Dear All,
Just to avoid confusion, the readNexus function is in the phylobase
package. And as Ben pointed out, other packages have their own functions
for reading the data part from a nexus-formatted file, see e.g., read.nex
in phyloch.
On a related note, I wrote read.nexus.data as a "temporary", crude parsing
function while waiting for the phylobase project to take off (phylobase
uses NCL by Lewis & Holder - _the_ nexus parser), so expect
read.nexus.data to have it's limitations.
Furthermore, if speed is the concern, it would perhaps be preferable to
first convert the Nexus data to Fasta, and then use one of the many
fast(er) parsers implemented in numerous R packages.
Cheers
Johan
On 04/07/2013 02:59 PM, Ben Bolker wrote:> On 13-04-05 01:29 PM, Jessica
Sabo wrote:
>> Hi All,
>>
>> I am wondering if there is anyway to increase the speed of the
>> read.nexus.data parser. Or if there is an alternative that is a
>> faster nexus file data parser.
>>
>> THanks, Jess
>>
>
> I don't know if it's faster or not, but there is ?readNexus in the
> 'ape' package. Also see library("sos"); findFn("read {nexus format}")
>
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