Biokey: Convert diagnostic keys and classification lists

In shipunov: Miscellaneous Functions from Alexey Shipunov

Convert diagnostic keys and classification lists

Description

Convert the oldest biological data structures: diagnostic keys ("keys") and classification lists ("classifs")

Usage

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

Arguments

data	Diagnostic keys ("keys"), classification lists ("classifs") and tables, or Newick phylogeny trees
from	Data type to convert from
to	Data type to convert to
recalculate	Recalculate the numeric ids?
internal	(For debugging) Output internal 4-column 'key' objects instead?
force	(For debugging) Ignore list of allowable conversion pairs?
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?

Details

Biokey() is a way to convert classification lists ("classifs") or diagnostic keys into each other. In addition, it handles species classification tables ("table") and Newick trees ("newick").

To know which conversions are allowed, simply type Biokey() without arguments (this will also induce the harmless 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 help for "classifs" and "keys".

Bracket keys (see help for "keys") could have more than two conditions, other keys not, so problems might arise during conversion (see examples).

Backreferenced keys (see help for "keys") is just a variety of bracket keys so the only possible way to make them is from bracket keys.

Branched key (see help for "keys") is an indented key with omitted "indent" column, therefore it does not require the separate conversion way. See examples about how to convert indent column into actual indents.

Classification "table" is the data frame where each column represent some particular rank (see examples to understand better). Similarly to "classif", "table" should use numerical ranks. In this case, numerical ranks should be column names (see examples).

When Biokey() converts "classif" to "newick", it keeps higher group names as node labels. It does not do that in all other cases.

It is an open question if phylogeny tree (Newick) should be converted into "classif" (see help for "classifs") with all intermediate ranks propagated (thus frequently become monotypic, i.e. with just one subgroup), or with only main ranks (whole numbers) propagated, or terminals (by default, they always have "species" rank = 1) could follow much bigger ranks (i.e., "species" = 1 might follow "family" = 3, not "genus" = 2). At the moment, the last variant is implemented.

Comparably, "newick" to "classif" conversion does _not_ remove names of monotypic intermediate taxa, this might result in "crowding" of node labels (see the example). Also, this conversion automatically propagates intermediate ranks to make all ranks concerted, this might result in empty labels.

Value

Typically, the data frame or just a character string (in case of Newick output). Output may contain column names but this is only to facilitate understanding of the format and could be stripped without consequences. 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.

Author(s)

Alexey Shipunov

References

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

See Also

classifs, keys

Examples

## Biokey() # makes (harmless) error message but also shows which conversions are available
Numranks() # shows the conversion table

## ===

Numranks(nums=1:7)
Numranks(ranks="kingdom") # "kingdom", "order", "family" and "tribe" translate 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 below
plot(read.tree(text=t1))
plot(read.tree(text=t2))
plot(read.tree(text=t3))

## ===

## Bracket keys
bracket1 <- keys[[1]]
bracket1
Biokey(bracket1, from="bracket", to="backreferenced")
(ii <- Biokey(bracket1, from="bracket", to="indented"))
## Remove third condition to avoid warnings:
Biokey(bracket1[bracket1[, 3] != "Horse", ], from="bracket", to="serial")
(nn <- Biokey(bracket1, from="bracket", to="newick"))
plot.phylo(read.tree(text=nn)) # plot newick as phylogeny trees

## Now convert indent column into actual indents:
for (i in 1:length(ii[, 1])) ii[i, 1] <- paste(rep(" ", ii[i, 1]), collapse="")
## and make also dot leaders
ifelse(!is.na(ii[, 3]), "...", "")
ii

## Branched keys
branched1 <- keys[[3]]
head(branched1)
Biokey(branched1, from="branched", to="bracket")[1:7, ]
Biokey(branched1, from="branched", to="indented")[1:7, ]
Biokey(branched1, from="branched", to="serial")[1:7, ]
(nn <- Biokey(branched1, from="branched", to="newick"))
plot.phylo(read.tree(text=nn))

## Indented keys (same as branched but with indent as first column)
indented0 <- c("0 1 Blue ", "1 2 Gas Sky", "1 2 Liquid ",
 "0 1 Yellow ", "2 3 Star Sun", "2 3 Buttecup Flower")
(indented1 <- read.table(textConnection(indented0), sep=" ", as.is=TRUE))
Biokey(indented1, from="indented", to="bracket")
Biokey(indented1, from="indented", to="serial")
(nn <- Biokey(indented1, from="indented", to="newick"))
plot.phylo(read.tree(text=nn))

## Serial keys
serial1 <- keys[[4]]
head(serial1)
Biokey(serial1, from="serial", to="bracket")[1:7, ]
Biokey(serial1, from="serial", to="indented")[1:7, ]
(nn <- Biokey(serial1, from="serial", to="newick"))
plot.phylo(read.tree(text=nn))

## Classifs
classif2 <- classifs[[2]]
classif2[, 1] <- Numranks(ranks=classif2[, 1], add=c(Series=1.1))
head(classif2)
Biokey(classif2, from="classif", to="table")[1:7, ]
(nn <- Biokey(classif2, from="classif", to="newick"))
tt <- read.tree(text=nn)
plot.phylo(tt, node.depth=2)
nodelabels(tt$node.label, frame="none", bg="transparent", adj=-0.05)

## Classification tables
table0 <- c("FAMILY SUBFAMILY TRIBE GENUS", "Hominidae Homininae Hominini Homo",
 "Hominidae Homininae Hominini Pan", "Hominidae Homininae Gorillini Gorilla",
 "Hominidae Ponginae Ponginini Pongo")
(table1 <- read.table(textConnection(table0), sep=" ", as.is=TRUE, h=TRUE))
names(table1) <- Numranks(ranks=names(table1))
table1
Biokey(table1, from="table", to="classif")

## Newick phylogeny trees
newick1 <- "((Coronopus,Plantago),(Bougueria,(Psyllium_s.str.,Albicans)),Littorella);"
plot.phylo(read.tree(text=newick1))
Biokey(newick1, from="newick", to="classif")

shipunov documentation built on Feb. 16, 2023, 9:05 p.m.