[R] Read a .sas7bdat file

2007-03-18 Thread David Hajage
Hello useRs,

I would like to import a data frame in a sas format (.sas7bdat).

I have installed foreign library, and tryed to use read.ssd function :

 read.ssd(these, fus9706.sas7bdat)
sh: sas: not found
SAS failed.  SAS program at /tmp/RtmpPdVSST/file2ae8944a.sas
a log and other error products should be in the vicinity
ls: file2ae8944a.log: Aucun fichier ou répertoire de ce type
NULL
Warning message:
Le code renvoyé par SAS est 32512 in: read.ssd(these, fus9706.sas7bdat)

Is it possible to read this file with R ?

Thank you for your help.

David

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Re: [R] Read a .sas7bdat file

2007-03-18 Thread David Hajage
Thank you for your answer.

The big problems are :
 - I don't have SAS
 - I work on a linux system

But, I've just found a solution :
 - I have downloaded SAS viewer (free) :
http://www.sas.com/apps/demosdownloads/sassysview_PROD_8.2_sysdep.jsp?packageID=000176
 - I have installed it with Wine.
 - Then, I can read my sas file and export it into a common format (csv...)

This program works perfectly with Wine.

Thank you very much.

2007/3/18, Peter Dalgaard [EMAIL PROTECTED]:

 David Hajage wrote:
  Hello useRs,
 
  I would like to import a data frame in a sas format (.sas7bdat).
 
  I have installed foreign library, and tryed to use read.ssd function
 :
 
 
  read.ssd(these, fus9706.sas7bdat)
 
  sh: sas: not found
  SAS failed.  SAS program at /tmp/RtmpPdVSST/file2ae8944a.sas
  a log and other error products should be in the vicinity
  ls: file2ae8944a.log: Aucun fichier ou répertoire de ce type
  NULL
  Warning message:
  Le code renvoyé par SAS est 32512 in: read.ssd(these, 
 fus9706.sas7bdat)
 
  Is it possible to read this file with R ?
 
 
 Not until SAS or someone else comes up with a description of the file
 format. Till then, you need SAS itself or one of a couple of
 special-purpose closed-source conversion tools (Stat/Transfer, DBMS/Copy).
  Thank you for your help.
 
  David
 
 




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[R] Install bioconductor

2006-11-11 Thread David Hajage

Hello useRs,

I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0.

I have some error messages during installation, in particular for the
package affy :

Error: package 'affy' required by 'makecdfenv' could not be found

I have tryed to install 'makecdfenv' with the command :

getBioC(makecdfenv)

But I have this message :

Running getBioC version 0.1.8 with R version 2.4.0
Running biocinstall version 1.9.9 with R version 2.4.0
Your version of R requires version 1.9 of Bioconductor.
Avis dans install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
argument 'lib' is missing: using /usr/local/lib/R/site-library
also installing the dependencies 'affy', 'affyio'

essai de l'URL '
http://bioconductor.org/packages/1.9/bioc/src/contrib/affy_1.12.1.tar.gz'
Content type 'application/x-gzip' length 1370295 bytes
URL ouverte
==
downloaded 1338Kb

essai de l'URL '
http://bioconductor.org/packages/1.9/bioc/src/contrib/affyio_1.2.0.tar.gz'
Content type 'application/x-gzip' length 57410 bytes
URL ouverte
==
downloaded 56Kb

essai de l'URL '
http://bioconductor.org/packages/1.9/bioc/src/contrib/makecdfenv_1.12.0.tar.gz
'
Content type 'application/x-gzip' length 3222836 bytes
URL ouverte
==
downloaded 3147Kb

* Installing *source* package 'affyio' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/usr/share/R/include -I/usr/share/R/include  -fpic  -g -O2
-std=gnu99 -c read_abatch.c -o read_abatch.o
read_abatch.c:151:18: error: zlib.h: Aucun fichier ou répertoire de ce type
read_abatch.c:1244: error: expected declaration specifiers or '...' before
'gzFile'
read_abatch.c: In function 'ReadgzFileLine':
read_abatch.c:1245: warning: implicit declaration of function 'gzgets'
read_abatch.c:1245: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1245: error: (Each undeclared identifier is reported only once
read_abatch.c:1245: error: for each function it appears in.)
read_abatch.c:1245: warning: comparison between pointer and integer
read_abatch.c: At top level:
read_abatch.c:1265: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'open_gz_cel_file'
read_abatch.c:1306: error: expected ')' before 'my_file'
read_abatch.c:1329: error: expected ')' before 'my_file'
read_abatch.c: In function 'check_gzcel_file':
read_abatch.c:1360: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1360: error: expected ';' before 'currentFile'
read_abatch.c:1364: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1364: warning: implicit declaration of function
'open_gz_cel_file'
read_abatch.c:1367: warning: implicit declaration of function
'gzAdvanceToSection'
read_abatch.c:1368: warning: implicit declaration of function
'gzfindStartsWith'
read_abatch.c:1393: warning: implicit declaration of function 'gzclose'
read_abatch.c: In function 'read_gzcel_file_intensities':
read_abatch.c:1421: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1421: error: expected ';' before 'currentFile'
read_abatch.c:1426: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1432: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'read_gzcel_file_stddev':
read_abatch.c:1495: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1495: error: expected ';' before 'currentFile'
read_abatch.c:1500: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1506: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'read_gzcel_file_npixels':
read_abatch.c:1579: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1579: error: expected ';' before 'currentFile'
read_abatch.c:1584: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1590: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'gz_apply_masks':
read_abatch.c:1669: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1669: error: expected ';' before 'currentFile'
read_abatch.c:1678: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1691: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c:1715: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'gz_get_header_info':
read_abatch.c:1749: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1749: error: expected ';' before 'currentFile'
read_abatch.c:1753: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c: In function 'gz_get_detailed_header_info':
read_abatch.c:1807: error: 'gzFile' undeclared (first use in this function)

Re: [R] Barplot legend position

2006-10-13 Thread David Hajage
For example :

x=matrix(1:10,2,5)
barplot(x,besid=T)
legend(topleft, c(left,right), density= c(0,1000))


2006/10/13, Ingmar Visser [EMAIL PROTECTED]:

 Dear useRs,

 I'm trying to create a barplot like so:

 x=matrix(1:10,2,5)
 barplot(x,leg=c(left,right),besid=T)

 The legend is placed in default position topright, however the data are
 plotted there too. I tried controlling the legend position by adding
 x=topleft but this results in an error that x matches multiple formal
 arguments.

 Leaving out the legend and making a separate call to legend leaves out the
 colors of bars ...

 Please advice, Ingmar

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-- 
David

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[R] install R on Sun Blade 2000

2006-09-13 Thread David Hajage
Hello useRs,

I would like to install R 2.3.1 on a computer : Sun Blade 2000.

Is there a precompiled version of R for this computer ?

Thank you very much.
-- 
David

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Re: [R] Output and Word

2006-07-19 Thread David Hajage
thank you Greg Snow for this information !

But I have this message :

 odfWeave(c:/simple.odt, c:/essai.odt)
  Setting wd
  Copying  c:/simple.odt
  Decompressing ODF file using unzip -o
C:\DOCUME~1\Maud\LOCALS~1\Temp\RtmpF0hdqb/simple.odt
Erreur dans odfWeave(c:/simple.odt, c:/essai.odt) :
Error unzipping file
De plus : Warning message:
unzip introuvable

R says that it doesn't find unzip... What is this program ?

2006/7/18, Greg Snow [EMAIL PROTECTED]:

 Others have suggested using R2HTML (which is a good option).

 Another option is to use Sweave and specifically the new odfWeave
 package for R.  This works on OpenOffice files rather than word files
 (but OpenOffice  http://www.openoffice.org/ can inport and export word
 documents).

 The basic idea is to write your report in OpenOffice (or LaTeX or HTML),
 but anywhere that you want statisticial output (graphs, tables) you
 include instead the R code to produce the table, graph, or whatever.
 Run this file through R (using Sweave or odfWeave) and the resulting
 file has replaced all the code segments with their output.

 The documentation with odfWeave has examples.

 Hope this helps,

 --
 Gregory (Greg) L. Snow Ph.D.
 Statistical Data Center
 Intermountain Healthcare
 [EMAIL PROTECTED]
 (801) 408-8111


 -Original Message-
 From: [EMAIL PROTECTED]
 [mailto:[EMAIL PROTECTED] On Behalf Of sharon snowdon
 Sent: Monday, July 17, 2006 2:36 PM
 To: r-help@stat.math.ethz.ch
 Subject: [R] Output and Word

 Hi

 I have just started to have a look at R. I have used most stats software
 packages and can use perl, visual basic etc. I am interested in how well
 it handles lots of output e.g. tables or charts. How would you get lots
 of output most easily and quickly into a Word document?

 Sharon Snowdon



 
 -






 --





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-- 
David

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[R] Name of a column

2006-06-15 Thread David Hajage
Hello,

My problem is quite simply, but I didn't find any solution...

I have a vector :

 truc
   longueur30 longueur40 longueur50 longueur60 longueur70 longueur80
longueur90
34  FALSE  FALSE  FALSE  FALSE   TRUE  FALSE
FALSE

I would like to have the name of the column where there is TRUE.

 colnames(truc)
[1] longueur30 longueur40 longueur50 longueur60 longueur70
[6] longueur80 longueur90

 truc[truc == T]
[1] TRUE

 colnames(truc[truc == T])
NULL

How can I do it ?

Thank you for your help.

-- 
David

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[R] problem with write.table

2006-06-13 Thread David Hajage
Hello,

I have a data frame :

 linkptpn[1:6,]
   pedigree id fa mo sex status rs3789604 rs3811021 rs1217413 ss38346942
1 1  1  0  0   1  2
2 1  2  0  0   2  2
3 1  3  1  2   2  3   3/3   2/2   3/34/4
4 1  4  1  2   2  3   3/3   2/4   3/32/2
5 2  1  0  0   1  2
6 2  2  0  0   2  3

I would like to use write.table :

 write.table(linkptpn, /home/biostat/david/genetique/linkptpn.csv)
Erreur dans write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec,
as.integer(quote),  :
type 'list' indisponible dans 'EncodeElement'

R says that my variables are 'list'. Indeed :

 apply(linkptpn, 2, class)
  pedigree id fa mosex status  rs3789604

list list list list list list list

 rs3811021  rs1217413 ss38346942  rs1217388 ss38346943  rs1310182 ss38346944

list list list

I would like to transform everything into a pure data.frame. I tried :

 apply(linkptpn, 2, unlist)
or
 apply(linkptpn, 2, as.data.frame)
or
linkptpn2 - data.frame(unlist(linkptpn$pedigree), unlist(linkptpn$id),
unlist(linkptpn$fa), unlist(linkptpn$mo), unlist(linkptpn$sex),
unlist(linkptpn$status), unlist(linkptpn$rs3789604),
unlist(linkptpn$rs3811021),unlist( linkptpn$rs1217413),
unlist(linkptpn$ss38346942))

But it doesn't work. The first and the second solution gives me another
list, and the third doesn't work because of missing data.

Do you have any idea to do this ?
-- 
David

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[R] reverse variables

2006-06-09 Thread David Hajage
Hello useRs,

Is there a way to reverse values of 2 variables (like with the language
Python) ? :

a - 1
b - 2

a, b - b, a

More specifically, I have a data frame :

   famnum generation germain1 germain2  fa  mo ptpn1 ptpn2 drb11 drb12
   1  2  200  201 101 102 1 1 1 1
   2  2  200  201 101 102 0 1 1 1
   3  2  200  201 101 102 1 0 1 1
...

I don't want 0 in the seventh column, so I would like to have :

   famnum generation germain1 germain2  fa  mo ptpn1 ptpn2 drb11 drb12
   1  2  200  201 101 102 1 1 1 1
   2  2  201  200 101 102 1 0 1 1
   3  2  200  201 101 102 1 0 1 1
...

I thought that a code like this would work :

if (ptpn1 == 0  ptpn2 == 1)
  {
germain1, germain2 - germain2, germain1
ptpn1, ptpn2 - ptpn2, ptpn1
drb11, drb12 - drb12n, drb11
  }

But R is not Python... Is there a way to do it easyly ?

Thank you.
-- 
David

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[R] Problem with Sweave

2006-06-05 Thread David Hajage
I was trying to use Sweave function.

Do you know why the following code in my .Rnw file:

results=tex, echo=FALSE=
print(xtable(stat.table(list(Couverture du livret = couv),  list(n =
count(), \\% = percent(couv, floating = F)
@
\\

NA = \Sexpr{table(is.na(couv))[2]}

gives me this result in my .tex file :

% latex table generated in R 2.3.1 by xtable 1.3-2 package
% Mon Jun  5 13:24:15 2006
\begin{tabular}{rrr}
\hline
  n  \% \\
\hline
Plutot negatif  8.00  21.62 \\
Plutot positif  29.00  78.38 \\
\hline
\end{tabular}\\

NA = \Sexpr{table( is.na(couv))[2]}

and not :

NA = 26

(where 26 is the result of table(is.na(couv))[2])

?

I don't understand !

-- 
David

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[R] Load a program from internet

2006-05-29 Thread David Hajage
Hello,

I know how to load a program from my computer with the command source.

example :
source(home/david/prog.r)

But is it possible to load a program from the internet ?

example :
source(http://davidblog/prog.r;)

-- 
David

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Re: [R] Load a program from internet

2006-05-29 Thread David Hajage
ok...

I've juste understood that my computer (at work) doesn't let R access to
internet... That's why I was wondering if it works !

I've made a function which adds exposed to risk on your survival curve...
If you want to try :

source(http://pepereblog.free.fr/blog/share/tigeR%202.0.r;)

tigeR.graph(aml$time, aml$status, aml$x, tps = seq(0,72, 24), IC = 24,
decalIC = 0.5, legend = names(table(aml$x)), main = Survival)

tigeR.results(aml$time, aml$status, aml$x, latex = F)

It's in french, but you can modify it if you want...

Thank you all for your answers, and sorry for my english.

2006/5/29, David Hajage [EMAIL PROTECTED]:

 and sorry for my english !...

 2006/5/29, David Hajage [EMAIL PROTECTED]:

   thank you.
 
  Same result... It doesn't work ! But i will try at home... I'm sure il
  will work !
 
  Or you can try : I've made a function which adds exposed to risk on
  your survival curve...
 
  source(http://pepereblog.free.fr/blog/share/tigeR%202.0.r )
 
  tigeR.graph(aml$time, aml$status, aml$x, tps = seq(0,72, 24), IC = 24,
  decalIC = 0.5, legend = names(table(aml$x)), main = Survival)
 
   tigeR.results(aml$time, aml$status, aml$x, latex = F)
 
  It's in french, but you can modify it if you want...
 
  Thank for your response.
  2006/5/29, Christian Ritz [EMAIL PROTECTED]:
 
   Hi David,
  
   try:
  
  
   source(url( http://davidblog/prog.r ))
  
  
   Christian
  
 
 
 
  --
 
  David
 



 --

 David




-- 
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[R] median of a survfit object

2006-05-24 Thread David Hajage
 Hello R users !

Here a survfit object :

library(survival)

essai - aml[aml$x == Maintained,]

calc - survfit(Surv(essai$time, 1 - essai$status))

calc

Call: survfit(formula = Surv(essai$time, 1 - essai$status))

  n  events  median 0.95LCL 0.95UCL
 11   4 103  28 Inf
I would like to get the median of the object calc...
For example,

med - calc$median

But it doesn't work... How can I do this ?

-- 
David


-- 
David

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Re: [R] median of a survfit object

2006-05-24 Thread David Hajage
It works ! thank you !

2006/5/24, Heinz Tuechler [EMAIL PROTECTED]:

 see: [R] How to access results of survival analysis Xiaochun Li (06 May
 2006)

 At 15:03 24.05.2006 +0200, David Hajage wrote:
  Hello R users !
 
 Here a survfit object :
 
 library(survival)
 
 essai - aml[aml$x == Maintained,]
 
 calc - survfit(Surv(essai$time, 1 - essai$status))
 
 calc
 
 Call: survfit(formula = Surv(essai$time, 1 - essai$status))
 
   n  events  median 0.95LCL 0.95UCL
  11   4 103  28 Inf
 I would like to get the median of the object calc...
 For example,
 
 med - calc$median
 
 But it doesn't work... How can I do this ?
 
 --
 David
 
 
 --
 David
 
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-- 
David

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[R] mc nemar test

2006-05-17 Thread David Hajage
Hello R users,

I would like to perform a mc nemar test.
There is my data :
__
x - matrix(4:1,2,2)

x

 [,1] [,2]
[1,]42
[2,]31
__

My population is too small for normal approximation.
__
library(concord)

mcnemar.mh(x)

$statistic
[1] 0.2

$p
[1] 0.6547208

Warning message:
low cell counts - consider binomial test in: mcnemar.mh(x)

___

Do you have an advice to perform this test ? Is there a non-parametric one ?
Thank you very much.

-- 
David

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[R] Create pdf and postscript files

2005-12-27 Thread David Hajage
Hello,



I would like to learn how to create a pdf and a postscript file from an R
graphic.

For example, I tried :



plot(1)  # example

pdf(H:/Perso/essai.pdf)

postscript(H:/Perso/essai.ps)



But the pdf document created is empty.



How do these functions work ?



Thank you very much.

--
David Hajage
Interne de santé publique
Institut Curie

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Re: [R] Create pdf and postscript files

2005-12-27 Thread David Hajage
... I'm so stupid !

Thank you very much.

David Hajage
Interne de santé publique
Institut Curie

2005/12/27, Ronnie Babigumira [EMAIL PROTECTED]:

 You need to open the pdf/poscript first and then plot...see ?postscript

  # open the file foo.ps for graphics output
  postscript(foo.ps)
  # produce the desired graph(s)
  dev.off()  # turn off the postscript device




 David Hajage wrote:
  Hello,
 
 
 
  I would like to learn how to create a pdf and a postscript file from an
 R
  graphic.
 
  For example, I tried :
 
 
 
  plot(1)  # example
 
  pdf(H:/Perso/essai.pdf)
 
  postscript(H:/Perso/essai.ps)
 
 
 
  But the pdf document created is empty.
 
 
 
  How do these functions work ?
 
 
 
  Thank you very much.
 
  --
  David Hajage
  Interne de santé publique
  Institut Curie
 
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David

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Re: [R] how to change a dataframe with characters to a numeric matrix?

2005-12-08 Thread David Hajage
A way to do it :

TEST$Y3[TEST$Y3==Z] - NA

TEST$Y3 - as.numeric(TEST$Y3)


2005/12/8, zhihua li [EMAIL PROTECTED]:

 hi netters,

 i have a dataframe TEST like this:

   Y1 Y2 Y3
 X1  4  7  8
 X2  6  2  Z
 X3  8  0  1

 i would like to change it to a numeric matrix, replacing Z with NA

   Y1 Y2 Y3
 X1  4  7  8
 X2  6  2  NA
 X3  8  0  1

 i've tried the function data.matrix but it didn't work. is there any easy
 way to do this?

 thanks a lot!



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Re: [R] how to change a dataframe with characters to a numeric matrix?

2005-12-08 Thread David Hajage
and then, if you want a matrix and not a data.frame :

TEST - as.matrix(TEST)


2005/12/8, David Hajage [EMAIL PROTECTED]:

 A way to do it :

 TEST$Y3[TEST$Y3==Z] - NA

 TEST$Y3 - as.numeric(TEST$Y3)


 2005/12/8, zhihua li [EMAIL PROTECTED]:
 
  hi netters,
 
  i have a dataframe TEST like this:
 
Y1 Y2 Y3
  X1  4  7  8
  X2  6  2  Z
  X3  8  0  1
 
  i would like to change it to a numeric matrix, replacing Z with NA
 
Y1 Y2 Y3
  X1  4  7  8
  X2  6  2  NA
  X3  8  0  1
 
  i've tried the function data.matrix but it didn't work. is there any
  easy
  way to do this?
 
  thanks a lot!
 
 
 
  __
  R-help@stat.math.ethz.ch mailing list
  https://stat.ethz.ch/mailman/listinfo/r-help
  PLEASE do read the posting guide!
  http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
 
 


 --
 David




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Re: [R] R newbie...

2005-12-07 Thread David Hajage
Thank you for all your answers...

I solved my problem thanks to you all !

david


2005/12/6, paul sorenson [EMAIL PROTECTED]:

 Return something that can hold more than one value, eg:

 calculate - function(x, y) {
list(a=x+y, b=x-y)
 }

 David Hajage wrote:
  Thank you for your answer.
 
  And what if my first function gives 2 results :
 
  calculate - function(x,y)
  {
  a - x + y
   b - x - y
  }
 
  How can I use both a and b in a new function ?




--
David

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[R] R newbie...

2005-12-06 Thread David Hajage
Hello,

I'm a new user...

I have a function :

calculate - function(x,y)
  {
 z - x + y
  }
I would like to use the result (z) with another function :

recalculate - function(...)
  {
 a - z^2
  }

But R says that z does not exist...

How can I use z in an another function ?

Thank you for your answer...

--
David

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Re: [R] R newbie...

2005-12-06 Thread David Hajage
Thank you for your answer.

And what if my first function gives 2 results :

calculate - function(x,y)
{
a - x + y
 b - x - y
}

How can I use both a and b in a new function ?




2005/12/6, Sarah Goslee [EMAIL PROTECTED]:

 First of all, you might try reading the manual.

 Second, you might try something like this:

 calculate - function(x,y)
 {
 z - x + y z
 }

 recalculate(z)
 {
a - z^2
a
 }

 z - calculate(x, y)
 recalculate(z)

 You need to return some value from your functions,
 and you need to assign that value to a variable.

 Sarah


 --
 Sarah Goslee
 http://www.stringpage.com




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