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manual.lyx
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#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
\textclass paper
\begin_preamble
\usepackage{fullpage}
\end_preamble
\use_default_options true
\language english
\inputencoding auto
\font_roman default
\font_sans default
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\font_default_family default
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
\graphics default
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\spacing single
\use_hyperref false
\papersize default
\use_geometry false
\use_amsmath 1
\use_esint 1
\cite_engine basic
\use_bibtopic false
\paperorientation portrait
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\defskip medskip
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle default
\tracking_changes false
\output_changes false
\author ""
\author ""
\end_header
\begin_body
\begin_layout Title
Lagrange C++ Manual
\end_layout
\begin_layout Author
Stephen A.
Smith and Richard Ree
\end_layout
\begin_layout Part
Introduction
\end_layout
\begin_layout Section
Impetus
\end_layout
\begin_layout Standard
Lagrange began as a Python library or program (however you want to look
at it) with Richard Ree.
I was coding along side this project a Java implementation (called AReA),
but we later joined forces and produced the paper with the explicitly solved
rate matrix,
\begin_inset ERT
status open
\begin_layout Plain Layout
$Q$
\end_layout
\end_inset
(Ree and Smith, 2008).
This package has been successfully used for a variety of projects including
some of our own.
However, development has continued.
Rick developed a nice web interface for the construction of input files.
This is especially helpful when describing more complex area connectivity
scenarios.
Nevertheless, some users, including the developers, have recognized the
speed limitations, and therefore dataset limitations, of the Python version.
In order to continue the development of more computationally intensive
procedures, we have moved to a C++ version.
There are/will be ways to use the Python files created from the website,
but you may also interact directly with the C++ program.
\end_layout
\begin_layout Section
What is here
\end_layout
\begin_layout Standard
In this document you will find descriptions of the 1) compilation and installati
on process, 2) configuration file construction, 3) some examples and 4)
some of the algorithmic advances.
\end_layout
\begin_layout Part
Compilation and Installation
\end_layout
\begin_layout Standard
The C++ version of Lagrange makes use of quite a few libraries to simplify
the code and limit the introduction of errors.
The hardest part of compilation will be getting those installed and the
difficulty will vary depending on the machine.
In some cases (Windows and certain versions of Mac and Linux), we do not
have access to machines in which to test compilation so you will be on
your own.
But please email with problems if they arise and we will try our best to
resolve those.
\end_layout
\begin_layout Standard
A more extensive discussion of the Makefile options is also below.
\end_layout
\begin_layout Standard
The libraries used in Lagrange include:
\end_layout
\begin_layout Itemize
Gnu Scientific Library (GSL) -- optimization
\end_layout
\begin_layout Itemize
armadillo -- linear algebra (which requires cmake)
\end_layout
\begin_layout Itemize
gmp -- optional, for calulating exceptionally large trees
\end_layout
\begin_layout Itemize
mpfr -- optional, for calculating exceptionally large trees
\end_layout
\begin_layout Itemize
gmpfrxx -- optional, for calculating exceptionally large trees
\end_layout
\begin_layout Standard
You will also have to be able to compile with a FORTRAN compiler (I have
been using gfortran).
\end_layout
\begin_layout Section
Linux
\end_layout
\begin_layout Standard
Compilation of Lagrange on a Linux machine will be the least painful.
This is mostly because both Rick and I develop on Linux machines and so
this is the operating system on which the most testing has occurred.
In particular it has been tested on both Ubuntu and Fedora distributions.
Because of the package management system on these machines, the vast majority
of the relevant packages can be installed from the package managers.
After downloading the packages, the current procedure for installation
on Ubuntu 10.04 is:
\end_layout
\begin_layout Enumerate
make sure that you have the basic compilation tools (
\family typewriter
sudo apt-get install build-essential
\family default
)
\end_layout
\begin_layout Enumerate
untar and install armadillo (contained in the downloaded package, this is
newer than the repository version)
\end_layout
\begin_deeper
\begin_layout Enumerate
this may require the installation of other packages (for example, cmake,
which can be installed with the command
\family typewriter
sudo apt-get install cmake
\family default
)
\end_layout
\begin_layout Enumerate
to get all the packages necessary you can run
\family typewriter
sudo apt-get build-dep armadillo
\end_layout
\end_deeper
\begin_layout Enumerate
install the gsl development libraries with the command
\family typewriter
sudo apt-get install libgsl0-dev
\end_layout
\begin_layout Enumerate
install the python development libraries so you can read in the web configuratio
n files with
\family typewriter
sudo apt-get install python2.6-dev
\end_layout
\begin_layout Enumerate
if you are going to use the big tree option for compilation (good for trees
over 1000 tips) you should do the following:
\end_layout
\begin_deeper
\begin_layout Enumerate
in the gmpfrxx directory, untar the gmp-4.3.1.tar.bz2 file and go inside and
install with
\family typewriter
sudo apt-get install m4
\family default
,
\family typewriter
./configure --enable-cxx
\family default
,
\family typewriter
make
\family default
,
\family typewriter
sudo make install
\family default
)
\end_layout
\begin_layout Enumerate
untar the mpfr-2.4.2.tar.gz and do the standard
\family typewriter
./configure
\family default
,
\family typewriter
make
\family default
,
\family typewriter
sudo make install
\family default
)
\end_layout
\begin_layout Enumerate
finally go back into the gmpfrxx and just type
\family typewriter
make
\end_layout
\end_deeper
\begin_layout Enumerate
make lagrange with the command
\family typewriter
make -f Makefile
\end_layout
\begin_layout Section
MacOSX
\end_layout
\begin_layout Standard
Most of the installation instructions are similar to Linux for MacOSX however
there are some differences.
\end_layout
\begin_layout Enumerate
install the developer tools for MacOSX (these should be on the disk that
comes with the computer or you can always download from apple.
You will need this to install anything from source code on the Mac.
You will also need cmake for armadillo (see below).
\end_layout
\begin_layout Enumerate
untar and install armadillo (contained in the downloaded package)
\end_layout
\begin_deeper
\begin_layout Enumerate
there are special instructions for the Mac so please look at the armadillo
README.txt within the directory
\end_layout
\end_deeper
\begin_layout Enumerate
install the GNU Gnu Scientific Library which can be found here
\begin_inset Flex URL
status open
\begin_layout Plain Layout
http://www.gnu.org/software/gsl/
\end_layout
\end_inset
.
\end_layout
\begin_layout Enumerate
if you are going to use the big tree option for compilation (good for trees
over 1000 tips) you should do the following:
\end_layout
\begin_deeper
\begin_layout Enumerate
in the gmpfrxx directory, untar the gmp-4.3.1.tar.bz2 file and go inside and
install with
\family typewriter
sudo apt-get install m4
\family default
,
\family typewriter
./configure --enable-cxx
\family default
,
\family typewriter
make
\family default
,
\family typewriter
sudo make install
\family default
)
\end_layout
\begin_layout Enumerate
untar the mpfr-2.4.2.tar.gz and do the standard
\family typewriter
./configure
\family default
,
\family typewriter
make
\family default
,
\family typewriter
sudo make install
\family default
)
\end_layout
\begin_layout Enumerate
finally go back into the gmpfrxx and just type
\family typewriter
make
\end_layout
\end_deeper
\begin_layout Enumerate
make lagrange with the command
\family typewriter
make -f Makefile.MAC
\end_layout
\begin_layout Standard
When available, a binary version of Lagrange is made available for Mac users
to bypass the need to compile it from source.
\end_layout
\begin_layout Section
Windows
\end_layout
\begin_layout Standard
Currently being test on a Windows 7 machines, but check out the instructions
for Linux and Mac and use CygWin.
\end_layout
\begin_layout Section
Makefile description
\end_layout
\begin_layout Standard
There are some configurable items in the Makefile for each system that you
should be aware of in case somethings goes wrong.
Below are some lines of which to be aware.
\end_layout
\begin_layout Subsection
Linux
\end_layout
\begin_layout Standard
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 0
width "85col%"
special "none"
height "1in"
height_special "totalheight"
status open
\begin_layout Plain Layout
#if you have an error related to python during compilation, check this line
\end_layout
\begin_layout Plain Layout
\family typewriter
PYTHON_LIB = -I/usr/include/python2.6/
\end_layout
\begin_layout Plain Layout
# requires fortran, gsl, and pthread -- and -ldl -lutil -lpython2.6 are for
python
\end_layout
\begin_layout Plain Layout
# if llapack lblas fail, try larmadillo
\end_layout
\begin_layout Plain Layout
LIBS := -llapack -lblas -lgfortran -lgsl -lgslcblas -lm -lpthread -lgmp
-ldl -lutil -lpython2.6
\end_layout
\begin_layout Plain Layout
###########
\end_layout
\begin_layout Plain Layout
# change to yes for bigtrees -- loses about 3x speed
\end_layout
\begin_layout Plain Layout
# if 64 bit GSL try CPPFLAGS="-arch x86_64" LDFLAGS="-arch x86_64" ./configure
\end_layout
\begin_layout Plain Layout
# need to install gmp (with ./configure --enable-cxx) and mpfr and gmpfrxx
\end_layout
\begin_layout Plain Layout
#######
\end_layout
\begin_layout Plain Layout
BIG = no
\end_layout
\begin_layout Plain Layout
#this is where the fortran compiler should be
\end_layout
\begin_layout Plain Layout
FC = /usr/bin/gfortran
\end_layout
\end_inset
\end_layout
\begin_layout Subsection
MacOSX
\end_layout
\begin_layout Standard
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 0
width "85col%"
special "none"
height "1in"
height_special "totalheight"
status open
\begin_layout Plain Layout
#if you have an error related to python during compilation, check these
lines
\end_layout
\begin_layout Plain Layout
\family typewriter
PYTHON_LIB = -I/System/Library/Frameworks/Python.framework/Headers/
\end_layout
\begin_layout Plain Layout
\family typewriter
#output of
\end_layout
\begin_layout Plain Layout
\family typewriter
#>>> import distutils.sysconfig
\end_layout
\begin_layout Plain Layout
\family typewriter
#>>> distutils.sysconfig.get_config_var('LINKFORSHARED')
\end_layout
\begin_layout Plain Layout
\family typewriter
\size footnotesize
PYTHON_REQ = -u _PyMac_Error /System/Library/Frameworks/Python.framework/Versions
/2.6/Python
\end_layout
\begin_layout Plain Layout
###########
\end_layout
\begin_layout Plain Layout
# change to yes for bigtrees -- loses about 3x speed
\end_layout
\begin_layout Plain Layout
# if 64 bit GSL try CPPFLAGS="-arch x86_64" LDFLAGS="-arch x86_64" ./configure
\end_layout
\begin_layout Plain Layout
# need to install gmp (with ./configure --enable-cxx) and mpfr and gmpfrxx
\end_layout
\begin_layout Plain Layout
#######
\end_layout
\begin_layout Plain Layout
BIG = no
\end_layout
\begin_layout Plain Layout
#this is where the fortran compiler should be
\end_layout
\begin_layout Plain Layout
FC = /usr/bin/gfortran
\end_layout
\end_inset
\end_layout
\begin_layout Part
Configuration file
\end_layout
\begin_layout Standard
In order for Lagrange to run it must be informed of your tree and data and
parameters.
This is done in a plain text file the options for which are described below.
\end_layout
\begin_layout Section
Typical configuration file
\end_layout
\begin_layout Standard
The configuration file is meant to have an extremely simple format where
there is a
\family typewriter
parameter = option
\family default
format.
\end_layout
\begin_layout Standard
So an example configuration file might look like:
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
\backslash
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 0
width "75col%"
special "none"
height "1in"
height_special "totalheight"
status open
\begin_layout Plain Layout
\family typewriter
treefile = aesculus.tre
\end_layout
\begin_layout Plain Layout
\family typewriter
datafile = aesculus.data
\end_layout
\begin_layout Plain Layout
\family typewriter
areanames = EA ENA WNA EU
\end_layout
\begin_layout Plain Layout
\family typewriter
ancstate = _all_
\end_layout
\begin_layout Plain Layout
\family typewriter
states
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
vspace{5 mm}
\end_layout
\end_inset
In this example, Lagrange will look for a treefile named aesculus.tre in
the current directory and a datafile named aesculus.data in the current
directory.
It will them assume that the area names corresponding to the data in the
aesculus.data file are called EA ENA WNA and EU respectfully.
It will then assume that you want ancestral range caluclations for all
the nodes and it will report the states at the nodes (as opposed to splits
which will report the splits at the nodes).
This is a simple file that might serve many of the needs of people using
Lagrange.
\end_layout
\begin_layout Standard
The treefile is assumed to contain newick tree(s) alone.
If more than one tree is in the file then it will assume that you want
to reconstruct across all those trees and will do so.
There is no other option for conducting the analyses on multiple trees.
In the case of Bayesian reconstructions, it will sample from those trees
for reconstruction ancestral ranges or for stochastic mapping.
An example treefile might look like:
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
\backslash
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 0
width "75col%"
special "none"
height "1in"
height_special "totalheight"
status open
\begin_layout Plain Layout
\family typewriter
((a:0.1,b:0.1):0.2,c:0.3);
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
vspace{5 mm}
\end_layout
\end_inset
Or in the case of many trees:
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
\backslash
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 0
width "75col%"
special "none"
height "1in"
height_special "totalheight"
status open
\begin_layout Plain Layout
\family typewriter
((a:0.1,b:0.1):0.2,c:0.3);
\end_layout
\begin_layout Plain Layout
\family typewriter
((a:0.1,b:0.1):0.15,c:0.25);
\end_layout
\begin_layout Plain Layout
\family typewriter
((a:0.1,c:0.1):0.15,b:0.25);
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
vspace{5 mm}
\end_layout
\end_inset
As a note, there should be no translation tables and of course the names
have to correspond to the datafile.
\end_layout
\begin_layout Standard
The datafile is also meant to be simple.
It is simply an extended Phylip format.
An example would be:
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
\backslash
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 0
width "75col%"
special "none"
height "1in"
height_special "totalheight"
status open
\begin_layout Plain Layout
\family typewriter
3 4
\end_layout
\begin_layout Plain Layout
\family typewriter
a 1100
\end_layout
\begin_layout Plain Layout
\family typewriter
b 0110
\end_layout
\begin_layout Plain Layout
\family typewriter
c 0011
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
vspace{5 mm}
\end_layout
\end_inset
The areanames are defined in the configuration file so there is no need
to place them here.
In the example above we might define in the configuration file that
\family typewriter
areanames = EA ENA WNA EU
\family default
.
\end_layout
\begin_layout Standard
With the two important bits being described (treefile and datafile), we
can now move on to other configuration options in the configuration file.
The two that need descriptions are the area connectivity options and period
disgnation options.
In the configuration file, these two may look like:
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
\backslash
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 0
width "75col%"
special "none"
height "1in"
height_special "totalheight"
status open
\begin_layout Plain Layout
\family typewriter
ratematrix = aesculus.rm
\end_layout
\begin_layout Plain Layout
\family typewriter
periods = 10 100
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
vspace{5 mm}
\end_layout
\end_inset
The first option is pointing to a file called aesculus.rm which contains
the rate matrix connectivity parameterization.
If no file is designated, then all connectivities will be considered or
unconstrained.
If a connectivity scenario is desired, then the file might look like:
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
\backslash
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Box Boxed
position "t"
hor_pos "c"
has_inner_box 1
inner_pos "t"
use_parbox 0
width "75col%"