Skip to contents

Example keys

Source: R/keys.R
exampleKeys.Rd

Ready-made dimoose keys built from the datasets that come with dimoose. All five are ordinary dimoose objects: they share the same fields (leads, df, meta, taxa, desc) and methods (print(), summary(), validate(), toDataTree(), toNewick()) and all work with exportWizard().

Usage

sharkKey()

arachnidaKey()

vibrioKey()

montanaKey()

Value

A dimoose object.

Details

  • sharkKey(): FishBase key 1, Key to the families of sharks in the Western Central Pacific (Compagno 1998), from saved FishBase pages in inst/extdata/fishbase/; 23 couplets, 24 families.

  • arachnidaKey(): the Key to the Orders of Arachnida from Triplehorn & Johnson (2005), the arachnida dataset; 11 couplets, 11 orders (Schizomida is reached from two couplets).

  • vibrioKey(): a key generated from the vibrio consensus matrix of Noguerola & Blanch (2008) with keyFromRpart(). Tests scored + or (+) count as positive and - or (-) as negative; variable (v, d) and not determined (ND) results are treated as missing, and rpart routes a species past such a test with surrogate splits, so a species that varies for a test appears on only one side of it. Species the tests cannot separate share a result.

  • montanaKey(): the native broadleaf trees of Montana, written for dimoose (the montana dataset); 10 couplets, 11 species, with photos from Wikimedia Commons. It is built with keyFromSpreadsheet() from inst/extdata/montana/montana-key.csv, a template for writing your own.

  • phylotreeKey(): PhyloTree Build 17.

References

Compagno LJV (1998). General remarks. In Carpenter KE, Niem VH (eds.), FAO species identification guide for fishery purposes. The living marine resources of the Western Central Pacific, vol. 2, pp. 1196-1207. FAO, Rome. FishBase key 1: https://www.fishbase.se/keys/description.php?keycode=1.

Triplehorn CA, Johnson NF (2005). Borror and DeLong's Introduction to the Study of Insects, 7th ed., chapter 5. Thomson Brooks/Cole. ISBN 0-03-096835-6.

Noguerola I, Blanch AR (2008). Identification of Vibrio spp. with a set of dichotomous keys. Journal of Applied Microbiology 105, 175-185. doi:10.1111/j.1365-2672.2008.03730.x

Examples

sharks <- sharkKey()
sharks
#> <dimoose key> Key to the families of sharks in the Western Central Pacific.
#>   23 couplets, 46 leads, 24 taxa, up to 12 steps deep
summary(arachnidaKey())
#>                            title couplets leads taxa depth problems
#> 1 Key to the Orders of Arachnida       11    22   11     6        0
vibrioKey()$validate()
if (FALSE) { # \dontrun{
exportWizard(sharkKey(), "sharks.html")
} # }