Re: [R-sig-phylo] Extinction series in bipartite

[Scott Chamberlain]

Apologies, meant to send to the R-ecolgy list serve!

Scott  


On Thursday, July 12, 2012 at 10:22 AM, Scott Chamberlain wrote:

> Hello,  
> 
> I am interested in calculating the consequences of removing species from a 
> bipartite network, specifically removing species from the least-connected to 
> the most-connected. The bipartite package in R has the second.extinct and 
> robustness functions which allows investigation of secondary extinctions but 
> does not allow for removing species from least-connected to the 
> most-connected. The only removal options are: 1) random, 2) least-abundant to 
> most-abundant 3) most-connected to least-connected. I am wondering if there 
> are any other programs in which I could run the extinction series that I 
> desire.
> 
> Thanks, 
> Scott Chamberlain
> Simon Fraser University
> 
> 



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Re: [R-sig-phylo] read.dna warnings and pitfalls

[Andrés Parada]

Hi all,

I obtained a using a vector with accession numbers and "read.GenBAnk
(namefile)" The names are "there" since I can obtain a list via attr
(namefile, "species") I couldn't find the way to use write.dna to save a
fasta file with those "species" labels instead of accession numbers.

I noticed seq.names is no more used under "ape".
*Could you tell me how to save a fasta with species names as labels?*
Thanks in advance,

a

2012/5/3 Emmanuel Paradis 

> I made some changes in read.dna which, I hope, solve the problems. The
> taxa names can be of any length and must be separated from the sequences by
> at least one space (or tabulation). write.dna() now follows the same rule.
> Files with less than 10 nucleotides can now be read by read.dna (bug fixed).
>
> I removed the option 'seq.names' of read.dna since it doesn't seem
> particularly useful and this helped to clarify the code.
>
> The new versions are now on ape's SVN:
>
> https://svn.mpl.ird.fr/ape/**dev/ape/R/read.dna.R
> https://svn.mpl.ird.fr/ape/**dev/ape/R/write.dna.R
>
> Tests welcome!
>
>
> Best,
>
> Emmanuel
>
> Dan Rabosky wrote on 26/04/2012 22:01:
>
>>
>> Hi Emmanuel-
>>
>> Thanks for fixing the whitespace issue. I think this fix will be useful
>> to many users.
>>
>> On the issue of recognizing 10 IUPAC characters: I think this is a real
>> problem, and may come up again in short order. Maybe it is just that use of
>> this function has been limited? In the single dataset with a modest number
>> of sequences that caused me problems yesterday, I had the following species
>> and/or genus names - all of which constitute 10 character strings drawn
>> from the set of IUPAC codes:
>>
>> brachyurus (x 2)
>> savannarum
>> graduacauda
>> caudacutus
>> Camarhynchus (x 3)
>> madagascariensis
>>
>> I don't suggest deprecating the phylip sequential, but rather, using
>> something that is compatible with raxml (surely one of the most widely used
>> phylogenetics programs today). I think raxml uses a relaxed sequential
>> version of the phylip format with whitespace delimitation. I could read the
>> same alignment in raxml with no problems, but I had multiple issues when
>> reading the same file with read.dna (including the whitespace character on
>> the first line). My guess is that very few people are using the original
>> phylip format, with its limit of 10 characters per taxon name, and with dna
>> seqs beginning immediately after this. So maybe deprecate "sequential
>> phylip", but you could use what Stamatakis calls "relaxed sequential
>> PHYLIP", which appears to be: (1) taxon names cannot include spaces but can
>> be up to 100 characters; and (2) names separated from sequences by
>> whitespace character (ideally, this should recognize any number of spaces
>> or tabs to prevent user confusion).
>>
>> For users with tab-delimited raxml files (eg each taxon name separated
>> from its dna sequence by a tab), you can use a regular-expressions enabled
>> text editor (like textwrangler) to quickly find potential problems. Just
>> search for
>>
>> [ACGTUMRWSYKVHDBN]{10}.+\t
>>
>> with grep matching enabled.
>>
>> Cheers,
>> ~Dan
>>
>>
>> On Apr 26, 2012, at 2:16 AM, Emmanuel Paradis wrote:
>>
>>  Hi Dan,
>>>
>>> The reason for this implementation (searching the first 10 IUPAC-coded
>>> bases) is because the exact formatting is not inconsistent among different
>>> programs. Some files have:
>>>
>>> 0123456789acgt.
>>>
>>> that is a 10-character name and the sequence starting on the 11th
>>> position. I think this is typical for Phylip. Other software (e.g., PhyML)
>>> accepts longer taxa names and require a space before the start of the
>>> sequence.
>>>
>>> About your example: it depends on the order of the data. The following
>>> file can be read:
>>>
>>> 2 10
>>> x AA
>>> madagascarAA
>>>
>>> But if you invert the two sequence lines, it fails.
>>>
>>> It is the first time I hear about this problem in 9 years, maybe because
>>> it requires a particular combination of circumstances. Another drawback of
>>> this implementation is that files with less than 10 bases cannot be read.
>>>
>>> How to solve this? If it were left only to me, I would deprecate the
>>> interleaved and sequential formats. FASTA is more flexible, more
>>> widespread, easier to parse, can store exactly the same information, and
>>> labels are only constrained to be on a single line (but can contain any
>>> characters including \n, \t, ...) But I guess many programs use the Phylip
>>> formats, so I'd be glad to read other suggestions.
>>>
>>> As for your 2nd problem, it is now fixed in ape.
>>>
>>> Best,
>>>
>>> Emmanuel
>>> -Original Message-
>>> From: Dan Rabosky
>>> Sender: 
>>> r-sig-phylo-bounces@r-project.**org
>>> Date: Wed, 25 Apr 2012 17:51:35
>>> To:
>>> Subject: [R-sig-phylo] read.dna warnings and pitfalls
>>>
>>>
>>> Hi All-
>>>
>>> I have

[R-sig-phylo] Extinction series in bipartite

[Scott Chamberlain]

Hello,  

I am interested in calculating the consequences of removing species from a 
bipartite network, specifically removing species from the least-connected to 
the most-connected. The bipartite package in R has the second.extinct and 
robustness functions which allows investigation of secondary extinctions but 
does not allow for removing species from least-connected to the most-connected. 
The only removal options are: 1) random, 2) least-abundant to most-abundant 3) 
most-connected to least-connected. I am wondering if there are any other 
programs in which I could run the extinction series that I desire.

Thanks, 
Scott Chamberlain
Simon Fraser University


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