Re: [R] Second axis on bottom of graph

2014-05-19 Thread Hurr
Thanks Jim, I see you are the author of staxlab.
In the second staxlab I have tried line=3.5 like in axis, and 
top.line=3.5, separately, with no apparent effect.
We should have to select the second axis somehow.
Hurr




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[R] converting a matrix to array

2014-05-19 Thread Effat Habibi
Dear Sir/ Madam,

I have a problem with converting a matrix (247 rows, 16 columns) to an array in 
R.

Would you please help me in this regard.

Thank you,
E. Habibi
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Re: [R] Second axis on bottom of graph

2014-05-19 Thread Jim Lemon
On Sun, 18 May 2014 11:12:21 PM Hurr wrote:
 Thanks Jim, I see you are the author of staxlab.
 In the second staxlab I have tried line=3.5 like in axis, and
 top.line=3.5, separately, with no apparent effect.
 We should have to select the second axis somehow.
 Hurr
 
 
You are correct, as I didn't run your code I forgot about the rotation. Here 
is a revised staxlab function that should correct the problem and will 
appear in the next version of plotrix. Thanks for alerting me to it.

Jim
# staxlab produces staggered axis tick labels
# note that barplot() tends to mess things up by plotting an X axis 
# even when axes=FALSE

staxlab-function(side=1,at,labels,nlines=2,top.line=0.5,
 line.spacing=0.8,srt=NA,ticklen=0.03,adj=1,...) {

 if(missing(labels)) labels-at
 nlabels-length(labels)
 if(missing(at)) at-1:nlabels
 axislim-par(usr)[3:4-2*side%%2]
 if(any(at  axislim[1]) || any(at  axislim[2]))
  warning(Some axis labels are off the plot)
 if(is.na(srt)) {
  linepos-rep(top.line,nlines)
  for(i in 2:nlines) linepos[i]-linepos[i-1]+line.spacing
  linepos-rep(linepos,ceiling(nlabels/nlines))[1:nlabels]
  axis(side=side,at=at,labels=rep(,nlabels))
  mtext(text=labels,side=side,line=linepos,at=at,...)
 }
 else {
  linewidth-strheight(M)
  xylim-par(usr)
  if(side == 1) {
   xpos-at
   if(par(ylog)) ypos-10^(xylim[3]-ticklen*(xylim[4]-xylim[3]))
   else ypos-xylim[3]-ticklen*(xylim[4]-xylim[3])-top.line*linewidth
  }
  if(side == 3) {
   xpos-at
   if(par(ylog)) ypos-10^(xylim[4]+ticklen*(xylim[4]-xylim[3]))
   else ypos-xylim[4]+ticklen*(xylim[4]-xylim[3])+top.line*linewidth
  }
  if(side == 2) {
   ypos-at
   if(par(xlog)) xpos-10^(xylim[1]-ticklen*(xylim[2]-xylim[1]))
   else xpos-xylim[1]-ticklen*(xylim[2]-xylim[1])-top.line*linewidth
  }
  if(side == 4) {
   ypos-at
   if(par(xlog)) xpos-10^(xylim[2]+ticklen*(xylim[2]-xylim[1]))
   else xpos-xylim[2]+ticklen*(xylim[2]-xylim[1])+top.line*linewidth
  }
  par(xpd=TRUE)
  text(xpos,ypos,labels,srt=srt,adj=adj,...)
  par(xpd=FALSE)
 }
}
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Re: [R] converting a matrix to array

2014-05-19 Thread Jim Lemon
On Sun, 18 May 2014 08:18:18 PM Effat Habibi wrote:
 Dear Sir/ Madam,
 
 I have a problem with converting a matrix (247 rows, 16 columns) to 
an array
 in R.
 
 Would you please help me in this regard.
 
Hi Effat,

A two-dimensional array is the same thing as a matrix.

From the help page for array.

Jim

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Re: [R] solution for r-help to the problem of yahoo addresses bouncing?

2014-05-19 Thread Jannis

Hi David,

thanks for your reply.


On 16.05.2014 23:07, David Winsemius wrote:

On May 16, 2014, at 2:25 AM, Jannis wrote:


Hi R users,



I suspect this is due to yahoo recently changing its handling of DMARC policies.

Yes. It is due to ISP bounces coming back to the ETHZ server. You do not say 
what you did with the rest of the message. Did you click on the re-enable 
hyperlink? About 250 people were recently forcibly unsubscribed on the same 
day, mostly with yahoo, gmail, or hotmail addresses,  because they had failed 
to re-enable their subscriptions. (This action by the mailserver filled up the 
mailboxes of all the moderators.)


I reenabled the mailadress at least 5 times at different times after the 
original reminder so I suspect this may not permanently solve the issue.





Is there anything I can do from my side to change this? Or is the only solution 
to change the mail provider?

Seek out methods of putting r-help on your whitemail list. Please do not ask me 
to describe this for you further. That is your and your ISP's responsibility to 
sort out.



There seems to be no indivdual whitelist for yahoo. I am no expert on 
these issues but as far as i understand it has more to do with the list 
mails not originating from the senders IP range. You are right that you 
(or the people hosting the list) are not responsible for all the 
individual receivers ISP setting, but in the yahoo case the information 
on these webpages  may solve the issue:


https://help.yahoo.com/kb/postmaster/SLN3435.html?impressions=true



I personally, however, can not fill in these forms.

Sorry for the hassle! If this issue prevails I will certainly contact 
the yahoo people to change the way they deal with mailing lists or just 
change the ISP.




Cheers
Jannis

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Re: [R] filename of current device

2014-05-19 Thread Andreas Leha


On 18/05/2014 18:08, Prof Brian Ripley wrote:
 On 14/05/2014 23:04, Andreas Leha wrote:
 Hi all,

 how do I find out about the filename, the currently open (let's say pdf)
 device is writing to?

 If I find 'dev.cur()' returning 'pdf 3' when I expect 'nulldevice 1' I
 would like to know, which file that pdf device is actually targeting.

 Any help for my poor organization is highly appreciated...
 
 You cannot know this for an arbitrary device, at least not from R.
 
 Most files in R are opened with the C call fopen() and thereafter
 referred to by a file handle: the file can be renamed, unlinked ...
 whilst the handle is open.  Some system utilities[*] may be able to tell
 you what filepaths are/were associated with file handles open in a
 process, but it cannot be done portably.
 
 However, in R-devel there is the possibility of a device recording extra
 information about itself.  See the NEWS item
 
 • Graphics devices can add attributes to their description in
   .Device and .Devices.  Several of those included with R use a
   filepath attribute.
 
 AFAIR the pdf() device does: let's see
 
 pdf('/tmp/foo.pdf')
 dev.cur()
 pdf
   2
 .Devices
 [[1]]
 [1] null device
 
 [[2]]
 [1] pdf
 attr(,filepath)
 [1] /tmp/foo.pdf
 
 
 There is at least one exception: for historical reasons locked in by
 undocumented use in package tkrplot, the win.metafile() device does
 include the file path in the device 'name'.
 
 [*] They have existed at least on Linux, Windows and OS X.
 


Very nice!  Thank you for pointing that out.  That's exactly what I was
hoping to see in R.  Good to know that this is already there.

Regards,
Andreas

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[R] could I smooth the geom_line output on ggplot2?

2014-05-19 Thread Klot Lee
hi,
I have got some data and draw a line graph with ggplot2 geom_line. The
output seems too sharp to me, is there any way to smooth it?
I mean smooth the line, NOT ADDING a smooth line. Or there is other
functions in ggplot2 can help me out with a smooth line?

Thank you.

-- 
Stand Alone Complex

[[alternative HTML version deleted]]

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Re: [R] help with xts

2014-05-19 Thread Pietro

Thanks to all for your ideas and inspirations

Il 18/05/2014 18.35, Joshua Ulrich ha scritto:

Using subset assignment with an array usually doesn't work well with
xts/zoo objects.  Your case wouldn't even work with a matrix because
you have NA in your array.

In this case, you can achieve the same result using multiplication:
pos.neg.1 - ((cond1  cond2)*-2+1)
test - test * pos.neg.1

Best,
--
Joshua Ulrich  |  about.me/joshuaulrich
FOSS Trading  |  www.fosstrading.com


On Sun, May 18, 2014 at 9:25 AM, Pete freeri...@gmail.com wrote:

I have 3 xts objects: test, cond1, cond2
You can download here:

https://dl.dropboxusercontent.com/u/102669/obj.rar

My problem is very simple.

test [ cond1  cond2] = NA   THIS WORKS

test [ cond1  cond2] = -test [ cond1  cond2]   THIS DOESN'T WORKS

Why?

My objective is to substitute all values in test (when cond1  cond2) with
the corresponding values of test but with negative sign

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.



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Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /

2014-05-19 Thread Henric Winell

On 2014-05-18 20:43, peter dalgaard wrote:


On 18 May 2014, at 07:38 , Jeff Newmiller jdnew...@dcn.davis.ca.us wrote:


Then you had best not do it again if you don't like that result.

1) This is not the right mailing list for issues having to do with 
bioconductor. Please go to the bioconductor mailing list for that.


Hmm, this is one case where I'd really rather not scare people off R-help. 
Non-BioC users do use BioC packages from time to time and what Juergen did is 
what the BioConductor web pages tells new users to do (probably minus the 
as-root bit). A warn-off on R-help seems entirely warranted. Good to see that 
Martin Morgan is taking the issue very seriously in his post below.


As a non-BioC user using BioC packages I've always wondered why the 
standard R functionality isn't enough.  Can someone, please, tell me why 
'biocLite()' should be used?


I've always succeeded installing BioC packages using the standard R 
tools (as indicated by Uwe in his reply).



Henric Winell







2) Running random scripts straight from the internet as root without reviewing 
them is exactly the kind of thing any experienced *nix user would never do. 
That is why user-level accounts have limits on the things they can do. I doubt 
you are supposed to be running anything with your current directory set to /, 
ever, especially not logged in as root.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
---
Sent from my phone. Please excuse my brevity.

On May 17, 2014 10:16:46 PM PDT, Juergen Rose r...@rz.uni-potsdam.de wrote:

I had the following files in /:

root@caiman:/root(8)# ll /
total 160301
drwxr-xr-x   2 root root  4096 May 16 12:23 bin/
drwxr-xr-x   6 root root  3072 May 14 13:58 boot/
-rw-r--r--   1 root root 38673 May 14 14:22 boot_local-d.log
lrwxrwxrwx   1 root root11 Jan 22  2011 data - data_caiman/
drwxr-xr-x   7 root root  4096 Mar  9 22:29 data_caiman/
lrwxrwxrwx   1 root root23 Dec 29 13:43 data_impala -
/net/impala/data_impala/
lrwxrwxrwx   1 root root21 Jan 27 08:13 data_lynx2 -
/net/lynx2/data_lynx2/
drwxr-xr-x  21 root root  4040 May 14 14:40 dev/
drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
-rw---   1 root root 15687 Dec 26 13:42 grub.cfg_old
lrwxrwxrwx   1 root root11 Jan 23  2011 home - home_caiman/
drwxr-xr-x   5 root root  4096 Dec 26 11:31 home_caiman/
lrwxrwxrwx   1 root root23 Dec 29 13:43 home_impala -
/net/impala/home_impala/
lrwxrwxrwx   1 root root21 Jan 27 08:13 home_lynx2 -
/net/lynx2/home_lynx2/
lrwxrwxrwx   1 root root 5 Mar 30 04:25 lib - lib64/
drwxr-xr-x   3 root root  4096 May 14 04:31 lib32/
drwxr-xr-x  17 root root 12288 May 16 12:23 lib64/
-rw-r--r--   1 root root   1797418 May 14 14:22 login.log
drwx--   2 root root 16384 Jan 20  2011 lost+found/
drwxr-xr-x   2 root root 0 May 14 14:21 misc/
drwxr-xr-x  10 root root  4096 Nov  4  2013 mnt/
drwxr-xr-x   4 root root 0 May 17 17:38 net/
drwxr-xr-x  13 root root  4096 Feb 13 13:25 opt/
dr-xr-xr-x 270 root root 0 May 14 14:21 proc/
drwx--  36 root root  4096 May 17 15:00 root/
drwxr-xr-x  30 root root   840 May 16 18:21 run/
drwxr-xr-x   2 root root 12288 May 16 12:23 sbin/
-rw-r--r--   1 root root 162191459 Jan 13  2011
stage3-amd64-20110113.tar.bz2
dr-xr-xr-x  12 root root 0 May 14 14:21 sys/
drwxrwxrwt  16 root root  1648 May 17 17:14 tmp/
drwxr-xr-x  19 root root  4096 May  6 04:40 usr/
drwxr-xr-x  16 root root  4096 Dec 26 11:17 var/


Then I did as root:
R

source(http://bioconductor.org/biocLite.R;)
biocLite(vsn)


Save workspace image? [y/n/c]: n
root@caiman:/root(15)# ll /
total 93
drwxr-xr-x   2 root root  4096 May 16 12:23 bin/
drwxr-xr-x   6 root root  3072 May 14 13:58 boot/
drwxr-xr-x   7 root root  4096 Mar  9 22:29 data_caiman/
drwxr-xr-x  21 root root  4040 May 14 14:40 dev/
drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
drwxr-xr-x   5 root root  4096 Dec 26 11:31 home_caiman/
drwxr-xr-x   3 root root  4096 May 14 04:31 lib32/
drwxr-xr-x  17 root root 12288 May 16 12:23 lib64/
drwx--   2 root root 16384 Jan 20  2011 lost+found/
drwxr-xr-x   2 root root 0 May 14 14:21 misc/
drwxr-xr-x  10 root root  4096 Nov  4  2013 mnt/
drwxr-xr-x   2 root root 0 May 17 17:38 net/
drwxr-xr-x  13 root root  4096 Feb 13 13:25 opt/
dr-xr-xr-x 272 root root 0 May 14 14:21 proc/
drwx--  36 root root  4096 May 17 15:00 root/
drwxr-xr-x  30 root root   840 May 16 18:21 

[R] Course: Introduction to GAM and GAMM with R

2014-05-19 Thread Highland Statistics Ltd

We would like to announce the following stats course:

Course: Introduction to Generalized Additive Models and Generalized 
Additive Mixed Effects Models with R

Where: Deakin University, Melbourne, Australia
When: 25 - 29 August, 2014

URL Flyer: http://www.highstat.com/Courses/Flyer2014_08Deakin.pdf
Further info: http://www.highstat.com/statscourse.htm

Kind regards,

Alain


--
Dr. Alain F. Zuur

First author of:
1. Beginner's Guide to GAMM with R (2014).
2. Beginner's Guide to GLM and GLMM with R (2013).
3. Beginner's Guide to GAM with R (2012).
4. Zero Inflated Models and GLMM with R (2012).
5. A Beginner's Guide to R (2009).
6. Mixed effects models and extensions in ecology with R (2009).
7. Analysing Ecological Data (2007).

Highland Statistics Ltd.
9 St Clair Wynd
UK - AB41 6DZ Newburgh
Tel:   0044 1358 788177
Email: highs...@highstat.com
URL:   www.highstat.com
blog: http://www.highstat.com/wordpress/

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Re: [R] Second axis on bottom of graph

2014-05-19 Thread Hurr
Thanks again Jim.
Sorry, again I'm enclosing incomplete not-runnable code.
Modified like this it works with the new staxlab function which 
I inserted before the second staxlab call. 
How long before I don't need to insert it?
I didn't see a way to select the specific axis, so
I used top.line=5. Is that what I should do?

axis(1,tick=TRUE,at=horTicLocs,labels=rep(,length(horLabels)),padj=0)
staxlab(1,at=horTicLocs,labels=horLabels,srt=90,adj=c(1,0)) 
nFrqTicInvls=9; frqTicLocs - vector(length=nFrqTicInvls+1); frqLabels -
vector(length=nFrqTicInvls+1); 
frqInvl=(horAxisLims[2]-horAxisLims[1])/nFrqTicInvls 
for(i in 1:(nFrqTicInvls+1))frqTicLocs[i]=horAxisLims[1]+(i-1)*frqInvl 
for(i in
1:(nFrqTicInvls+1))frqLabels[i]=.jcall(OuWid,S,sR,frqTicLocs[i],as.integer(4))
 
for(i in 1:(nFrqTicInvls+1))print(frqLabels[i]) 
axis(1,tick=TRUE,line=3.5,at=frqTicLocs,labels=rep(,length(frqLabels)),padj=0)
 
staxlab(1,top.line=5,at=frqTicLocs,labels=frqLabels,srt=90) 
title(xlab=Cycles/Yr,line=6)

Hurr




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[R] extract duplications from list

2014-05-19 Thread Assa Yeroslaviz
Hi,

I have a list of 40 data.frames.

I would like to identify duplicated entries in the whole list, not only in
one specific data.frame, but in all 40.

Here is my list:

 myList
[[1]]
XNAME  MEM.SHIP
1 FBgn008 FBgn008 0.9304502
2 FBgn014 FBgn014 1.000
3 FBgn028 FBgn028 1.000
4 FBgn109 FBgn109 1.000
5 FBgn114 FBgn114 0.4839886
6 FBgn120 FBgn120 1.000

[[2]]
XNAME  MEM.SHIP
1 FBgn251 FBgn251 0.3138650
2 FBgn0001168 FBgn0001168 0.8995011
3 FBgn0001941 FBgn0001941 0.7485548
4 FBgn0003053 FBgn028 0.4426997
5 FBgn0003159 FBgn0003159 0.4843226
6 FBgn120 FBgn0003162 0.6556290


I would like to know whether there are duplicated entries in the first
and/or second column of all. In this list I have two duplications one is
FBgn120 in both lines Nr. 6 and the second is FBgn028 in line 3 and
line 4 in df1 and df2 respectively.


Is there a way to do it. With unique I don't get any results. and I cannot
convert the list into a data.frame, as the number of items in each df is
different.

Thanks
Assa

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[R] Spatial Quantile Regression: Extracting residuals

2014-05-19 Thread Marie-Line GLAESENER
Dear R users,

Could anyone tell me if there is a way to obtain the residuals from a model 
fitted by

qregspiv(y ~  x,wmat=wmat,inst=NULL,tau=.5,rhomat = 
seq(-1,1,.01),printsariv=T,silent=F,   nboot=300,data=)

in McSpatial, using the Chernozhukov and Hansen (2006) method.

Many thanks in advance and kind regards,

Marie-Line

Ph.D. Candidate
Institute of Geography and Spatial Planning

UNIVERSITÉ DU LUXEMBOURG
CAMPUS WALFERDANGE
Route de Diekirch / BP 2
L-7201 Walferdange
Luxembourg
marie-line.glaese...@uni.lumailto:marie-line.glaese...@uni.lu
www.geo.ipse.uni.luhttp://www.geo.ipse.uni.lu/


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Re: [R] Second axis on bottom of graph

2014-05-19 Thread Jim Lemon
On Mon, 19 May 2014 05:23:20 AM Hurr wrote:
 Thanks again Jim.
 Sorry, again I'm enclosing incomplete not-runnable code.
 Modified like this it works with the new staxlab function which
 I inserted before the second staxlab call.
 How long before I don't need to insert it?
 I didn't see a way to select the specific axis, so
 I used top.line=5. Is that what I should do?
 
 
axis(1,tick=TRUE,at=horTicLocs,labels=rep(,length(horLabels)),padj=0)
 staxlab(1,at=horTicLocs,labels=horLabels,srt=90,adj=c(1,0))
 nFrqTicInvls=9; frqTicLocs - vector(length=nFrqTicInvls+1); frqLabels 
-
 vector(length=nFrqTicInvls+1);
 frqInvl=(horAxisLims[2]-horAxisLims[1])/nFrqTicInvls
 for(i in 1:(nFrqTicInvls+1))frqTicLocs[i]=horAxisLims[1]+(i-1)*frqInvl
 for(i in
 1:
(nFrqTicInvls+1))frqLabels[i]=.jcall(OuWid,S,sR,frqTicLocs[i],as.integ
 er(4)) for(i in 1:(nFrqTicInvls+1))print(frqLabels[i])
 
axis(1,tick=TRUE,line=3.5,at=frqTicLocs,labels=rep(,length(frqLabels)),pad
 j=0) staxlab(1,top.line=5,at=frqTicLocs,labels=frqLabels,srt=90)
 title(xlab=Cycles/Yr,line=6)
 
 Hurr

I guess top.line=5 would be almost off the bottom of the plot. I assume 
that you know how it should look (I don't) and can adjust the top.line 
value until it looks right. the next version of plotrix will probably be out 
in a week or two.

Jim

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[R] substring if value starts with a character

2014-05-19 Thread Mat
Hello togehter, 

i have a litte problem to convert a data.frame. My data.frame looks like
this one
  A
1  R5000
2  R4800
3  R4700
4  3500
5  3800

I need now a command, which outputs all the numbers, without the character
in front.
The solution look like this one:

 A
1  5000
2  4800
3  4700
4  3500
5  3800

Thanks.

Best regards. Mat



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Re: [R] Testing parallel regression assumption

2014-05-19 Thread Rui Barradas

Hello,

Take a look at

http://stats.stackexchange.com/questions/58772/brant-test-in-r

Hope this helps,

Rui Barradas

Em 19-05-2014 01:40, caoweina escreveu:

Dear Rose :
 I saw your questions about the R function that performs brant test. Have 
you worked out ?  Please give some advice. I need to do  the brant test in R . 
Thank you very much!
sincerely!

Anna
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Re: [R] substring if value starts with a character

2014-05-19 Thread Rui Barradas

Hello,

Try the following.

dat - read.table(text = 
 A
1  R5000
2  R4800
3  R4700
4  3500
5  3800
, header = TRUE)

dat

dat2 - dat
dat2[] - lapply(dat, function(x) sub(^[[:alpha:]]*(.*$), \\1, x))
dat2


Hope this helps,

Rui Barradas

Em 19-05-2014 14:00, Mat escreveu:

Hello togehter,

i have a litte problem to convert a data.frame. My data.frame looks like
this one
   A
1  R5000
2  R4800
3  R4700
4  3500
5  3800

I need now a command, which outputs all the numbers, without the character
in front.
The solution look like this one:

  A
1  5000
2  4800
3  4700
4  3500
5  3800

Thanks.

Best regards. Mat



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Re: [R] extract duplications from list

2014-05-19 Thread jim holtman
Here is one way of doing it:


##
 files - list(file1 = XNAME  MEM.SHIP
+ 1 FBgn008 FBgn008 0.9304502
+ 2 FBgn014 FBgn014 1.000
+ 3 FBgn028 FBgn028 1.000
+ 4 FBgn109 FBgn109 1.000
+ 5 FBgn114 FBgn114 0.4839886
+ 6 FBgn120 FBgn120 1.000,
+ file2 = XNAME  MEM.SHIP
+ 1 FBgn251 FBgn251 0.3138650
+ 2 FBgn0001168 FBgn0001168 0.8995011
+ 3 FBgn0001941 FBgn0001941 0.7485548
+ 4 FBgn0003053 FBgn028 0.4426997
+ 5 FBgn0003159 FBgn0003159 0.4843226
+ 6 FBgn120 FBgn0003162 0.6556290)

 # read in all the files (dummies in this case)
 # append file name
 allFiles - do.call(rbind, lapply(names(files), function(.name){
+ input - read.table(text = files[[.name]], as.is = TRUE)
+ input$file - .name
+ input  # return value
+ }))

 # function to mark all duplicate entries
 allDup -
+ function (value)
+ {
+ duplicated(value) | duplicated(value, fromLast = TRUE)
+ }
 allFiles$col1 - allDup(allFiles$X)
 allFiles$col2 - allDup(allFiles$NAME)
 allFiles
 XNAME  MEM.SHIP  file  col1  col2
1  FBgn008 FBgn008 0.9304502 file1 FALSE FALSE
2  FBgn014 FBgn014 1.000 file1 FALSE FALSE
3  FBgn028 FBgn028 1.000 file1 FALSE  TRUE
4  FBgn109 FBgn109 1.000 file1 FALSE FALSE
5  FBgn114 FBgn114 0.4839886 file1 FALSE FALSE
6  FBgn120 FBgn120 1.000 file1  TRUE FALSE
11 FBgn251 FBgn251 0.3138650 file2 FALSE FALSE
21 FBgn0001168 FBgn0001168 0.8995011 file2 FALSE FALSE
31 FBgn0001941 FBgn0001941 0.7485548 file2 FALSE FALSE
41 FBgn0003053 FBgn028 0.4426997 file2 FALSE  TRUE
51 FBgn0003159 FBgn0003159 0.4843226 file2 FALSE FALSE
61 FBgn120 FBgn0003162 0.6556290 file2  TRUE FALSE




Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.


On Mon, May 19, 2014 at 8:48 AM, Assa Yeroslaviz fry...@gmail.com wrote:

 Hi,

 I have a list of 40 data.frames.

 I would like to identify duplicated entries in the whole list, not only in
 one specific data.frame, but in all 40.

 Here is my list:

  myList
 [[1]]
 XNAME  MEM.SHIP
 1 FBgn008 FBgn008 0.9304502
 2 FBgn014 FBgn014 1.000
 3 FBgn028 FBgn028 1.000
 4 FBgn109 FBgn109 1.000
 5 FBgn114 FBgn114 0.4839886
 6 FBgn120 FBgn120 1.000

 [[2]]
 XNAME  MEM.SHIP
 1 FBgn251 FBgn251 0.3138650
 2 FBgn0001168 FBgn0001168 0.8995011
 3 FBgn0001941 FBgn0001941 0.7485548
 4 FBgn0003053 FBgn028 0.4426997
 5 FBgn0003159 FBgn0003159 0.4843226
 6 FBgn120 FBgn0003162 0.6556290


 I would like to know whether there are duplicated entries in the first
 and/or second column of all. In this list I have two duplications one is
 FBgn120 in both lines Nr. 6 and the second is FBgn028 in line 3 and
 line 4 in df1 and df2 respectively.


 Is there a way to do it. With unique I don't get any results. and I cannot
 convert the list into a data.frame, as the number of items in each df is
 different.

 Thanks
 Assa

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Re: [R] substring if value starts with a character

2014-05-19 Thread Ivan Calandra

Hi Mat,

Try that:
gsub([A-Za-z], , df$A)

This is a regular expression that looks for all characters (A to Z and a 
to z) and replaces it with nothing ()

You will need to convert the column to numeric after this operation.

HTH,
Ivan

--
Ivan Calandra
University of Franche-Comté
Laboratoire Chrono-Environnement
Bureau ATER -107L
16, Route de Gray
25030 Besançon Cedex, France
ivan.calan...@univ-fcomte.fr
+33 (0) 381 66 20 60
http://chrono-environnement.univ-fcomte.fr/spip.php?article1830

Le 19/05/14 15:00, Mat a écrit :

Hello togehter,

i have a litte problem to convert a data.frame. My data.frame looks like
this one
   A
1  R5000
2  R4800
3  R4700
4  3500
5  3800

I need now a command, which outputs all the numbers, without the character
in front.
The solution look like this one:
 
  A

1  5000
2  4800
3  4700
4  3500
5  3800

Thanks.

Best regards. Mat



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[R] K-mean Clustering in URL's

2014-05-19 Thread Ashis Deb
Hi  ,  I  have some   URL's  like :-



  2

   facebook
http://www.facebook.com http://www.facebook.com/
http://twitter.com/facebook http://twitter.com/facebook
http://en.wikipedia.org/wiki/Facebook
http://play.google.com/store/apps/developer?id=Facebookhl=en
http://mashable.com/category/facebook  http://www.facebookstories.com
 How   to  find  kmean clusterring of this text  URL data?


THanks

ASHIS

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[R] Boxplots

2014-05-19 Thread Shane Carey
Hi,

I have boxplots by factors for a dataset and trying to include a boxplot to
represent the entire dataset.

Any idea how this would be done?

Thanks

-- 
Shane

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Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /

2014-05-19 Thread Martin Morgan

On 05/19/2014 01:09 AM, Henric Winell wrote:

On 2014-05-18 20:43, peter dalgaard wrote:


On 18 May 2014, at 07:38 , Jeff Newmiller jdnew...@dcn.davis.ca.us wrote:


Then you had best not do it again if you don't like that result.

1) This is not the right mailing list for issues having to do with
bioconductor. Please go to the bioconductor mailing list for that.


Hmm, this is one case where I'd really rather not scare people off R-help.
Non-BioC users do use BioC packages from time to time and what Juergen did is
what the BioConductor web pages tells new users to do (probably minus the
as-root bit). A warn-off on R-help seems entirely warranted. Good to see that
Martin Morgan is taking the issue very seriously in his post below.


As a non-BioC user using BioC packages I've always wondered why the standard R
functionality isn't enough.  Can someone, please, tell me why 'biocLite()'
should be used?

I've always succeeded installing BioC packages using the standard R tools (as
indicated by Uwe in his reply).


Conversely, I've always succeeded in installing CRAN and Bioc packages via

  source(http://bioconductor.org/biocLite.R;)
  biocLite(...)

and am more-or-less flummoxed by the extra steps I'm asked to perform (to choose 
and set repositories) when I take that rare foray into install.packages()-land! 
One point is that http://bioconductor.org actually points to an Amazon 
CloudFront address, which means that the content comes from a geographically 
proximate and reliable location (this makes choice of repository mostly 
irrelevant for normal users, just point to bioconductor.org)




Bioconductor has a repository and release schedule that differs from R 
(Bioconductor has a 'devel' branch to which new packages and updates are 
introduced, and a stable 'release' branch emitted once every 6 months to which 
bug fixes but not new features are introduced).


A consequences of the mismatch between R and Bioconductor release schedules is 
that the Bioconductor version identified by Uwe's method is sometimes not the 
most recent 'release' available. For instance, R 3.1.1 will likely be introduced 
some months before the next Bioc release. After the Bioc release, 3.1.1 users 
will be pointed to an out-of-date version of Bioconductor.


A consequence of the distinct 'devel' branch is that Uwe's method sometimes 
points only to the 'release' repository, whereas Bioconductor developers and 
users wanting leading-edge features wish to access the Bioconductor 'devel' 
repository. For instance, the next Bioc release will be available for R.3.1.x, 
so Bioconductor developers and leading-edge users need to be able to install the 
devel version of Bioconductor packages into the same version (though perhaps 
different instance or at least library location) of R that currently supports 
the release version.


An indirect consequence of the structured release is that Bioconductor packages 
generally have more extensive dependencies with one another, both explicitly via 
the usual package mechanisms and implicitly because the repository, release 
structure, and Bioconductor community  interactions favor re-use of data 
representations and analysis concepts across packages. There is thus a higher 
premium on knowing that packages are from the same release, and that all 
packages are current within the release.




These days, the main purpose of source(http://bioconductor.org/biocLite.R;) is 
to install and attach the 'BiocInstaller' package.


In a new installation, the script installs the most recent version of the 
BiocInstaller package relevant to the version of R in use, regardless of the 
relative times of R and Bioconductor release cycles. The BiocInstaller package 
serves as the primary way to identify the version of Bioconductor in use


   library(BiocInstaller)
  Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help

Since new features are often appealing to users, but at the same time require an 
updated version of Bioconductor, the source() command evaluated in an 
out-of-date R will nudge users to upgrade, e.g., in R-2.15.3


   source(http://bioconductor.org/biocLite.R;)
  A new version of Bioconductor is available after installing the most
recent version of R; see http://bioconductor.org/install

The biocLite() function is provided by BiocInstaller. This is a wrapper around 
install.packages, but with the repository chosen according to the version of 
Bioconductor in use, rather than to the version relevant at the time of the 
release of R.


biocLite also nudges users to remain current within a release, by default 
checking for out-of-date packages and asking if the user would like to update


 biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
  3.1.0.
Old packages: 'BBmisc', 'genefilter', 'GenomicAlignments',
  'GenomicRanges', 'IRanges', 'MASS', 'reshape2', 'Rgraphviz',
  'RJSONIO', 'rtracklayer'
Update all/some/none? 

Re: [R] Boxplots

2014-05-19 Thread Jeff Newmiller
Read the posting guide, which tells you to provide a minimal reproducible 
example [1] (there it's more than one way to accomplish what you have done 
already) and post using plain text (so your R code comes through without being 
corrupted).

[1] 
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

On May 19, 2014 7:08:00 AM PDT, Shane Carey careys...@gmail.com wrote:
Hi,

I have boxplots by factors for a dataset and trying to include a
boxplot to
represent the entire dataset.

Any idea how this would be done?

Thanks

__
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[R] level for confint (nls)

2014-05-19 Thread Jun Shen
Dear list,

I have this nls model and trying to calculate the confidence interval for
some parameter. I found if I use the default value level=0.95, confint can
calculate a value; when I change the level=0.9, then it return  :Error in
prof$getProfile() : number of iterations exceeded maximum of 50.

The strange thing is if I use level=0.8, it is working again. Why is that?
How do I get an CI value for any level? Thanks.

Jun Shen

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[R] How to define and calculate volume of 3D polygon?

2014-05-19 Thread Alexander Shenkin

Hi Folks,

I have a set of x,y,z points in 3D space that defines the outline of a 
tree crown (5 - 15 perimeter points + 1 top  bottom point). I would 
like to calculate the volume of the corresponding 3D polygon based on 
those points.  I have been able to use geometry::convhulln, but I think 
this isn't the right algorithm, since the polygon needs to pass through 
each point in order, and not just snap a rubber-band around the outer 
points.


Any suggestions for alternative algorithms and packages would be most 
welcome!


Thanks,
Allie

   seq  x  yz
11 -1.7310065  2.4502278 11.1
22 -1.9048260 -0.6096212  9.0
33  2.8652209  0.8891057 11.0
44  2.3929514 -3.4516349 11.2
55 -2.6436343  5.2745803 11.7
66 -4.3521504  4.6924180 11.7
77  6.1441732 -4.8051156 11.6
88 -6.2157823 -3.2193244  8.0
99  1.0024961 -2.8275434  9.0
10  10 -3.9656821  3.0452201  8.0
11  11  4.2070518 -1.5970958 11.0
12  12 -0.9461915  1.2902409  9.8
13  13  2.2792265  0.7517491 11.4

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Re: [R] How to Optimize two functions together in R

2014-05-19 Thread Mingxuan Han
I try to use NSGAII function in the mco but I am kind of confusing about the
numbers of input and output dimension in the argument. Could you explain a
little about this? Thank you. 



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[R] XML pkg. Namespace message

2014-05-19 Thread Timothy W. Cook
I am getting messages like:

Namespace prefix ccd on el-418bd009-f19a-4107-bc7b-2abb83748bbb is not defined
Namespace prefix mlhim244 on interval-type is not defined


when retrieving nodesets like this:
pct - getNodeSet(root, '//ccd:el-6acf3ae9-222c-4f71-8120-76375db84177',
nsDEF)

nsDEF is defined as:

nsDEF - function(){
  return(c(ccd='http://www.mlhim.org/ccd',mlhim244='
http://www.mlhim.org/xmlns/mlhim2/2_4_4'))
}

Which clearly has both namespaces defined and they match the definitions in
the XML.

The returned nodesets are correct. In fact, when I do not see these
messages, I know that I have a namespace problem.

So my questions is: Are these normal return messages?  They sure look like
error messages.

Thanks for any clarification.

--Tim







Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org

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Re: [R] level for confint (nls)

2014-05-19 Thread Bert Gunter
I believe this has to do with numeric issues in nonlinear fitting and
interpolation, and is neither concerned with R programming nor trivial
to answer. I therefore suggest you post on the stats.stackexchange.com
for a fuller discussion of the issues.

Cheers,
Bert

Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
H. Gilbert Welch




On Mon, May 19, 2014 at 7:42 AM, Jun Shen jun.shen...@gmail.com wrote:
 Dear list,

 I have this nls model and trying to calculate the confidence interval for
 some parameter. I found if I use the default value level=0.95, confint can
 calculate a value; when I change the level=0.9, then it return  :Error in
 prof$getProfile() : number of iterations exceeded maximum of 50.

 The strange thing is if I use level=0.8, it is working again. Why is that?
 How do I get an CI value for any level? Thanks.

 Jun Shen

 [[alternative HTML version deleted]]

 __
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Re: [R] How to define and calculate volume of 3D polygon?

2014-05-19 Thread Duncan Murdoch

On 19/05/2014, 10:42 AM, Alexander Shenkin wrote:

Hi Folks,

I have a set of x,y,z points in 3D space that defines the outline of a
tree crown (5 - 15 perimeter points + 1 top  bottom point). I would
like to calculate the volume of the corresponding 3D polygon based on
those points.  I have been able to use geometry::convhulln, but I think
this isn't the right algorithm, since the polygon needs to pass through
each point in order, and not just snap a rubber-band around the outer
points.

Any suggestions for alternative algorithms and packages would be most
welcome!


If you aren't using the convex hull, you need to specify more 
information.  The vertices of a polyhedron don't have a natural order, 
so passing through them in order doesn't make sense.


One way to specify this information is to specify which triples of 
vertices form triangular faces, as convhulln does.


I don't know of a package containing code to compute the volume, but a 
description of the algorithm is on this page:


http://www.ecse.rpi.edu/~wrf/Research/Short_Notes/volume.html

Duncan Murdoch




Thanks,
Allie

 seq  x  yz
11 -1.7310065  2.4502278 11.1
22 -1.9048260 -0.6096212  9.0
33  2.8652209  0.8891057 11.0
44  2.3929514 -3.4516349 11.2
55 -2.6436343  5.2745803 11.7
66 -4.3521504  4.6924180 11.7
77  6.1441732 -4.8051156 11.6
88 -6.2157823 -3.2193244  8.0
99  1.0024961 -2.8275434  9.0
10  10 -3.9656821  3.0452201  8.0
11  11  4.2070518 -1.5970958 11.0
12  12 -0.9461915  1.2902409  9.8
13  13  2.2792265  0.7517491 11.4

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Re: [R] How to Optimize two functions together in R

2014-05-19 Thread Suzen, Mehmet
Use defaul values initially, to see if you got reasonable results. See
here for the details of nsga2
http://dx.doi.org/10.1109/4235.996017

On 19 May 2014 16:42, Mingxuan Han han...@purdue.edu wrote:
 I try to use NSGAII function in the mco but I am kind of confusing about the
 numbers of input and output dimension in the argument. Could you explain a
 little about this? Thank you.



 --
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Re: [R] extract duplications from list

2014-05-19 Thread arun
Hi,

You may try:

myList - list(structure(list(X = c(FBgn008, FBgn014, 
FBgn028, 
FBgn109, FBgn114, FBgn120), NAME = c(FBgn008, 
FBgn014, FBgn028, FBgn109, FBgn114, FBgn120
), MEM.SHIP = c(0.9304502, 1, 1, 1, 0.4839886, 1)), .Names = c(X, 
NAME, MEM.SHIP), class = data.frame, row.names = c(1, 
2, 3, 4, 5, 6)), structure(list(X = c(FBgn251, 
FBgn0001168, FBgn0001941, FBgn0003053, FBgn0003159, FBgn120
), NAME = c(FBgn251, FBgn0001168, FBgn0001941, FBgn028, 
FBgn0003159, FBgn0003162), MEM.SHIP = c(0.313865, 0.8995011, 
0.7485548, 0.4426997, 0.4843226, 0.655629)), .Names = c(X, 
NAME, MEM.SHIP), class = data.frame, row.names = c(1, 
2, 3, 4, 5, 6)))

library(data.table)
 dt1 - rbindlist(myList)
fun1 - function(val){duplicated(val)|duplicated(val,fromLast=TRUE)}
dt1[,paste0(Col,1:2):=lapply(.SD, fun1),.SDcols=1:2]
dt1

A.K.




On Monday, May 19, 2014 8:50 AM, Assa Yeroslaviz fry...@gmail.com wrote:
Hi,

I have a list of 40 data.frames.

I would like to identify duplicated entries in the whole list, not only in
one specific data.frame, but in all 40.

Here is my list:

 myList
[[1]]
            X        NAME  MEM.SHIP
1 FBgn008 FBgn008 0.9304502
2 FBgn014 FBgn014 1.000
3 FBgn028 FBgn028 1.000
4 FBgn109 FBgn109 1.000
5 FBgn114 FBgn114 0.4839886
6 FBgn120 FBgn120 1.000

[[2]]
            X        NAME  MEM.SHIP
1 FBgn251 FBgn251 0.3138650
2 FBgn0001168 FBgn0001168 0.8995011
3 FBgn0001941 FBgn0001941 0.7485548
4 FBgn0003053 FBgn028 0.4426997
5 FBgn0003159 FBgn0003159 0.4843226
6 FBgn120 FBgn0003162 0.6556290


I would like to know whether there are duplicated entries in the first
and/or second column of all. In this list I have two duplications one is
FBgn120 in both lines Nr. 6 and the second is FBgn028 in line 3 and
line 4 in df1 and df2 respectively.


Is there a way to do it. With unique I don't get any results. and I cannot
convert the list into a data.frame, as the number of items in each df is
different.

Thanks
Assa

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Re: [R] Boxplots

2014-05-19 Thread S Ellison


 I have boxplots by factors for a dataset and trying to include a boxplot to
 represent the entire dataset.

Have a look at last the example in ?boxplot which plots a second set of values 
beside a first set. In your case, specifying xlim larger than needed by one and 
then using boxplot(x, at=n+1) is the kind of thing you'd need to do.

S Ellison



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Re: [R] Boxplots

2014-05-19 Thread Richard M. Heiberger
tmp - data.frame(y=c(rnorm(20), rnorm(20), c=rnorm(20)),
g=rep(letters[1:3], each=20))

library(lattice)
library(latticeExtra)
A - bwplot(y ~ g, data=tmp)
B - bwplot(y ~ rep(Y,60), data=tmp, horizontal=FALSE)

resizePanels(c(Individual=A, All Together=B, layout=c(2,1)), w=c(3,1))


## for even more options, you can look at the examples in
## the HH package
## install.packages(HH) ## if necessary
library(HH)
demo(bwplot.examples, package=HH)
example(panel.bwplot.superpose, package=HH)
?panel.bwplot.intermediate.hh
?panel.bwplot.superpose

On Mon, May 19, 2014 at 10:08 AM, Shane Carey careys...@gmail.com wrote:
 Hi,

 I have boxplots by factors for a dataset and trying to include a boxplot to
 represent the entire dataset.

 Any idea how this would be done?

 Thanks

 --
 Shane

 [[alternative HTML version deleted]]

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Re: [R] Is there an easier way than this to list all functions in the global environment?

2014-05-19 Thread Byron Dom


Thanks. Good suggestion. I completely forgot about the *apply() functions -- a 
symptom of my R-neophyte status. ;-) 





 From: Peter Alspach peter.alsp...@plantandfood.co.nz

ct.org 
Sent: Sunday, May 18, 2014 4:24 PM
Subject: RE: [R] Is there an easier way than this to list all functions in the  
global environment?


Tena koe Byron

Many years ago, I came across the following function by Simon Fear:

function (splitby = mode, pos = 1, ...)
{
    lsout - ls(pos = pos, ...)
    tapply(lsout, sapply(lsout, function(x) {
        splitby(get(x))
    }), invisible)
}

from which one can deduce that, given your obj, the following line could 
replace your loop:

obj[sapply(obj, function(x) mode(get(x))=='function')]

For future reference, it can be slow in R to  continually append to an object:

test - character(0)
system.time(for (i in 1:10^5) test - c(test, as.character(i)))
#   user  system elapsed
#  47.86    0.02   47.89
test - character(10^5)
system.time(for (i in 1:10^5) test[i] - as.character(i))
#   user  system elapsed
#   0.25    0.00    0.25

HTH 

Peter Alspach

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Byron Dom
Sent: Monday, 19 May 2014 10:50 a.m.
To: r-help@r-project.org
Subject: [R] Is there an easier way than this to list all functions in the 
global environment?



After an unsuccessful search thru several books plus online documentation, I 
was unable to find a simple way to do this, so I wrote my own function (see 
below) to do it.  I'm relatively new to R however, so I'm guessing that there 
must be an easier way to do it.

I want to list all functions and only the functions (not other objects also) in 
the global environment.

I'm working with several old R workspaces that contain a very large number of 
objects -- functions, data structures, etc. and I would to be able to easily 
find out which objects are functions.

The function below (listfunc()) works fine. I'm just asking this for future 
reference.

+++
listfunc - function() {
# lists names of all function objects in the global environment obj - 
objects(.GlobalEnv) funclist - character(length = 0) for (i in 1:length(obj)) {
    if (mode(get(obj[i])) == function) funclist - c(funclist,obj[i])
  }
return(funclist)
}
+++

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Re: [R] Is there an easier way than this to list all functions in the global environment?

2014-05-19 Thread Byron Dom


Thanks. That's the answer I was looking for. It not only lists the function 
names by also the arguments required. 

I wonder why I was unable to find that command in all the searching I did (?).

    - - Byron






To: r-help@r-project.org r-help@r-project.org 
Cc: Peter Alspach peter.alsp...@plantandfood.co.nz; Byron Dom 
byron_...@yahoo.com 
Sent: Sunday, May 18, 2014 7:01 PM
Subject: Re: [R] Is there an easier way than this to list all functions in the  
global environment?




Hi,

You may also check ?lsf.str()
c(lsf.str())
A.K.


On Sunday, May 18, 2014 7:27 PM, Peter Alspach 
peter.alsp...@plantandfood.co.nz wrote:
Tena koe Byron

Many years ago, I came across the following function by Simon Fear:

function (splitby = mode, pos = 1, ...) 
{
    lsout - ls(pos = pos, ...)
    tapply(lsout, sapply(lsout, function(x) {
        splitby(get(x))
    }), invisible)
}

from which one can deduce that, given your obj, the following line could 
replace your loop:

obj[sapply(obj, function(x) mode(get(x))=='function')]

For future reference, it can be slow in R to  continually append to an object:

test - character(0)
system.time(for (i in 1:10^5) test - c(test, as.character(i)))
#   user  system elapsed 
#  47.86    0.02   47.89 
test - character(10^5)
system.time(for (i in 1:10^5) test[i] - as.character(i))
#   user  system elapsed 
#   0.25    0.00    0.25

HTH 

Peter Alspach
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Byron Dom
Sent: Monday, 19 May 2014 10:50 a.m.
To: r-help@r-project.org
Subject: [R] Is there an easier way than this to list all functions in the 
global environment?



After an unsuccessful search thru several books plus online documentation, I 
was unable to find a simple way to do this, so I wrote my own function (see 
below) to do it.  I'm relatively new to R however, so I'm guessing that there 
must be an easier way to do it.

I want to list all functions and only the functions (not other objects also) in 
the global environment.

I'm working with several old R workspaces that contain a very large number of 
objects -- functions, data structures, etc. and I would to be able to easily 
find out which objects are functions.

The function below (listfunc()) works fine. I'm just asking this for future 
reference.

+++
listfunc - function() {
# lists names of all function objects in the global environment obj - 
objects(.GlobalEnv) funclist - character(length = 0) for (i in 1:length(obj)) {
    if (mode(get(obj[i])) == function) funclist - c(funclist,obj[i])
  }
return(funclist)
}
+++

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Re: [R] substring if value starts with a character

2014-05-19 Thread arun


Hi,
Try:
 dat - read.table(text=A
1  R5000
2  R4800
3  R4700
4  3500
5  3800,sep=,header=TRUE,stringsAsFactors=FALSE)
 dat$A - as.numeric(gsub([[:alpha:]]+,,dat$A))
A.K.



On Monday, May 19, 2014 9:02 AM, Mat matthias.we...@fnt.de wrote:
Hello togehter, 

i have a litte problem to convert a data.frame. My data.frame looks like
this one
      A
1  R5000
2  R4800
3  R4700
4  3500
5  3800

I need now a command, which outputs all the numbers, without the character
in front.
The solution look like this one:
    
     A
1  5000
2  4800
3  4700
4  3500
5  3800

Thanks.

Best regards. Mat



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Sent from the R help mailing list archive at Nabble.com.

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[R] solve scalar linear equation

2014-05-19 Thread message

Readers,

The function 'solve' states that it is applicable to a vector or matrix 
object.


Please what is the syntax to solve a very simple equation like:

5x + 1 = 56

The books read so far give explanations for simultaneous linear 
equations or differential equations, but there have not been able to 
find a very basic description to solve simple equations (as an initial 
learning stage). Thanks.


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Re: [R] converting a matrix to array

2014-05-19 Thread arun


Hi,


If you meant to convert the matrix to a 3D array, check this link:

http://stackoverflow.com/questions/9572656/how-to-convert-matrix-into-array

A.K.



On Monday, May 19, 2014 2:18 AM, Effat Habibi habibi...@gmail.com wrote:
Dear Sir/ Madam,

I have a problem with converting a matrix (247 rows, 16 columns) to an array in 
R.

Would you please help me in this regard.

Thank you,
E. Habibi
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[R] R save with encoding...

2014-05-19 Thread Alexsandro Cândido de Oliveira Silva
Hello everybody!!



I'm trying to plot a graphic with the title: INTERVALS λ.

But the special character λ can't be encoded using ISO8859-1.



Which another encoding I need to choose?



Att.

Alexsandro Cândido de Oliveira Silva

___





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Re: [R] Boxplots

2014-05-19 Thread Shane Carey
Great,

Thanks everyone :-)

On Monday, May 19, 2014, Richard M. Heiberger r...@temple.edu wrote:

 tmp - data.frame(y=c(rnorm(20), rnorm(20), c=rnorm(20)),
 g=rep(letters[1:3], each=20))

 library(lattice)
 library(latticeExtra)
 A - bwplot(y ~ g, data=tmp)
 B - bwplot(y ~ rep(Y,60), data=tmp, horizontal=FALSE)

 resizePanels(c(Individual=A, All Together=B, layout=c(2,1)), w=c(3,1))


 ## for even more options, you can look at the examples in
 ## the HH package
 ## install.packages(HH) ## if necessary
 library(HH)
 demo(bwplot.examples, package=HH)
 example(panel.bwplot.superpose, package=HH)
 ?panel.bwplot.intermediate.hh
 ?panel.bwplot.superpose

 On Mon, May 19, 2014 at 10:08 AM, Shane Carey 
 careys...@gmail.comjavascript:;
 wrote:
  Hi,
 
  I have boxplots by factors for a dataset and trying to include a boxplot
 to
  represent the entire dataset.
 
  Any idea how this would be done?
 
  Thanks
 
  --
  Shane
 
  [[alternative HTML version deleted]]
 
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  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.



-- 
Shane

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Re: [R] solve scalar linear equation

2014-05-19 Thread Rui Barradas

Hello,

Try ?uniroot instead.
Your equation is equivalent to 5x - 55 = 0, so the instruction would be

uniroot(function(x) 5*x - 55, c(0, 20))

Hope this helps,

Rui Barradas

Em 19-05-2014 14:46, message escreveu:

Readers,

The function 'solve' states that it is applicable to a vector or matrix
object.

Please what is the syntax to solve a very simple equation like:

5x + 1 = 56

The books read so far give explanations for simultaneous linear
equations or differential equations, but there have not been able to
find a very basic description to solve simple equations (as an initial
learning stage). Thanks.

__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


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[R] Subsets of a function

2014-05-19 Thread Marlin Keith Cox
Hi all, this is a reoccurring theme in my programming and I need some help
with it.  When I use a built in function and need to use it on a subset of
my data frame, I always end up using the subset function first, but this
seems very clunky.  For example, if I have years 2003:2013 with season a
and b within each year, and I want to create a smooth.spline, I end up
creating a subset for each year and season, and then have a smooth spline
function for each year and season.  Can I do this more efficiently?


The subsets are below:


size.2003-subset(size,Year==2003Season==a)

size.2004-subset(size,Year==2004Season==a)

size.2005-subset(size,Year==2005Season==a)

size.2006-subset(size,Year==2006Season==a)

size.2007-subset(size,Year==2007Season==a)

size.2008-subset(size,Year==2008Season==a)

size.2009-subset(size,Year==2009Season==a)

size.2010-subset(size,Year==2010Season==a)

size.2011-subset(size,Year==2011Season==a)

size.2012-subset(size,Year==2012Season==a)

size.2013-subset(size,Year==2013Season==a)

size.2003b-subset(size,Year==2003Season==b)

size.2004b-subset(size,Year==2004Season==b)

size.2005b-subset(size,Year==2005Season==b)

size.2006b-subset(size,Year==2006Season==b)

size.2007b-subset(size,Year==2007Season==b)

size.2008b-subset(size,Year==2008Season==b)

size.2009b-subset(size,Year==2009Season==b)

size.2010b-subset(size,Year==2010Season==b)

size.2011b-subset(size,Year==2011Season==b)

size.2012b-subset(size,Year==2012Season==b)

size.2013b-subset(size,Year==2013Season==b)

The smooth.spline is below

2003-with(size.2003,smooth.spline(Size,Prop,spar=0.25))

2004-with(size.2004,smooth.spline(Size,Prop,spar=0.25))
2005-with(size.2005,smooth.spline(Size,Prop,spar=0.25))
etc. etc.

M. Keith Cox, Ph.D.
Principal
MKConsulting
17105 Glacier Hwy
Juneau, AK 99801
U.S. 907.957.4606

[[alternative HTML version deleted]]

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Re: [R] Subsets of a function

2014-05-19 Thread Bert Gunter
Have you read An Introduction to R and sections on indexing (?[)
where this is discussed. Have you read about apply type functions
there like ?tapply.  If not, don't you think you should. If so, read
again.

Cheers,
Bert

Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
H. Gilbert Welch




On Mon, May 19, 2014 at 5:34 PM, Marlin Keith Cox marlink...@gmail.com wrote:
 Hi all, this is a reoccurring theme in my programming and I need some help
 with it.  When I use a built in function and need to use it on a subset of
 my data frame, I always end up using the subset function first, but this
 seems very clunky.  For example, if I have years 2003:2013 with season a
 and b within each year, and I want to create a smooth.spline, I end up
 creating a subset for each year and season, and then have a smooth spline
 function for each year and season.  Can I do this more efficiently?


 The subsets are below:


 size.2003-subset(size,Year==2003Season==a)

 size.2004-subset(size,Year==2004Season==a)

 size.2005-subset(size,Year==2005Season==a)

 size.2006-subset(size,Year==2006Season==a)

 size.2007-subset(size,Year==2007Season==a)

 size.2008-subset(size,Year==2008Season==a)

 size.2009-subset(size,Year==2009Season==a)

 size.2010-subset(size,Year==2010Season==a)

 size.2011-subset(size,Year==2011Season==a)

 size.2012-subset(size,Year==2012Season==a)

 size.2013-subset(size,Year==2013Season==a)

 size.2003b-subset(size,Year==2003Season==b)

 size.2004b-subset(size,Year==2004Season==b)

 size.2005b-subset(size,Year==2005Season==b)

 size.2006b-subset(size,Year==2006Season==b)

 size.2007b-subset(size,Year==2007Season==b)

 size.2008b-subset(size,Year==2008Season==b)

 size.2009b-subset(size,Year==2009Season==b)

 size.2010b-subset(size,Year==2010Season==b)

 size.2011b-subset(size,Year==2011Season==b)

 size.2012b-subset(size,Year==2012Season==b)

 size.2013b-subset(size,Year==2013Season==b)

 The smooth.spline is below

 2003-with(size.2003,smooth.spline(Size,Prop,spar=0.25))

 2004-with(size.2004,smooth.spline(Size,Prop,spar=0.25))
 2005-with(size.2005,smooth.spline(Size,Prop,spar=0.25))
 etc. etc.

 M. Keith Cox, Ph.D.
 Principal
 MKConsulting
 17105 Glacier Hwy
 Juneau, AK 99801
 U.S. 907.957.4606

 [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
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Re: [R] Subsets of a function

2014-05-19 Thread jim holtman
It would have been nice if you at least supplied a subset of the data, but
here is a try at it:

myList - split(size, list(size$Year, size$Season))
result - lapply(myList, function(.sub){
smooth.spline(.sub$Size, spar = 0.25)
})




Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.


On Mon, May 19, 2014 at 8:34 PM, Marlin Keith Cox marlink...@gmail.comwrote:

 Hi all, this is a reoccurring theme in my programming and I need some help
 with it.  When I use a built in function and need to use it on a subset of
 my data frame, I always end up using the subset function first, but this
 seems very clunky.  For example, if I have years 2003:2013 with season a
 and b within each year, and I want to create a smooth.spline, I end up
 creating a subset for each year and season, and then have a smooth spline
 function for each year and season.  Can I do this more efficiently?


 The subsets are below:


 size.2003-subset(size,Year==2003Season==a)

 size.2004-subset(size,Year==2004Season==a)

 size.2005-subset(size,Year==2005Season==a)

 size.2006-subset(size,Year==2006Season==a)

 size.2007-subset(size,Year==2007Season==a)

 size.2008-subset(size,Year==2008Season==a)

 size.2009-subset(size,Year==2009Season==a)

 size.2010-subset(size,Year==2010Season==a)

 size.2011-subset(size,Year==2011Season==a)

 size.2012-subset(size,Year==2012Season==a)

 size.2013-subset(size,Year==2013Season==a)

 size.2003b-subset(size,Year==2003Season==b)

 size.2004b-subset(size,Year==2004Season==b)

 size.2005b-subset(size,Year==2005Season==b)

 size.2006b-subset(size,Year==2006Season==b)

 size.2007b-subset(size,Year==2007Season==b)

 size.2008b-subset(size,Year==2008Season==b)

 size.2009b-subset(size,Year==2009Season==b)

 size.2010b-subset(size,Year==2010Season==b)

 size.2011b-subset(size,Year==2011Season==b)

 size.2012b-subset(size,Year==2012Season==b)

 size.2013b-subset(size,Year==2013Season==b)

 The smooth.spline is below

 2003-with(size.2003,smooth.spline(Size,Prop,spar=0.25))

 2004-with(size.2004,smooth.spline(Size,Prop,spar=0.25))
 2005-with(size.2005,smooth.spline(Size,Prop,spar=0.25))
 etc. etc.

 M. Keith Cox, Ph.D.
 Principal
 MKConsulting
 17105 Glacier Hwy
 Juneau, AK 99801
 U.S. 907.957.4606

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Re: [R] Boxplots

2014-05-19 Thread William Dunlap
Another method uses the core boxplot() function but replaces the usual
call to split() with a variant that puts all the data at the end of
the list of splits:

 splitPlusAll - function(x, ...) c(split(x, ...), list(All=x))
 boxplot(with(mtcars, splitPlusAll(wt, list(gear,am), drop=TRUE)))
 boxplot(with(mtcars, split(wt, list(gear,am), drop=TRUE)))

(It helps if you show what you have done when your question arose, as
there are several R functions for drawing boxplots.)

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Mon, May 19, 2014 at 2:41 PM, Shane Carey careys...@gmail.com wrote:
 Great,

 Thanks everyone :-)

 On Monday, May 19, 2014, Richard M. Heiberger r...@temple.edu wrote:

 tmp - data.frame(y=c(rnorm(20), rnorm(20), c=rnorm(20)),
 g=rep(letters[1:3], each=20))

 library(lattice)
 library(latticeExtra)
 A - bwplot(y ~ g, data=tmp)
 B - bwplot(y ~ rep(Y,60), data=tmp, horizontal=FALSE)

 resizePanels(c(Individual=A, All Together=B, layout=c(2,1)), w=c(3,1))


 ## for even more options, you can look at the examples in
 ## the HH package
 ## install.packages(HH) ## if necessary
 library(HH)
 demo(bwplot.examples, package=HH)
 example(panel.bwplot.superpose, package=HH)
 ?panel.bwplot.intermediate.hh
 ?panel.bwplot.superpose

 On Mon, May 19, 2014 at 10:08 AM, Shane Carey 
 careys...@gmail.comjavascript:;
 wrote:
  Hi,
 
  I have boxplots by factors for a dataset and trying to include a boxplot
 to
  represent the entire dataset.
 
  Any idea how this would be done?
 
  Thanks
 
  --
  Shane
 
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 --
 Shane

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[R] How could I graph a special coordinate

2014-05-19 Thread Klot Lee
hi,

I'v got some data attached as apx.csv.  It shows the relationship about a
kind of enzyme and the temperature.
yhf and xbt are 2 kind of cowpea. apx is the kind of enzyme and low
means the lowest temperature intraday. date means 1 to 121 days.

What I want to show with it is how is apx changes with low on 2 kind of
cowpeas. And date is better not missing in graph.
I have made one by ggplot2 using apx2.csv (reshaped by melt).

apx- read.csv(apx2.csv)
p- ggplot(apx, aes(x= dat, y=apx, colour= factor(var)))
p + geom_line()+facet_wrap(~var,ncol=1, scales= free_y)

The graph is NOT good enough. It is not easy to find the relationship
between apx and low. How could I do better? Is it possible to show
low data as graph background color changing with date? Thank you.

-- 
Stand Alone Complex
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Re: [R] R save with encoding...

2014-05-19 Thread Frede Aakmann Tøgersen
Hi

See ?plotmath.

Something like this:

plot(1, 1, main = expression(paste(INTERVALS , lambda)))



Yours sincerely / Med venlig hilsen


Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant Performance  Modeling

Technology  Service Solutions
T +45 9730 5135
M +45 2547 6050
fr...@vestas.com
http://www.vestas.com

Company reg. name: Vestas Wind Systems A/S
This e-mail is subject to our e-mail disclaimer statement.
Please refer to www.vestas.com/legal/notice
If you have received this e-mail in error please contact the sender. 


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of Alexsandro Cândido de Oliveira Silva
 Sent: 19. maj 2014 19:41
 To: r-help@r-project.org
 Subject: [R] R save with encoding...
 
 Hello everybody!!
 
 
 
 I'm trying to plot a graphic with the title: INTERVALS λ.
 
 But the special character λ can't be encoded using ISO8859-1.
 
 
 
 Which another encoding I need to choose?
 
 
 
 Att.
 
 Alexsandro Cândido de Oliveira Silva
 
 __
 _
 
 
 
 
 
 ---
 Este email está limpo de vírus e malwares porque a proteção do avast!
 Antivírus está ativa.
 http://www.avast.com
 
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Re: [R] How could I graph a special coordinate

2014-05-19 Thread Bert Gunter
Check out the R Graph Gallery for ideas.

http://rgraphgallery.blogspot.com/

Cheers,
Bert

Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
H. Gilbert Welch




On Mon, May 19, 2014 at 5:48 PM, Klot Lee fff200...@gmail.com wrote:
 hi,

 I'v got some data attached as apx.csv.  It shows the relationship about a
 kind of enzyme and the temperature.
 yhf and xbt are 2 kind of cowpea. apx is the kind of enzyme and low
 means the lowest temperature intraday. date means 1 to 121 days.

 What I want to show with it is how is apx changes with low on 2 kind of
 cowpeas. And date is better not missing in graph.
 I have made one by ggplot2 using apx2.csv (reshaped by melt).

 apx- read.csv(apx2.csv)
 p- ggplot(apx, aes(x= dat, y=apx, colour= factor(var)))
 p + geom_line()+facet_wrap(~var,ncol=1, scales= free_y)

 The graph is NOT good enough. It is not easy to find the relationship
 between apx and low. How could I do better? Is it possible to show
 low data as graph background color changing with date? Thank you.

 --
 Stand Alone Complex

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


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Re: [R-es] Utilizar scripts de PHP en R

2014-05-19 Thread Xavier de Pedro
Hola Álvaro:

Hace años había más programas que relacionaban php y r (en uno u otro
sentido), pero acabo de buscar en el CRAN Task View: Web Technologies
and Services, y parece que no hay ninguno que haga referencia explícita
a php allí:
http://cran.r-project.org/web/views/WebTechnologies.html

De todas formas, si lo que buscases pudiera ser también lo contrario,
como usar un script de R desde PHP, puedes echar una ojeada a como
está desarrollado el PluginR de Tiki (hay varios enlaces desde el CRAN
Task View citado anteriormente; Tiki está hecho con PHP y JQuery como
lenguages de programación, fundamentalmente).

Saludos

Xavier


On 18/05/14 17:34, Alvaro Franquet wrote:
 Hola a todos, Estoy interesado en usar un Script de PHP desde R y me
 gustaría saber si eso es posible y como se hace. Muchas gracias de antemano
 por las respuestas.

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Re: [R-es] Utilizar bs.data

2014-05-19 Thread Omar Salas Jácome
Buen día a todos. Tengo un problema.Podría ayudarme diciendóme cómo se llama la 
paquetería para encontrar el comando bs.data, lo he estado buscando para ver 
como escribir el comando en R y no me aparece una paquetería para ver la 
descripción. Saludos. 
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Re: [R-es] Utilizar bs.data

2014-05-19 Thread Carlos Ortega
Hola,

Prueba con esta búsqueda y sírvete tu mismo

http://www.rseek.org/?cx=010923144343702598753%3Aboaz1reyxd4q=bs.datasa=Search+functions%2C+lists%2C+and+morecof=FORID%3A11siteurl=rseek.org%2Fref=ss=888j162752j7

Saludos,
Carlos Ortega
www.qualityexcellence.es


El 19 de mayo de 2014, 12:57, Omar Salas Jácome
omar_salas...@hotmail.comescribió:

 Buen día a todos. Tengo un problema.Podría ayudarme diciendóme cómo se
 llama la paquetería para encontrar el comando bs.data, lo he estado
 buscando para ver como escribir el comando en R y no me aparece una
 paquetería para ver la descripción. Saludos.
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-- 
Saludos,
Carlos Ortega
www.qualityexcellence.es

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