shipunov (version 1.17.1)

keys: Diagnostic keys

Description

Diagnostic keys are data structures which help to identify biological samples, i.e. give them (scientific) names. They are old but still very popular because they are simple and efficient, sometimes even for not very experienced user.

The second goal of these keys is the compact representation of biological diversity. Diagnostic keys are not very far from classification lists (see 'classifs'), phylogeny trees (like 'phylo' objects in 'ape' package), from core R 'dendrogram' and 'hclust' objects, and especially from recursive partitioning objects (e.g., from 'tree' or 'rpart' packages).

In biology, diagnostic keys exist in many flavors which are possible to reduce into two main types:

I. Branched keys, where alternatives are separated.

You compare your sample with the first description. Then, if the sample agrees with first description, you go to second description (these keys are usually fully dichotomous), then to the third, until you reach the temninal (name of the organism). If not, you find the alternative description of the _same level_ (same depth). The main difficulty here is how to find it.

To help user find descriptions of the same depths, branched keys are usually presented as _indented_ where each line starts with an indent. Bigger indent means bigger depth.

Branched or indented keys could be traced at least to 1668, to one of John Wilkins books:

(and maybe to much earlier scholastic works.)

Indented keys are widely used, especially in English-language publications.

Another modification could be traced to 1892 when A. Semenow-Tjan-Shanskij published his serial key:

Serial keys are similar to all branched keys but numbering style is different. All steps are numbered sequentially but each has a back-reference to the alternative so user is not required to find the description of the same depth, they are already here. Serial keys are strictly dichotomous. They are probably the most space-saving keys, and still in use, especially in entomology.

II. Bracket keys, where alternatives are together, and user required to use 'goto' references to take the next step.

They can be traced to the famous "Flora Francoise" (1778) where J.-B. Lamarck likely used them the first time:

You compare your sample with first description, and if it agrees, go to where 'goto' reference says. If not, go to second (alternative) description, and then again use its 'goto'. On the last steps, 'goto' is just the terminal, the name you want. Sometimes, bracket keys have more than one alternative (e.g., not fully dichotomous).

Bracket keys pose another difficulty: it is not easy to go back (up) if you by mistake went into the wrong direction. Williamson (1922) proposed backreferenced keys where each step supplied with back-reference:

Sometimes, back-references exist only in case where the referenced step is not immediately before the current.

Bracket keys (backreferenced or not) are probably most popular in biology, and most international as well.

Here bracket, branched and serial keys are standardized as rectangular tables (data frames). Each feature (id, backreference, description, terminal, 'goto') is just one column. In bracket keys, terminal and 'goto' are combined. For example, if you need a bracket key without backreferences, use three columns: id, description and terminal+'goto'. Order of columns is important, column name is not. Please see examples to understand better.

Note that while this format is human-readable, it is not typographic. To make keys more typographic, user might want to convert them into LaTeX where several packages allow for typesetting diagnostic keys (for example, my 'biokey' package.)

Usage

keys

Format

The list which contains four data frames representing three different flavors of biological diagnostic keys: two simple bracket keys, one branched (indented variant) and one serial key. Last two keys are real-world keys, first to determine Plantago (ribworts, plantains) from European Russia (Shipunov, 2000), second -- from North America (Shipunov, 2019).

See Also

Biokey

Examples

attach(keys)

head(bracket1)
head(bracket2)
head(branched)
head(serial)

## convert keys with Biokey()
sii <- Biokey(serial, from="serial", to="indented")
sbb <- Biokey(serial, from="serial", to="bracket")
bbr <- Biokey(branched, from="branched", to="bracket")

## convert keys and visualize them as trees
library(ape) # load 'ape' library to plot Newick trees
plot(read.tree(text=Biokey(bracket1, from="bracket", to="newick")))
plot(read.tree(text=Biokey(bracket2, from="bracket", to="newick")))
plot(read.tree(text=Biokey(branched, from="branched", to="newick")))
plot(read.tree(text=Biokey(serial, from="serial", to="newick")))

detach(keys)

## to make a new bracket key (without backreferences)
## supply three columns: id, description and 'goto'+terminal
bracket3 <- read.table(as.is=TRUE, text="
1 Small Ant
1 Big 2
2 Blue Sky
2 Green Grass
")
bracket3
Biokey(bracket3, from="bracket", to="newick")
cophenetic(ape::read.tree(text=Biokey(bracket3, from="bracket", to="newick")))