Maybe
methods(class=class(myobjetc))
for example:
>library(ape)
> data(bird.families)
> class(bird.families)
[1] "phylo"
> methods(class=class(bird.families))
[1] +.phylo all.equal.phylo
[3] as.hclust.phylo as.matching.phylo
[5] c.phylo coalescent.intervals.phylo
[7] cophenetic.phylo identify.phylo
[9] makeLabel.phylo plot.phylo
[11] print.phylo reorder.phylo
[13] skyline.phylo summary.phylo
[15] vcv.phylo
Cheers,
Marcelino
At 20:39 07/03/2011, Rob Lanfear wrote:
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>
>Hi All,
>
>On the issue of visibility of functions in R, I definitely find it a
>struggle to 'discover' things that I could do with a particular object.
>Python has this worked out in a really nice way - if I have an object I can
>simply put a full-stop after it and hit tab, and I get a list of all
>currently loaded functions which could apply to that object. Does R have
>anything similar to this? For instance, if I have a "phylo" object, is there
>any straightforward way to see which functions currently loaded in R can
>take that object as input? If not, would it be hard to write a function to
>do this?
>
>Often I find myself reading through the full help pdf for a given of
>libraries to see if I can find what I'm looking for. Depending on what
>people have named their functions this can sometimes be a painful process
>too!
>
>Rob
>
>On 8 March 2011 03:35, David Bapst <dwba...@uchicago.edu> wrote:
>
> > Emmanuel, all-
> > That's pretty fast, even on my cheap laptop!
> >
> > > system.time(desc1<-c(as.list(1:Ntip(res_tree)),prop.part(res_tree)))
> > user system elapsed
> > 0.65 0.00 0.66
> >
> > As far as why I didn't try prop.part, to be honest, I had no idea that
> > prop.part() did that. The help file says:
> >
> > Description
> > These functions analyse bipartitions found in a series of trees.
> > prop.part counts the number of bipartitions found in a series of trees
> > given as ....
> >
> > and
> >
> > Value
> > prop.part returns an object of class "prop.part" which is a list with
> > an attribute "number". The elements of this list are the observed
> > clades, and the attribute their respective numbers. If the default
> > check.labels = FALSE is used, an attribute "labels" is added, and the
> > vectors of the returned object contains the indices of these labels
> > instead of the labels themselves.
> >
> > That doesn't suggest to me that it gives the tip descendants of every
> > internal node, although that is part of what it does. Until you
> > suggested I run it, I had no idea it could give the information I
> > wanted. Perhaps a little bit of clarifying of the help file,
> > particularly the specific bits of the output, would go a long way.
> >
> > Cheers!
> > -Dave
> >
> >
> >
> > On Sun, Mar 6, 2011 at 10:11 PM, Emmanuel Paradis
> > <emmanuel.para...@ird.fr> wrote:
> > > Hi David and others,
> > >
> > > prop.part() with a single tree does what you want:
> > >
> > >> set.seed(123)
> > >> res_tree <- rtree(1700)
> > >> system.time(desc2 <- prop.part(res_tree))
> > >
> > > user system elapsed
> > > 0.050 0.000 0.053
> > >>
> > >> edge_end <- unique(res_tree$edge[,1])
> > >> system.time(desc1 <- Descendants(res_tree,edge_end))
> > >
> > > user system elapsed
> > > 0.400 0.000 0.406
> > >
> > > This gives the same answer than Descendants:
> > >
> > >> for (i in seq_along(desc1))
> > >
> > > + stopifnot(all(sort(desc1[[i]]) == sort(desc2[[i]])))
> > >>
> > >
> > > Klaus makes an excellent reminder about R programming: use vectorisation
> > > whenever possible (you'll almost always win to do it).
> > >
> > > Your examples are very instructive. One lesson is that it is quite easy
> > > to write R code that tends to be slow. Another one is that it is also
> > > easy to write different functions doing the same thing. I'm quite
> > > impressed to see that several packages have re-implemented something
> > > that has been in ape for some time.
> > >
> > > I wish developpers (and users as well) could use these tools from ape
> > > which have been developed specifically for this kind of objectives (fast,
> > > efficient, and reliable). Is it an issue of 'visibility' of these
> > functions?
> > > This could be a project idea for the next GSoC.
> > >
> > > Cheers,
> > >
> > > Emmanuel
> > >
> > > PS: if you want to speed-up your computations and you have a multi-core
> > > processor on your machine (which are common on laptops nowadays), you
> > could
> > > try the multicore package (phangorn already supports it):
> > >
> > >> library(multicore)
> > >> job <- parallel(prop.part(res_tree))
> > >> system.time(out <- collect(job))
> > > user system elapsed
> > > 0.080 0.010 0.002
> > >> out <- out[[1]]
> > >> identical(out, desc2)
> > > [1] TRUE
> > >
> > > This might be even more interesting with lists of trees.
> > >
> > >
> > > David Bapst wrote on 07/03/2011 04:32:
> > >>
> > >> Klaus-
> > >> Oh, that worked rather splendid! Thanks for letting me know.
> > >>
> > >>> system.time(desc<-Descendants(res_tree,edge_end))
> > >>
> > >> user system elapsed
> > >> 1.56 0.00 1.56
> > >>
> > >> -Dave
> > >>
> > >> On Sun, Mar 6, 2011 at 3:22 PM, Klaus Schliep <klaus.schl...@gmail.com>
> > >> wrote:
> > >>>
> > >>> Hi David,
> > >>>
> > >>> you can supply Descendents (from phangorn) with a vector instead of
> > >>> using sapply. I should have mentioned this in the help file.
> > >>> If your vector (edge_end) is long enough (I don't have a exact number
> > >>> here) this can be much faster than using sapply as some results are
> > >>> reused.
> > >>> Here are some timings:
> > >>>
> > >>>> set.seed(123)
> > >>>> res_tree = rtree(1700)
> > >>>> edge_end = unique(res_tree$edge[,1])
> > >>>> system.time(desc1<-sapply(edge_end,function(x)
> > Descendants(res_tree,x)))
> > >>>
> > >>> user system elapsed
> > >>> 54.51 0.00 54.87
> > >>>>
> > >>>> system.time(desc2<-Descendants(res_tree,edge_end))
> > >>>
> > >>> user system elapsed
> > >>> 0.75 0.00 0.75
> > >>>>
> > >>>> system.time(desc3<-sapply(edge_end,function(x) node.tips(res_tree,x)))
> > >>>
> > >>> user system elapsed
> > >>> 4.07 0.00 4.07
> > >>>
> > >>>
> > >>> Cheers,
> > >>> Klaus
> > >>>
> > >>>
> > >>>
> > >>> On 3/6/11, David Bapst <dwba...@uchicago.edu> wrote:
> > >>>>
> > >>>> Hello all,
> > >>>> I'm currently trying to measure a parameter over a large number of
> > >>>> large trees (>1700 tips), and part of this calculation requires
> > >>>> knowing the tip taxa descended from each node (I must compare the
> > >>>> difference in tip values among taxa descended from a node). Because I
> > >>>> must do this many times, I decided to compare the efficiency of
> > >>>> several methods for doing this in various R libraries with
> > >>>> system.time() (as Liam did recently with some BM simulation functions
> > >>>> in some recent blog posts). As I feel that others may benefit from
> > >>>> this comparison of methods, I am posting the results to this list.
> > >>>>
> > >>>> Geiger's node.leaves() is much faster than the alternatives, although
> > >>>> at ~13s a run, it is still not a particularly speedy process. I didn't
> > >>>> need the actual tip.labels, so I took node.leaves() and made it as
> > >>>> lean as possible, to produce node.tips(), below. That cut the run time
> > >>>> down to ~9 sec.
> > >>>>
> > >>>> node.tips<-function (phy, node){
> > >>>> n <- length(phy$tip.label)
> > >>>> if (node <= n){node}else{
> > >>>> l<- numeric()
> > >>>> d<- phy$edge[which(phy$edge[,1]==node),2]
> > >>>> for(j in d){if(j <= n){l <- c(l, j)}else{l<-c(l,
> > >>>> node.tips(phy,j))}}
> > >>>> l}}
> > >>>>
> > >>>> If anyone knows of another alternative that might be faster, I would
> > >>>> greatly appreciate any suggestions.
> > >>>> -Dave Bapst, UChicago Geosci
> > >>>>
> > >>>> Using the modified node.leaves() function from geiger, node.tips()
> > >>>>
> > >>>>> system.time(desc<-sapply(edge_end,function(x) node.tips(res_tree,x)))
> > >>>>
> > >>>> user system elapsed
> > >>>> 9.39 0.00 9.44
> > >>>>
> > >>>> Using node.leaves() in geiger
> > >>>>
> > >>>>> system.time(desc<-sapply(edge_end,function(x)
> > node.leaves(res_tree,x)))
> > >>>>
> > >>>> user system elapsed
> > >>>> 13.29 0.02 13.34
> > >>>>
> > >>>> Using Descendants() in phangorn
> > >>>>
> > >>>>> system.time(desc<-sapply(edge_end,function(x)
> > Descendants(res_tree,x)))
> > >>>>
> > >>>> user system elapsed
> > >>>> 75.60 0.10 76.83
> > >>>>
> > >>>> Using listTips() in adephylo
> > >>>>
> > >>>>>
> > system.time(desc_list<-c(as.list(1:Ntip(res_tree)),listTips(res_tree)))
> > >>>>
> > >>>> user system elapsed
> > >>>> 75.27 2.93 87.28
> > >>>>
> > >>>> Using descendants() in phylobase
> > >>>>
> > >>>>> system.time(desc<-sapply(edge_end,function(x)
> > >>>>> descendants(res_tree4,x,type="tips")))
> > >>>>
> > >>>> user system elapsed
> > >>>> 149.56 0.67 155.15
> > >>>>
> > >>>> Using nodeDecendants() in maticce (note that translating the tree
> > >>>> into ouchtree format was prohibitively very lengthy)
> > >>>>
> > >>>>> system.time(res_tree_ou<-ape2ouch(res_tree))
> > >>>>
> > >>>> user system elapsed
> > >>>> 84.01 0.13 85.34
> > >>>>>
> > >>>>> system.time(desc<-sapply(edge_end,function(x)
> > >>>>> nodeDescendents(res_tree_ou,x)))
> > >>>>
> > >>>> user system elapsed
> > >>>> 65.91 0.23 68.47
> > >>>>
> > >>>> --
> > >>>> David Bapst
> > >>>> Dept of Geophysical Sciences
> > >>>> University of Chicago
> > >>>> 5734 S. Ellis
> > >>>> Chicago, IL 60637
> > >>>> http://home.uchicago.edu/~dwbapst/
> > >>>>
> > >>>> _______________________________________________
> > >>>> R-sig-phylo mailing list
> > >>>> R-sig-phylo@r-project.org
> > >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > >>>>
> > >>>
> > >>> --
> > >>> Klaus Schliep
> > >>> Université Paris 6 (Pierre et Marie Curie)
> > >>> 9, Quai Saint-Bernard, 75005 Paris
> > >>>
> > >>
> > >>
> > >>
> > >
> > > --
> > > Emmanuel Paradis
> > > IRD, Jakarta, Indonesia
> > > http://ape.mpl.ird.fr/
> > >
> > >
> > >
> >
> >
> >
> > --
> > David Bapst
> > Dept of Geophysical Sciences
> > University of Chicago
> > 5734 S. Ellis
> > Chicago, IL 60637
> > http://home.uchicago.edu/~dwbapst/
> >
> > _______________________________________________
> > R-sig-phylo mailing list
> > R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> >
>
>
>
>--
>Rob Lanfear
>Postdoc,
>Centre for Macroevolution and Macroecology,
>Research School of Biology,
>Australian National University
>
>Tel: +61 2 6125 7270
>www.robertlanfear.com
>
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>
>
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____________________________________
Marcelino de la Cruz Rot
Depto. Biologia Vegetal
EUIT Agricola
Universidad Politecnica de Madrid
tel: 34 + 913365435
____________________________________
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