taxa (version 0.1.0)

span: Span taxa

Description

Select a range of taxa, either by two names, or relational operators

Usage

span(.data, ...)

Arguments

.data

Input, object of class Hierarchy, or hierarchies

...

quoted rank names (e.g., family) via ranks(), taxon names (e.g., Poa annua) via nms(), or taxonomic IDs (e.g., 93036) via ids(). You can't pass in arbitrary strings or numbers.

Value

an object of the same class as passed in

Details

supports Hierarchy and hierarchies objects

See Also

See filtering-helpers, including for more explanation of how this function works.

Examples

Run this code
# NOT RUN {
# Hierarchy class
ex_hierarchy1

## ranks
### keep all taxa between family and genus
span(ex_hierarchy1, ranks("family", "genus"))
span(ex_hierarchy1, nms("Poaceae", "Poa"))
span(ex_hierarchy1, ids(4479, 4544))

### keep all taxa between genus and species
span(ex_hierarchy1, ranks("genus", "species"))

### keep all taxa greater than genus
span(ex_hierarchy1, ranks("> genus"))

### keep all taxa greater than or equal to genus
span(ex_hierarchy1, ranks(">= genus"))

### keep all taxa less than genus
span(ex_hierarchy1, ranks("< genus"))

### keep all taxa less than or equal to genus
span(ex_hierarchy1, ranks("<= genus"))

### same as above, with different dataset
span(ex_hierarchy2, ranks("> genus"))
span(ex_hierarchy2, ranks(">= genus"))
span(ex_hierarchy2, ranks("< genus"))
span(ex_hierarchy2, ranks("<= genus"))

# using taxonomic names
span(ex_hierarchy2, nms("< Felidae"))

# using taxonomic ids
span(ex_hierarchy2, ids("< 9681"))

## Multiple operator statements - useful with larger classifications
ex_hierarchy3
span(ex_hierarchy3, ranks("> genus"), ranks("< phylum"))
span(ex_hierarchy3, ids("> 161994"), ids("< 158852"))


## taxon names
### keep all taxa between Poaceae and Poa
### - matches to ranks first
ex_hierarchy1 %>% span(nms("Poaceae", "Poa"))

## taxon ids
### keep all taxa between 4479 and 4544 taxonomic IDs
### - matches to ranks first
ex_hierarchy1 %>% span(ids(4479, 4544))


# hierarchies class
invisible(lapply(ex_hierarchies, print))
ex_hierarchies %>% span(ranks("family", "genus")) %>% lapply(., print) %>%
invisible
# }

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