Let's get some tools installed.

Following the steps (modified) from http://www.phytools.org/eqg/Exercise_3.2/



In [5]:

    
if (!require('ctv')) {
    # this install is pretty quick
    install.packages('ctv', repos = 'http://cran.r-project.org/')
}
library('ctv')









    



The downloaded binary packages are in
	/var/folders/bm/hwt7p96n2_ngh1_pr8g7dl2m0000gn/T//Rtmpe4Wc5D/downloaded_packages



In [131]:

    
install.views('Phylogenetics', repos = 'http://cran.r-project.org/')









    



Warning message:
: dependencies ‘Biostrings’, ‘phyloseq’ are not availablePackage which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘SigTree’






    



The downloaded binary packages are in
	/var/folders/bm/hwt7p96n2_ngh1_pr8g7dl2m0000gn/T//Rtmpe4Wc5D/downloaded_packages






    



installing the source packages ‘pmc’, ‘SigTree’

Warning message:
In install.packages(pkgs[[i]], repos = names(pkgs)[i], ...): installation of package ‘SigTree’ had non-zero exit status





    



The downloaded source packages are in
	‘/private/var/folders/bm/hwt7p96n2_ngh1_pr8g7dl2m0000gn/T/Rtmpe4Wc5D/downloaded_packages’

This installed (most of) a bundle of phylo-related R packages. Now let's tinker with phylo structures.



In [132]:

    
library(ape)
tree <- rtree(n=20)
tree









    





Phylogenetic tree with 20 tips and 19 internal nodes.

Tip labels:
	t11, t6, t19, t9, t8, t14, ...

Rooted; includes branch lengths.



In [16]:

    
plot(tree, type = 'cladogram', edge.width = 2)



In [20]:

    
str(tree)









    



List of 4
 $ edge       : int [1:38, 1:2] 21 22 23 24 24 23 22 25 26 27 ...
 $ tip.label  : chr [1:20] "t7" "t8" "t11" "t12" ...
 $ edge.length: num [1:38] 0.063 0.53 0.834 0.114 0.934 ...
 $ Nnode      : int 19
 - attr(*, "class")= chr "phylo"
 - attr(*, "order")= chr "cladewise"



In [133]:

    
tree <- read.tree(text = "(((A,B),(C,D)),E);")
plot(tree, type = "cladogram", edge.width = 2)



In [22]:

    
tree









    





Phylogenetic tree with 5 tips and 4 internal nodes.

Tip labels:
[1] "A" "B" "C" "D" "E"

Rooted; no branch lengths.



In [23]:

    
str(tree)









    



List of 3
 $ edge     : int [1:8, 1:2] 6 7 8 8 7 9 9 6 7 8 ...
 $ tip.label: chr [1:5] "A" "B" "C" "D" ...
 $ Nnode    : int 4
 - attr(*, "class")= chr "phylo"
 - attr(*, "order")= chr "cladewise"



In [24]:

    
tree$edge



In [25]:

    
tree$tip.label









    





	'A'
	'B'
	'C'
	'D'
	'E'



In [26]:

    
tree$Nnode



In [30]:

    
plot(tree, edge.width = 2, label.offset = 0.1, type = "cladogram")
nodelabels()
tiplabels()
# N.B. these must be called here to render labels!



In [34]:

    
is.binary.tree(tree)









    




TRUE



In [42]:

    
library(jsonlite)
# N.B. 'mtcars' is a built-in sample data frame
x <- toJSON(mtcars, pretty=TRUE)
cat(x)









    



[
  {
    "mpg": 21,
    "cyl": 6,
    "disp": 160,
    "hp": 110,
    "drat": 3.9,
    "wt": 2.62,
    "qsec": 16.46,
    "vs": 0,
    "am": 1,
    "gear": 4,
    "carb": 4,
    "_row": "Mazda RX4"
  },
  {
    "mpg": 21,
    "cyl": 6,
    "disp": 160,
    "hp": 110,
    "drat": 3.9,
    "wt": 2.875,
    "qsec": 17.02,
    "vs": 0,
    "am": 1,
    "gear": 4,
    "carb": 4,
    "_row": "Mazda RX4 Wag"
  },
  {
    "mpg": 22.8,
    "cyl": 4,
    "disp": 108,
    "hp": 93,
    "drat": 3.85,
    "wt": 2.32,
    "qsec": 18.61,
    "vs": 1,
    "am": 1,
    "gear": 4,
    "carb": 1,
    "_row": "Datsun 710"
  },
  {
    "mpg": 21.4,
    "cyl": 6,
    "disp": 258,
    "hp": 110,
    "drat": 3.08,
    "wt": 3.215,
    "qsec": 19.44,
    "vs": 1,
    "am": 0,
    "gear": 3,
    "carb": 1,
    "_row": "Hornet 4 Drive"
  },
  {
    "mpg": 18.7,
    "cyl": 8,
    "disp": 360,
    "hp": 175,
    "drat": 3.15,
    "wt": 3.44,
    "qsec": 17.02,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 2,
    "_row": "Hornet Sportabout"
  },
  {
    "mpg": 18.1,
    "cyl": 6,
    "disp": 225,
    "hp": 105,
    "drat": 2.76,
    "wt": 3.46,
    "qsec": 20.22,
    "vs": 1,
    "am": 0,
    "gear": 3,
    "carb": 1,
    "_row": "Valiant"
  },
  {
    "mpg": 14.3,
    "cyl": 8,
    "disp": 360,
    "hp": 245,
    "drat": 3.21,
    "wt": 3.57,
    "qsec": 15.84,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 4,
    "_row": "Duster 360"
  },
  {
    "mpg": 24.4,
    "cyl": 4,
    "disp": 146.7,
    "hp": 62,
    "drat": 3.69,
    "wt": 3.19,
    "qsec": 20,
    "vs": 1,
    "am": 0,
    "gear": 4,
    "carb": 2,
    "_row": "Merc 240D"
  },
  {
    "mpg": 22.8,
    "cyl": 4,
    "disp": 140.8,
    "hp": 95,
    "drat": 3.92,
    "wt": 3.15,
    "qsec": 22.9,
    "vs": 1,
    "am": 0,
    "gear": 4,
    "carb": 2,
    "_row": "Merc 230"
  },
  {
    "mpg": 19.2,
    "cyl": 6,
    "disp": 167.6,
    "hp": 123,
    "drat": 3.92,
    "wt": 3.44,
    "qsec": 18.3,
    "vs": 1,
    "am": 0,
    "gear": 4,
    "carb": 4,
    "_row": "Merc 280"
  },
  {
    "mpg": 17.8,
    "cyl": 6,
    "disp": 167.6,
    "hp": 123,
    "drat": 3.92,
    "wt": 3.44,
    "qsec": 18.9,
    "vs": 1,
    "am": 0,
    "gear": 4,
    "carb": 4,
    "_row": "Merc 280C"
  },
  {
    "mpg": 16.4,
    "cyl": 8,
    "disp": 275.8,
    "hp": 180,
    "drat": 3.07,
    "wt": 4.07,
    "qsec": 17.4,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 3,
    "_row": "Merc 450SE"
  },
  {
    "mpg": 17.3,
    "cyl": 8,
    "disp": 275.8,
    "hp": 180,
    "drat": 3.07,
    "wt": 3.73,
    "qsec": 17.6,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 3,
    "_row": "Merc 450SL"
  },
  {
    "mpg": 15.2,
    "cyl": 8,
    "disp": 275.8,
    "hp": 180,
    "drat": 3.07,
    "wt": 3.78,
    "qsec": 18,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 3,
    "_row": "Merc 450SLC"
  },
  {
    "mpg": 10.4,
    "cyl": 8,
    "disp": 472,
    "hp": 205,
    "drat": 2.93,
    "wt": 5.25,
    "qsec": 17.98,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 4,
    "_row": "Cadillac Fleetwood"
  },
  {
    "mpg": 10.4,
    "cyl": 8,
    "disp": 460,
    "hp": 215,
    "drat": 3,
    "wt": 5.424,
    "qsec": 17.82,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 4,
    "_row": "Lincoln Continental"
  },
  {
    "mpg": 14.7,
    "cyl": 8,
    "disp": 440,
    "hp": 230,
    "drat": 3.23,
    "wt": 5.345,
    "qsec": 17.42,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 4,
    "_row": "Chrysler Imperial"
  },
  {
    "mpg": 32.4,
    "cyl": 4,
    "disp": 78.7,
    "hp": 66,
    "drat": 4.08,
    "wt": 2.2,
    "qsec": 19.47,
    "vs": 1,
    "am": 1,
    "gear": 4,
    "carb": 1,
    "_row": "Fiat 128"
  },
  {
    "mpg": 30.4,
    "cyl": 4,
    "disp": 75.7,
    "hp": 52,
    "drat": 4.93,
    "wt": 1.615,
    "qsec": 18.52,
    "vs": 1,
    "am": 1,
    "gear": 4,
    "carb": 2,
    "_row": "Honda Civic"
  },
  {
    "mpg": 33.9,
    "cyl": 4,
    "disp": 71.1,
    "hp": 65,
    "drat": 4.22,
    "wt": 1.835,
    "qsec": 19.9,
    "vs": 1,
    "am": 1,
    "gear": 4,
    "carb": 1,
    "_row": "Toyota Corolla"
  },
  {
    "mpg": 21.5,
    "cyl": 4,
    "disp": 120.1,
    "hp": 97,
    "drat": 3.7,
    "wt": 2.465,
    "qsec": 20.01,
    "vs": 1,
    "am": 0,
    "gear": 3,
    "carb": 1,
    "_row": "Toyota Corona"
  },
  {
    "mpg": 15.5,
    "cyl": 8,
    "disp": 318,
    "hp": 150,
    "drat": 2.76,
    "wt": 3.52,
    "qsec": 16.87,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 2,
    "_row": "Dodge Challenger"
  },
  {
    "mpg": 15.2,
    "cyl": 8,
    "disp": 304,
    "hp": 150,
    "drat": 3.15,
    "wt": 3.435,
    "qsec": 17.3,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 2,
    "_row": "AMC Javelin"
  },
  {
    "mpg": 13.3,
    "cyl": 8,
    "disp": 350,
    "hp": 245,
    "drat": 3.73,
    "wt": 3.84,
    "qsec": 15.41,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 4,
    "_row": "Camaro Z28"
  },
  {
    "mpg": 19.2,
    "cyl": 8,
    "disp": 400,
    "hp": 175,
    "drat": 3.08,
    "wt": 3.845,
    "qsec": 17.05,
    "vs": 0,
    "am": 0,
    "gear": 3,
    "carb": 2,
    "_row": "Pontiac Firebird"
  },
  {
    "mpg": 27.3,
    "cyl": 4,
    "disp": 79,
    "hp": 66,
    "drat": 4.08,
    "wt": 1.935,
    "qsec": 18.9,
    "vs": 1,
    "am": 1,
    "gear": 4,
    "carb": 1,
    "_row": "Fiat X1-9"
  },
  {
    "mpg": 26,
    "cyl": 4,
    "disp": 120.3,
    "hp": 91,
    "drat": 4.43,
    "wt": 2.14,
    "qsec": 16.7,
    "vs": 0,
    "am": 1,
    "gear": 5,
    "carb": 2,
    "_row": "Porsche 914-2"
  },
  {
    "mpg": 30.4,
    "cyl": 4,
    "disp": 95.1,
    "hp": 113,
    "drat": 3.77,
    "wt": 1.513,
    "qsec": 16.9,
    "vs": 1,
    "am": 1,
    "gear": 5,
    "carb": 2,
    "_row": "Lotus Europa"
  },
  {
    "mpg": 15.8,
    "cyl": 8,
    "disp": 351,
    "hp": 264,
    "drat": 4.22,
    "wt": 3.17,
    "qsec": 14.5,
    "vs": 0,
    "am": 1,
    "gear": 5,
    "carb": 4,
    "_row": "Ford Pantera L"
  },
  {
    "mpg": 19.7,
    "cyl": 6,
    "disp": 145,
    "hp": 175,
    "drat": 3.62,
    "wt": 2.77,
    "qsec": 15.5,
    "vs": 0,
    "am": 1,
    "gear": 5,
    "carb": 6,
    "_row": "Ferrari Dino"
  },
  {
    "mpg": 15,
    "cyl": 8,
    "disp": 301,
    "hp": 335,
    "drat": 3.54,
    "wt": 3.57,
    "qsec": 14.6,
    "vs": 0,
    "am": 1,
    "gear": 5,
    "carb": 8,
    "_row": "Maserati Bora"
  },
  {
    "mpg": 21.4,
    "cyl": 4,
    "disp": 121,
    "hp": 109,
    "drat": 4.11,
    "wt": 2.78,
    "qsec": 18.6,
    "vs": 1,
    "am": 1,
    "gear": 4,
    "carb": 2,
    "_row": "Volvo 142E"
  }
]

OK, so let's try a straightforward conversion using the pattern above:



In [53]:

    
toJSON(tree, pretty=TRUE)









    



Error: No method asJSON S3 class: phylo
Traceback:

1. toJSON(tree, pretty = TRUE)
2. asJSON(x, dataframe = dataframe, Date = Date, POSIXt = POSIXt, 
 .     factor = factor, complex = complex, raw = raw, matrix = matrix, 
 .     auto_unbox = auto_unbox, digits = digits, na = na, null = null, 
 .     force = force, indent = indent, ...)
3. asJSON(x, dataframe = dataframe, Date = Date, POSIXt = POSIXt, 
 .     factor = factor, complex = complex, raw = raw, matrix = matrix, 
 .     auto_unbox = auto_unbox, digits = digits, na = na, null = null, 
 .     force = force, indent = indent, ...)
4. .local(x, ...)
5. stop("No method asJSON S3 class: ", class(x))
6. base::stop(..., call. = FALSE)

No dice! If only there was a way to force a liberal interpretation of obscure classes. (SPOILER: There is.)



In [51]:

    
toJSON(tree, force=TRUE)









    





{"edge":[[6,7],[7,8],[8,1],[8,2],[7,9],[9,3],[9,4],[6,5]],"tip.label":["A","B","C","D","E"],"Nnode":[4]}

Is that all there is in tree !? It just doesn't seem like enough data. But it's true! See this explanation.



In [52]:

    
str(tree)









    



List of 3
 $ edge     : int [1:8, 1:2] 6 7 8 8 7 9 9 6 7 8 ...
 $ tip.label: chr [1:5] "A" "B" "C" "D" ...
 $ Nnode    : int 4
 - attr(*, "class")= chr "phylo"
 - attr(*, "order")= chr "cladewise"

If force won't do the trick for some reason, here's an example of how to walk an R object piecemeal and serialize its parts more selectively.

For more background, here are the design objectives of the jsonlite R package and a wonderful "package vignette" that describes its class-based (de)serialization in detail. Here they briefly mention adding methods for new classes:

Users in R can extend this system by implementing additional methods for other classes.

It's a bit hazy on how this could be implemented, but the jsonlite source seems to be on GitHub. But this discussion in their issue tracker tells me that this extensibility was a hoped-for feature they've been unable to deliver.

Still, it offers an intriguing possibility: We could write toJSON/fromJSON for phylo objects, using NexSON as the serialization schema in JSON! I'm not sure this is a good idea, but it's food for thought.

We can do more piecemeal conversion using flexible functions like lapply() or by borrowing (de)serialization innards from jsonlite like so:



In [69]:

    
temp.string = jsonlite::serializeJSON(x=list("foo",2))
temp.string









    




'{"type":"list","attributes":{},"value":[{"type":"character","attributes":{},"value":["foo"]},{"type":"double","attributes":{},"value":[2]}]}'



In [70]:

    
temp.restored = jsonlite::unserializeJSON(temp.string)
str(temp.restored)









    



List of 2
 $ : chr "foo"
 $ : num 2

Anyway, we might never use this. Let's move on.

Importing the Tree Illustrator!

So it turns out "magics" like %%javascript are really specific to the IPython kernel, and there are no plans to implement them in the R kernel. I struggled with how to inject Javascript in an R notebook, and finally stumbled onto an example of simply echoing the SCRIPT tag as a string. Since R is so naive about Javascript, it simply parrots the markup into the cell's output and the script runs!



In [1]:

    
# To use Javascript in an R notebook, just spell it out and run the cell!
'<SCRIPT TYPE="text/javascript">
    var element = $(IPython.notebook.container).find(".cell.running .output_subarea");
    //$.getScript("//rawgit.com/OpenTreeOfLife/tree-illustrator/1a5e8db/stylist/ipynb-tree-illustrator.js",
    $.getScript("//rawgit.com/OpenTreeOfLife/tree-illustrator/9480fc59e72212685ccbd85ce3f16bff3e8f6802/stylist/ipynb-tree-illustrator.js",
        function() {
            /* This function is called once the IPythonTreeIllustrator module has loaded. 
             * N.B. we mimic the `element` value (a jQuery selection of the output area of
             * this cell) defined by %%javascript magic, which is only available in the 
             * IPython kernel. 
             */
            IPythonTreeIllustrator.initNotebookUI(element);
        }
    );
</SCRIPT>'

''

Now we can launch the Tree Illustrator and try (fail) to load R variables. So it's time to add that option to ipynb-tree-illustrator.js!



In [110]:

    
ls









    




function (name, pos = -1L, envir = as.environment(pos), all.names = FALSE, 
    pattern, sorted = TRUE) 
{
    if (!missing(name)) {
        pos <- tryCatch(name, error = function(e) e)
        if (inherits(pos, "error")) {
            name <- substitute(name)
            if (!is.character(name)) 
                name <- deparse(name)
            warning(gettextf("%s converted to character string", 
                sQuote(name)), domain = NA)
            pos <- name
        }
    }
    all.names <- .Internal(ls(envir, all.names, sorted))
    if (!missing(pattern)) {
        if ((ll <- length(grep("[", pattern, fixed = TRUE))) && 
            ll != length(grep("]", pattern, fixed = TRUE))) {
            if (pattern == "[") {
                pattern <- "\\["
                warning("replaced regular expression pattern '[' by  '\\\\['")
            }
            else if (length(grep("[^\\\\]\\[<-", pattern))) {
                pattern <- sub("\\[<-", "\\\\\\[<-", pattern)
                warning("replaced '[<-' by '\\\\[<-' in regular expression pattern")
            }
        }
        grep(pattern, all.names, value = TRUE)
    }
    else all.names
}



In [111]:

    
ls()









    





	'q'
	'quit'
	'temp.restored'
	'temp.string'
	'tree'
	'x'



In [112]:

    
require('OOFOO')









    



Loading required package: OOFOO
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘OOFOO’



In [130]:

    
if (!require('FOOFOO')) {
    cat(TRUE)
}









    



Loading required package: FOOFOO
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘FOOFOO’





    



TRUE



In [147]:

    
library(jsonlite)
.local.vars = ls()
toJSON( c(.local.vars) )









    





["local.vars","q","quit","temp.restored","temp.string","tree","x"]



In [170]:

    
get('tree')









    





Phylogenetic tree with 5 tips and 4 internal nodes.

Tip labels:
[1] "A" "B" "C" "D" "E"

Rooted; no branch lengths.



In [217]:

    
.ti.locals = ls()
.ti.locals <- lapply( .ti.locals, function(varName) {
    print(paste("STARTING with", varName))
    varValue = get(varName)
    print(paste(">>> ", varName, " is a <", class(varValue), ">:"))
    #print(varValue)    
    return( c(varName, class(varValue), 'R') )
})

#results









    



[1] "STARTING with local.vars"
[1] ">>>  local.vars  is a < character >:"
[1] "STARTING with q"
[1] ">>>  q  is a < function >:"
[1] "STARTING with quit"
[1] ">>>  quit  is a < function >:"
[1] "STARTING with results"
[1] ">>>  results  is a < list >:"
[1] "STARTING with S"
[1] ">>>  S  is a < numeric >:"
[1] "STARTING with temp.restored"
[1] ">>>  temp.restored  is a < list >:"
[1] "STARTING with temp.string"
[1] ">>>  temp.string  is a < character >:"
[1] "STARTING with tree"
[1] ">>>  tree  is a < phylo >:"
[1] "STARTING with x"
[1] ">>>  x  is a < integer >:"
[1] "STARTING with Z"
[1] ">>>  Z  is a < numeric >:"



In [218]:

    
.ti.locals









    





	
	'local.vars'
	'character'
	'R'


	
	'q'
	'function'
	'R'


	
	'quit'
	'function'
	'R'


	
	'results'
	'list'
	'R'


	
	'S'
	'numeric'
	'R'


	
	'temp.restored'
	'list'
	'R'


	
	'temp.string'
	'character'
	'R'


	
	'tree'
	'phylo'
	'R'


	
	'x'
	'integer'
	'R'


	
	'Z'
	'numeric'
	'R'



In [219]:

    
toJSON(.ti.locals, force=TRUE)









    





[["local.vars","character","R"],["q","function","R"],["quit","function","R"],["results","list","R"],["S","numeric","R"],["temp.restored","list","R"],["temp.string","character","R"],["tree","phylo","R"],["x","integer","R"],["Z","numeric","R"]]

Converting R phylo objects to NexSON for use in Tree Illustrator

At this point we have a few options:

write a JS converter (Vega data transform) to do this from scratch
teach peyotl to import R phylo objects and convert to NexSON
look for more help in R packages

Not surprisingly, ape knows how to write phylo objects out as Newick or NEXUS:



In [293]:

    
testnewick = write.tree(tree)
testnewick









    




'(((A,B),(C,D)),E);'



In [250]:

    
write.nexus(tree)









    



#NEXUS
[R-package APE, Sat Mar 26 20:24:51 2016]

BEGIN TAXA;
	DIMENSIONS NTAX = 5;
	TAXLABELS
		A
		B
		C
		D
		E
	;
END;
BEGIN TREES;
	TRANSLATE
		1	A,
		2	B,
		3	C,
		4	D,
		5	E
	;
	TREE * UNTITLED = [&R] (((1,2),(3,4)),5);
END;

Since NEXUS is the richer of the two formats, we should try this first and pass the result to peyotl for conversion to NexSON.

Note that there's also a method write.nexus.data() to generate NEXUS from sequences (character data). We can read this directly into the Tree Illustrator, then pass it on to peyotl for conversion to NexSON. But will peyotl capture anything beyond the basic tree structure and labels? Let's find out!

Here are some BAMM snippets provided by @rhr:



In [299]:

    
# Extract DTrates from BAMM object

library(BAMMtools)
data(primates)
data(events.primates)
edata <- getEventData(primates, events.primates, burnin=0.25, type = 'trait')
dtrates = dtRates(edata, tau=0.01, tmat=T)

# tmat is the matrix of branch segments
tmat = dtrates$dtrates$tmat
# reconstructed rates. Each entry corresponds to a branch segment
rates = dtrates$dtrates$rates









    



Processing event data from data.frame

Discarded as burnin: GENERATIONS <  4990000
Analyzing  1501  samples from posterior

Setting recursive sequence on tree...

Done with recursive sequence



In [310]:

    
write.nexus(primates)









    



#NEXUS
[R-package APE, Sun Mar 27 17:21:57 2016]

BEGIN TAXA;
	DIMENSIONS NTAX = 233;
	TAXLABELS
		Galago_matschiei
		Euoticus_pallidus
		Euoticus_elegantulus
		Galagoides_zanzibaricus
		Galagoides_demidoff
		Galago_alleni
		Galago_senegalensis
		Galago_moholi
		Galago_gallarum
		Otolemur_garnettii
		Otolemur_crassicaudatus
		Perodicticus_potto
		Arctocebus_aureus
		Arctocebus_calabarensis
		Loris_tardigradus
		Nycticebus_pygmaeus
		Nycticebus_coucang
		Daubentonia_madagascariensis
		Lepilemur_mustelinus
		Lepilemur_septentrionalis
		Lepilemur_ruficaudatus
		Lepilemur_leucopus
		Lepilemur_edwardsi
		Lepilemur_microdon
		Lepilemur_dorsalis
		Lemur_catta
		Hapalemur_aureus
		Hapalemur_simus
		Hapalemur_griseus
		Varecia_variegata
		Eulemur_rubriventer
		Eulemur_mongoz
		Eulemur_coronatus
		Eulemur_macaco
		Eulemur_fulvus
		Avahi_laniger
		Indri_indri
		Propithecus_diadema
		Propithecus_verreauxi
		Propithecus_tattersalli
		Phaner_furcifer
		Allocebus_trichotis
		Microcebus_coquereli
		Microcebus_rufus
		Microcebus_murinus
		Cheirogaleus_medius
		Cheirogaleus_major
		Tarsius_dianae
		Tarsius_pumilus
		Tarsius_spectrum
		Tarsius_syrichta
		Tarsius_bancanus
		Chiropotes_satanas
		Chiropotes_albinasus
		Cacajao_melanocephalus
		Cacajao_calvus
		Pithecia_pithecia
		Pithecia_irrorata
		Pithecia_aequatorialis
		Pithecia_monachus
		Pithecia_albicans
		Callicebus_torquatus
		Callicebus_modestus
		Callicebus_oenanthe
		Callicebus_olallae
		Callicebus_donacophilus
		Callicebus_personatus
		Callicebus_dubius
		Callicebus_cupreus
		Callicebus_caligatus
		Callicebus_hoffmannsi
		Callicebus_brunneus
		Callicebus_moloch
		Callicebus_cinerascens
		Alouatta_palliata
		Alouatta_coibensis
		Alouatta_caraya
		Alouatta_pigra
		Alouatta_fusca
		Alouatta_seniculus
		Alouatta_sara
		Alouatta_belzebul
		Ateles_paniscus
		Ateles_belzebuth
		Ateles_geoffroyi
		Ateles_fusciceps
		Ateles_marginatus
		Ateles_chamek
		Brachyteles_arachnoides
		Lagothrix_lagotricha
		Lagothrix_flavicauda
		Cebus_olivaceus
		Cebus_apella
		Cebus_capucinus
		Cebus_albifrons
		Saimiri_boliviensis
		Saimiri_vanzolinii
		Saimiri_sciureus
		Saimiri_ustus
		Saimiri_oerstedii
		Aotus_lemurinus
		Aotus_hershkovitzi
		Aotus_vociferans
		Aotus_brumbacki
		Aotus_nancymaae
		Aotus_miconax
		Aotus_infulatus
		Aotus_nigriceps
		Aotus_trivirgatus
		Aotus_azarai
		Callimico_goeldii
		Callithrix_pygmaea
		Callithrix_humeralifera
		Callithrix_argentata
		Callithrix_flaviceps
		Callithrix_aurita
		Callithrix_kuhlii
		Callithrix_geoffroyi
		Callithrix_penicillata
		Callithrix_jacchus
		Leontopithecus_chrysomela
		Leontopithecus_caissara
		Leontopithecus_rosalia
		Leontopithecus_chrysopygus
		Saguinus_oedipus
		Saguinus_geoffroyi
		Saguinus_midas
		Saguinus_bicolor
		Saguinus_leucopus
		Saguinus_imperator
		Saguinus_mystax
		Saguinus_labiatus
		Saguinus_inustus
		Saguinus_nigricollis
		Saguinus_tripartitus
		Saguinus_fuscicollis
		Pongo_pygmaeus
		Gorilla_gorilla
		Homo_sapiens
		Pan_troglodytes
		Pan_paniscus
		Hylobates_hoolock
		Hylobates_moloch
		Hylobates_lar
		Hylobates_agilis
		Hylobates_pileatus
		Hylobates_muelleri
		Hylobates_klossii
		Hylobates_syndactylus
		Hylobates_gabriellae
		Hylobates_leucogenys
		Hylobates_concolor
		Trachypithecus_geei
		Trachypithecus_auratus
		Trachypithecus_francoisi
		Trachypithecus_cristatus
		Trachypithecus_pileatus
		Trachypithecus_phayrei
		Trachypithecus_obscurus
		Semnopithecus_entellus
		Presbytis_potenziani
		Presbytis_comata
		Presbytis_frontata
		Presbytis_femoralis
		Presbytis_melalophos
		Presbytis_rubicunda
		Presbytis_thomasi
		Presbytis_hosei
		Trachypithecus_johnii
		Trachypithecus_vetulus
		Pygathrix_nemaeus
		Pygathrix_avunculus
		Pygathrix_roxellana
		Pygathrix_brelichi
		Pygathrix_bieti
		Nasalis_larvatus
		Nasalis_concolor
		Procolobus_preussi
		Procolobus_verus
		Procolobus_rufomitratus
		Procolobus_pennantii
		Procolobus_badius
		Colobus_satanas
		Colobus_angolensis
		Colobus_polykomos
		Colobus_guereza
		Mandrillus_sphinx
		Mandrillus_leucophaeus
		Cercocebus_torquatus
		Cercocebus_agilis
		Cercocebus_galeritus
		Lophocebus_albigena
		Theropithecus_gelada
		Papio_hamadryas
		Macaca_sylvanus
		Macaca_tonkeana
		Macaca_maura
		Macaca_ochreata
		Macaca_nigra
		Macaca_silenus
		Macaca_nemestrina
		Macaca_arctoides
		Macaca_radiata
		Macaca_assamensis
		Macaca_thibetana
		Macaca_sinica
		Macaca_fascicularis
		Macaca_fuscata
		Macaca_mulatta
		Macaca_cyclopis
		Allenopithecus_nigroviridis
		Miopithecus_talapoin
		Erythrocebus_patas
		Chlorocebus_aethiops
		Cercopithecus_solatus
		Cercopithecus_preussi
		Cercopithecus_lhoesti
		Cercopithecus_hamlyni
		Cercopithecus_neglectus
		Cercopithecus_mona
		Cercopithecus_campbelli
		Cercopithecus_wolfi
		Cercopithecus_pogonias
		Cercopithecus_erythrotis
		Cercopithecus_sclateri
		Cercopithecus_cephus
		Cercopithecus_ascanius
		Cercopithecus_petaurista
		Cercopithecus_erythrogaster
		Cercopithecus_nictitans
		Cercopithecus_mitis
		Cercopithecus_dryas
		Cercopithecus_diana
	;
END;
BEGIN TREES;
	TRANSLATE
		1	Galago_matschiei,
		2	Euoticus_pallidus,
		3	Euoticus_elegantulus,
		4	Galagoides_zanzibaricus,
		5	Galagoides_demidoff,
		6	Galago_alleni,
		7	Galago_senegalensis,
		8	Galago_moholi,
		9	Galago_gallarum,
		10	Otolemur_garnettii,
		11	Otolemur_crassicaudatus,
		12	Perodicticus_potto,
		13	Arctocebus_aureus,
		14	Arctocebus_calabarensis,
		15	Loris_tardigradus,
		16	Nycticebus_pygmaeus,
		17	Nycticebus_coucang,
		18	Daubentonia_madagascariensis,
		19	Lepilemur_mustelinus,
		20	Lepilemur_septentrionalis,
		21	Lepilemur_ruficaudatus,
		22	Lepilemur_leucopus,
		23	Lepilemur_edwardsi,
		24	Lepilemur_microdon,
		25	Lepilemur_dorsalis,
		26	Lemur_catta,
		27	Hapalemur_aureus,
		28	Hapalemur_simus,
		29	Hapalemur_griseus,
		30	Varecia_variegata,
		31	Eulemur_rubriventer,
		32	Eulemur_mongoz,
		33	Eulemur_coronatus,
		34	Eulemur_macaco,
		35	Eulemur_fulvus,
		36	Avahi_laniger,
		37	Indri_indri,
		38	Propithecus_diadema,
		39	Propithecus_verreauxi,
		40	Propithecus_tattersalli,
		41	Phaner_furcifer,
		42	Allocebus_trichotis,
		43	Microcebus_coquereli,
		44	Microcebus_rufus,
		45	Microcebus_murinus,
		46	Cheirogaleus_medius,
		47	Cheirogaleus_major,
		48	Tarsius_dianae,
		49	Tarsius_pumilus,
		50	Tarsius_spectrum,
		51	Tarsius_syrichta,
		52	Tarsius_bancanus,
		53	Chiropotes_satanas,
		54	Chiropotes_albinasus,
		55	Cacajao_melanocephalus,
		56	Cacajao_calvus,
		57	Pithecia_pithecia,
		58	Pithecia_irrorata,
		59	Pithecia_aequatorialis,
		60	Pithecia_monachus,
		61	Pithecia_albicans,
		62	Callicebus_torquatus,
		63	Callicebus_modestus,
		64	Callicebus_oenanthe,
		65	Callicebus_olallae,
		66	Callicebus_donacophilus,
		67	Callicebus_personatus,
		68	Callicebus_dubius,
		69	Callicebus_cupreus,
		70	Callicebus_caligatus,
		71	Callicebus_hoffmannsi,
		72	Callicebus_brunneus,
		73	Callicebus_moloch,
		74	Callicebus_cinerascens,
		75	Alouatta_palliata,
		76	Alouatta_coibensis,
		77	Alouatta_caraya,
		78	Alouatta_pigra,
		79	Alouatta_fusca,
		80	Alouatta_seniculus,
		81	Alouatta_sara,
		82	Alouatta_belzebul,
		83	Ateles_paniscus,
		84	Ateles_belzebuth,
		85	Ateles_geoffroyi,
		86	Ateles_fusciceps,
		87	Ateles_marginatus,
		88	Ateles_chamek,
		89	Brachyteles_arachnoides,
		90	Lagothrix_lagotricha,
		91	Lagothrix_flavicauda,
		92	Cebus_olivaceus,
		93	Cebus_apella,
		94	Cebus_capucinus,
		95	Cebus_albifrons,
		96	Saimiri_boliviensis,
		97	Saimiri_vanzolinii,
		98	Saimiri_sciureus,
		99	Saimiri_ustus,
		100	Saimiri_oerstedii,
		101	Aotus_lemurinus,
		102	Aotus_hershkovitzi,
		103	Aotus_vociferans,
		104	Aotus_brumbacki,
		105	Aotus_nancymaae,
		106	Aotus_miconax,
		107	Aotus_infulatus,
		108	Aotus_nigriceps,
		109	Aotus_trivirgatus,
		110	Aotus_azarai,
		111	Callimico_goeldii,
		112	Callithrix_pygmaea,
		113	Callithrix_humeralifera,
		114	Callithrix_argentata,
		115	Callithrix_flaviceps,
		116	Callithrix_aurita,
		117	Callithrix_kuhlii,
		118	Callithrix_geoffroyi,
		119	Callithrix_penicillata,
		120	Callithrix_jacchus,
		121	Leontopithecus_chrysomela,
		122	Leontopithecus_caissara,
		123	Leontopithecus_rosalia,
		124	Leontopithecus_chrysopygus,
		125	Saguinus_oedipus,
		126	Saguinus_geoffroyi,
		127	Saguinus_midas,
		128	Saguinus_bicolor,
		129	Saguinus_leucopus,
		130	Saguinus_imperator,
		131	Saguinus_mystax,
		132	Saguinus_labiatus,
		133	Saguinus_inustus,
		134	Saguinus_nigricollis,
		135	Saguinus_tripartitus,
		136	Saguinus_fuscicollis,
		137	Pongo_pygmaeus,
		138	Gorilla_gorilla,
		139	Homo_sapiens,
		140	Pan_troglodytes,
		141	Pan_paniscus,
		142	Hylobates_hoolock,
		143	Hylobates_moloch,
		144	Hylobates_lar,
		145	Hylobates_agilis,
		146	Hylobates_pileatus,
		147	Hylobates_muelleri,
		148	Hylobates_klossii,
		149	Hylobates_syndactylus,
		150	Hylobates_gabriellae,
		151	Hylobates_leucogenys,
		152	Hylobates_concolor,
		153	Trachypithecus_geei,
		154	Trachypithecus_auratus,
		155	Trachypithecus_francoisi,
		156	Trachypithecus_cristatus,
		157	Trachypithecus_pileatus,
		158	Trachypithecus_phayrei,
		159	Trachypithecus_obscurus,
		160	Semnopithecus_entellus,
		161	Presbytis_potenziani,
		162	Presbytis_comata,
		163	Presbytis_frontata,
		164	Presbytis_femoralis,
		165	Presbytis_melalophos,
		166	Presbytis_rubicunda,
		167	Presbytis_thomasi,
		168	Presbytis_hosei,
		169	Trachypithecus_johnii,
		170	Trachypithecus_vetulus,
		171	Pygathrix_nemaeus,
		172	Pygathrix_avunculus,
		173	Pygathrix_roxellana,
		174	Pygathrix_brelichi,
		175	Pygathrix_bieti,
		176	Nasalis_larvatus,
		177	Nasalis_concolor,
		178	Procolobus_preussi,
		179	Procolobus_verus,
		180	Procolobus_rufomitratus,
		181	Procolobus_pennantii,
		182	Procolobus_badius,
		183	Colobus_satanas,
		184	Colobus_angolensis,
		185	Colobus_polykomos,
		186	Colobus_guereza,
		187	Mandrillus_sphinx,
		188	Mandrillus_leucophaeus,
		189	Cercocebus_torquatus,
		190	Cercocebus_agilis,
		191	Cercocebus_galeritus,
		192	Lophocebus_albigena,
		193	Theropithecus_gelada,
		194	Papio_hamadryas,
		195	Macaca_sylvanus,
		196	Macaca_tonkeana,
		197	Macaca_maura,
		198	Macaca_ochreata,
		199	Macaca_nigra,
		200	Macaca_silenus,
		201	Macaca_nemestrina,
		202	Macaca_arctoides,
		203	Macaca_radiata,
		204	Macaca_assamensis,
		205	Macaca_thibetana,
		206	Macaca_sinica,
		207	Macaca_fascicularis,
		208	Macaca_fuscata,
		209	Macaca_mulatta,
		210	Macaca_cyclopis,
		211	Allenopithecus_nigroviridis,
		212	Miopithecus_talapoin,
		213	Erythrocebus_patas,
		214	Chlorocebus_aethiops,
		215	Cercopithecus_solatus,
		216	Cercopithecus_preussi,
		217	Cercopithecus_lhoesti,
		218	Cercopithecus_hamlyni,
		219	Cercopithecus_neglectus,
		220	Cercopithecus_mona,
		221	Cercopithecus_campbelli,
		222	Cercopithecus_wolfi,
		223	Cercopithecus_pogonias,
		224	Cercopithecus_erythrotis,
		225	Cercopithecus_sclateri,
		226	Cercopithecus_cephus,
		227	Cercopithecus_ascanius,
		228	Cercopithecus_petaurista,
		229	Cercopithecus_erythrogaster,
		230	Cercopithecus_nictitans,
		231	Cercopithecus_mitis,
		232	Cercopithecus_dryas,
		233	Cercopithecus_diana
	;
	TREE * UNTITLED = [&R] (((((1:3.644984273,(2:1.449862152,3:1.449862152):2.19512212):4.875712214,((4:3.574103734,5:3.574103734):3.753222182,((6:5.403508585,((7:1.46115685,8:1.46115685):0.9031863282,9:2.364343178):3.039165407):0.9126765822,(10:4.242644127,11:4.242644127):2.07354104):1.011140749):1.19337057):12.40170848,((12:4.703629279,(13:1.881771918,14:1.881771918):2.821857361):11.63769999,(15:9.200565853,(16:2.672476766,17:2.672476766):6.528089088):7.140763412):4.581075703):30.9481165,(18:39.48238529,((((19:11.19994092,(20:7.600895938,(21:5.028627182,(22:3.00293009,((23:0.4532281942,24:0.4532281942):0.9099348266,25:1.363163021):1.639767069):2.025697092):2.572268756):3.599044977):5.972299255,((26:6.229068058,((27:5.342908924,28:5.342908924):0.3195365339,29:5.662445458):0.5666226004):6.830461251,(30:11.89273831,((31:3.074034512,32:3.074034512):3.302548494,(33:3.756910335,(34:3.684015058,35:3.684015058):0.07289527772):2.61967267):5.516155306):1.166790997):4.112710861):4.862567529,(36:13.61679482,(37:7.435235336,(38:5.879825205,(39:1.54141842,40:1.54141842):4.338406785):1.555410131):6.181559482):8.418012881):5.481371118,(41:17.03543968,((42:7.053370093,(43:4.099785478,(44:2.737419707,45:2.737419707):1.362365772):2.953584615):4.41733529,(46:9.4004694,47:9.4004694):2.070235983):5.564734292):10.48073914):11.96620647):12.38813618):13.22116451,((((48:0.2574238833,49:0.2574238833):15.04352481,50:15.30094869):19.88152752,(51:8.683554425,52:8.683554425):26.49892178):27.41764581,(((((((53:3.688446923,54:3.688446923):4.43397097,(55:3.700510722,56:3.700510722):4.421907171):3.758327519,(57:10.23381691,(58:6.549583463,(59:3.789893236,(60:1.755629589,61:1.755629589):2.034263646):2.759690228):3.684233443):1.646928507):9.091857379,(62:16.4714104,((63:7.328813932,((64:0.6554084888,65:0.6554084888):2.430400428,66:3.085808916):4.243005015):5.974162265,(67:10.30345572,((68:4.724420572,(69:1.982769904,70:1.982769904):2.741650669):3.275942328,((71:2.3505473,72:2.3505473):2.976743205,(73:2.323716931,74:2.323716931):3.003573574):2.673072396):2.30309282):2.999520477):3.168434207):4.501192388):4.343687065,(((75:0.5022628648,76:0.5022628648):12.22768188,(77:6.926354953,(78:4.52730596,(79:2.947096325,((80:0.7931449028,81:0.7931449028):0.9655421863,82:1.758687089):1.188409236):1.580209636):2.399048993):5.803589795):7.953558288,(((83:3.038404989,(84:2.0373527,(85:1.215004191,86:1.215004191):0.8223485097):1.001052288):1.654543136,(87:2.885071027,88:2.885071027):1.807877097):6.593561648,(89:9.030844567,(90:2.921910319,91:2.921910319):6.108934248):2.255665205):9.396993264):4.632786821):4.835889797,((((92:3.963779494,93:3.963779494):3.298610745,(94:0.1411841561,95:0.1411841561):7.121206083):15.92417684,(96:8.42086612,(97:6.824135378,(98:3.943009428,(99:1.765312829,100:1.765312829):2.177696599):2.88112595):1.596730742):14.76570096):2.506309495,(((101:3.41619118,102:3.41619118):12.37114501,((103:4.522715102,104:4.522715102):7.223381154,(105:8.668907477,(106:6.289866555,(107:4.164301987,(108:2.631524193,(109:1.237794698,110:1.237794698):1.393729496):1.532777793):2.125564568):2.379040922):3.077188779):4.041239934):6.241568413,((111:18.37696755,((112:3.706008951,(113:2.079201914,114:2.079201914):1.626807038):7.659029351,((115:3.433355688,116:3.433355688):7.766883693,((117:0.2655427553,118:0.2655427553):0.2450028896,(119:0.2563476922,120:0.2563476922):0.2541979527):10.68969374):0.1647989214):7.011929249):0.6106466388,((121:7.67864797,(122:6.625267777,(123:3.83733791,124:3.83733791):2.787929867):1.053380192):7.967671715,(((125:3.279130893,126:3.279130893):4.599071641,(127:3.309205777,128:3.309205777):4.568996757):4.804458654,(129:9.81877075,((130:4.38688854,(131:1.953791812,132:1.953791812):2.433096728):3.291138283,(133:5.079922827,(134:3.038858259,(135:1.38319711,136:1.38319711):1.655661149):2.041064568):2.598103996):2.140743928):2.863890437):2.963658497):3.341294506):3.041290413):3.663971968):4.459303084):21.07285881,(((137:15.84463358,(138:6.414492353,(139:5.067395296,(140:1.95369081,141:1.95369081):3.113704486):1.347097057):9.430141232):3.792242626,((142:4.011578905,((143:3.516831702,(144:3.100837056,145:3.100837056):0.415994646):0.02217424005,(146:2.029256113,(147:0.8819271649,148:0.8819271649):1.147328948):1.50974983):0.4725729627):1.864277026,(149:4.018969267,(150:1.806528048,(151:0.7882422843,152:0.7882422843):1.018285764):2.212441219):1.856886664):13.76102028):12.78015491,(((((((153:5.122402371,(154:3.734662847,(155:2.896936803,(156:0.7948482703,(157:0.7521180596,(158:0.6943398071,159:0.6943398071):0.05777825247):0.04273021076):2.102088533):0.8377260442):1.387739524):1.686236098,160:6.808638469):0.1210272121,(((161:1.894279439,((162:0.2207630615,163:0.2207630615):1.368093801,((164:0.5271822714,165:0.5271822714):1.023551706,(166:0.5324439811,167:0.5324439811):1.018289997):0.03812288497):0.3054225766):1.913113649,168:3.807393089):2.744710106,(169:5.199385085,170:5.199385085):1.35271811):0.3775624863):1.956935552,(171:8.00141983,(172:3.871092153,(173:2.609689257,(174:1.037846215,175:1.037846215):1.571843042):1.261402895):4.130327677):0.8851814025):0.005580154993,(176:3.483864376,177:3.483864376):5.408317012):4.714508807,(((178:3.495012927,179:3.495012927):1.765829351,(180:4.31325428,(181:1.755080673,182:1.755080673):2.558173607):0.9475879969):6.697248224,(183:6.037347054,(184:3.490571445,(185:0.8052450953,186:0.8052450953):2.68532635):2.546775609):5.920743447):1.648599693):4.73007412,(((((187:1.965891197,188:1.965891197):3.476292126,(189:2.313096216,(190:0.5032383396,191:0.5032383396):1.809857876):3.129087107):1.267822239,(192:2.228040923,(193:1.542748547,194:1.542748547):0.6852923762):4.48196464):2.530843414,(195:7.491106738,((((196:0.1352766979,197:0.1352766979):2.512987258,(198:1.653294976,199:1.653294976):0.99496898):0.9324480106,(200:2.244767628,201:2.244767628):1.335944338):2.67575395,((202:2.801002741,((203:0.7161250138,204:0.7161250138):0.9920128354,(205:1.055381942,206:1.055381942):0.6527559075):1.092864892):1.631659175,(207:2.229595922,(208:0.9127479862,(209:0.2690107063,210:0.2690107063):0.6437372799):1.316847935):2.203065995):1.823803999):1.234640822):1.749742238):2.0137033,(211:8.282985373,(212:6.749635282,((213:5.180706992,214:5.180706992):0.5443901029,((215:0.8414405469,(216:0.008617084965,217:0.008617084965):0.832823462):4.070831472,(218:4.215320983,((219:2.558834212,((220:0.786479238,221:0.786479238):0.4537817958,(222:0.7782538441,223:0.7782538441):0.4620071896):1.318573178):1.074499161,(((((224:0.5027196302,225:0.5027196302):0.5295782726,(226:0.488649295,227:0.488649295):0.5436486077):0.6762807982,(228:0.7530173817,229:0.7530173817):0.9555613192):0.6143894491,(230:0.9547751556,231:0.9547751556):1.368192994):0.6306031166,(232:1.234458241,233:1.234458241):1.719113026):0.6797621058):0.5819876103):0.6969510358):0.8128250763):1.024538187):1.533350091):2.971566903):7.082212039):14.0802668):18.80800735):11.37508356):2.491563952);
END;



In [313]:

    
write.nexus(edata, file='')









    



#NEXUS
[R-package APE, Sun Mar 27 17:28:42 2016]







    



Error in obj[[1]]$tip.label: $ operator is invalid for atomic vectors
Traceback:

1. write.nexus(edata, file = "")



In [315]:

    
write.nexus(dtrates)









    



#NEXUS
[R-package APE, Sun Mar 27 17:28:56 2016]







    



Error in obj[[1]]$tip.label: $ operator is invalid for atomic vectors
Traceback:

1. write.nexus(dtrates)



In [326]:

    
class(dtrates$tip.label)









    




'character'



In [327]:

    
dtrates$tip.label









    





	'Galago_matschiei'
	'Euoticus_pallidus'
	'Euoticus_elegantulus'
	'Galagoides_zanzibaricus'
	'Galagoides_demidoff'
	'Galago_alleni'
	'Galago_senegalensis'
	'Galago_moholi'
	'Galago_gallarum'
	'Otolemur_garnettii'
	'Otolemur_crassicaudatus'
	'Perodicticus_potto'
	'Arctocebus_aureus'
	'Arctocebus_calabarensis'
	'Loris_tardigradus'
	'Nycticebus_pygmaeus'
	'Nycticebus_coucang'
	'Daubentonia_madagascariensis'
	'Lepilemur_mustelinus'
	'Lepilemur_septentrionalis'
	'Lepilemur_ruficaudatus'
	'Lepilemur_leucopus'
	'Lepilemur_edwardsi'
	'Lepilemur_microdon'
	'Lepilemur_dorsalis'
	'Lemur_catta'
	'Hapalemur_aureus'
	'Hapalemur_simus'
	'Hapalemur_griseus'
	'Varecia_variegata'
	'Eulemur_rubriventer'
	'Eulemur_mongoz'
	'Eulemur_coronatus'
	'Eulemur_macaco'
	'Eulemur_fulvus'
	'Avahi_laniger'
	'Indri_indri'
	'Propithecus_diadema'
	'Propithecus_verreauxi'
	'Propithecus_tattersalli'
	'Phaner_furcifer'
	'Allocebus_trichotis'
	'Microcebus_coquereli'
	'Microcebus_rufus'
	'Microcebus_murinus'
	'Cheirogaleus_medius'
	'Cheirogaleus_major'
	'Tarsius_dianae'
	'Tarsius_pumilus'
	'Tarsius_spectrum'
	'Tarsius_syrichta'
	'Tarsius_bancanus'
	'Chiropotes_satanas'
	'Chiropotes_albinasus'
	'Cacajao_melanocephalus'
	'Cacajao_calvus'
	'Pithecia_pithecia'
	'Pithecia_irrorata'
	'Pithecia_aequatorialis'
	'Pithecia_monachus'
	'Pithecia_albicans'
	'Callicebus_torquatus'
	'Callicebus_modestus'
	'Callicebus_oenanthe'
	'Callicebus_olallae'
	'Callicebus_donacophilus'
	'Callicebus_personatus'
	'Callicebus_dubius'
	'Callicebus_cupreus'
	'Callicebus_caligatus'
	'Callicebus_hoffmannsi'
	'Callicebus_brunneus'
	'Callicebus_moloch'
	'Callicebus_cinerascens'
	'Alouatta_palliata'
	'Alouatta_coibensis'
	'Alouatta_caraya'
	'Alouatta_pigra'
	'Alouatta_fusca'
	'Alouatta_seniculus'
	'Alouatta_sara'
	'Alouatta_belzebul'
	'Ateles_paniscus'
	'Ateles_belzebuth'
	'Ateles_geoffroyi'
	'Ateles_fusciceps'
	'Ateles_marginatus'
	'Ateles_chamek'
	'Brachyteles_arachnoides'
	'Lagothrix_lagotricha'
	'Lagothrix_flavicauda'
	'Cebus_olivaceus'
	'Cebus_apella'
	'Cebus_capucinus'
	'Cebus_albifrons'
	'Saimiri_boliviensis'
	'Saimiri_vanzolinii'
	'Saimiri_sciureus'
	'Saimiri_ustus'
	'Saimiri_oerstedii'
	'Aotus_lemurinus'
	'Aotus_hershkovitzi'
	'Aotus_vociferans'
	'Aotus_brumbacki'
	'Aotus_nancymaae'
	'Aotus_miconax'
	'Aotus_infulatus'
	'Aotus_nigriceps'
	'Aotus_trivirgatus'
	'Aotus_azarai'
	'Callimico_goeldii'
	'Callithrix_pygmaea'
	'Callithrix_humeralifera'
	'Callithrix_argentata'
	'Callithrix_flaviceps'
	'Callithrix_aurita'
	'Callithrix_kuhlii'
	'Callithrix_geoffroyi'
	'Callithrix_penicillata'
	'Callithrix_jacchus'
	'Leontopithecus_chrysomela'
	'Leontopithecus_caissara'
	'Leontopithecus_rosalia'
	'Leontopithecus_chrysopygus'
	'Saguinus_oedipus'
	'Saguinus_geoffroyi'
	'Saguinus_midas'
	'Saguinus_bicolor'
	'Saguinus_leucopus'
	'Saguinus_imperator'
	'Saguinus_mystax'
	'Saguinus_labiatus'
	'Saguinus_inustus'
	'Saguinus_nigricollis'
	'Saguinus_tripartitus'
	'Saguinus_fuscicollis'
	'Pongo_pygmaeus'
	'Gorilla_gorilla'
	'Homo_sapiens'
	'Pan_troglodytes'
	'Pan_paniscus'
	'Hylobates_hoolock'
	'Hylobates_moloch'
	'Hylobates_lar'
	'Hylobates_agilis'
	'Hylobates_pileatus'
	'Hylobates_muelleri'
	'Hylobates_klossii'
	'Hylobates_syndactylus'
	'Hylobates_gabriellae'
	'Hylobates_leucogenys'
	'Hylobates_concolor'
	'Trachypithecus_geei'
	'Trachypithecus_auratus'
	'Trachypithecus_francoisi'
	'Trachypithecus_cristatus'
	'Trachypithecus_pileatus'
	'Trachypithecus_phayrei'
	'Trachypithecus_obscurus'
	'Semnopithecus_entellus'
	'Presbytis_potenziani'
	'Presbytis_comata'
	'Presbytis_frontata'
	'Presbytis_femoralis'
	'Presbytis_melalophos'
	'Presbytis_rubicunda'
	'Presbytis_thomasi'
	'Presbytis_hosei'
	'Trachypithecus_johnii'
	'Trachypithecus_vetulus'
	'Pygathrix_nemaeus'
	'Pygathrix_avunculus'
	'Pygathrix_roxellana'
	'Pygathrix_brelichi'
	'Pygathrix_bieti'
	'Nasalis_larvatus'
	'Nasalis_concolor'
	'Procolobus_preussi'
	'Procolobus_verus'
	'Procolobus_rufomitratus'
	'Procolobus_pennantii'
	'Procolobus_badius'
	'Colobus_satanas'
	'Colobus_angolensis'
	'Colobus_polykomos'
	'Colobus_guereza'
	'Mandrillus_sphinx'
	'Mandrillus_leucophaeus'
	'Cercocebus_torquatus'
	'Cercocebus_agilis'
	'Cercocebus_galeritus'
	'Lophocebus_albigena'
	'Theropithecus_gelada'
	'Papio_hamadryas'
	'Macaca_sylvanus'
	'Macaca_tonkeana'
	'Macaca_maura'
	'Macaca_ochreata'
	'Macaca_nigra'
	'Macaca_silenus'
	'Macaca_nemestrina'
	'Macaca_arctoides'
	'Macaca_radiata'
	'Macaca_assamensis'
	'Macaca_thibetana'
	'Macaca_sinica'
	'Macaca_fascicularis'
	'Macaca_fuscata'
	'Macaca_mulatta'
	'Macaca_cyclopis'
	'Allenopithecus_nigroviridis'
	'Miopithecus_talapoin'
	'Erythrocebus_patas'
	'Chlorocebus_aethiops'
	'Cercopithecus_solatus'
	'Cercopithecus_preussi'
	'Cercopithecus_lhoesti'
	'Cercopithecus_hamlyni'
	'Cercopithecus_neglectus'
	'Cercopithecus_mona'
	'Cercopithecus_campbelli'
	'Cercopithecus_wolfi'
	'Cercopithecus_pogonias'
	'Cercopithecus_erythrotis'
	'Cercopithecus_sclateri'
	'Cercopithecus_cephus'
	'Cercopithecus_ascanius'
	'Cercopithecus_petaurista'
	'Cercopithecus_erythrogaster'
	'Cercopithecus_nictitans'
	'Cercopithecus_mitis'
	'Cercopithecus_dryas'
	'Cercopithecus_diana'



In [328]:

    
dtrates









    





Phylogenetic tree with 233 tips and 232 internal nodes.

Tip labels:
	Galago_matschiei, Euoticus_pallidus, Euoticus_elegantulus, Galagoides_zanzibaricus, Galagoides_demidoff, Galago_alleni, ...

Rooted; includes branch lengths.

Posterior samples: 1501 

List elements:
	 edge Nnode tip.label edge.length begin end downseq lastvisit numberEvents eventData	 eventVectors tipStates tipLambda meanTipLambda eventBranchSegs tipMu meanTipMu type dtrates



In [332]:

    
class(dtrates)









    




'bammdata'



In [334]:

    
as.phylo(dtrates)









    





Phylogenetic tree with 233 tips and 232 internal nodes.

Tip labels:
	Galago_matschiei, Euoticus_pallidus, Euoticus_elegantulus, Galagoides_zanzibaricus, Galagoides_demidoff, Galago_alleni, ...

Rooted; includes branch lengths.



In [335]:

    
str(as.phylo(dtrates))









    



List of 4
 $ edge       : int [1:464, 1:2] 234 235 236 237 238 238 239 239 237 240 ...
 $ Nnode      : int 232
 $ tip.label  : chr [1:233] "Galago_matschiei" "Euoticus_pallidus" "Euoticus_elegantulus" "Galagoides_zanzibaricus" ...
 $ edge.length: num [1:464] 13.22 30.95 12.4 4.88 3.64 ...
 - attr(*, "class")= chr "phylo"
 - attr(*, "order")= chr "cladewise"



In [336]:

    
str(dtrates)









    



List of 19
 $ edge           : int [1:464, 1:2] 234 235 236 237 238 238 239 239 237 240 ...
 $ Nnode          : int 232
 $ tip.label      : chr [1:233] "Galago_matschiei" "Euoticus_pallidus" "Euoticus_elegantulus" "Galagoides_zanzibaricus" ...
 $ edge.length    : num [1:464] 13.22 30.95 12.4 4.88 3.64 ...
 $ begin          : num [1:464] 0 13.2 44.2 56.6 61.4 ...
 $ end            : num [1:464] 13.2 44.2 56.6 61.4 65.1 ...
 $ downseq        : int [1:465] 234 235 236 237 238 1 239 2 3 240 ...
 $ lastvisit      : int [1:465] 1 2 3 4 5 6 7 8 9 10 ...
 $ numberEvents   : int [1:1501] 6 11 4 4 12 5 7 7 7 10 ...
 $ eventData      :List of 1501
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 281 421 348 212 230
  .. ..$ time : num [1:6] 0 2.25 55.12 56.67 60.36 ...
  .. ..$ lam1 : num [1:6] 0.0905 0.0949 0.1019 0.0715 0.1397 ...
  .. ..$ lam2 : num [1:6] -0.00626 -0.03418 0.00258 -0.01041 0.00654 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	11 obs. of  7 variables:
  .. ..$ node : int [1:11] 234 281 311 348 421 248 408 112 145 55 ...
  .. ..$ time : num [1:11] 0 0.16 46.09 55.3 55.63 ...
  .. ..$ lam1 : num [1:11] 0.08512 0.11015 0.00387 0.03582 0.07289 ...
  .. ..$ lam2 : num [1:11] -0.00626 -0.03418 -0.00253 -0.02267 0.00917 ...
  .. ..$ mu1  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:11] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 235 288 420
  .. ..$ time : num [1:4] 0 6.61 37.83 50.47
  .. ..$ lam1 : num [1:4] 0.0948 0.0479 0.0275 0.0671
  .. ..$ lam2 : num [1:4] -0.02238 0.008 -0.05714 -0.00418
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 281 421 431
  .. ..$ time : num [1:4] 0 1.22 54.03 60.65
  .. ..$ lam1 : num [1:4] 0.0588 0.1237 0.0715 0.0675
  .. ..$ lam2 : num [1:4] -0.00626 -0.03418 0 -0.03048
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	12 obs. of  7 variables:
  .. ..$ node : int [1:12] 234 286 386 328 356 373 417 465 212 112 ...
  .. ..$ time : num [1:12] 0 9.16 34.64 49.35 50.53 ...
  .. ..$ lam1 : num [1:12] 0.032557 0.160751 0.038497 0.089296 0.000608 ...
  .. ..$ lam2 : num [1:12] 0.01021 -0.05343 0.00422 0 0 ...
  .. ..$ mu1  : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:12] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 235 276 420 112
  .. ..$ time : num [1:5] 0 11.7 49.7 50.5 61.9
  .. ..$ lam1 : num [1:5] 0.063 0.0329 0.1026 0.0635 0.4212
  .. ..$ lam2 : num [1:5] -0.02238 0 0.01305 0.00508 -0.02934
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 286 372 420 36 52 112
  .. ..$ time : num [1:7] 0 8.99 48.32 51.31 53.51 ...
  .. ..$ lam1 : num [1:7] 0.042 0.0608 0.1965 0.0901 0.0206 ...
  .. ..$ lam2 : num [1:7] 0.01784 -0.03543 0.02439 -0.01952 0.00691 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 281 420 430 425 31 110
  .. ..$ time : num [1:7] 0 1.1 53.6 58.7 60.8 ...
  .. ..$ lam1 : num [1:7] 0.0761 0.1271 0.05533 0.11522 0.00681 ...
  .. ..$ lam2 : num [1:7] -0.00626 -0.03418 -0.01837 -0.00252 0.01966 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 235 370 430 427 29 112
  .. ..$ time : num [1:7] 0 7.18 28.82 57.7 62.13 ...
  .. ..$ lam1 : num [1:7] 0.0443 0.0443 0.0452 0.1532 0.3181 ...
  .. ..$ lam2 : num [1:7] -0.02238 0.00229 -0.01306 -0.00551 0.03214 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	10 obs. of  7 variables:
  .. ..$ node : int [1:10] 234 281 252 327 386 372 421 139 112 212
  .. ..$ time : num [1:10] 0 0.785 18.262 41.486 42.358 ...
  .. ..$ lam1 : num [1:10] 0.0397 0.1825 0.0894 0.037 0.0334 ...
  .. ..$ lam2 : num [1:10] 0.00733 -0.04901 -0.01938 0.01552 -0.00152 ...
  .. ..$ mu1  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:10] 1 2 3 4 5 6 7 8 9 10
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 235 370 421 112 126 433
  .. ..$ time : num [1:7] 0 8.47 22.9 54.55 63.77 ...
  .. ..$ lam1 : num [1:7] 0.039 0.055 0.033 0.0907 0.4696 ...
  .. ..$ lam2 : num [1:7] -2.24e-02 -1.24e-05 -1.31e-02 -8.64e-03 7.98e-03 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 281 372 420 444 277 330 348
  .. ..$ time : num [1:8] 0 0.686 45.899 49.795 55.818 ...
  .. ..$ lam1 : num [1:8] 0.0333 0.0847 0.1351 0.1496 0.0843 ...
  .. ..$ lam2 : num [1:8] 0.0216 -0.0354 -0.0227 -0.0274 -0.0266 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 235 370 337 421 111 348 103 53
  .. ..$ time : num [1:9] 0 4.85 18.86 54.04 54.08 ...
  .. ..$ lam1 : num [1:9] 0.04891 0.07753 0.04317 0.00777 0.09693 ...
  .. ..$ lam2 : num [1:9] -0.022384 0.000387 -0.015295 -0.012357 0.021043 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 281 285 372 421 91 382 212
  .. ..$ time : num [1:8] 0 1.96 41.26 48.19 53.93 ...
  .. ..$ lam1 : num [1:8] 0.0519 0.2956 0.0112 0.1133 0.0761 ...
  .. ..$ lam2 : num [1:8] 0.0149 -0.04901 -0.0027 0.01125 0.00262 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 281 421 212 112
  .. ..$ time : num [1:5] 0 1.03 55.69 60.05 61.77
  .. ..$ lam1 : num [1:5] 0.0468 0.2215 0.0886 0.2428 0.1236
  .. ..$ lam2 : num [1:5] 0.01066 -0.04901 0.00262 0.00471 0.00664
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 235 370 421 348 71 330
  .. ..$ time : num [1:7] 0 2.47 14.96 55.57 59.74 ...
  .. ..$ lam1 : num [1:7] 0.0358 0.0611 0.0425 0.0613 0.0626 ...
  .. ..$ lam2 : num [1:7] -0.022384 0.000399 -0.015295 0 0.00189 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 235 370 347 36 421 330 18
  .. ..$ time : num [1:8] 0 10 19.2 51.6 55.1 ...
  .. ..$ lam1 : num [1:8] 0.0449 0.0541 0.0526 0.0579 0.0234 ...
  .. ..$ lam2 : num [1:8] -0.02521 0 -0.01529 0.00189 0.0196 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 235 370 347 421 51 5 330
  .. ..$ time : num [1:8] 0 2.82 22.5 50 54.38 ...
  .. ..$ lam1 : num [1:8] 0.0506 0.0685 0.0631 0.0839 0.0924 ...
  .. ..$ lam2 : num [1:8] -0.02521 0.0014 -0.01529 0.00189 0.02823 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 235 370 346 421 212 368 63
  .. ..$ time : num [1:8] 0 4.64 20.45 46.56 54.16 ...
  .. ..$ lam1 : num [1:8] 0.043 0.0445 0.0447 0.0533 0.0538 ...
  .. ..$ lam2 : num [1:8] -0.02521 0.0014 -0.01483 -0.00407 0.01552 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	10 obs. of  7 variables:
  .. ..$ node : int [1:10] 234 281 372 328 299 430 348 212 268 10
  .. ..$ time : num [1:10] 0 2.42 47.86 49.78 49.81 ...
  .. ..$ lam1 : num [1:10] 0.0383 0.0521 0.0323 0.0374 0.0021 ...
  .. ..$ lam2 : num [1:10] 0.00816 -0.0199 -0.01189 0.00562 -0.01842 ...
  .. ..$ mu1  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:10] 1 2 3 4 5 6 7 8 9 10
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 281 420 138
  .. ..$ time : num [1:4] 0 0.093 48.064 63.872
  .. ..$ lam1 : num [1:4] 0.0841 0.1523 0.0555 0.2354
  .. ..$ lam2 : num [1:4] -0.00578 -0.03855 -0.00523 0.01499
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	11 obs. of  7 variables:
  .. ..$ node : int [1:11] 234 281 386 328 275 348 430 246 138 12 ...
  .. ..$ time : num [1:11] 0 1.87 41.22 43.32 46.51 ...
  .. ..$ lam1 : num [1:11] 0.0254 0.2259 0.0242 0.019 0.1699 ...
  .. ..$ lam2 : num [1:11] -0.00309 -0.04949 0.00176 0.00782 -0.04031 ...
  .. ..$ mu1  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:11] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 281 298 429 348 427 97 405
  .. ..$ time : num [1:8] 0 1.49 47.23 57.15 60.61 ...
  .. ..$ lam1 : num [1:8] 0.04654 0.0576 0.00194 0.10505 0.13798 ...
  .. ..$ lam2 : num [1:8] 0.001933 -0.019899 0.000558 0.004825 0.004509 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 281 298 421 28
  .. ..$ time : num [1:5] 0 0.00157 48.2995 55.7547 64.1634
  .. ..$ lam1 : num [1:5] 0.04364 0.05362 0.00326 0.05352 0.08937
  .. ..$ lam2 : num [1:5] 0.001933 -0.019899 0.000558 0.021107 0.006409
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 370 18 253 236 421 278 112 465
  .. ..$ time : num [1:9] 0 27 31.1 33.3 42.5 ...
  .. ..$ lam1 : num [1:9] 0.0368 0.042 0.0959 0.0906 0.1762 ...
  .. ..$ lam2 : num [1:9] -0.026104 -0.014827 -0.000879 -0.030573 -0.020232 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 286 282 421 212 103 137
  .. ..$ time : num [1:7] 0 4.1 6.25 55.84 61.14 ...
  .. ..$ lam1 : num [1:7] 0.08524 0.16415 0.00432 0.06821 0.05467 ...
  .. ..$ lam2 : num [1:7] -0.00668 -0.03855 0.01607 0.00142 0 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 281 421 212 112
  .. ..$ time : num [1:5] 0 1.39 55.43 61.43 62.87
  .. ..$ lam1 : num [1:5] 0.0301 0.054 0.0831 0.4161 0.2106
  .. ..$ lam2 : num [1:5] 0.0221 -0.0199 -0.0196 -0.0388 0.0148
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 286 386 430 244 112
  .. ..$ time : num [1:6] 0 8.76 34.74 57.8 59.78 ...
  .. ..$ lam1 : num [1:6] 0.0711 0.14 0.0189 0.1958 0.0141 ...
  .. ..$ lam2 : num [1:6] -0.00398 -0.04949 0.00142 0.00423 0.01161 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 282 286 386 30 340 430 128 112
  .. ..$ time : num [1:9] 0 9.21 12.37 37.78 53.89 ...
  .. ..$ lam1 : num [1:9] 0.0509 0.0464 0.1026 0.0207 0.1941 ...
  .. ..$ lam2 : num [1:9] -0.00398 -0.02467 -0.04949 0.00142 0.0099 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 286 370 282 429 419 112
  .. ..$ time : num [1:7] 0 7.4 26.2 26.6 57 ...
  .. ..$ lam1 : num [1:7] 0.0761 0.1243 0.0542 0.0142 0.1436 ...
  .. ..$ lam2 : num [1:7] -0.00398 -0.04949 -0.0173 -0.02467 0.00778 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 253 370 236 137 421 112 58 103
  .. ..$ time : num [1:9] 0 27.6 32.2 32.7 52.2 ...
  .. ..$ lam1 : num [1:9] 0.0458 0.097 0.0363 0.0799 0.1848 ...
  .. ..$ lam2 : num [1:9] -0.026104 -0.019086 -0.014827 -0.000939 0.007197 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 236 253 370 18 429 112 44 228
  .. ..$ time : num [1:9] 0 14.8 29.4 31.3 38.1 ...
  .. ..$ lam1 : num [1:9] 0.0413 0.3065 0.103 0.0423 0.1153 ...
  .. ..$ lam2 : num [1:9] -0.0261 -0.01273 -0.02371 -0.01483 0.00274 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 236 287 275 376 18 429 112
  .. ..$ time : num [1:8] 0 13.6 19.5 47.2 48.9 ...
  .. ..$ lam1 : num [1:8] 0.0318 0.0949 0.0708 0.2797 0.0172 ...
  .. ..$ lam2 : num [1:8] -0.00398 0.01338 -0.04949 -0.00717 -0.05415 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	14 obs. of  7 variables:
  .. ..$ node : int [1:14] 234 287 236 328 276 376 429 328 130 112 ...
  .. ..$ time : num [1:14] 0 24.1 41.8 43.6 49.7 ...
  .. ..$ lam1 : num [1:14] 0.0376 0.0372 0.0457 0.0989 0.2831 ...
  .. ..$ lam2 : num [1:14] -0.00398 -0.04949 0.01338 0.02009 -0.00717 ...
  .. ..$ mu1  : num [1:14] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:14] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:14] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 287 275 303 376 430 251 112 9
  .. ..$ time : num [1:9] 0 25.4 47.6 53.9 54.3 ...
  .. ..$ lam1 : num [1:9] 0.03721 0.05809 0.18866 0.00503 0.00656 ...
  .. ..$ lam2 : num [1:9] -0.00398 -0.04949 -0.01365 -0.00306 -0.02947 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	12 obs. of  7 variables:
  .. ..$ node : int [1:12] 234 287 275 328 111 19 137 105 430 246 ...
  .. ..$ time : num [1:12] 0 24.1 44.8 48.4 54.6 ...
  .. ..$ lam1 : num [1:12] 0.0353 0.0434 0.3495 0.091 0.0322 ...
  .. ..$ lam2 : num [1:12] -0.00398 -0.04949 -0.01365 -0.0234 0.01699 ...
  .. ..$ mu1  : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:12] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 235 370 285 429 111 278 38 112
  .. ..$ time : num [1:9] 0 0.759 15.509 55.643 57.399 ...
  .. ..$ lam1 : num [1:9] 5.78e-02 1.26e-01 9.84e-02 2.65e-05 7.94e-02 ...
  .. ..$ lam2 : num [1:9] -0.02895 -0.01273 -0.0318 0.00882 0.01524 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 235 370 429 52 112
  .. ..$ time : num [1:6] 0 12.4 18.3 57.1 57.8 ...
  .. ..$ lam1 : num [1:6] 0.0562 0.095 0.1074 0.0925 0.3071 ...
  .. ..$ lam2 : num [1:6] -0.029 -0.0127 -0.0318 0.0224 0.0031 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 235 370 421 431 112 330
  .. ..$ time : num [1:7] 0 9.03 22.78 55.7 59.9 ...
  .. ..$ lam1 : num [1:7] 0.0482 0.2004 0.1015 0.0767 0.222 ...
  .. ..$ lam2 : num [1:7] -0.02895 -0.01514 -0.0318 -0.02085 -0.00132 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 281 287 255 346 41 421 330 212
  .. ..$ time : num [1:9] 0 1.41 25.61 45.15 46.11 ...
  .. ..$ lam1 : num [1:9] 0.0861 0.2113 0.0136 0.1289 0.0573 ...
  .. ..$ lam2 : num [1:9] -0.00113 -0.03855 -0.0149 -0.01609 0.00113 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 281 287 347 421 330 138
  .. ..$ time : num [1:7] 0 2.26 28.82 51.56 55.39 ...
  .. ..$ lam1 : num [1:7] 0.0583 0.2141 0.0162 0.0633 0.1502 ...
  .. ..$ lam2 : num [1:7] 0.00562 -0.03855 -0.0149 0.00526 -0.01056 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 235 370 111 348 430 30 330
  .. ..$ time : num [1:8] 0 8.54 24.67 54.99 56.96 ...
  .. ..$ lam1 : num [1:8] 0.0428 0.1192 0.0839 0.0829 0.1527 ...
  .. ..$ lam2 : num [1:8] -0.029 -0.0151 -0.0318 0.0083 0.0119 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 235 370 348 430 278 111 330
  .. ..$ time : num [1:8] 0 9.74 23.78 57.85 58.37 ...
  .. ..$ lam1 : num [1:8] 0.0431 0.1208 0.0877 0.3275 0.1406 ...
  .. ..$ lam2 : num [1:8] -0.028951 -0.01514 -0.031799 0.000533 0.004812 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 287 277 348 207 219
  .. ..$ time : num [1:6] 0 27 54.4 55.6 64.4 ...
  .. ..$ lam1 : num [1:6] 0.0509 0.0162 0.1193 0.1104 0.1226 ...
  .. ..$ lam2 : num [1:6] -0.00685 -0.01343 0.03201 0.0168 -0.03408 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 287 348 63 431 26 144
  .. ..$ time : num [1:7] 0 34.5 57.9 58.6 59.2 ...
  .. ..$ lam1 : num [1:7] 0.05496 0.01747 0.24932 0.00838 0.19754 ...
  .. ..$ lam2 : num [1:7] -0.00685 -0.01343 0.0168 0.01837 0.01782 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 287 275 347 277 430 248 402
  .. ..$ time : num [1:8] 0 33.1 39.4 47.6 57.9 ...
  .. ..$ lam1 : num [1:8] 0.0484 0.0122 0.1897 0.1661 0.0698 ...
  .. ..$ lam2 : num [1:8] -0.00685 -0.01343 -0.00249 -0.00895 0.01051 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 287 237 347 430 25
  .. ..$ time : num [1:6] 0 25.3 47.7 51.7 57.7 ...
  .. ..$ lam1 : num [1:6] 0.0524 0.0211 0.0722 0.0373 0.1062 ...
  .. ..$ lam2 : num [1:6] -0.00685 -0.01343 0.02299 -0.00877 0.00603 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	3 obs. of  7 variables:
  .. ..$ node : int [1:3] 234 281 421
  .. ..$ time : num [1:3] 0 2.01 54.29
  .. ..$ lam1 : num [1:3] 0.0521 0.1674 0.0775
  .. ..$ lam2 : num [1:3] 0.00254 -0.03855 -0.00733
  .. ..$ mu1  : num [1:3] 0 0 0
  .. ..$ mu2  : num [1:3] 0 0 0
  .. ..$ index: int [1:3] 1 2 3
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 281 252 421 19
  .. ..$ time : num [1:5] 0 1.92 15.84 55.38 63.14
  .. ..$ lam1 : num [1:5] 0.1034 0.1809 0.0501 0.1347 0.1351
  .. ..$ lam2 : num [1:5] 0.000568 -0.03855 0.011727 -0.00733 -0.000247
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	10 obs. of  7 variables:
  .. ..$ node : int [1:10] 234 287 285 36 242 436 431 41 144 11
  .. ..$ time : num [1:10] 0 27 38.2 53.9 58.3 ...
  .. ..$ lam1 : num [1:10] 0.0466 0.0239 0.0295 0.0384 0.1086 ...
  .. ..$ lam2 : num [1:10] -0.00685 -0.01343 0.01067 -0.00426 0.00663 ...
  .. ..$ mu1  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:10] 1 2 3 4 5 6 7 8 9 10
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 252 236 287 429 4
  .. ..$ time : num [1:6] 0 22.5 26.2 30.2 56.3 ...
  .. ..$ lam1 : num [1:6] 0.0408 0.0826 0.0973 0.0134 0.1462 ...
  .. ..$ lam2 : num [1:6] -0.00685 -0.01893 -0.01643 -0.01343 0.02227 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 235 386 429 199
  .. ..$ time : num [1:5] 0 5.26 33.43 57.54 63.88
  .. ..$ lam1 : num [1:5] 0.0966 0.1158 0.0735 0.11 0.3029
  .. ..$ lam2 : num [1:5] -0.03153 -0.00725 -0.02784 -0.02293 -0.00785
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 286 386 348
  .. ..$ time : num [1:4] 0 11.5 45.9 54.2
  .. ..$ lam1 : num [1:4] 0.0438 0.0759 0.0463 0.0709
  .. ..$ lam2 : num [1:4] 0.0106 -0.0385 0 0.0195
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 281 289 18 429 437
  .. ..$ time : num [1:6] 0 0.0116 41.2693 49.1356 57.5512 ...
  .. ..$ lam1 : num [1:6] 0.0468 0.08472 0.00414 0.27228 0.05972 ...
  .. ..$ lam2 : num [1:6] 0.00775 -0.01992 -0.0107 -0.03644 0.01881 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 235 287 328 300 373 429 112 4
  .. ..$ time : num [1:9] 0 2.45 31.49 43.67 55.67 ...
  .. ..$ lam1 : num [1:9] 0.034538 0.166418 0.013098 0.38498 0.000568 ...
  .. ..$ lam2 : num [1:9] -0.00685 -0.01682 -0.01535 -0.01102 0.00396 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 235 287 421 300 348 348
  .. ..$ time : num [1:7] 0 0.184 30.851 54.602 56.033 ...
  .. ..$ lam1 : num [1:7] 0.05231 0.19067 0.01449 0.06827 0.00088 ...
  .. ..$ lam2 : num [1:7] -0.00685 -0.01682 -0.01211 -0.02057 -0.03531 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	11 obs. of  7 variables:
  .. ..$ node : int [1:11] 234 286 253 370 253 236 328 347 429 47 ...
  .. ..$ time : num [1:11] 0 10.2 27.6 28 32.3 ...
  .. ..$ lam1 : num [1:11] 0.091513 0.0426 0.000116 0.054792 0.049719 ...
  .. ..$ lam2 : num [1:11] 0.01879 -0.03855 0 -0.02094 -0.00136 ...
  .. ..$ mu1  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:11] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 286 370 347 430 238 212 361 43
  .. ..$ time : num [1:9] 0 2.82 27.34 51.79 57.99 ...
  .. ..$ lam1 : num [1:9] 0.057 0.0841 0.0425 0.0337 0.2669 ...
  .. ..$ lam2 : num [1:9] 0 -0.0382 -0.02094 0.01377 -0.00085 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 287 37 112
  .. ..$ time : num [1:4] 0 20.1 58.1 62.3
  .. ..$ lam1 : num [1:4] 0.0644 0.0149 0.4119 0.0569
  .. ..$ lam2 : num [1:4] -0.00376 -0.01211 0.00952 0.00306
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 286 287 248 430 212 384 112 3
  .. ..$ time : num [1:9] 0 8.15 16.35 51.74 58.25 ...
  .. ..$ lam1 : num [1:9] 0.0576 0.0665 0.0135 0.1599 0.0902 ...
  .. ..$ lam2 : num [1:9] -0.00376 -0.01752 -0.01211 -0.01248 0.03507 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	11 obs. of  7 variables:
  .. ..$ node : int [1:11] 234 281 370 285 284 347 421 212 465 330 ...
  .. ..$ time : num [1:11] 0 2.45 22.54 35.09 51.77 ...
  .. ..$ lam1 : num [1:11] 7.00e-02 9.09e-02 4.23e-02 8.83e-06 2.14e-02 ...
  .. ..$ lam2 : num [1:11] 0.00103 -0.03849 -0.01851 0.01415 -0.0333 ...
  .. ..$ mu1  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:11] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 235 370 429 27
  .. ..$ time : num [1:5] 0 9.81 22.06 55.92 63.03
  .. ..$ lam1 : num [1:5] 0.05326 0.06497 0.11976 0.09891 0.00244
  .. ..$ lam2 : num [1:5] -0.02844 -0.00176 -0.03692 -0.01711 -0.02002
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 286 370 282 285 347 250 429 212
  .. ..$ time : num [1:9] 0 10.1 28.2 28.4 33.5 ...
  .. ..$ lam1 : num [1:9] 4.30e-02 6.09e-02 3.99e-02 6.03e-02 6.32e-06 ...
  .. ..$ lam2 : num [1:9] 0.00943 -0.03849 -0.02005 0.01478 0.0167 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	11 obs. of  7 variables:
  .. ..$ node : int [1:11] 234 287 370 285 352 430 427 104 54 212 ...
  .. ..$ time : num [1:11] 0 16.7 25.8 40.7 56.4 ...
  .. ..$ lam1 : num [1:11] 5.01e-02 4.62e-02 4.15e-02 5.01e-06 1.58e-01 ...
  .. ..$ lam2 : num [1:11] 0.00943 -0.03849 -0.02005 0.00805 0.00149 ...
  .. ..$ mu1  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:11] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 287 370 429 348 149 330 141
  .. ..$ time : num [1:8] 0 19.1 30.2 57.6 59.1 ...
  .. ..$ lam1 : num [1:8] 0.0621 0.014 0.0593 0.0927 0.139 ...
  .. ..$ lam2 : num [1:8] -0.0041 -0.00758 -0.01974 0.0011 0.02751 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 287 370 285 347 429 330
  .. ..$ time : num [1:7] 0 19 32.4 46.1 48 ...
  .. ..$ lam1 : num [1:7] 2.54e-02 3.84e-02 4.84e-02 5.63e-05 4.81e-02 ...
  .. ..$ lam2 : num [1:7] 0.016727 -0.038492 -0.020049 -0.001307 -0.000303 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 235 370 430 348 330 122 366
  .. ..$ time : num [1:8] 0 7.2 29.3 58.4 58.5 ...
  .. ..$ lam1 : num [1:8] 0.0757 0.1002 0.1008 0.1035 0.3729 ...
  .. ..$ lam2 : num [1:8] -0.02879 -0.00649 -0.04399 -0.01456 0.02774 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	10 obs. of  7 variables:
  .. ..$ node : int [1:10] 234 287 370 347 256 429 291 19 38 330
  .. ..$ time : num [1:10] 0 23.4 26.4 47 53.2 ...
  .. ..$ lam1 : num [1:10] 0.0404 0.0359 0.0505 0.0729 0.0627 ...
  .. ..$ lam2 : num [1:10] 0.01973 -0.03849 -0.02005 -0.00878 -0.00936 ...
  .. ..$ mu1  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:10] 1 2 3 4 5 6 7 8 9 10
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 235 370 137 348 429 330
  .. ..$ time : num [1:7] 0 8.3 21.5 50 55.6 ...
  .. ..$ lam1 : num [1:7] 0.0533 0.1018 0.1973 0.1422 0.2344 ...
  .. ..$ lam2 : num [1:7] -0.02879 -0.00649 -0.04399 0.00474 0.00941 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	11 obs. of  7 variables:
  .. ..$ node : int [1:11] 234 281 370 282 283 421 112 6 212 449 ...
  .. ..$ time : num [1:11] 0 1.91 14.66 27.78 31.75 ...
  .. ..$ lam1 : num [1:11] 0.079 0.0141 0.0659 0.091 0.0215 ...
  .. ..$ lam2 : num [1:11] -0.0041 -0.00758 -0.02284 -0.00701 0.0088 ...
  .. ..$ mu1  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:11] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 281 370 430 112
  .. ..$ time : num [1:5] 0 0.142 15.196 58.706 64.058
  .. ..$ lam1 : num [1:5] 0.0589 0.0517 0.0661 0.1039 0.1598
  .. ..$ lam2 : num [1:5] 0.00346 -0.02596 -0.02097 0.00413 0.0034
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 286 370 347 328 30 429
  .. ..$ time : num [1:7] 0 11.5 18 46.8 55.6 ...
  .. ..$ lam1 : num [1:7] 0.0397 0.0574 0.0667 0.0419 0.0615 ...
  .. ..$ lam2 : num [1:7] 0.01161 -0.04296 -0.02005 0.00325 0.02688 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 281 370 18 429 112
  .. ..$ time : num [1:6] 0 2.38 16.59 56.27 56.47 ...
  .. ..$ lam1 : num [1:6] 0.06 0.0538 0.0537 0.0792 0.2204 ...
  .. ..$ lam2 : num [1:6] 0.00346 -0.02596 -0.02097 0.01836 -0.02494 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 235 370 285 277 50 430 179 112
  .. ..$ time : num [1:9] 0 0.504 15.169 31.728 53.838 ...
  .. ..$ lam1 : num [1:9] 0.0703 0.1384 0.1535 0.2417 0.2803 ...
  .. ..$ lam2 : num [1:9] -0.02879 -0.00923 -0.04399 0.01632 0.02153 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	10 obs. of  7 variables:
  .. ..$ node : int [1:10] 234 286 370 285 328 347 267 431 103 50
  .. ..$ time : num [1:10] 0 12.5 29.8 43.5 45.4 ...
  .. ..$ lam1 : num [1:10] 0.0854 0.0537 0.0682 0.0282 0.0941 ...
  .. ..$ lam2 : num [1:10] 0.00316 -0.04296 -0.02005 0.00699 -0.02026 ...
  .. ..$ mu1  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:10] 1 2 3 4 5 6 7 8 9 10
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 286 421 348 212 323 179
  .. ..$ time : num [1:7] 0 12.1 55.2 58.6 60.4 ...
  .. ..$ lam1 : num [1:7] 0.0922 0.019 0.0847 0.0778 0.1569 ...
  .. ..$ lam2 : num [1:7] -0.00988 -0.00758 -0.00388 0 -0.02871 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	9 obs. of  7 variables:
  .. ..$ node : int [1:9] 234 235 370 421 63 1 112 30 138
  .. ..$ time : num [1:9] 0 7.19 26.94 53.9 61.73 ...
  .. ..$ lam1 : num [1:9] 0.0866 0.1007 0.1298 0.1095 0.074 ...
  .. ..$ lam2 : num [1:9] -0.03456 -0.00728 -0.04499 -0.00805 0.00952 ...
  .. ..$ mu1  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:9] 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:9] 1 2 3 4 5 6 7 8 9
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 286 347 421 240 212
  .. ..$ time : num [1:6] 0 10.4 47.5 55.7 56.6 ...
  .. ..$ lam1 : num [1:6] 0.0769 0.0283 0.0953 0.1129 0.0808 ...
  .. ..$ lam2 : num [1:6] -0.009881 -0.008591 -0.006618 -0.036587 0.000985 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	6 obs. of  7 variables:
  .. ..$ node : int [1:6] 234 235 370 420 137 330
  .. ..$ time : num [1:6] 0 4.8 24.6 51.1 51.3 ...
  .. ..$ lam1 : num [1:6] 0.096 0.0949 0.1138 0.0494 0.1655 ...
  .. ..$ lam2 : num [1:6] -0.03456 -0.00969 -0.04499 0 0 ...
  .. ..$ mu1  : num [1:6] 0 0 0 0 0 0
  .. ..$ mu2  : num [1:6] 0 0 0 0 0 0
  .. ..$ index: int [1:6] 1 2 3 4 5 6
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 281 236 421 16
  .. ..$ time : num [1:5] 0 0.823 31.418 55.384 62.824
  .. ..$ lam1 : num [1:5] 0.0463 0.0269 0.0456 0.1017 0.46
  .. ..$ lam2 : num [1:5] -0.00388 -0.00859 0.01836 -0.02308 0.0236
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 235 370 328 421 97 212 112
  .. ..$ time : num [1:8] 0 4.32 26.67 46.9 53.87 ...
  .. ..$ lam1 : num [1:8] 0.0856 0.0993 0.0797 0.0872 0.0684 ...
  .. ..$ lam2 : num [1:8] -0.03456 -0.00969 -0.04499 -0.00479 0.00877 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 281 275 421 240 240 212
  .. ..$ time : num [1:7] 0 1.03 39.4 54.39 56.73 ...
  .. ..$ lam1 : num [1:7] 0.0556 0.0276 0.1258 0.0986 0.0249 ...
  .. ..$ lam2 : num [1:7] -0.00234 -0.00859 -0.00824 -0.00792 0 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 281 370 370 347 421 330
  .. ..$ time : num [1:7] 0 0.968 22.915 24.89 51.717 ...
  .. ..$ lam1 : num [1:7] 0.0399 0.1106 0.0888 0.0299 0.0525 ...
  .. ..$ lam2 : num [1:7] 0.00542 -0.04726 -0.00718 -0.00899 -0.02643 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 235 429 47
  .. ..$ time : num [1:4] 0 3.07 56.14 63.37
  .. ..$ lam1 : num [1:4] 0.1246 0.0723 0.0928 0.1409
  .. ..$ lam2 : num [1:4] -0.02814 -0.00969 -0.00906 -0.00507
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 235 356 429
  .. ..$ time : num [1:4] 0 11.8 49.9 56.4
  .. ..$ lam1 : num [1:4] 0.09223 0.10071 0.00162 0.16363
  .. ..$ lam2 : num [1:4] -0.02814 -0.00969 -0.01509 -0.02217
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 286 421 123
  .. ..$ time : num [1:4] 0 6.63 55.65 64.71
  .. ..$ lam1 : num [1:4] 0.0906 0.084 0.0597 0.027
  .. ..$ lam2 : num [1:4] -0.00423 -0.03073 0 -0.00942
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 281 421 10
  .. ..$ time : num [1:4] 0 0.471 55.758 63.27
  .. ..$ lam1 : num [1:4] 0.0693 0.0914 0.0763 0.1387
  .. ..$ lam2 : num [1:4] -0.00223 -0.03073 0.01855 0.00714
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 281 370 371 347 429 330
  .. ..$ time : num [1:7] 0 0.865 32.498 44.565 47.381 ...
  .. ..$ lam1 : num [1:7] 0.0654 0.1006 0.0506 0.0243 0.0486 ...
  .. ..$ lam2 : num [1:7] -0.00406 -0.04193 -0.01252 -0.00506 -0.00662 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  ..$ :'data.frame':	5 obs. of  7 variables:
  .. ..$ node : int [1:5] 234 235 355 421 212
  .. ..$ time : num [1:5] 0 3.45 46.8 54.12 61.52
  .. ..$ lam1 : num [1:5] 0.09918 0.09693 0.00545 0.06557 0.12451
  .. ..$ lam2 : num [1:5] -0.02814 -0.00943 0.01428 0.00314 0.01547
  .. ..$ mu1  : num [1:5] 0 0 0 0 0
  .. ..$ mu2  : num [1:5] 0 0 0 0 0
  .. ..$ index: int [1:5] 1 2 3 4 5
  ..$ :'data.frame':	10 obs. of  7 variables:
  .. ..$ node : int [1:10] 234 281 370 370 376 429 348 418 330 13
  .. ..$ time : num [1:10] 0 0.993 24.522 29.925 56.214 ...
  .. ..$ lam1 : num [1:10] 0.0619 0.0999 0.0554 0.0516 0.0103 ...
  .. ..$ lam2 : num [1:10] -0.00406 -0.04193 -0.02284 -0.01252 0.02383 ...
  .. ..$ mu1  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:10] 0 0 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:10] 1 2 3 4 5 6 7 8 9 10
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 286 421 43
  .. ..$ time : num [1:4] 0 9.05 54.74 63.07
  .. ..$ lam1 : num [1:4] 0.0794 0.0268 0.0892 0.292
  .. ..$ lam2 : num [1:4] -0.00402 -0.0086 -0.04586 0.01304
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	12 obs. of  7 variables:
  .. ..$ node : int [1:12] 234 286 235 370 283 284 330 430 348 67 ...
  .. ..$ time : num [1:12] 0 8.28 13.04 22.06 37.23 ...
  .. ..$ lam1 : num [1:12] 0.1602 0.0565 0.2342 0.0519 0.1208 ...
  .. ..$ lam2 : num [1:12] -0.00406 -0.04193 -0.03051 -0.01252 -0.0053 ...
  .. ..$ mu1  : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:12] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 235 253 18 429 212 112 16
  .. ..$ time : num [1:8] 0 1.32 36.24 51.41 56.34 ...
  .. ..$ lam1 : num [1:8] 0.0893 0.1483 0.0391 0.5113 0.0961 ...
  .. ..$ lam2 : num [1:8] -0.02814 -0.0114 0.03615 0.00485 0.00314 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	11 obs. of  7 variables:
  .. ..$ node : int [1:11] 234 286 370 283 348 429 160 212 330 123 ...
  .. ..$ time : num [1:11] 0 7.74 19.16 45.45 56.27 ...
  .. ..$ lam1 : num [1:11] 0.0677 0.1073 0.0328 0.0188 0.0754 ...
  .. ..$ lam2 : num [1:11] -0.00158 -0.04193 -0.01252 -0.00368 0.00422 ...
  .. ..$ mu1  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:11] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:11] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	12 obs. of  7 variables:
  .. ..$ node : int [1:12] 234 281 18 372 421 436 268 348 212 114 ...
  .. ..$ time : num [1:12] 0 0.0908 47.2335 48.9745 54.1404 ...
  .. ..$ lam1 : num [1:12] 0.0707 0.0198 0.1098 0.2819 0.0742 ...
  .. ..$ lam2 : num [1:12] -9.84e-03 -8.60e-03 3.08e-02 7.15e-05 1.22e-02 ...
  .. ..$ mu1  : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ mu2  : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..$ index: int [1:12] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 286 370 429 171 330 112 133
  .. ..$ time : num [1:8] 0 7.3 17.9 56 59.1 ...
  .. ..$ lam1 : num [1:8] 0.0459 0.0718 0.0447 0.1058 0.1989 ...
  .. ..$ lam2 : num [1:8] -0.00158 -0.04193 -0.01252 0 0 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	8 obs. of  7 variables:
  .. ..$ node : int [1:8] 234 286 372 421 212 91 112 99
  .. ..$ time : num [1:8] 0 9.39 46.01 54.49 62.31 ...
  .. ..$ lam1 : num [1:8] 0.1002 0.0181 0.1477 0.0759 0.1969 ...
  .. ..$ lam2 : num [1:8] -0.00984 -0.0086 0 0.01493 0.01816 ...
  .. ..$ mu1  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:8] 0 0 0 0 0 0 0 0
  .. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
  ..$ :'data.frame':	4 obs. of  7 variables:
  .. ..$ node : int [1:4] 234 235 421 233
  .. ..$ time : num [1:4] 0 6.38 54.3 64.12
  .. ..$ lam1 : num [1:4] 0.0742 0.1107 0.1273 0.1341
  .. ..$ lam2 : num [1:4] -0.02567 -0.0114 0.00792 -0.0014
  .. ..$ mu1  : num [1:4] 0 0 0 0
  .. ..$ mu2  : num [1:4] 0 0 0 0
  .. ..$ index: int [1:4] 1 2 3 4
  ..$ :'data.frame':	7 obs. of  7 variables:
  .. ..$ node : int [1:7] 234 281 370 328 421 241 112
  .. ..$ time : num [1:7] 0 0.467 18.399 47.159 53.909 ...
  .. ..$ lam1 : num [1:7] 0.09 0.0862 0.045 0.0247 0.0825 ...
  .. ..$ lam2 : num [1:7] -0.00158 -0.04193 -0.01552 -0.01498 0.02417 ...
  .. ..$ mu1  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ mu2  : num [1:7] 0 0 0 0 0 0 0
  .. ..$ index: int [1:7] 1 2 3 4 5 6 7
  .. [list output truncated]
 $ eventVectors   :List of 1501
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 5 5 5 5 5 5 5 5 5 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 4 4 4 4 4 4 4 4 4 ...
  ..$ : num [1:464] 1 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 3 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 3 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 6 6 6 6 6 6 6 6 6 ...
  ..$ : num [1:464] 1 1 1 6 6 6 6 6 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 9 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 6 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 5 5 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 3 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 6 6 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 3 3 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:464] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:464] 1 1 1 1 1 1 1 1 1 6 ...
  .. [list output truncated]
 $ tipStates      :List of 1501
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 7 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 10 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 8 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 5 5 5 5 5 5 5 5 5 5 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 5 5 5 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 4 4 4 4 4 4 4 4 4 4 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 3 3 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 9 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 10 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 3 3 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 5 5 5 5 5 ...
  ..$ : num [1:233] 3 3 3 6 3 3 3 3 3 3 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 9 2 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 6 6 6 6 6 6 6 6 6 6 ...
  ..$ : num [1:233] 6 6 6 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 9 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 8 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 6 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 5 5 5 5 5 5 5 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 3 3 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 6 6 6 6 6 6 6 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 4 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 3 3 3 3 3 3 3 3 3 3 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ : num [1:233] 2 2 2 2 2 2 2 2 2 2 ...
  ..$ : num [1:233] 1 1 1 6 6 1 1 1 1 1 ...
  .. [list output truncated]
 $ tipLambda      :List of 1501
  ..$ : num [1:233] 0.0602 0.0602 0.0602 0.0602 0.0602 ...
  ..$ : num [1:233] 0.0566 0.0566 0.0566 0.0566 0.0566 ...
  ..$ : num [1:233] 0.0658 0.0658 0.0658 0.0658 0.0658 ...
  ..$ : num [1:233] 0.0391 0.0391 0.0391 0.0391 0.0391 ...
  ..$ : num [1:233] 0.0484 0.0484 0.0484 0.0484 0.0484 ...
  ..$ : num [1:233] 0.0329 0.0329 0.0329 0.0329 0.0329 ...
  ..$ : num [1:233] 0.0709 0.0709 0.0709 0.0709 0.0709 ...
  ..$ : num [1:233] 0.0506 0.0506 0.0506 0.0506 0.0506 ...
  ..$ : num [1:233] 0.0498 0.0498 0.0498 0.0498 0.0498 ...
  ..$ : num [1:233] 0.0548 0.0548 0.0548 0.0548 0.0548 ...
  ..$ : num [1:233] 0.055 0.055 0.055 0.055 0.055 ...
  ..$ : num [1:233] 0.0584 0.0584 0.0584 0.0584 0.0584 ...
  ..$ : num [1:233] 0.0793 0.0793 0.0793 0.0793 0.0793 ...
  ..$ : num [1:233] 0.0842 0.0842 0.0842 0.0842 0.0842 ...
  ..$ : num [1:233] 0.0703 0.0703 0.0703 0.0703 0.0703 ...
  ..$ : num [1:233] 0.0626 0.0626 0.0626 0.0626 0.0626 ...
  ..$ : num [1:233] 0.0541 0.0541 0.0541 0.0541 0.0541 ...
  ..$ : num [1:233] 0.07421 0.07421 0.07421 0.07421 0.00277 ...
  ..$ : num [1:233] 0.0481 0.0481 0.0481 0.0481 0.0481 ...
  ..$ : num [1:233] 0.0541 0.0541 0.0541 0.0541 0.0541 ...
  ..$ : num [1:233] 0.0577 0.0577 0.0577 0.0577 0.0577 ...
  ..$ : num [1:233] 0.0208 0.0208 0.0208 0.0208 0.0208 ...
  ..$ : num [1:233] 0.052 0.052 0.052 0.052 0.052 ...
  ..$ : num [1:233] 0.0488 0.0488 0.0488 0.0488 0.0488 ...
  ..$ : num [1:233] 0.112 0.112 0.112 0.112 0.112 ...
  ..$ : num [1:233] 0.0552 0.0552 0.0552 0.0552 0.0552 ...
  ..$ : num [1:233] 0.053 0.053 0.053 0.053 0.053 ...
  ..$ : num [1:233] 0.0549 0.0549 0.0549 0.0549 0.0549 ...
  ..$ : num [1:233] 0.0393 0.0393 0.0393 0.0393 0.0393 ...
  ..$ : num [1:233] 0.0587 0.0587 0.0587 0.0587 0.0587 ...
  ..$ : num [1:233] 0.0775 0.0775 0.0775 0.0775 0.0775 ...
  ..$ : num [1:233] 0.162 0.162 0.162 0.162 0.162 ...
  ..$ : num [1:233] 0.142 0.142 0.142 0.142 0.142 ...
  ..$ : num [1:233] 0.0579 0.0579 0.0579 0.0579 0.0579 ...
  ..$ : num [1:233] 0.0287 0.0287 0.0287 0.0287 0.0287 ...
  ..$ : num [1:233] 0.0273 0.0273 0.0273 0.0273 0.0273 ...
  ..$ : num [1:233] 0.0555 0.0555 0.0555 0.0555 0.0555 ...
  ..$ : num [1:233] 0.0486 0.0486 0.0486 0.0486 0.0486 ...
  ..$ : num [1:233] 0.0858 0.0858 0.0858 0.0858 0.0858 ...
  ..$ : num [1:233] 0.08 0.08 0.08 0.08 0.08 ...
  ..$ : num [1:233] 0.0762 0.0762 0.0762 0.0762 0.0762 ...
  ..$ : num [1:233] 0.0506 0.0506 0.0506 0.0506 0.0506 ...
  ..$ : num [1:233] 0.0523 0.0523 0.0523 0.0523 0.0523 ...
  ..$ : num [1:233] 0.0326 0.0326 0.0326 0.0326 0.0326 ...
  ..$ : num [1:233] 0.0352 0.0352 0.0352 0.0352 0.0352 ...
  ..$ : num [1:233] 0.031 0.031 0.031 0.031 0.031 ...
  ..$ : num [1:233] 0.096 0.096 0.096 0.096 0.096 ...
  ..$ : num [1:233] 0.0601 0.0601 0.0601 0.0601 0.0601 ...
  ..$ : num [1:233] 0.107 0.107 0.107 0.107 0.107 ...
  ..$ : num [1:233] 0.0298 0.0298 0.0298 0.0298 0.0298 ...
  ..$ : num [1:233] 0.0513 0.0513 0.0513 0.3683 0.0513 ...
  ..$ : num [1:233] 0.0751 0.0751 0.0751 0.0751 0.0751 ...
  ..$ : num [1:233] 0.0655 0.0655 0.0655 0.0655 0.0655 ...
  ..$ : num [1:233] 0.0653 0.0653 0.0653 0.0653 0.0653 ...
  ..$ : num [1:233] 0.058 0.058 0.058 0.049 0.058 ...
  ..$ : num [1:233] 0.064 0.064 0.064 0.064 0.064 ...
  ..$ : num [1:233] 0.122 0.122 0.122 0.122 0.122 ...
  ..$ : num [1:233] 0.0104 0.0104 0.0104 0.057 0.057 ...
  ..$ : num [1:233] 0.0504 0.0504 0.0504 0.0504 0.0504 ...
  ..$ : num [1:233] 0.0451 0.0451 0.0037 0.0451 0.0451 ...
  ..$ : num [1:233] 0.0746 0.0746 0.0746 0.0746 0.0746 ...
  ..$ : num [1:233] 0.059 0.059 0.059 0.059 0.059 ...
  ..$ : num [1:233] 0.0627 0.0627 0.0627 0.0627 0.0627 ...
  ..$ : num [1:233] 0.0731 0.0731 0.0731 0.0731 0.0731 ...
  ..$ : num [1:233] 0.0475 0.0475 0.0475 0.0475 0.0475 ...
  ..$ : num [1:233] 0.0422 0.0422 0.0422 0.0422 0.0422 ...
  ..$ : num [1:233] 0.0688 0.0688 0.0688 0.0688 0.0688 ...
  ..$ : num [1:233] 0.0696 0.0696 0.0696 0.0696 0.0696 ...
  ..$ : num [1:233] 0.0704 0.0704 0.0704 0.0704 0.0704 ...
  ..$ : num [1:233] 0.0605 0.0605 0.0605 0.0605 0.0605 ...
  ..$ : num [1:233] 0.0708 0.0708 0.0708 0.0708 0.0708 ...
  ..$ : num [1:233] 0.0608 0.0608 0.0608 0.0608 0.0608 ...
  ..$ : num [1:233] 0.0722 0.0722 0.0722 0.0722 0.0722 ...
  ..$ : num [1:233] 0.0763 0.0763 0.0763 0.0763 0.0763 ...
  ..$ : num [1:233] 0.101 0.101 0.101 0.101 0.101 ...
  ..$ : num [1:233] 0.0485 0.0485 0.0485 0.0485 0.0485 ...
  ..$ : num [1:233] 0.0712 0.066 0.066 0.066 0.066 ...
  ..$ : num [1:233] 0.0404 0.0404 0.0404 0.0815 0.0815 ...
  ..$ : num [1:233] 0.0529 0.0529 0.0529 0.0529 0.0529 ...
  ..$ : num [1:233] 0.0667 0.0667 0.0667 0.0667 0.0667 ...
  ..$ : num [1:233] 0.0551 0.0551 0.0551 0.0551 0.0551 ...
  ..$ : num [1:233] 0.0477 0.0477 0.0477 0.0394 0.0394 ...
  ..$ : num [1:233] 0.0518 0.0518 0.0518 0.0518 0.0518 ...
  ..$ : num [1:233] 0.0396 0.0396 0.0396 0.0396 0.0396 ...
  ..$ : num [1:233] 0.0601 0.0601 0.0601 0.0601 0.0601 ...
  ..$ : num [1:233] 0.0688 0.0688 0.0688 0.0688 0.0688 ...
  ..$ : num [1:233] 0.06 0.06 0.06 0.06 0.06 ...
  ..$ : num [1:233] 0.0502 0.0502 0.0502 0.0502 0.0502 ...
  ..$ : num [1:233] 0.0542 0.0542 0.0542 0.0542 0.0542 ...
  ..$ : num [1:233] 0.0476 0.0476 0.0476 0.0476 0.0476 ...
  ..$ : num [1:233] 0.0612 0.0612 0.0612 0.0612 0.0612 ...
  ..$ : num [1:233] 0.0478 0.0478 0.0478 0.0478 0.0478 ...
  ..$ : num [1:233] 0.0717 0.0717 0.0717 0.0717 0.0717 ...
  ..$ : num [1:233] 0.061 0.061 0.061 0.061 0.061 ...
  ..$ : num [1:233] 0.0373 0.0373 0.0373 0.0373 0.0373 ...
  ..$ : num [1:233] 0.0414 0.0414 0.0414 0.0414 0.0414 ...
  ..$ : num [1:233] 0.0528 0.0528 0.0528 0.0528 0.0528 ...
  ..$ : num [1:233] 0.0567 0.0567 0.0567 0.0567 0.0567 ...
  ..$ : num [1:233] 0.0812 0.0812 0.0812 0.0263 0.0263 ...
  .. [list output truncated]
 $ meanTipLambda  : num [1:233] 0.0631 0.0625 0.0622 0.0668 0.0689 ...
 $ eventBranchSegs:List of 1501
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:474, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:475, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:473, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 5 6 7 8 9 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:473, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:474, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:477, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 9 ...
  ..$ : num [1:475, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:466, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:473, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 4 5 6 7 8 9 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 4 5 6 7 8 9 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:474, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 3 4 5 6 7 8 9 ...
  ..$ : num [1:474, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:474, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:473, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:474, 1:4] 1 2 3 4 5 6 6 7 8 9 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:473, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:472, 1:4] 1 1 2 3 4 5 6 7 8 9 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:469, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:468, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:473, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:475, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:474, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:475, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:471, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:467, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ : num [1:470, 1:4] 1 2 3 4 5 6 7 8 9 10 ...
  .. [list output truncated]
 $ tipMu          :List of 1501
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
  .. [list output truncated]
 $ meanTipMu      : num [1:233] 0 0 0 0 0 0 0 0 0 0 ...
 $ type           : chr "trait"
 $ dtrates        :List of 3
  ..$ tau  : num 0.01
  ..$ rates: num [1:3042] 0.0786 0.0779 0.0773 0.0768 0.0763 ...
  ..$ tmat : num [1:3042, 1:3] 235 235 235 235 235 235 235 235 235 235 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:3042] "1" "2" "3" "4" ...
  .. .. ..$ : NULL
 - attr(*, "class")= chr "bammdata"
 - attr(*, "order")= chr "cladewise"



In [331]:

    
write.nexus(as.phylo(dtrates))









    



#NEXUS
[R-package APE, Sun Mar 27 17:33:19 2016]

BEGIN TAXA;
	DIMENSIONS NTAX = 233;
	TAXLABELS
		Galago_matschiei
		Euoticus_pallidus
		Euoticus_elegantulus
		Galagoides_zanzibaricus
		Galagoides_demidoff
		Galago_alleni
		Galago_senegalensis
		Galago_moholi
		Galago_gallarum
		Otolemur_garnettii
		Otolemur_crassicaudatus
		Perodicticus_potto
		Arctocebus_aureus
		Arctocebus_calabarensis
		Loris_tardigradus
		Nycticebus_pygmaeus
		Nycticebus_coucang
		Daubentonia_madagascariensis
		Lepilemur_mustelinus
		Lepilemur_septentrionalis
		Lepilemur_ruficaudatus
		Lepilemur_leucopus
		Lepilemur_edwardsi
		Lepilemur_microdon
		Lepilemur_dorsalis
		Lemur_catta
		Hapalemur_aureus
		Hapalemur_simus
		Hapalemur_griseus
		Varecia_variegata
		Eulemur_rubriventer
		Eulemur_mongoz
		Eulemur_coronatus
		Eulemur_macaco
		Eulemur_fulvus
		Avahi_laniger
		Indri_indri
		Propithecus_diadema
		Propithecus_verreauxi
		Propithecus_tattersalli
		Phaner_furcifer
		Allocebus_trichotis
		Microcebus_coquereli
		Microcebus_rufus
		Microcebus_murinus
		Cheirogaleus_medius
		Cheirogaleus_major
		Tarsius_dianae
		Tarsius_pumilus
		Tarsius_spectrum
		Tarsius_syrichta
		Tarsius_bancanus
		Chiropotes_satanas
		Chiropotes_albinasus
		Cacajao_melanocephalus
		Cacajao_calvus
		Pithecia_pithecia
		Pithecia_irrorata
		Pithecia_aequatorialis
		Pithecia_monachus
		Pithecia_albicans
		Callicebus_torquatus
		Callicebus_modestus
		Callicebus_oenanthe
		Callicebus_olallae
		Callicebus_donacophilus
		Callicebus_personatus
		Callicebus_dubius
		Callicebus_cupreus
		Callicebus_caligatus
		Callicebus_hoffmannsi
		Callicebus_brunneus
		Callicebus_moloch
		Callicebus_cinerascens
		Alouatta_palliata
		Alouatta_coibensis
		Alouatta_caraya
		Alouatta_pigra
		Alouatta_fusca
		Alouatta_seniculus
		Alouatta_sara
		Alouatta_belzebul
		Ateles_paniscus
		Ateles_belzebuth
		Ateles_geoffroyi
		Ateles_fusciceps
		Ateles_marginatus
		Ateles_chamek
		Brachyteles_arachnoides
		Lagothrix_lagotricha
		Lagothrix_flavicauda
		Cebus_olivaceus
		Cebus_apella
		Cebus_capucinus
		Cebus_albifrons
		Saimiri_boliviensis
		Saimiri_vanzolinii
		Saimiri_sciureus
		Saimiri_ustus
		Saimiri_oerstedii
		Aotus_lemurinus
		Aotus_hershkovitzi
		Aotus_vociferans
		Aotus_brumbacki
		Aotus_nancymaae
		Aotus_miconax
		Aotus_infulatus
		Aotus_nigriceps
		Aotus_trivirgatus
		Aotus_azarai
		Callimico_goeldii
		Callithrix_pygmaea
		Callithrix_humeralifera
		Callithrix_argentata
		Callithrix_flaviceps
		Callithrix_aurita
		Callithrix_kuhlii
		Callithrix_geoffroyi
		Callithrix_penicillata
		Callithrix_jacchus
		Leontopithecus_chrysomela
		Leontopithecus_caissara
		Leontopithecus_rosalia
		Leontopithecus_chrysopygus
		Saguinus_oedipus
		Saguinus_geoffroyi
		Saguinus_midas
		Saguinus_bicolor
		Saguinus_leucopus
		Saguinus_imperator
		Saguinus_mystax
		Saguinus_labiatus
		Saguinus_inustus
		Saguinus_nigricollis
		Saguinus_tripartitus
		Saguinus_fuscicollis
		Pongo_pygmaeus
		Gorilla_gorilla
		Homo_sapiens
		Pan_troglodytes
		Pan_paniscus
		Hylobates_hoolock
		Hylobates_moloch
		Hylobates_lar
		Hylobates_agilis
		Hylobates_pileatus
		Hylobates_muelleri
		Hylobates_klossii
		Hylobates_syndactylus
		Hylobates_gabriellae
		Hylobates_leucogenys
		Hylobates_concolor
		Trachypithecus_geei
		Trachypithecus_auratus
		Trachypithecus_francoisi
		Trachypithecus_cristatus
		Trachypithecus_pileatus
		Trachypithecus_phayrei
		Trachypithecus_obscurus
		Semnopithecus_entellus
		Presbytis_potenziani
		Presbytis_comata
		Presbytis_frontata
		Presbytis_femoralis
		Presbytis_melalophos
		Presbytis_rubicunda
		Presbytis_thomasi
		Presbytis_hosei
		Trachypithecus_johnii
		Trachypithecus_vetulus
		Pygathrix_nemaeus
		Pygathrix_avunculus
		Pygathrix_roxellana
		Pygathrix_brelichi
		Pygathrix_bieti
		Nasalis_larvatus
		Nasalis_concolor
		Procolobus_preussi
		Procolobus_verus
		Procolobus_rufomitratus
		Procolobus_pennantii
		Procolobus_badius
		Colobus_satanas
		Colobus_angolensis
		Colobus_polykomos
		Colobus_guereza
		Mandrillus_sphinx
		Mandrillus_leucophaeus
		Cercocebus_torquatus
		Cercocebus_agilis
		Cercocebus_galeritus
		Lophocebus_albigena
		Theropithecus_gelada
		Papio_hamadryas
		Macaca_sylvanus
		Macaca_tonkeana
		Macaca_maura
		Macaca_ochreata
		Macaca_nigra
		Macaca_silenus
		Macaca_nemestrina
		Macaca_arctoides
		Macaca_radiata
		Macaca_assamensis
		Macaca_thibetana
		Macaca_sinica
		Macaca_fascicularis
		Macaca_fuscata
		Macaca_mulatta
		Macaca_cyclopis
		Allenopithecus_nigroviridis
		Miopithecus_talapoin
		Erythrocebus_patas
		Chlorocebus_aethiops
		Cercopithecus_solatus
		Cercopithecus_preussi
		Cercopithecus_lhoesti
		Cercopithecus_hamlyni
		Cercopithecus_neglectus
		Cercopithecus_mona
		Cercopithecus_campbelli
		Cercopithecus_wolfi
		Cercopithecus_pogonias
		Cercopithecus_erythrotis
		Cercopithecus_sclateri
		Cercopithecus_cephus
		Cercopithecus_ascanius
		Cercopithecus_petaurista
		Cercopithecus_erythrogaster
		Cercopithecus_nictitans
		Cercopithecus_mitis
		Cercopithecus_dryas
		Cercopithecus_diana
	;
END;
BEGIN TREES;
	TRANSLATE
		1	Galago_matschiei,
		2	Euoticus_pallidus,
		3	Euoticus_elegantulus,
		4	Galagoides_zanzibaricus,
		5	Galagoides_demidoff,
		6	Galago_alleni,
		7	Galago_senegalensis,
		8	Galago_moholi,
		9	Galago_gallarum,
		10	Otolemur_garnettii,
		11	Otolemur_crassicaudatus,
		12	Perodicticus_potto,
		13	Arctocebus_aureus,
		14	Arctocebus_calabarensis,
		15	Loris_tardigradus,
		16	Nycticebus_pygmaeus,
		17	Nycticebus_coucang,
		18	Daubentonia_madagascariensis,
		19	Lepilemur_mustelinus,
		20	Lepilemur_septentrionalis,
		21	Lepilemur_ruficaudatus,
		22	Lepilemur_leucopus,
		23	Lepilemur_edwardsi,
		24	Lepilemur_microdon,
		25	Lepilemur_dorsalis,
		26	Lemur_catta,
		27	Hapalemur_aureus,
		28	Hapalemur_simus,
		29	Hapalemur_griseus,
		30	Varecia_variegata,
		31	Eulemur_rubriventer,
		32	Eulemur_mongoz,
		33	Eulemur_coronatus,
		34	Eulemur_macaco,
		35	Eulemur_fulvus,
		36	Avahi_laniger,
		37	Indri_indri,
		38	Propithecus_diadema,
		39	Propithecus_verreauxi,
		40	Propithecus_tattersalli,
		41	Phaner_furcifer,
		42	Allocebus_trichotis,
		43	Microcebus_coquereli,
		44	Microcebus_rufus,
		45	Microcebus_murinus,
		46	Cheirogaleus_medius,
		47	Cheirogaleus_major,
		48	Tarsius_dianae,
		49	Tarsius_pumilus,
		50	Tarsius_spectrum,
		51	Tarsius_syrichta,
		52	Tarsius_bancanus,
		53	Chiropotes_satanas,
		54	Chiropotes_albinasus,
		55	Cacajao_melanocephalus,
		56	Cacajao_calvus,
		57	Pithecia_pithecia,
		58	Pithecia_irrorata,
		59	Pithecia_aequatorialis,
		60	Pithecia_monachus,
		61	Pithecia_albicans,
		62	Callicebus_torquatus,
		63	Callicebus_modestus,
		64	Callicebus_oenanthe,
		65	Callicebus_olallae,
		66	Callicebus_donacophilus,
		67	Callicebus_personatus,
		68	Callicebus_dubius,
		69	Callicebus_cupreus,
		70	Callicebus_caligatus,
		71	Callicebus_hoffmannsi,
		72	Callicebus_brunneus,
		73	Callicebus_moloch,
		74	Callicebus_cinerascens,
		75	Alouatta_palliata,
		76	Alouatta_coibensis,
		77	Alouatta_caraya,
		78	Alouatta_pigra,
		79	Alouatta_fusca,
		80	Alouatta_seniculus,
		81	Alouatta_sara,
		82	Alouatta_belzebul,
		83	Ateles_paniscus,
		84	Ateles_belzebuth,
		85	Ateles_geoffroyi,
		86	Ateles_fusciceps,
		87	Ateles_marginatus,
		88	Ateles_chamek,
		89	Brachyteles_arachnoides,
		90	Lagothrix_lagotricha,
		91	Lagothrix_flavicauda,
		92	Cebus_olivaceus,
		93	Cebus_apella,
		94	Cebus_capucinus,
		95	Cebus_albifrons,
		96	Saimiri_boliviensis,
		97	Saimiri_vanzolinii,
		98	Saimiri_sciureus,
		99	Saimiri_ustus,
		100	Saimiri_oerstedii,
		101	Aotus_lemurinus,
		102	Aotus_hershkovitzi,
		103	Aotus_vociferans,
		104	Aotus_brumbacki,
		105	Aotus_nancymaae,
		106	Aotus_miconax,
		107	Aotus_infulatus,
		108	Aotus_nigriceps,
		109	Aotus_trivirgatus,
		110	Aotus_azarai,
		111	Callimico_goeldii,
		112	Callithrix_pygmaea,
		113	Callithrix_humeralifera,
		114	Callithrix_argentata,
		115	Callithrix_flaviceps,
		116	Callithrix_aurita,
		117	Callithrix_kuhlii,
		118	Callithrix_geoffroyi,
		119	Callithrix_penicillata,
		120	Callithrix_jacchus,
		121	Leontopithecus_chrysomela,
		122	Leontopithecus_caissara,
		123	Leontopithecus_rosalia,
		124	Leontopithecus_chrysopygus,
		125	Saguinus_oedipus,
		126	Saguinus_geoffroyi,
		127	Saguinus_midas,
		128	Saguinus_bicolor,
		129	Saguinus_leucopus,
		130	Saguinus_imperator,
		131	Saguinus_mystax,
		132	Saguinus_labiatus,
		133	Saguinus_inustus,
		134	Saguinus_nigricollis,
		135	Saguinus_tripartitus,
		136	Saguinus_fuscicollis,
		137	Pongo_pygmaeus,
		138	Gorilla_gorilla,
		139	Homo_sapiens,
		140	Pan_troglodytes,
		141	Pan_paniscus,
		142	Hylobates_hoolock,
		143	Hylobates_moloch,
		144	Hylobates_lar,
		145	Hylobates_agilis,
		146	Hylobates_pileatus,
		147	Hylobates_muelleri,
		148	Hylobates_klossii,
		149	Hylobates_syndactylus,
		150	Hylobates_gabriellae,
		151	Hylobates_leucogenys,
		152	Hylobates_concolor,
		153	Trachypithecus_geei,
		154	Trachypithecus_auratus,
		155	Trachypithecus_francoisi,
		156	Trachypithecus_cristatus,
		157	Trachypithecus_pileatus,
		158	Trachypithecus_phayrei,
		159	Trachypithecus_obscurus,
		160	Semnopithecus_entellus,
		161	Presbytis_potenziani,
		162	Presbytis_comata,
		163	Presbytis_frontata,
		164	Presbytis_femoralis,
		165	Presbytis_melalophos,
		166	Presbytis_rubicunda,
		167	Presbytis_thomasi,
		168	Presbytis_hosei,
		169	Trachypithecus_johnii,
		170	Trachypithecus_vetulus,
		171	Pygathrix_nemaeus,
		172	Pygathrix_avunculus,
		173	Pygathrix_roxellana,
		174	Pygathrix_brelichi,
		175	Pygathrix_bieti,
		176	Nasalis_larvatus,
		177	Nasalis_concolor,
		178	Procolobus_preussi,
		179	Procolobus_verus,
		180	Procolobus_rufomitratus,
		181	Procolobus_pennantii,
		182	Procolobus_badius,
		183	Colobus_satanas,
		184	Colobus_angolensis,
		185	Colobus_polykomos,
		186	Colobus_guereza,
		187	Mandrillus_sphinx,
		188	Mandrillus_leucophaeus,
		189	Cercocebus_torquatus,
		190	Cercocebus_agilis,
		191	Cercocebus_galeritus,
		192	Lophocebus_albigena,
		193	Theropithecus_gelada,
		194	Papio_hamadryas,
		195	Macaca_sylvanus,
		196	Macaca_tonkeana,
		197	Macaca_maura,
		198	Macaca_ochreata,
		199	Macaca_nigra,
		200	Macaca_silenus,
		201	Macaca_nemestrina,
		202	Macaca_arctoides,
		203	Macaca_radiata,
		204	Macaca_assamensis,
		205	Macaca_thibetana,
		206	Macaca_sinica,
		207	Macaca_fascicularis,
		208	Macaca_fuscata,
		209	Macaca_mulatta,
		210	Macaca_cyclopis,
		211	Allenopithecus_nigroviridis,
		212	Miopithecus_talapoin,
		213	Erythrocebus_patas,
		214	Chlorocebus_aethiops,
		215	Cercopithecus_solatus,
		216	Cercopithecus_preussi,
		217	Cercopithecus_lhoesti,
		218	Cercopithecus_hamlyni,
		219	Cercopithecus_neglectus,
		220	Cercopithecus_mona,
		221	Cercopithecus_campbelli,
		222	Cercopithecus_wolfi,
		223	Cercopithecus_pogonias,
		224	Cercopithecus_erythrotis,
		225	Cercopithecus_sclateri,
		226	Cercopithecus_cephus,
		227	Cercopithecus_ascanius,
		228	Cercopithecus_petaurista,
		229	Cercopithecus_erythrogaster,
		230	Cercopithecus_nictitans,
		231	Cercopithecus_mitis,
		232	Cercopithecus_dryas,
		233	Cercopithecus_diana
	;
	TREE * UNTITLED = [&R] (((((1:3.644984273,(2:1.449862152,3:1.449862152):2.19512212):4.875712214,((4:3.574103734,5:3.574103734):3.753222182,((6:5.403508585,((7:1.46115685,8:1.46115685):0.9031863282,9:2.364343178):3.039165407):0.9126765822,(10:4.242644127,11:4.242644127):2.07354104):1.011140749):1.19337057):12.40170848,((12:4.703629279,(13:1.881771918,14:1.881771918):2.821857361):11.63769999,(15:9.200565853,(16:2.672476766,17:2.672476766):6.528089088):7.140763412):4.581075703):30.9481165,(18:39.48238529,((((19:11.19994092,(20:7.600895938,(21:5.028627182,(22:3.00293009,((23:0.4532281942,24:0.4532281942):0.9099348266,25:1.363163021):1.639767069):2.025697092):2.572268756):3.599044977):5.972299255,((26:6.229068058,((27:5.342908924,28:5.342908924):0.3195365339,29:5.662445458):0.5666226004):6.830461251,(30:11.89273831,((31:3.074034512,32:3.074034512):3.302548494,(33:3.756910335,(34:3.684015058,35:3.684015058):0.07289527772):2.61967267):5.516155306):1.166790997):4.112710861):4.862567529,(36:13.61679482,(37:7.435235336,(38:5.879825205,(39:1.54141842,40:1.54141842):4.338406785):1.555410131):6.181559482):8.418012881):5.481371118,(41:17.03543968,((42:7.053370093,(43:4.099785478,(44:2.737419707,45:2.737419707):1.362365772):2.953584615):4.41733529,(46:9.4004694,47:9.4004694):2.070235983):5.564734292):10.48073914):11.96620647):12.38813618):13.22116451,((((48:0.2574238833,49:0.2574238833):15.04352481,50:15.30094869):19.88152752,(51:8.683554425,52:8.683554425):26.49892178):27.41764581,(((((((53:3.688446923,54:3.688446923):4.43397097,(55:3.700510722,56:3.700510722):4.421907171):3.758327519,(57:10.23381691,(58:6.549583463,(59:3.789893236,(60:1.755629589,61:1.755629589):2.034263646):2.759690228):3.684233443):1.646928507):9.091857379,(62:16.4714104,((63:7.328813932,((64:0.6554084888,65:0.6554084888):2.430400428,66:3.085808916):4.243005015):5.974162265,(67:10.30345572,((68:4.724420572,(69:1.982769904,70:1.982769904):2.741650669):3.275942328,((71:2.3505473,72:2.3505473):2.976743205,(73:2.323716931,74:2.323716931):3.003573574):2.673072396):2.30309282):2.999520477):3.168434207):4.501192388):4.343687065,(((75:0.5022628648,76:0.5022628648):12.22768188,(77:6.926354953,(78:4.52730596,(79:2.947096325,((80:0.7931449028,81:0.7931449028):0.9655421863,82:1.758687089):1.188409236):1.580209636):2.399048993):5.803589795):7.953558288,(((83:3.038404989,(84:2.0373527,(85:1.215004191,86:1.215004191):0.8223485097):1.001052288):1.654543136,(87:2.885071027,88:2.885071027):1.807877097):6.593561648,(89:9.030844567,(90:2.921910319,91:2.921910319):6.108934248):2.255665205):9.396993264):4.632786821):4.835889797,((((92:3.963779494,93:3.963779494):3.298610745,(94:0.1411841561,95:0.1411841561):7.121206083):15.92417684,(96:8.42086612,(97:6.824135378,(98:3.943009428,(99:1.765312829,100:1.765312829):2.177696599):2.88112595):1.596730742):14.76570096):2.506309495,(((101:3.41619118,102:3.41619118):12.37114501,((103:4.522715102,104:4.522715102):7.223381154,(105:8.668907477,(106:6.289866555,(107:4.164301987,(108:2.631524193,(109:1.237794698,110:1.237794698):1.393729496):1.532777793):2.125564568):2.379040922):3.077188779):4.041239934):6.241568413,((111:18.37696755,((112:3.706008951,(113:2.079201914,114:2.079201914):1.626807038):7.659029351,((115:3.433355688,116:3.433355688):7.766883693,((117:0.2655427553,118:0.2655427553):0.2450028896,(119:0.2563476922,120:0.2563476922):0.2541979527):10.68969374):0.1647989214):7.011929249):0.6106466388,((121:7.67864797,(122:6.625267777,(123:3.83733791,124:3.83733791):2.787929867):1.053380192):7.967671715,(((125:3.279130893,126:3.279130893):4.599071641,(127:3.309205777,128:3.309205777):4.568996757):4.804458654,(129:9.81877075,((130:4.38688854,(131:1.953791812,132:1.953791812):2.433096728):3.291138283,(133:5.079922827,(134:3.038858259,(135:1.38319711,136:1.38319711):1.655661149):2.041064568):2.598103996):2.140743928):2.863890437):2.963658497):3.341294506):3.041290413):3.663971968):4.459303084):21.07285881,(((137:15.84463358,(138:6.414492353,(139:5.067395296,(140:1.95369081,141:1.95369081):3.113704486):1.347097057):9.430141232):3.792242626,((142:4.011578905,((143:3.516831702,(144:3.100837056,145:3.100837056):0.415994646):0.02217424005,(146:2.029256113,(147:0.8819271649,148:0.8819271649):1.147328948):1.50974983):0.4725729627):1.864277026,(149:4.018969267,(150:1.806528048,(151:0.7882422843,152:0.7882422843):1.018285764):2.212441219):1.856886664):13.76102028):12.78015491,(((((((153:5.122402371,(154:3.734662847,(155:2.896936803,(156:0.7948482703,(157:0.7521180596,(158:0.6943398071,159:0.6943398071):0.05777825247):0.04273021076):2.102088533):0.8377260442):1.387739524):1.686236098,160:6.808638469):0.1210272121,(((161:1.894279439,((162:0.2207630615,163:0.2207630615):1.368093801,((164:0.5271822714,165:0.5271822714):1.023551706,(166:0.5324439811,167:0.5324439811):1.018289997):0.03812288497):0.3054225766):1.913113649,168:3.807393089):2.744710106,(169:5.199385085,170:5.199385085):1.35271811):0.3775624863):1.956935552,(171:8.00141983,(172:3.871092153,(173:2.609689257,(174:1.037846215,175:1.037846215):1.571843042):1.261402895):4.130327677):0.8851814025):0.005580154993,(176:3.483864376,177:3.483864376):5.408317012):4.714508807,(((178:3.495012927,179:3.495012927):1.765829351,(180:4.31325428,(181:1.755080673,182:1.755080673):2.558173607):0.9475879969):6.697248224,(183:6.037347054,(184:3.490571445,(185:0.8052450953,186:0.8052450953):2.68532635):2.546775609):5.920743447):1.648599693):4.73007412,(((((187:1.965891197,188:1.965891197):3.476292126,(189:2.313096216,(190:0.5032383396,191:0.5032383396):1.809857876):3.129087107):1.267822239,(192:2.228040923,(193:1.542748547,194:1.542748547):0.6852923762):4.48196464):2.530843414,(195:7.491106738,((((196:0.1352766979,197:0.1352766979):2.512987258,(198:1.653294976,199:1.653294976):0.99496898):0.9324480106,(200:2.244767628,201:2.244767628):1.335944338):2.67575395,((202:2.801002741,((203:0.7161250138,204:0.7161250138):0.9920128354,(205:1.055381942,206:1.055381942):0.6527559075):1.092864892):1.631659175,(207:2.229595922,(208:0.9127479862,(209:0.2690107063,210:0.2690107063):0.6437372799):1.316847935):2.203065995):1.823803999):1.234640822):1.749742238):2.0137033,(211:8.282985373,(212:6.749635282,((213:5.180706992,214:5.180706992):0.5443901029,((215:0.8414405469,(216:0.008617084965,217:0.008617084965):0.832823462):4.070831472,(218:4.215320983,((219:2.558834212,((220:0.786479238,221:0.786479238):0.4537817958,(222:0.7782538441,223:0.7782538441):0.4620071896):1.318573178):1.074499161,(((((224:0.5027196302,225:0.5027196302):0.5295782726,(226:0.488649295,227:0.488649295):0.5436486077):0.6762807982,(228:0.7530173817,229:0.7530173817):0.9555613192):0.6143894491,(230:0.9547751556,231:0.9547751556):1.368192994):0.6306031166,(232:1.234458241,233:1.234458241):1.719113026):0.6797621058):0.5819876103):0.6969510358):0.8128250763):1.024538187):1.533350091):2.971566903):7.082212039):14.0802668):18.80800735):11.37508356):2.491563952);
END;

OK, so coercing a bammdata object to phylo lets us generate NEXUS output. But it seems very lossy, unless we just need branch lengths. Let's look at the "raw" JSON for each:



In [ ]:

    
# This JSON output is WAAAY too big for a Jupyter notebook! We can use it on the server, 
# but do *not* attempt to render its output here!
test = toJSON(dtrates, force=TRUE)



In [350]:

    
gdata::object.size(test)

23072168

Yes, that's 23 MB of JSON, which nicely chokes the Chrome browser and probably any others. What is all this stuff?!

edge: [   // 2545 bytes
    [234,235], 
    [235,236], 
    ...
]
Nnode: [232]
tip.label: ["Galago_matschiei", "Euoticus_pallidus", ...]   // 4909 bytes
edge.length: [13.2212,30.9481,12.4017,4.8757,3.645,2.1951,1.4499,1.4499,1.1934, ...]  // 3259 bytes
begin: [0,13.2212, 44.1693, ...]  // 3672 bytes
end: [0,13.2212, 44.1693, ...]    // 3703 bytes
downseq: [234,235,236, ...]   // 1768 bytes
lastvisit: [1,2,3 ...]        // 1673 bytes
numberEvents: [6,11,4,4 ...]  // 3509 bytes
eventData: [                  // 1027938 bytes (1 MB)
    [
        {"node":234,"time":0,"lam1":0.0905,"lam2":-0.0063,"mu1":0,"mu2":0,"index":1},
        {"node":281,"time":2.2503,"lam1":0.0949,"lam2":-0.0342,"mu1":0,"mu2":0,"index":2},
        ...
    ],
    ...
]
eventVectors: [                 // 1399423 bytes (1.4 MB)
    [1,1,1, ...],
    [1,1,1, ...],
    ...
]
tipStates: [                    // 704907 bytes (700 KB)
    [1,1,1, ...],
    [1,1,1, ...],
    ...
]
tipLambda: [                    // 2413245 bytes (2.4 MB)
    [0.0602,0.0602,0.0602, ...],
    [0.0602,0.0602,0.0602, ...],
    ...
]
meanTipLambda: [                // 1624 bytes
    [0.0602,0.0602,0.0602, ...],
    [0.0602,0.0602,0.0602, ...],
    ...
]
eventBranchSegs: [[[...], ...], ...]   // 16708306 bytes (16.7 MB)
tipMu: [[...], ...]                    // 702482 bytes (700 KB)
meanTipMu: [0,0,0, ...]                // 483 bytes
type: ["trait"]                         
dtrates: {
    "tau":[0.01],
    "rates": [0.0786, ...]             // 20989 bytes (21 KB)
    "tmat": [[235,0,0.6509],[235,0.6509,1.3018], ...]  // 65456 bytes (65 KB)
    "

So the main culprits are eventData, eventVectors, tipLambda, and especially eventBranchSegs (the lion's share at almost 17 MB).

Clearly most of this data is lost in the NEXUS output. If we want to pass JSON to the Tree Illustrator, perhaps we can weed out these fields during a piecemeal conversion to JSON. But which are the fields we need?

Based on the source code for plot.bammdata, the important information for coloring edges is contained in dtrates$dtrates$rates. These values must correspond to branches/edges somehow, but the numbers don't match and are not visible:



In [409]:

    
length(dtrates$dtrates$rates)



In [410]:

    
dtrates$Nnode

Let's mimic the code in plot.bammdata and see what it reveals. First, what does assignColorBreaks really do? It seems to map an inbound range of rate values (arbitrary decimal numbers) to a set of threshold values that map to a preset palette, e.g. 16 equidistant hues in the ROYGBIV spectrum.



In [422]:

    
assignColorBreaks(dtrates$dtrates$rates, NCOLORS=16)









    





	0.00891625545951066
	0.0171185643546078
	0.0253208732497049
	0.033523182144802
	0.0417254910398991
	0.0499277999349962
	0.0581301088300933
	0.0663324177251904
	0.0745347266202875
	0.0827370355153846
	0.0909393444104817
	0.0991416533055788
	0.107343962200676
	0.115546271095773
	0.12374857999087
	0.131950888885967
	0.140153197781064



In [424]:

    
length(assignColorBreaks(dtrates$dtrates$rates, NCOLORS=16))

NOTE that it always includes the upper and lower bounds, so the number of color break values is always NCOLORS + 1.



In [428]:

    
min(dtrates$dtrates$rates)









    




0.00891625545951066



In [429]:

    
max(dtrates$dtrates$rates)









    




0.140153197781064

A close look at the SVG output of plot.bammdata shows that edges have been rendered as a series of short line segments (or arcs) in solid colors. A high value for tau results in fewer, coarser segments.



In [416]:

    
plot(edata, method="polar", pal=c("darkgreen","yellow2","red"),tau=0.1)



In [407]:

    
names(dtrates)









    





	'edge'
	'Nnode'
	'tip.label'
	'edge.length'
	'begin'
	'end'
	'downseq'
	'lastvisit'
	'numberEvents'
	'eventData'
	'eventVectors'
	'tipStates'
	'tipLambda'
	'meanTipLambda'
	'eventBranchSegs'
	'tipMu'
	'meanTipMu'
	'type'
	'dtrates'



In [436]:

    
dtrates$dtrates$rates[[5]]









    




0.0762798795755268



In [437]:

    
colorMap(dtrates$dtrates$rates)









    



Error in eval(expr, envir, enclos): could not find function "colorMap"
Traceback:

Hm, it seems the interesting stuff is in method colorMap, which is a hidden internal method of BAMMtools.



In [453]:

    
?BAMMtools









    





BAMMtools-package {BAMMtools} R Documentation


BAMMtools


Description

An R package for the analysis and visualization of complex macroevolutionary dynamics. Functions in BAMMtools are oriented entirely around analysis of results obtained using the BAMM software (bamm-project.org).



Details




 
Package:  BAMMtools


 
Type:  Package


 
Version:  2.1.1


 
Date:  2016-03-02


 
License:  GPL-2 | GPL-3


 







Author(s)

Dan Rabosky, Mike Grundler, Pascal Title, Jonathan Mitchell, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang

Maintainer: Pascal Title <ptitle@umich.edu>



References

bamm-project.org

Rabosky, D., M. Grundler, C. Anderson, P. Title, J. Shi, J. Brown, H. Huang and J. Larson. 2014. BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods in Ecology and Evolution 5: 701-707.

Rabosky, D. L. 2014. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE 9: e89543

Shi, J. J., and D. L. Rabosky. 2015. Speciation dynamics during the global radiation of extant bats. Evolution 69: 1528-1545.

Rabosky, D. L., F. Santini, J. T. Eastman, S. A. Smith, B. L. Sidlauskas, J. Chang, and M. E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications DOI: 10.1038/ncomms2958 


[Package BAMMtools version 2.1.1 ]



In [ ]:

Package:	BAMMtools
Type:	Package
Version:	2.1.1
Date:	2016-03-02
License:	GPL-2 \| GPL-3