shipunov (version 1.5)

classifs: Classification lists

Description

Classification lists ('classifs') are probably one of the most ancient attempts to represent biological diversity, the ordered heterogeneity of living things. In biological systematics, they dated from 1753 when Linnaeus published his "Species Plantarum":

(here on the first page of this book four ranks and five names are represented: class ("Monandria"), order ("Monogynia"), genus ("Canna") and species ("Canna indica" and "Canna angustilolia"))

In essence, classifs require only two columns: rank and name (in that order) so they are easy to standardize as two-column data frames. However, we need to know how to order the ranks. One way is to convert ranks into numbers (Shipunov, 2017). Numranks() implements this functionality.

It is possible to extend classifs with more columns: synonyms, name comments and taxonomic comments. Synonyms (the third column) are especially useful; each synonym will be then one row where second position is a valid name and third position is (one of) synonyms.

Please note that while 'classifs' as data frames are human-readable, they are not typographic. To make them better suited for publication, one might convert them into LaTeX where many packages could be used to typeset classifications (for example, my 'classif2' package).

Note also that in classif, species names must be given in full (in biology, species name consists of two words, (a) genus name and (b) species epithet). One of examples below shows how to replace abbreviations with full genus names.

Usage

classifs

Format

The list with two data frames representing 'classifs', classification lists. First is the classif with textual ranks, second with numerical ranks. Both based on some classifications of Plantago (ribworts, plantains), first (Shipunov, 2000) include species only from European Russia, the other is from the oldest Plantago monograph (Barneoud, 1845).

See Also

Biokey, Numranks

Examples

# NOT RUN {
## European Russian species classif
plevru <- classifs$plevru
## convert rank names into numbers
plevru[, 1] <- Numranks(ranks=plevru[, 1], add=c(Series=1.1))

## now convert into Newick tree and plot it
plevru.n <- Biokey(plevru, from="classif", to="newick")
library(ape) # to plot, load the 'ape' package
plot(read.tree(text=plevru.n))

## Barneoud classif
brn.n <- Biokey(classifs$plbarn, from="classif", to="newick")
plot((read.tree(text=brn.n)), no.margin=TRUE)

## convert classif to taxonomic table
plevru.t <- Biokey(plevru, from="classif", to="table")
colnames(plevru.t) <- Numranks(nums=as.numeric(colnames(plevru.t)))
plevru.t

## two Newick trees
aa <- "(A,(B,C),(D,E));"
bb <- "((A,(B,C)),(D,E));"
## convert them to classif
aa.c <- Biokey(aa, from="newick", to="classif")
bb.c <- Biokey(bb, from="newick", to="classif")
## ... and back to Newick
aa.n <- Biokey(aa.c, from="classif", to="newick")
bb.n <- Biokey(bb.c, from="classif", to="newick")

## how to convert abbreviated species names
spp <- c ("Plantago afra", "P. arborescens", "P. arenaria")
stt <- do.call(rbind, strsplit(spp, " "))
stt[, 1] <- Fill(stt[, 1], "P.")
(res <- apply(stt, 1, paste, collapse=" "))
# }

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