shipunov (version 1.3)

Biokey: Convert diagnostic keys and classification lists

Description

Convert the oldest biological data structures: diagnostic keys and classification lists

Usage

Biokey(data, from=NULL, to=NULL, recalculate=TRUE, internal=FALSE)
Numranks(nums=NULL, ranks=NULL, add=NULL, empty="Species")

Arguments

data

Key-like data (see 'keys'), or other hierarchical data (see 'classifs') and also in details below

from

Data type to convert from

to

Data type to convert to

recalculate

Recalculate the numeric ids?

internal

Output internal 4-column 'key' objects instead?

nums

Numbers to convert into ranks

ranks

Ranks to convert into numbers

add

Rank-number conversion rule to add (overrides embedded rules)

empty

What rank to use for empty number?

Value

Typically, the data frame or just a character string (in case of Newick output). If 'internal=TRUE', outputs a standardized 4-column data frame in a form of branched key (columns 'id', 'description', 'terminal'), plus 'goto' column which might be just NAs.

Details

Biokey() is a way to convert classification lists ('classifs') or diagnostic keys into keys of other types or classifs. Biokey() is able also to convert keys or classifs into more external data structures: classification tables ('to="table"') or Newick trees ('to="newick"'.) To know which conversions are allowed, simply type Biokey() whithout arguments (this will also induce the error message).

Numranks() converts biological rank names into numbers and numbers into rank names (Shipunov, 2017). To see the embedded conversion table, type Numranks() without arguments.

To know more about keys and classifs, read 'classifs' and 'keys' help files.

References

Shipunov A. 2017. "Numerical ranks" to improve biological nomenclature of higher groups. 2017. URL: 'https://arxiv.org/abs/1708.07260'

See Also

classifs, keys

Examples

# NOT RUN {
## Biokey() # will induce error message but also show which conversions are available
Numranks() # will show the conversion table

Numranks(nums=1:7)
Numranks(ranks="kingdom") # "kingdom", "order" and "family" will be translated into Latin

## three branched keys
i1 <- c("1 A ", "2 B Name1", "2 BB Name2", "1 AA ", "3 C Name3", "3 CC Name4")
i2 <- c("1 A Name1", "2 B Name2", "2 BB ", "3 C Name3", "3 CC Name4")
i3 <- c("1 A Name1", "2 B Name2", "2 BB ", "3 C Name3",
 "3 CC Name4", "2 BBB ", "4 D Name5", "4 DD Name6", "4 DDD Name7")
k1 <- read.table(textConnection(i1), sep=" ", as.is=TRUE)
k2 <- read.table(textConnection(i2), sep=" ", as.is=TRUE)
k3 <- read.table(textConnection(i3), sep=" ", as.is=TRUE)

## convert them into phylogeny trees and plot
t1 <- Biokey(k1, from="branched", to="newick")
t2 <- Biokey(k2, from="branched", to="newick")
t3 <- Biokey(k3, from="branched", to="newick")
library(ape) # load 'ape' to plot Newick trees
plot(read.tree(text=t1))
plot(read.tree(text=t2))
plot(read.tree(text=t3))
# }