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<b style="font-weight:normal;"
id="docs-internal-guid-78a4e8c4-0c50-57e0-7108-f060ddbaac2e">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">You’re
receiving this message from a private list I’ve set up to help
keep us all coordinated over this summer’s GSoC project. All
of the mentors and the student are subscribed and can send
mail to the list.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Using
the list will let everyone communicate with just one address
(the list address), and will make it easier to sort these
communications out in our inboxes (I'm sure all of you, like
me, get lots of emails every day). It should also lessen the
pressure on everyone, as any of the mentors can respond if we
have an answer to a student query, when we have a moment to do
so.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Please
use this list for all ‘general’ or non-time-critical
discussions about the project, so that everyone stays
informed. Obviously, if you are local to one of the mentors,
face to face meetings are encouraged. Please do inform the
rest of us of major decisions though. </span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">I
anticipate that we will discuss design decisions,
implementation roadblocks, and various implementation choices
that need to be made as the summer progresses. These
discussions should take place on </span><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">this
</span><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">mailing
list as much as possible.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">As
you know, the schedule has several milestones:</span></p>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Community
Bonding Period: Today, May 27th</span></p>
</li>
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Official
Coding Start: June 17th</span></p>
</li>
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Mid
Term Evaluation: Jul 29th - Aug 2nd</span></p>
</li>
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Pencils
Down: Sept 23rd</span></p>
</li>
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Final
Evaluations Due: Sept 27th</span></p>
</li>
</ul>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Please
add these to your calendar (or add the </span><a
href="http://www.google-melange.com/gsoc/events/google/gsoc2013"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">Google
Calendar overlay</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[0]
to yours for the summer from melange)</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">As
the first phase starts today, we want to re-emphasize what our
objectives are for the short term. This first phase is
intended for you to get your bearings and firm up your coding
plan. To do that, you’ll need to identify and obtain any
source and background reading materials. Start reading and
and asking questions. Early on, you’ll want to identify what
data you need for tests and examples. Inventory any existing
code. Familiarize yourself with packages you will use for
development, and packages you will be committing code into.
Get set up with R-forge and SVN, and make your first commits
(no matter how minor). List out what you want to start
implementing and why. Sketch out a project plan in more detail
than you have previously. Start communicating about what you
are going to do when you start coding. </span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">This
project will use </span><a
href="http://r-forge.r-project.org/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">R-Forge</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[1]
extensively. R-Forge provides a set of tools for source code
management (Subversion) and various web-based features. To
use Subversion (svn) on R-Forge you'll need to</span><a
href="https://r-forge.r-project.org/account/register.php"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">
register as a site user</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[2]
and then</span><a
href="https://r-forge.r-project.org/account/login.php"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">
login</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[3].
If you are unfamiliar with R-Forge, you may want to review a
copy of the</span><a
href="http://download.r-forge.r-project.org/R-Forge_Manual.pdf"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">User's
Manual</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[4].
To get you set up with svn commit access on R-Forge, we will
need your r-forge id. </span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">R-Forge
uses svn for version control, and it will be very important
for everyone (both mentors and students) to quickly get adept
at using svn. For more specifics about how to use svn, take a
look at the book </span><a
href="http://svnbook.red-bean.com/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">Version
Control with Subversion</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[5].
You will need to install the client of your choice (e.g., </span><a
href="http://tortoisesvn.tigris.org/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">Tortoise
SVN</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[6]
on Windows or svnX on Mac OSX) and check out the repository.
Please do not hesitate to ask for help if you get stuck -
this is a critical component of our workflow and will be
important for keeping everyone up to date with current code.
If you’ve previously checked out the code anonymously, you’ll
need to check it out again using your R-Forge id (and ssh key)
before you’ll be able to commit your changes.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">In
addition, everyone should join the r-forge commit list for the
project the code is being submitted into. For example, go to
the </span><a
href="https://r-forge.r-project.org/projects/returnanalytics/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">returnanalytics</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[7]
project on R-Forge. You’ll see a link for mailing lists, with
one public mailing list called “returnanalytics-commits”.
Subscribe to that, and you’ll be notified by email of any
commits made to the project.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Please
try to make commits to svn at least daily while coding. If
you make an improvement and it works - check it in. This way
mentors will be able to test code continuously, and we’ll know
quickly if something is broken. We suggest an iterative
approach to development: first make it work, then make it work
*correctly*, and finally make it work fast (if needed). Do
not try to make it perfect or even pretty before checking
something in. Make sure you provide a log message for each
commit. Look at the log of the repository you will be working
with to get a feel for the logging style. Make small changes,
frequently. We know from past years that students who make
incremental, small progress have a much greater chance of
successfully finishing the summer. </span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Document
as you write. It is really important to write the
documentation as you write functions, perhaps even *before*
you write the function, at least to describe what it should
do. </span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">When
documenting a function:</span></p>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">make
sure equations are correct and cited,</span></p>
</li>
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">make
sure all user-facing functions have examples,</span></p>
</li>
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">make
sure you know the expected results of the examples (these
will become tests),</span></p>
</li>
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">make
sure relevant literature is cited everywhere, and</span></p>
</li>
<li dir="ltr"
style="list-style-type:disc;font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">apply
a standard mathematical notation. In most cases, follow
the notation from the original paper. </span></p>
</li>
</ul>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">We
either have or are currently converting all of our packages’
documentation to </span><a
href="http://cran.r-project.org/web/packages/roxygen2/index.html"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">roxygen2</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[8],
an in-source </span><a
href="http://en.wikipedia.org/wiki/Literate_programming"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">‘literate
programming’</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[9]
documentation system for generating Rd, collation, and
NAMESPACE files. What that means is that the documentation
will be in the same file as the functions (as comments before
each function) which will make writing and synchronizing the
documentation easier for everyone. Every function file will
have the documentation and roxygen tags in the file, and
roxygenize() will be run before the package build process to
generate the Rd documentation files required by R. Roxygen2
is available on CRAN. </span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Equations
in documentation should have both full LaTeX code for printing
in the PDF and a text representation that will be used in the
console help. Use:</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">\eqn{\LaTeX}{ascii}
</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">or
</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">\deqn{\LaTeX}{ascii}</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Greek
letters will also be rendered in the HTML help. However, the
only way to get the full mathematical equation layout is in
the PDF rendered from LaTeX.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">For
more information on documentation and R package development in
general, read '</span><a
href="http://cran.r-project.org/doc/manuals/R-exts.pdf"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">Writing
R Extensions</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">'[10].</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Although
preferences for code style do vary, when there are a number of
contributors to the package it can be important for
readability and future maintainability of the code. You
should strive (as much as is practical) to match the style in
the existing code. When in doubt, rely on </span><a
href="http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">Google’s
R Style Guide</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[11]
or ask the mailing list.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Everyone
should know how to build packages from source, although
once-daily builds may be available on R-Forge. A *nix machine
should have everything needed (see Appendix A of ‘</span><a
href="http://cran.r-project.org/doc/manuals/R-admin.pdf"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">R
Installation and Administration</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">’[13]),
but a regular Windows machine will not. Windows users will
need to install </span><a
href="http://cran.r-project.org/bin/windows/Rtools/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">RTools</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">
[12], a collection of resources for building packages for R
under Microsoft Windows (see Appendix D of ‘</span><a
href="http://cran.r-project.org/doc/manuals/R-admin.pdf"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">R
Installation and Administration</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">’[13]).
Once all tools are in place, you should be able to build the
package by opening a shell, moving to the directory of the
package, and typing ‘R CMD INSTALL packagename’. The R-Forge
Manual provides more detail in section 4.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">I
know this was a lot of information, but we thought it would
make sense to get most of it out of the way immediately, in a
format that is easily referred to throughout the summer.
Please don’t hesitate to use the list to ask any questions,
that’s what it is here for.</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span><br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Regards,</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Brian</span></p>
<br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span><br>
<span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">References:</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[0]
Google Calendar overlay</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://www.google-melange.com/gsoc/events/google/gsoc2013"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://www.google-melange.com/gsoc/events/google/gsoc2013</span></a><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[1]
R-Forge</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://r-forge.r-project.org/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://r-forge.r-project.org</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[2]
R-Forge registration</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="https://r-forge.r-project.org/account/register.php"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">https://r-forge.r-project.org/account/register.php</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[3]
R-Forge login</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="https://r-forge.r-project.org/account/login.php"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">https://r-forge.r-project.org/account/login.php</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[4]
R-Forge User Manual</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://download.r-forge.r-project.org/R-Forge_Manual.pdf"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://download.r-forge.r-project.org/R-Forge_Manual.pdf</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[5]
SVN Book</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://svnbook.red-bean.com/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://svnbook.red-bean.com</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[6]
Tortoise SVN</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://tortoisesvn.tigris.org/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://tortoisesvn.tigris.org</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[7]
ReturnAnalytics on R-Forge</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="https://r-forge.r-project.org/projects/returnanalytics/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">https://r-forge.r-project.org/projects/returnanalytics/</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[8]
roxygen2</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://cran.r-project.org/web/packages/roxygen2/index.html"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://cran.r-project.org/web/packages/roxygen2/index.html</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[9]
literate programming</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://en.wikipedia.org/wiki/Literate_programming"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://en.wikipedia.org/wiki/Literate_programming</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[10]
Writing R Extensions</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://cran.r-project.org/doc/manuals/R-exts.pdf"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://cran.r-project.org/doc/manuals/R-exts.pdf</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[11]
Google’s R style guide</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[12]
Rtools</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://cran.r-project.org/bin/windows/Rtools/"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://cran.r-project.org/bin/windows/Rtools/</span></a></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><span
style="font-size:13px;font-family:Arial;color:#000000;background-color:#ffffff;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">[13]
R Installation and Administration</span></p>
<p dir="ltr"
style="line-height:1.15;margin-top:0pt;margin-bottom:0pt;"><a
href="http://cran.r-project.org/doc/manuals/R-admin.pdf"
style="text-decoration:none;"><span
style="font-size:13px;font-family:Arial;color:#1155cc;background-color:#ffffff;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap;">http://cran.r-project.org/doc/manuals/R-admin.pdf</span></a></p>
<br>
<span
style="font-size:15px;font-family:Arial;color:#000000;background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"></span></b>
<pre class="moz-signature" cols="72">--
Brian G. Peterson
<a class="moz-txt-link-freetext" href="http://braverock.com/brian/">http://braverock.com/brian/</a>
Ph: 773-459-4973
IM: bgpbraverock</pre>
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