Re: [R] Excel

2007-08-28 Thread J Dougherty
On Monday 27 August 2007 22:21, David Scott wrote:
> On Tue, 28 Aug 2007, Robert A LaBudde wrote:
> > If you format the column as "Text", you won't have this problem. By
> > leaving the cells as "General", you leave it up to Excel to guess at
> > the correct interpretation.
>
> Not true actually. I had converted the column to Text because I saw the
> interpretation as a date in the .xls file. I saved the .csv file *after*
> the column had been converted to Text. Looking at the .csv file in a text
> editor, the entry is correct.
>
> I have just rechecked this.
>
> On reopening the .csv using Excel, the entry AUG2699 had been interpreted
> as a date, and was showing as Aug-99. Most bizarre is that the NHI value
> of AUG1838 has *not* been interpreted as a date.
>
Actually, in Excel 2000, he's right.  What you have to is be sure of is that 
the "'" that denotes a text entry precedes EVERY entry that can be confused 
with a date.  Selecting the entire column and setting the format to "text" 
*before* data is entered does this.  It will also create an appropriate *.csv 
file.  Excel is notable too because it will automatically convert "date-like" 
entries as you type.  In a column of IDs or similar critical data, that 
behaviour is really bad.  I have never tried the MS site, but I haven't been 
able to find any entry about how to turn that particular automatic behaviour 
off. 

However, while I have not experimented extensively, as far as I have 
experimented, OpenOffice spreadsheet does not behave this way.

JWDougherty

PS, I quit using Excel for most important work after it returned a negative 
variance on some data I was collecting descriptive statistics on.

JWD

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Re: [R] Mann-Whitney U

2007-08-14 Thread J Dougherty
Natalie,

It's best to provide at least a sample of your data.  Your field names suggest 
that your data might be collected in units of mm^2 or some similar 
measurement of area.  Why do you want to use Mann-Whitney, which will rank 
your data and then use those ranks rather than your actual data?  Unless your 
sample is quite small, why not use a two sample t-test?  Also,are your 
samples paired?  If they aren't, did you use the "paired = FALSE" option?

JWDougherty

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[R] JGR starter problems

2007-04-30 Thread J Dougherty
I'm running R 2.4.1 on SuSE Linux 10.2.  My system is an AMD based PC with 2 
Gigs of ram and abundant HD space. 

I have always run R from the console without problems, but in the interests of 
broadening R's user-base, and reducing the complexity of my computing 
environment, I am hoping to convince my PTB that R is a viable alternative to 
Excel under Windows - heh.  Since they like pretty pictures I'm experimenting 
with graphic interfaces for R in linux.  The Windows interface is fine, but I 
would prefer to stick to linux if at all possible.  I've been trying the JGR 
environment and so far it loads and looks nice but it doesn't seem to be able 
to find the key libraries such as "base."  There are two errors that appear 
in the initial messages - one being that JGR can't load .../stats.so, and 
that R_GlobalEnv is an undefined symbol.  And the other is that 
options("defaultPackages") is not as shown below.  I presume this is probably 
a compilation error on my part and would like to know what I've done wrong.  
The initial messages when JGR loads are below.

Thanks, JWDougherty

Error in dyn.load(x, as.logical(local), as.logical(now)) : 
unable to load shared library 
'/usr/local/lib/R/library/stats/libs/stats.so':
  /usr/local/lib/R/library/stats/libs/stats.so: undefined symbol: R_GlobalEnv
Loading required package: JavaGD
Loading required package: iplots
Creating per-session help links...
Loading required package: grDevices
During startup - Warning message:
package stats in options("defaultPackages") was not found

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Re: [R] RODBC compile error with R 2.4.1

2007-01-03 Thread J Dougherty
Matthew,

You don't seem to say what linux release you are using,  They can't very well 
help you without that information.  Not all releases are equal.

JWD

On Wednesday 03 January 2007 03:49, Matthew Dowle wrote:
> Hi All,
>
> I'm getting the following error,  could anyone help please?
>
> $ R CMD INSTALL RODBC_1.1-7.tar.gz
> * Installing *source* package 'RODBC' ...
> checking for gcc... gcc -std=gnu99
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking sql.h usability... yes
> checking sql.h presence... yes
> checking for sql.h... yes
> checking sqlext.h usability... yes
> checking sqlext.h presence... yes
> checking for sqlext.h... yes
> checking for library containing SQLTables... -lodbc
> checking for SQLLEN... yes
> checking for SQLULEN... yes
> checking for long... yes
> checking size of long... configure: error: cannot compute sizeof (long),
> 77
> See `config.log' for more details.
> ERROR: configuration failed for package 'RODBC'
> ** Removing '/usr/local/lib/R/library/RODBC'
> ** Restoring previous '/usr/local/lib/R/library/RODBC'
>
> > version
>
>_
> platform   x86_64-unknown-linux-gnu
> arch   x86_64
> os linux-gnu
> system x86_64, linux-gnu
> status
> major  2
> minor  4.1
> year   2006
> month  12
> day18
> svn rev40228
> language   R
> version.string R version 2.4.1 (2006-12-18)
>
>
>
> Regards,
> Matthew
>
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[R] Obiously obsolete

2006-12-13 Thread J Dougherty
On Tuesday 12 December 2006 07:59, javier garcia-pintado wrote:
> "beta max"

Sorry, couldn't resist.

JD

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Re: [R] Books

2006-06-18 Thread J Dougherty
On Sunday 18 June 2006 08:27, Anderson de Rezende Rocha wrote:
> Dears,
>
> I saw in the R-project site some R-books. However, I'm new in this
> community and I didn't figure out what are the best books.
>
> Can you suggest me some "reference" books? My intentions with R is
> concerned to Artificial Intelligence simulations, Classification and
> general Statistics (e.g., regression, multivariate regression, etc).
>

Four books:

- Introductory Statistics with R by Peter Daalgard
- Modern Applied Statistics with S by Venables and Ripley
- Data Analysis and Graphics Using R by Maindonald and Braun
another very useful introductory book is
- Statistics, an Introduction using R by Crawley

You may also want to track down a hard copy of the R manuals.  It comes free 
along with R, but the pdf is almost 1400 pages long, so it can be worthwhile 
having someone else do the printing and binding.

JDougherty

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Re: [R] R kicking us out

2006-06-13 Thread J Dougherty
On Tuesday 13 June 2006 13:00, Erin Hodgess wrote:
> Dear R People:
>
> I am using R for teaching purposes in a large classroom.
>
> Each computer has its own copy of R.
>
> However, every once in a while, about half of us will get
> thrown out of R, for no apparent reason.
>
> By the way, it has happened in other classrooms as well.
>
>
> Has anyone else run into this, please?
>
> If so, how have you solved this problem, please?
>
> Thanks in advance!
>
> R for Windows
>
You will need to provide a good deal more information before a useful answer 
is likely.  For instance, what operating system do these computers use?  If 
the computers are all running networked in a lab, is there some automatic 
maintenance being run?  What hardware specifications (CPU, memory, harddisk 
storage, etc.)?  What size data sets are being used?  And, more importantly, 
what does "kicking you out" actually mean in terms of computer behaviour?  
Does R simply crash?  When you "about half of us"  is it always the same 
half?  Does it occur at the same time of day?  There are far too many 
unknowns for a diagnosis.

JD

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Re: [R] How can you buy R?

2006-05-19 Thread J Dougherty
On Thursday 18 May 2006 14:51, Damien Joly wrote:
> Hi all,
>
> This may seem like a dumb question, but I work for an entity that is soon
> converting to XP across the board, and I will lose the ability to install
> software on my own.  The entity has a policy of only using software that
> has been purchased and "properly licensed" (whatever that means).
>
> This means I will soon lose the ability to use R at work - something I
> can't do without at this point.
>
> HOWEVER, I might be able to work around this policy if I can find a
> licensed software vendor, preferably in Canada, that sells R.
>
> I tried googling R vendors but was unsuccessful.
>
> Any ideas?
>
Well, first, have you pointed out to whatever limited neurons came up with 
that specification, that this will mean that part of your job can no longer 
be done because their specifications appear to rule out a key tool?  

Second, R is available for windows and works quite well.  While there is no 
charge for R, it IS properly licensed properly licensed under the GPL.  
Theoretically, is system security is the actual issue, then the individual in 
charge of software acquisition can download and install it for you.  All of 
that should be clear and above board and shouldn't compromise anything unless 
the "entity" you work for has become contractually constrained to avoid using 
OS ware for some obscure and irrational reason.

What do they actually expect to gain from this policy?

The _expensive_ alternative is to have them purchase S-Plus for you.  If you 
present them with an estimated cost and l imagine they might think having the 
BOFH download R for windows for you might be the cost-effective way to go.

JD

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Re: [R] The mysterious e1071

2006-04-09 Thread J Dougherty
On Saturday 08 April 2006 11:51, Chelsea Ellis wrote:
> Hi,
>
> I'm trying to use the svm function in R, but I can't find the e1071
> package. When I type library(e1071), I get the error message that the
> package doesn't exist.  I've searched all over the CRAN website, but I
> can't find anything.  Did it change names?
>
> Thanks for your help,
>
> Chelsea
You'll have to download it off CRAN.  It IS there.  Go to CRAN, choose your 
server, and then on the left pane, you will see a link named "packages."  The 
link will be http://[your server name]/src/contrib/PACKAGES.html.  Chose 
that.  On the right pane, which is not visually well differentiated from the 
rest of the page, scroll down.  e1071 is there right at the beginning of the 
packages whose names begin with "e".

Have fun,
JD

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Re: [R] small sample size confidence interval by bootstrap

2006-04-01 Thread J Dougherty
On Friday 31 March 2006 18:21, Urania Sun wrote:
> Hi, All:
>
> I only have 4 samples. I wish to get a confidence interval around the mean.
> Is it reasonable? If not, is there a way to compute a confidence interval
> for such small sample size's mean?
>
> Many thanks,
>
With a sample that small, it is far safer to simply consider them as four 
examples and leave it at that.  In a population where there is little 
variation (say an archaeological projectile point type with a nech width that 
varies between 3 and 5 mm), the examples are likely to be close to typical, 
and the difference isn't really llikely to be important anyway.  However, in 
a population with considerable variation (for example height in humans) you 
can see that trying to make any generalizations from 4 examples is going to 
be more likely to be misleading than anything else.  

If your sample of four is your entire population, you have all the information 
possible through simple measurements.  But, if the population were 100 the 
number of possible samples of size 4 is, as Gnumeric assures me, about 4 x 
10^306, which, to put it scientifically, is a whole bunch.  It'is better not 
to generalize from small samples.

JD

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Re: [R] R and packages

2006-02-20 Thread J Dougherty
You want to take the sysad by the hairy of his chinny-chin-chin and explain 
the issue in short sentences.  He or she ought to be able produce a solution 
without difficulty, and should not have any problems about doing so.  It IS 
their job.  

JD  

On Monday 20 February 2006 17:07, Erin Hodgess wrote:
> Dear R People:
>
> Here is yet another strange problem.
>
> I'm using R in one of my classes.  However, the computer lab has something
> called "Deep Freeze" and the students cannot save anything to the hard
> drive.
>
> I had R installed and things were working well.  They would save their
> .Rdata files to disks.
>
> Now, we need to add more packages.  We can't download and we can't
> bring them in via zip files (already tried both!)  When the zip files
> are expanded, of course they build new directories..
>
> I'm completely annoyed because learning to download packages
> and installing them from local zips are actually important tasks!
> We're also losing good teaching/learning time!
>
> Anyhow, what I would like to do is produce a sort of combination R
> installation exe with our extra libraries as part of the package.
>
> Does anyone have any suggestions on how this could be done, please?
>
> This is R for Windows, Version 2.2.1
>
> Thanks for any help!  Sorry about the totally weird problem!
>
> Sincerely,
> Erin Hodgess
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: [EMAIL PROTECTED]
>
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Re: [R] Variance for Vector of Constants is Not Zero

2006-02-16 Thread J Dougherty
On Thursday 16 February 2006 11:29, Barry Zajdlik wrote:
> 1.337451e-35

Well, its nearly zero ;-)

JD

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Re: [R] Loading Excel file into Limma

2006-01-11 Thread J Dougherty
R won't read an Excel sheet directly.  You need to export it, saving it as a 
CSV or tab delimited file.  You can then import using read.table.  The entire 
path and file have to be in double-quotes as well.  Try ?read.table for more 
info.

JWD

On Wednesday 11 January 2006 19:48, N. Goodacre wrote:
> Dear mailing group,
>
>   This is my first time here. Glad to have this resource!
>
>   I am currently trying to load an Excel file into R (limma package loaded)
> using the source(*name of directory*) command, but it cannot open the file.
> I renamed the file as .R and .RData, to no avail. The Excel data contains
> one gene name per row and about 100 data points per gene (columns).
>
>   I am only used to loading preprepared microarray data with all the t's
> crossed and i's dotted, with the read.maimages command. Can anyone help me
> out with this silly-sounding "challenge"?
>
>   Sincerely - in the truest sense -
>
> Norman Goodacre
>
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Re: [R] wicked wikis for R

2006-01-09 Thread J Dougherty
On Monday 09 January 2006 05:16, Jean-Christophe BOUETTE wrote:
> > From: "Arin Basu" <[EMAIL PROTECTED]>
> > To: r-help@stat.math.ethz.ch
> > Date: 8 Jan 2006 19:18:17 -
> > Subject: [R] wicked wikis for R
> >
> > >Message: 41
> > >Date: Sun, 08 Jan 2006 13:52:33 +1100
> > > From: paul sorenson <[EMAIL PROTECTED]>
> > >Subject: Re: [R] Wikis etc.
> > >To: Frank E Harrell Jr <[EMAIL PROTECTED]>, r-help
> > >   
>
> -snip-
>
> > Among others, here's one long-term benefit for the newbies. Instead of
> > people getting admonished/thrashed with harsh expressions/advices like
> > "go see the mailing list publishing etiquettes", or "you should search
> > the archives and help files, and read all manuals, and ask others first
> > before posting here..." (which can turn away many a newcomer from posting
> > or using the mailing list or using R for that matter), wiki could make
> > life a little easy for newbies/less experienced who could then receive
> > more polite one liners like, "please check the wikipages...", or
> > "solution #xyz in the wikipages for the solution".
>
> Sorry, I don't get the point here. Some people will keep feeling
> offensed when they're just told to read the man/wiki pages, and others
> will simply change their answers from RTFM to RTFW.
> Nobody can force people into reading the manuals, or reading the
> posting guide. This is definitely one problem that the wiki will not
> solve.
>
>
The real issue is indexing and cross-referencing.  Quite often requestors HAVE 
tried the manuals, but without a real clue about where to look, that can be 
unproductive.  On the other hand, being pulled up short and Ripleyed can have 
a salutary effect on analyzing the problem first and researching carefully 
before posting a clueless query.  You could see as a useful part of the 
learning process.

JD

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Re: [R] Wikis etc.

2006-01-09 Thread J Dougherty
On Monday 09 January 2006 11:31, Gabor Grothendieck wrote:
> . . .
>
> I certainly was not disparaging books.  I said _in addition to_ books,
> not _insted of_.  The reason I pointed this out is that I think
> most people already read the books.  What many people don't
> do as far as can tell is read the code.  Obviously if you are just
> starting out you are going to be relying on the documentation,
> books, etc. but once you get past the intro stage you need to get
> into code.  One repeatedly sees questions on this list where just
> a minute or two spent with the code would have answered the
> question.
>
Gabor,  

The issue IS the INTRO stage though, in fact well beyond the intro stage.  
Reading the code is well and good for a programmer, but many are not and 
never will be coders, and this group is going to continue to expand.  Even an 
advanced statistician migrating from a proprietary system like SPSS to R is 
going to need documentation.  They would not even know where in the code to 
look!  Code is cool, but it really isn't expository.

John

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Re: [R] A comment about R:

2006-01-05 Thread J Dougherty
On Thursday 05 January 2006 12:13, Achim Zeileis wrote:
> . . . snip
> Whether you find this simple or not depends on what you might want to
> have. Personally, I always find it very limiting if I've only got a switch
> to choose one or another vcov matrix when there is a multitude of vcov
> matrices in use in the literature. What if you would want to do HC3
> instead of the HC(0) that is offered by Eviews...or HC4...or HAC...or
> something bootstrapped...or...
> In my view, this is the stengths of many implementation in R: you can make
> programs very modular so that the user can easily extend the software or
> re-use it for other purposes. The price you pay for that is that it is not
> as easy to as a point-and-click software that offers some standard tools.
> Of course, both sides have advantages or disadvantages.
> . . .snip

Stata's ADO scripting language has the ability to access intermediate steps 
and local variables used by various commands.  These are typically held in 
memory until they are purged.  The difference between Stata and R is more 
that Stata has been streamlined into an application, the nuts and bolts 
hidden away, the rivet heads counter sunk and polished, so that unless you 
really need to use them, they aren't visible.  It only LOOKS like you are 
constrained to the readily available results of specific commands.  Stata 
output will tend to look very much like the standard output one becomes 
accustomed to in undergraduate stat courses.  

R assumes you _will_ want access to the nuts and bolts, and don't much care 
about visible rivets if the system is both accurate and functional.  R is 
much more a programming environment in that sense.  It is an important 
difference.  There is going to be a continuing growth in users of R as 
companies see cost savings in OS.  They will often be people who happily 
dragged .xls files into SPSS or SPSS for analysis and then printed the 
resulting reports.  (Personally, I became a strong believer in statistical 
analysis packages after receiving a _negative_ variance in Excel once upon a 
time.  I don't see how that could even be possible, but apparently it was a 
known issue.  Some ad hoc experimentation then demonstrated that no 
spreadsheet was all that precise).

One place where R and Stata have a great deal in common is in the manner in 
which graphs and charts are formatted.  Stata is perhaps slightly less 
bizantine, but only slightly.  Both systems emphasize flexibility and quality 
graphics at the price of learning to know what you are doing.  That said, you 
can still do a lot more with R in some areas than Stata, especially in 
spatial graphics and analysis.

JD

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Re: [R] Help: chisq.test

2005-12-10 Thread J Dougherty
On Saturday 10 December 2005 17:37, Thanjavur Bragadeesh wrote:
> I have two groups of patients (improved or not improved) named x and y
> group respectively after being treated with 5 different drugs
>
> X<-c(43,52,25,48,57) and
>
> Y<-c(237,198,245,212,233)
>
> when I run
>
> chisq.test(cbind(x,y))

X and Y here are read as two columns of data when you use cbind with five 
rows.  With cbind you have 4 DOF.
>
> I get a p value of <0.0024
>
> but if I run
>
> chisq.test(x,y)   I get a p value of 0.22 not significant at 5%

When not using cbind, you have 16 DOF.  The numbers may look the same to you, 
but you are specifying two quite different sets of data,
>
>
> what is the difference between the two
>
> thanks
>
> bragadeesh

JWDougherty

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[R] Problem compiling R 2.1.* on SUSE 9.2

2005-07-07 Thread J Dougherty
I have been unable to compile either R 2.1.0 or 2.1.1 under SUSE 9.2.  The 
system simply hangs as far as I can tell.  All key board and mouse 
service dies.  I have had no problem compiling earlier versions of R through 
2.0.1, aside from remembering to include readline in the configuration.  
Configure runs without any warnings except that Info or html versions of the 
R Manuals.  The SUSE 9.2 install is generic with KDE 3.3 as the principal 
GUI.  Compiling also crashes under GNOME.  Because of the system hang, I 
can't provide any error codes.  Perusing /var/log/messages doesn't seem to 
yield any clues.  The system is a KDE AMD XP 2100, there is 1 GB of system 
ram, less than 10% of the harddisk space is in use, videocard is an nVidia 
GeForce4 Ti 4400.  The OS is SUSE 9.2 and it has current updates for 
security.

JWDougherty

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