort] 4 column(s) manually sorted from position 2: kingdom -> order -> family -> species
#>   id  kingdom     order    family      species
#> 1  1 Animalia  Primates Hominidae Homo sapiens
#> 2  2 Animalia Carnivora   Felidae Panthera leo
#> 3  3 Animalia Carnivora   Canidae  Canis lupus

# Inspect rank assignments first if sort returns a warning
taxon_column(df, output = "list")
#> $family
#> $family$family
#> [1] 4
#> 
#> 
#> $kingdom
#> $kingdom$kingdom
#> [1] 3
#> 
#> 
#> $order
#> $order$order
#> [1] 5
#> 
#> 
#> $species
#> $species$species
#> [1] 2
#> 
#>