Dear All,<div><br></div><div>I have composed a short report from UseR! conference, see </div><div><br></div><div><a href="http://www.genabel.org/news20130714">http://www.genabel.org/news20130714</a></div><div><br></div><div>
for the links.</div><div><br></div><div>best wishes, and thanks again for your help,</div><div><br></div><div>Yurii<br clear="all"></div><div><br></div><br><div class="gmail_quote">On Wed, Jul 10, 2013 at 8:42 PM, Yurii Aulchenko <span dir="ltr"><<a href="mailto:yurii.aulchenko@gmail.com" target="_blank">yurii.aulchenko@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear All,<div><br></div><div>The last variant of presentation - the one I presented at UseR!-2013 this morning - is available at previous link. The presentation went fine (though I was slightly over time and therefore was wrapping up a bit too quickly). Several people contacted me after the talk. </div>
<div><br></div><div>Later, we should probably move that presentation to our web-site. (what section? showcase?..)</div><div><br></div><div>Lennart, Maarten, many thanks for your input!</div><span class="HOEnZb"><font color="#888888"><div>
<br></div></font></span><div><span class="HOEnZb"><font color="#888888">YA</font></span><div><div class="h5"><br><br><div class="gmail_quote">
On Sun, Jul 7, 2013 at 3:40 AM, Yurii Aulchenko <span dir="ltr"><<a href="mailto:yurii.aulchenko@gmail.com" target="_blank">yurii.aulchenko@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thank you very much, Lennart! - not sure I will manage to use this data for current presentation - it is getting rather big now, and I am getting tired... I probably can use these numbers to make a figure "how the community sets off", but not sure, did not have time to present these numbers graphically yet. <div>
<br></div><div>You can find the current draft of presentation at my public Dropbox, <a href="https://dl.dropboxusercontent.com/u/13260693/GenABEL-1.odp" target="_blank">https://dl.dropboxusercontent.com/u/13260693/GenABEL-1.odp</a></div>
<div><br></div><div>Comments/suggestions/improvements are welcome! </div><div><br></div><div>Note that I have 15-17 minutes for the presentation, so slide count is already too high. Can probably cut short on the "history". Also wonder if this presentation will be interesting for the R people - it is kind of very general one at the moment. <br>
<div><br></div><div>YA<div><div><br><br><div class="gmail_quote">On Sat, Jul 6, 2013 at 6:10 PM, L.C. Karssen <span dir="ltr"><<a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Yurii,<br>
<br>
Please find attached the output of the MySQL statement. I added another<br>
column in which the week numbers are separated from the year by a dash,<br>
that makes it easier to read in e.g. R:<br>
<br>
posts <- read.table("tmp/posts_per_week_converted.out", header=TRUE,<br>
sep=" ", row.names=NULL)<br>
<br>
colnames(posts) <- c("date", "num_posts")<br>
<br>
# Convert year-week to year-month-day<br>
posts$weekdate <- as.Date(paste(posts$date, 1), format="%Y-%U %u")<br>
<br>
head(posts)<br>
date num_posts weekdate<br>
1 2011-01 1 2011-01-03<br>
2 2011-04 15 2011-01-24<br>
3 2011-05 7 2011-01-31<br>
4 2011-06 24 2011-02-07<br>
5 2011-07 10 2011-02-14<br>
6 2011-08 7 2011-02-21<br>
<br>
<br>
This should help making a bar plot of "weekdate" vs. "num_posts".<br>
<br>
<br>
By the way, the SQL script is in the ~/scripts/ directory on the SSH<br>
server of our hoster. You can execute it like this:<br>
mysql -u USERNAME --password=PASSWORD -h HOSTNAME <<br>
get_weekly_posts.sql > posts_per_week.out<br>
<br>
The user name, password and host name can be found in the backup scripts<br>
in that same directory.<br>
<br>
<br>
Best,<br>
<br>
Lennart.<br>
<div><br>
<br>
On 05-07-13 14:04, Yurii Aulchenko wrote:<br>
><br>
><br>
> On Fri, Jul 5, 2013 at 12:30 PM, L.C. Karssen <<a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a><br>
</div><div><div>> <mailto:<a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a>>> wrote:<br>
><br>
> Hi Yurii,<br>
><br>
> On 07/05/2013 11:04 AM, Yurii Aulchenko wrote:<br>
> > Dear All,<br>
> ><br>
> > I am now drafting my presentation for UseR!-2013 (<br>
> > <a href="http://www.edii.uclm.es/~useR-2013/" target="_blank">http://www.edii.uclm.es/~useR-2013/</a>). My presentation about "The<br>
> GenABEL<br>
> > suite for genome-wide association analyses" is scheduled for Wed<br>
> July 10<br>
> > morning. I will send it to the list for the discussion as soon as<br>
> I have a<br>
> > draft (most likely by Saturday eve).<br>
> ><br>
> > I thought it may be a good idea to present the evolution of the<br>
> GenABEL in<br>
> > number, so the idea is to get the numbers by years/quartes of the year<br>
> > (say, #posts in 2009=x1, 2010=x2...) and present them graphically.<br>
> For some<br>
> > of growth metrics I can get the dynamics by years easily, but for<br>
> some I<br>
> > have no idea and hope you could help me (may be also by providing the<br>
> > numbers directly).<br>
> ><br>
> > Here a small list of metrics I thought of:<br>
> ><br>
> > #packages: very easy to count :)<br>
> > #posts on GenABEL-devel: possible to count<br>
> > #posts on forum: no idea how to do that for defined time periods<br>
><br>
> I guess you need to run a query on the database to get those. Our hoster<br>
> has a phpmyadmin interface yuo can use for that (or you could probably<br>
> use the SSH account and run the MySQL client from the command line).<br>
> Probably a query along this line:<br>
><br>
> SELECT yearweek(date(from_unixtime(post_time))) AS week, COUNT(*) AS<br>
> num_posts FROM phpbb_posts GROUP BY<br>
> yearweek(date(from_unixtime(post_time)))<br>
><br>
><br>
> arrgh... probably I can figure this out if I had enough time, but gonna<br>
> to invest into presentation now. If you/someone could give a hand, would<br>
> be great :)<br>
><br>
><br>
><br>
><br>
> > #number of lines of code in our SVN repo: no idea<br>
><br>
> Probably SLOCcount will help: <a href="http://www.dwheeler.com/sloccount/" target="_blank">http://www.dwheeler.com/sloccount/</a><br>
><br>
><br>
> This is a nice one! Two problems: it does not count/recognize R; did not<br>
> see how to use it to see the dynamics (what was there in repo 2 years<br>
> ago?..)<br>
><br>
> But I like that even without the R code counts (which is 148,000 lines),<br>
> for ~65,000 lines of mostly C/C++ I get the message indicating that<br>
> GenABEL is worth few millions of dollars:<br>
><br>
> Development Effort Estimate, Person-Years (Person-Months) = 15.44 (185.24)<br>
> (Basic COCOMO model, Person-Months = 2.4 * (KSLOC**1.05))<br>
> Schedule Estimate, Years (Months) = 1.05 (12.61)<br>
> (Basic COCOMO model, Months = 2.5 * (person-months**0.38))<br>
> Total Estimated Cost to Develop = $ 2,085,323<br>
> (average salary = $56,286/year, overhead = 2.40).<br>
><br>
> So I think I should use these figures in my presentation :)<br>
><br>
> > #citations (GenA, ProbA...): easy to count thanks to Google Scholar<br>
> > #mentions on the Web: ???<br>
> ><br>
> > Any other nice and easily computed metrics?<br>
> ><br>
> > I will appreciate your help and suggestions, and sorry for late<br>
> notice.<br>
> ><br>
><br>
><br>
> Good luck,<br>
><br>
> Lennart.<br>
><br>
> > best,<br>
> > Yurii<br>
> ><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > genabel-devel mailing list<br>
> > <a href="mailto:genabel-devel@lists.r-forge.r-project.org" target="_blank">genabel-devel@lists.r-forge.r-project.org</a><br>
</div></div>> <mailto:<a href="mailto:genabel-devel@lists.r-forge.r-project.org" target="_blank">genabel-devel@lists.r-forge.r-project.org</a>><br>
<div>> ><br>
> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel</a><br>
> ><br>
><br>
><br>
> --<br>
> -----------------------------------------------------------------<br>
> L.C. Karssen<br>
> Utrecht<br>
> The Netherlands<br>
><br>
</div>> <a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a> <mailto:<a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a>><br>
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><br>
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><br>
><br>
><br>
><br>
> --<br>
> -----------------------------------------------------<br>
> Yurii S. Aulchenko<br>
><br>
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<div><div><br>
--<br>
-----------------------------------------------------------------<br>
L.C. Karssen<br>
Utrecht<br>
The Netherlands<br>
<br>
<a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a><br>
<a href="http://blog.karssen.org" target="_blank">http://blog.karssen.org</a><br>
<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>-----------------------------------------------------<br>Yurii S. Aulchenko<br><div><br></div></div></div><div>[ <a href="http://nl.linkedin.com/in/yuriiaulchenko" target="_blank">LinkedIn</a> ] [ <a href="http://twitter.com/YuriiAulchenko" target="_blank">Twitter</a> ] [ <a href="http://yurii-aulchenko.blogspot.nl/" target="_blank">Blog</a> ]</div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>-----------------------------------------------------<br>Yurii S. Aulchenko<br><div><br></div><div>[ <a href="http://nl.linkedin.com/in/yuriiaulchenko" target="_blank">LinkedIn</a> ] [ <a href="http://twitter.com/YuriiAulchenko" target="_blank">Twitter</a> ] [ <a href="http://yurii-aulchenko.blogspot.nl/" target="_blank">Blog</a> ]</div>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>-----------------------------------------------------<br>Yurii S. Aulchenko<br><div><br></div><div>[ <a href="http://nl.linkedin.com/in/yuriiaulchenko" target="_blank">LinkedIn</a> ] [ <a href="http://twitter.com/YuriiAulchenko" target="_blank">Twitter</a> ] [ <a href="http://yurii-aulchenko.blogspot.nl/" target="_blank">Blog</a> ]</div>