[GenABEL-dev] presentation at UseR!-2013
Yurii Aulchenko
yurii.aulchenko at gmail.com
Sun Jul 7 03:40:06 CEST 2013
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.
You can find the current draft of presentation at my public Dropbox,
https://dl.dropboxusercontent.com/u/13260693/GenABEL-1.odp
Comments/suggestions/improvements are welcome!
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.
YA
On Sat, Jul 6, 2013 at 6:10 PM, L.C. Karssen <lennart at karssen.org> wrote:
> Hi Yurii,
>
> Please find attached the output of the MySQL statement. I added another
> column in which the week numbers are separated from the year by a dash,
> that makes it easier to read in e.g. R:
>
> posts <- read.table("tmp/posts_per_week_converted.out", header=TRUE,
> sep=" ", row.names=NULL)
>
> colnames(posts) <- c("date", "num_posts")
>
> # Convert year-week to year-month-day
> posts$weekdate <- as.Date(paste(posts$date, 1), format="%Y-%U %u")
>
> head(posts)
> date num_posts weekdate
> 1 2011-01 1 2011-01-03
> 2 2011-04 15 2011-01-24
> 3 2011-05 7 2011-01-31
> 4 2011-06 24 2011-02-07
> 5 2011-07 10 2011-02-14
> 6 2011-08 7 2011-02-21
>
>
> This should help making a bar plot of "weekdate" vs. "num_posts".
>
>
> By the way, the SQL script is in the ~/scripts/ directory on the SSH
> server of our hoster. You can execute it like this:
> mysql -u USERNAME --password=PASSWORD -h HOSTNAME <
> get_weekly_posts.sql > posts_per_week.out
>
> The user name, password and host name can be found in the backup scripts
> in that same directory.
>
>
> Best,
>
> Lennart.
>
>
> On 05-07-13 14:04, Yurii Aulchenko wrote:
> >
> >
> > On Fri, Jul 5, 2013 at 12:30 PM, L.C. Karssen <lennart at karssen.org
> > <mailto:lennart at karssen.org>> wrote:
> >
> > Hi Yurii,
> >
> > On 07/05/2013 11:04 AM, Yurii Aulchenko wrote:
> > > Dear All,
> > >
> > > I am now drafting my presentation for UseR!-2013 (
> > > http://www.edii.uclm.es/~useR-2013/). My presentation about "The
> > GenABEL
> > > suite for genome-wide association analyses" is scheduled for Wed
> > July 10
> > > morning. I will send it to the list for the discussion as soon as
> > I have a
> > > draft (most likely by Saturday eve).
> > >
> > > I thought it may be a good idea to present the evolution of the
> > GenABEL in
> > > number, so the idea is to get the numbers by years/quartes of the
> year
> > > (say, #posts in 2009=x1, 2010=x2...) and present them graphically.
> > For some
> > > of growth metrics I can get the dynamics by years easily, but for
> > some I
> > > have no idea and hope you could help me (may be also by providing
> the
> > > numbers directly).
> > >
> > > Here a small list of metrics I thought of:
> > >
> > > #packages: very easy to count :)
> > > #posts on GenABEL-devel: possible to count
> > > #posts on forum: no idea how to do that for defined time periods
> >
> > I guess you need to run a query on the database to get those. Our
> hoster
> > has a phpmyadmin interface yuo can use for that (or you could
> probably
> > use the SSH account and run the MySQL client from the command line).
> > Probably a query along this line:
> >
> > SELECT yearweek(date(from_unixtime(post_time))) AS week, COUNT(*) AS
> > num_posts FROM phpbb_posts GROUP BY
> > yearweek(date(from_unixtime(post_time)))
> >
> >
> > arrgh... probably I can figure this out if I had enough time, but gonna
> > to invest into presentation now. If you/someone could give a hand, would
> > be great :)
> >
> >
> >
> >
> > > #number of lines of code in our SVN repo: no idea
> >
> > Probably SLOCcount will help: http://www.dwheeler.com/sloccount/
> >
> >
> > This is a nice one! Two problems: it does not count/recognize R; did not
> > see how to use it to see the dynamics (what was there in repo 2 years
> > ago?..)
> >
> > But I like that even without the R code counts (which is 148,000 lines),
> > for ~65,000 lines of mostly C/C++ I get the message indicating that
> > GenABEL is worth few millions of dollars:
> >
> > Development Effort Estimate, Person-Years (Person-Months) = 15.44
> (185.24)
> > (Basic COCOMO model, Person-Months = 2.4 * (KSLOC**1.05))
> > Schedule Estimate, Years (Months) = 1.05 (12.61)
> > (Basic COCOMO model, Months = 2.5 * (person-months**0.38))
> > Total Estimated Cost to Develop = $ 2,085,323
> > (average salary = $56,286/year, overhead = 2.40).
> >
> > So I think I should use these figures in my presentation :)
> >
> > > #citations (GenA, ProbA...): easy to count thanks to Google Scholar
> > > #mentions on the Web: ???
> > >
> > > Any other nice and easily computed metrics?
> > >
> > > I will appreciate your help and suggestions, and sorry for late
> > notice.
> > >
> >
> >
> > Good luck,
> >
> > Lennart.
> >
> > > best,
> > > Yurii
> > >
> > >
> > >
> > > _______________________________________________
> > > genabel-devel mailing list
> > > genabel-devel at lists.r-forge.r-project.org
> > <mailto:genabel-devel at lists.r-forge.r-project.org>
> > >
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> > >
> >
> >
> > --
> > -----------------------------------------------------------------
> > L.C. Karssen
> > Utrecht
> > The Netherlands
> >
> > lennart at karssen.org <mailto:lennart at karssen.org>
> > http://blog.karssen.org
> >
> > Stuur mij aub geen Word of Powerpoint bestanden!
> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> > ------------------------------------------------------------------
> >
> >
> > _______________________________________________
> > genabel-devel mailing list
> > genabel-devel at lists.r-forge.r-project.org
> > <mailto:genabel-devel at lists.r-forge.r-project.org>
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
> >
> >
> >
> > --
> > -----------------------------------------------------
> > Yurii S. Aulchenko
> >
> > [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> > <http://twitter.com/YuriiAulchenko> ] [ Blog
> > <http://yurii-aulchenko.blogspot.nl/> ]
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
--
-----------------------------------------------------
Yurii S. Aulchenko
[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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