R help - Nov 2009 - splitting scientific names into genus, species, and subspecies

I have a list of scientific names in a data set.  I would like to split the
names into genus, species and subspecies.  Not all names include a
subspecies.  Could someone show me how to do this?

My example code is:


a <- matrix(c('genusA speciesA', 10,   
              'genusB speciesAA', 20,   
              'genusC speciesAAA subspeciesA', 15, 
              'genusC speciesAAA subspeciesB', 25), nrow=4, byrow=TRUE)

aa <- data.frame(a)

colnames(aa) <- c('species', 'counts')

aa


# The code returns

                                   species  counts
1                     genusA speciesA     10
2                    genusB speciesAA     20
3 genusC speciesAAA subspeciesA     15
4 genusC speciesAAA subspeciesB     25



# I would like there to be 4 columns as below

genus  species    subspecies    counts

genusA speciesA   no.subspecies   10
genusB speciesAA  no.subspecies   20
genusC speciesAAA subspeciesA     15
genusC speciesAAA subspeciesB     25


I have tried using 'strsplit', but cannot get the desired result.  Thank
you
for any help with this.


Mark Miller
Gainesville, Florida

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On 04-Nov-09 21:09:42, Mark W. Miller wrote:
> I have a list of scientific names in a data set. I would like
> to split the names into genus, species and subspecies.
> Not all names include a subspecies.  Could someone show me how
> to do this?
> 
> My example code is:
> a <- matrix(c('genusA speciesA', 10,   
>               'genusB speciesAA', 20,   
>               'genusC speciesAAA subspeciesA', 15, 
>               'genusC speciesAAA subspeciesB', 25), nrow=4,
byrow=TRUE)
> aa <- data.frame(a)
> colnames(aa) <- c('species', 'counts')
> aa
> 
># The code returns
>                                    species  counts
> 1                     genusA speciesA     10
> 2                    genusB speciesAA     20
> 3 genusC speciesAAA subspeciesA     15
> 4 genusC speciesAAA subspeciesB     25
> 
># I would like there to be 4 columns as below
> genus  species    subspecies    counts
> genusA speciesA   no.subspecies   10
> genusB speciesAA  no.subspecies   20
> genusC speciesAAA subspeciesA     15
> genusC speciesAAA subspeciesB     25
> 
> I have tried using 'strsplit', but cannot get the desired result. 
> Thank you for any help with this.
> 
> Mark Miller
> Gainesville, Florida
The following seems to work for your example. However, others
can probably propose a less clumsy version (but at least this
one breaks it down into its elements):

a <- matrix(c('genusA speciesA', 10,
              'genusB speciesAA', 20,   
              'genusC speciesAAA subspeciesA', 15, 
              'genusC speciesAAA subspeciesB', 25), nrow=4, byrow=TRUE)

a
#      [,1]                            [,2]
# [1,] "genusA speciesA"               "10"
# [2,] "genusB speciesAA"              "20"
# [3,] "genusC speciesAAA subspeciesA" "15"
# [4,] "genusC speciesAAA subspeciesB" "25"

A <- NULL
for( i in (1:nrow(a))){
  Names <- unlist(strsplit(a[i,1],"[ ]+"))
  if(length(Names)==2) Names <- c(Names,"no.subspecies")
  A <- rbind(A,c(Names,a[i,2]))
}
colnames(A) <-
c("Genus","Species","Subspecies","Count")
A <- as.data.frame(A)
A$Count <- as.numeric(A$Count)

A
#    Genus    Species    Subspecies Count
# 1 genusA   speciesA no.subspecies     1
# 2 genusB  speciesAA no.subspecies     3
# 3 genusC speciesAAA   subspeciesA     2
# 4 genusC speciesAAA   subspeciesB     4

Hoping this helps!
Ted.


--------------------------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 04-Nov-09                                       Time: 21:37:03
------------------------------ XFMail ------------------------------

Mark W. Miller wrote:
> 
> I have a list of scientific names in a data set.  I would like to split
> the names into genus, species and subspecies.  Not all names include a
> subspecies.  Could someone show me how to do this?
> 
strsplit should work for your example...

data.frame( 
  genus=sapply(strsplit(aa, " "), "[", 1),
species=sapply(strsplit(aa, " "), "[", 2),
subspecies=sapply(strsplit(aa, " "), "[", 3)   ## will be NA
for missing
subsp 
 ) 

However, scientific names are often pretty messy - I often have datasets
like this...
x
 [1] "Aquilegia caerulea James var. caerulea"
 [2] "Aquilegia caerulea James var. ochroleuca Hook."
 [3] "Aquilegia caerulea James var. pinetorum (Tidestrom) Payson ex Kearney
& Peebles"
 [4] "Aquilegia caerulea James"
 [5] "Aquilegia chaplinei Standl."
 [6] "Aquilegia chaplinei Standley ex Payson"
 [7] "Aquilegia chrysantha Gray var. chrysantha"
 [8] "Aquilegia chrysantha Gray"       

So I first strip out author names using strsplit and use grep to find
subspecies/variety abbreviations 

noauthor<-function(x){
  ## split name into vector of separate words
  y<-strsplit(x, " ")
  sapply(y, function(x){  
        n<-grep( "^var\\.$|^ssp\\.$|^var$|^f\\.$",x)
# apply a function to paste together the first and second elements
# plus element after matching var., spp., f. (or and others) 
# use sort in case the name includes both var and spp -sometimes happens
        paste( x[sort(c(1:2, n,n+1))], collapse=" ")  })}


noauthor(x[1:8])
[1] "Aquilegia caerulea var. caerulea"    
[2] "Aquilegia caerulea var. ochroleuca"  
[3] "Aquilegia caerulea var. pinetorum"   
[4] "Aquilegia caerulea"                  
[5] "Aquilegia chaplinei"                 
[6] "Aquilegia chaplinei"                 
[7] "Aquilegia chrysantha var. chrysantha"
[8] "Aquilegia chrysantha"    


Chris






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