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$edge
6 7
7 8
8 1
8 2
7 9
9 3
9 4
6 5
In [25]:
tree$tip.label
- 'A'
- 'B'
- 'C'
- 'D'
- 'E'
In [26]:
tree$Nnode
4
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.
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"]]
At this point we have a few options:
phylo
objects and convert to NexSONNot 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
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.. ..$ lam1 : num [1:12] 0.032557 0.160751 0.038497 0.089296 0.000608 ...
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.. ..$ 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 ...
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.. ..$ lam1 : num [1:5] 0.063 0.0329 0.1026 0.0635 0.4212
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ lam1 : num [1:5] 0.0468 0.2215 0.0886 0.2428 0.1236
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ lam1 : num [1:5] 0.0301 0.054 0.0831 0.4161 0.2106
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ node : int [1:9] 234 281 287 255 346 41 421 330 212
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ time : num [1:6] 0 25.3 47.7 51.7 57.7 ...
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.. ..$ lam2 : num [1:6] -0.00685 -0.01343 0.02299 -0.00877 0.00603 ...
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.. ..$ time : num [1:3] 0 2.01 54.29
.. ..$ lam1 : num [1:3] 0.0521 0.1674 0.0775
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.. ..$ 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
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.. ..$ 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 ...
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.. ..$ mu2 : num [1:10] 0 0 0 0 0 0 0 0 0 0
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ time : num [1:4] 0 11.5 45.9 54.2
.. ..$ lam1 : num [1:4] 0.0438 0.0759 0.0463 0.0709
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.. ..$ 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 ...
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.. ..$ mu2 : num [1:6] 0 0 0 0 0 0
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.. ..$ 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 ...
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.. ..$ mu2 : num [1:9] 0 0 0 0 0 0 0 0 0
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.. ..$ 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 ...
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.. ..$ index: int [1:7] 1 2 3 4 5 6 7
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ time : num [1:4] 0 20.1 58.1 62.3
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.. ..$ lam2 : num [1:4] -0.00376 -0.01211 0.00952 0.00306
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.. ..$ 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 ...
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.. ..$ mu2 : num [1:9] 0 0 0 0 0 0 0 0 0
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ mu2 : num [1:5] 0 0 0 0 0
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ mu2 : num [1:7] 0 0 0 0 0 0 0
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.. ..$ 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 ...
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.. ..$ mu2 : num [1:8] 0 0 0 0 0 0 0 0
.. ..$ index: int [1:8] 1 2 3 4 5 6 7 8
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ 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 ...
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.. ..$ index: int [1:7] 1 2 3 4 5 6 7
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ index: int [1:5] 1 2 3 4 5
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.. ..$ 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 ...
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.. ..$ index: int [1:7] 1 2 3 4 5 6 7
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.. ..$ 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 ...
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.. ..$ mu2 : num [1:6] 0 0 0 0 0 0
.. ..$ index: int [1:6] 1 2 3 4 5 6
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ index: int [1:6] 1 2 3 4 5 6
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.. ..$ 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
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.. ..$ index: int [1:5] 1 2 3 4 5
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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 ...
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.. ..$ 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
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.. ..$ 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)
3042
In [410]:
dtrates$Nnode
232
Let's mimic the code in plot.bammdata
and see what it reveals. First, what does assignColorBreaks
really do? It seems to map an inbound range of rate values (arbitrary decimal numbers) to a set of threshold values that map to a preset palette, e.g. 16 equidistant hues in the ROYGBIV spectrum.
In [422]:
assignColorBreaks(dtrates$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$rates, NCOLORS=16))
17
NOTE that it always includes the upper and lower bounds, so the number of color break values is always NCOLORS + 1
.
In [428]:
min(dtrates$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
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 [ ]:
Content source: OpenTreeOfLife/tree-illustrator
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