date:20091122


On 22/11/2009 1:07 AM, Marc Chiarini (Tufts) wrote:

Dear R Community:

Recently, I have managed to plot some really useful graphs of my 
research data using persp().  I have even figured out how to overplot 
rectangular regions (corresponding to submatrices) with a different 
color.  This is accomplished by using par(new=T).  I am now searching 
for a way to highlight a set of (possibly non-contiguous) facets with 
a specific color, e.g., the facet between each set of four points whose 
values are all above a certain threshold.  An example would be coloring 
the raised corners of the classic sombrero (found in example(persp)) 
differently from the rest of the sombrero.  I feel like the last example 
in persp() is pointing me in the right direction, but I'm not quite 
getting it.  Any help is much appreciated.


Think of the facets as an nx-1 by ny-1 matrix.  Pass the col arg by 
creating a matrix of this shape.  (A vector version of the data in the 
matrix would also be good enough.)


If you pass something shorter, it will be recycled to that length.

You could also use persp3d from the rgl package, but an important 
difference is that it colours all nx by ny vertices, and interpolates 
colours on the facets.  So you can't use the same colour matrix as in persp.


Duncan Murdoch

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] other decriptive stats packages

Here is one more function for the list:
whatis
from the package:
YaleToolkit
See:
http://cran.r-project.org/web/packages/YaleToolkit/



I also like using:
ls()
ls.str()
And sometimes (for just one variable):
stem (which can be viewd as an ascii histogram)


Wonderful question and list, I hope for more answers.


Tal

Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com/ (English)
--




On Sun, Nov 22, 2009 at 12:01 AM, frenchcr frenc...@btinternet.com wrote:


 i just found the following list, i wondered if anybody could add to this as
 i
 have to characterize a large data set and am new to R...the list below was
 so helpfulcan you add to this???

 Just to forestall confusion amongst those who would like to use one of
 the functions called describe...

 Hmisc package - describe
 numeric
  name
  count of observations
  count of missing values
  count of unique values
  mean
  seven quantiles
  five lowest and highest values
 discrete (factor or numeric with = 10 unique values) -
  as for numeric, but
  no mean, quantiles or low/high values and
  including a frequency/percent display for each value.

 psych package - describe
  item name
  item number
  number of valid cases
  mean
  standard deviation
  median
  mad: median absolute deviation (from the median)
  minimum
  maximum
  skew (optional)
  kurtosis (optional)
  standard error

 prettyR package - describe
 numeric
  name
  mean
  median
  var
  sd
  valid.n
 the above are the defaults - the user can specify the name(s) of any
 function(s) as an argument to the function to customize the display.
 factor
  name
  count for each value
  percent for each value
  modal value
  count of missing values
 logical
  name
  count of FALSE
  count of TRUE
  percent of TRUE
  count of missing values



 are there any more packages that help decribe and explore data sets
 
 --
 View this message in context:
 http://old.nabble.com/other-decriptive-stats-packages-tp26460757p26460757.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 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.


[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] other decriptive stats packages

A few more came to mind:

VIM package (for exploring missing data):
http://cran.r-project.org/web/packages/VIM/index.html
http://bm2.genes.nig.ac.jp/RGM2/index.php?scope=namequery=VIM

And the basic commands:
* edit (for seeing the dataframe as in a spreadsheet)
And the commands:
* head   (and)   tail


Tal




Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com/ (English)
--




On Sun, Nov 22, 2009 at 3:15 PM, Tal Galili tal.gal...@gmail.com wrote:

 Here is one more function for the list:
 whatis
 from the package:
 YaleToolkit
 See:
 http://cran.r-project.org/web/packages/YaleToolkit/



 I also like using:
 ls()
 ls.str()
 And sometimes (for just one variable):
 stem (which can be viewd as an ascii histogram)


 Wonderful question and list, I hope for more answers.


 Tal

 Contact
 Details:---
 Contact me: tal.gal...@gmail.com |  972-52-7275845
 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
 www.r-statistics.com/ (English)

 --





 On Sun, Nov 22, 2009 at 12:01 AM, frenchcr frenc...@btinternet.comwrote:


 i just found the following list, i wondered if anybody could add to this
 as i
 have to characterize a large data set and am new to R...the list below was
 so helpfulcan you add to this???

 Just to forestall confusion amongst those who would like to use one of
 the functions called describe...

 Hmisc package - describe
 numeric
  name
  count of observations
  count of missing values
  count of unique values
  mean
  seven quantiles
  five lowest and highest values
 discrete (factor or numeric with = 10 unique values) -
  as for numeric, but
  no mean, quantiles or low/high values and
  including a frequency/percent display for each value.

 psych package - describe
  item name
  item number
  number of valid cases
  mean
  standard deviation
  median
  mad: median absolute deviation (from the median)
  minimum
  maximum
  skew (optional)
  kurtosis (optional)
  standard error

 prettyR package - describe
 numeric
  name
  mean
  median
  var
  sd
  valid.n
 the above are the defaults - the user can specify the name(s) of any
 function(s) as an argument to the function to customize the display.
 factor
  name
  count for each value
  percent for each value
  modal value
  count of missing values
 logical
  name
  count of FALSE
  count of TRUE
  percent of TRUE
  count of missing values



 are there any more packages that help decribe and explore data sets
 
 --
 View this message in context:
 http://old.nabble.com/other-decriptive-stats-packages-tp26460757p26460757.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 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.




[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Define return values of a function



On Nov 22, 2009, at 6:26 AM, soeren.vo...@eawag.ch wrote:


I have created a function to do something:

i - factor(sample(c(A, B, C, NA), 793, rep=T, prob=c(8, 7, 5,  
1)))
k - factor(sample(c(X, Y, Z, NA), 793, rep=T, prob=c(12, 7,  
9, 1)))

mytable - function(x){
 xtb - x
 btx - x
 # do more with x, not relevant here
 cat(The table has been created, see here:\n)
 print(xtb)
 list(table=xtb, elbat=btx)
}
tbl - table(i, k)
mytable(tbl) # (1)
z - mytable(tbl) # (2)
str(z) # (3)

(1) Wanted: outputs the string and the table properly. *Unwanted*:  
outputs the list elements.




Whet the author of a function wants a particular object that exists  
insode a function to be returned they may warp it in the function  
return(). Otherwise R returns the result of the last evaluation which  
in this case was list(table=xtb, elbat=btx).


If you want the function to return something else. then you could   
put something else last in the sequence. If you want it to return  
nothing than put this at the end:


return()

If you want the results to not be printed the use invisible()

Perhaps:
 invisible(list( elbat=btx))   #substituted for list(table=xtb,  
elbat=btx) after the print line


 tbl - table(i, k)
 mytable(tbl) # (1)
The table has been created, see here:
   k
i X   Y   Z
  A 119  69  89
  B 116  70  97
  C  80  36  52
 z - mytable(tbl) # (2)
The table has been created, see here:
   k
i X   Y   Z
  A 119  69  89
  B 116  70  97
  C  80  36  52
 str(z) # (3)
List of 1
 $ elbat: 'table' int [1:3, 1:3] 119 116 80 69 70 36 89 97 52
  ..- attr(*, dimnames)=List of 2
  .. ..$ i: chr [1:3] A B C
  .. ..$ k: chr [1:3] X Y Z



(2) and (3) Wanted: outputs the string properly. Wanted: assigns the  
list properly.


If you want to return the list, elbat, then just put the name of the  
list last in your case inside invisible or put it inside return().





How can I get rid of the *unwanted* part? That is, how do I define  
what the functions prints


That set by cat and print in your case.


and -- on the other hand -- what it returns without printing?


By return()  or the order of evaluation




--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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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.

Re: [R] other decriptive stats packages

2009-11-22 Thread Liviu Andronic

On 11/21/09, frenchcr frenc...@btinternet.com wrote:
  are there any more packages that help decribe and explore data sets 

See numSummary() in Rcmdr.
Liviu

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Over-coloring facets on persp() plot



On Nov 22, 2009, at 7:07 AM, Duncan Murdoch wrote:


On 22/11/2009 1:07 AM, Marc Chiarini (Tufts) wrote:

Dear R Community:
Recently, I have managed to plot some really useful graphs of my  
research data using persp().  I have even figured out how to  
overplot rectangular regions (corresponding to submatrices) with a  
different color.  This is accomplished by using par(new=T).  I am  
now searching for a way to highlight a set of (possibly non- 
contiguous) facets with a specific color, e.g., the facet between  
each set of four points whose values are all above a certain  
threshold.  An example would be coloring the raised corners of the  
classic sombrero (found in example(persp)) differently from the  
rest of the sombrero.  I feel like the last example in persp() is  
pointing me in the right direction, but I'm not quite getting it.   
Any help is much appreciated.


Think of the facets as an nx-1 by ny-1 matrix.  Pass the col arg by  
creating a matrix of this shape.  (A vector version of the data in  
the matrix would also be good enough.)


I came close to coloring the top facet, but did not quite get there  
with:


x - seq(-10, 10, length= 30)
y - x
f - function(x,y) { r - sqrt(x^2+y^2); 10 * sin(r)/r }
z - outer(x, y, f)
z[is.na(z)] - 1
op - par(bg = white)

 zcol - as.vector( z[-1,-1] == max(z) )  # Need to exclude two  
sides, I think


persp(x, y, z, theta = 30, phi = 30, expand = 0.5, col = ifelse(zcol ,  
red, lightblue),

  ltheta = 120, shade = 0.75, ticktype = detailed,
  xlab = X, ylab = Y, zlab = Sinc( r )
 )
par(op)

I did not get precisely the top facet in part, because there are 4 z  
elements at the max.


--
David.




If you pass something shorter, it will be recycled to that length.

You could also use persp3d from the rgl package, but an important  
difference is that it colours all nx by ny vertices, and  
interpolates colours on the facets.  So you can't use the same  
colour matrix as in persp.


Duncan Murdoch

__
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.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
R-help@r-project.org mailing list
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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.

Re: [R] Over-coloring facets on persp() plot



On Nov 22, 2009, at 9:18 AM, David Winsemius wrote:



On Nov 22, 2009, at 7:07 AM, Duncan Murdoch wrote:


On 22/11/2009 1:07 AM, Marc Chiarini (Tufts) wrote:

Dear R Community:
Recently, I have managed to plot some really useful graphs of my  
research data using persp().  I have even figured out how to  
overplot rectangular regions (corresponding to submatrices) with a  
different color.  This is accomplished by using par(new=T).  I am  
now searching for a way to highlight a set of (possibly non- 
contiguous) facets with a specific color, e.g., the facet between  
each set of four points whose values are all above a certain  
threshold.  An example would be coloring the raised corners of the  
classic sombrero (found in example(persp)) differently from the  
rest of the sombrero.  I feel like the last example in persp() is  
pointing me in the right direction, but I'm not quite getting it.   
Any help is much appreciated.


Think of the facets as an nx-1 by ny-1 matrix.  Pass the col arg by  
creating a matrix of this shape.  (A vector version of the data in  
the matrix would also be good enough.)


I came close to coloring the top facet, but did not quite get  
there with:


x - seq(-10, 10, length= 30)
y - x
f - function(x,y) { r - sqrt(x^2+y^2); 10 * sin(r)/r }
z - outer(x, y, f)
z[is.na(z)] - 1
op - par(bg = white)

zcol - as.vector( z[-1,-1] == max(z) )  # Need to exclude two side  
edges, I think


persp(x, y, z, theta = 30, phi = 30, expand = 0.5, col =  
ifelse(zcol , red, lightblue),

 ltheta = 120, shade = 0.75, ticktype = detailed,
 xlab = X, ylab = Y, zlab = Sinc( r )
)
par(op)

I did not get precisely the top facet in part, because there are 4 z  
elements at the max.


Specifying row and column == 15 for z[-1,-1] does color just the top  
facet. Conditional level coloring can be achieved as above with  
suitable limits on the z values:


zcol - as.vector( z[-1,-1] 1  z[-1,-1] 3 )




--
David.




If you pass something shorter, it will be recycled to that length.

You could also use persp3d from the rgl package, but an important  
difference is that it colours all nx by ny vertices, and  
interpolates colours on the facets.  So you can't use the same  
colour matrix as in persp.


Duncan Murdoch

__
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.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
R-help@r-project.org mailing list
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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.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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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.

[R] How to make a matrix of a number of factors?

I use the following code to generate a matrix of factors. I'm
wondering if there is a way to make it more general so that I can have
any number of factors (not necessarily 5).

a=3
b=4
c=5
d=6
e=7

A=1:a
B=1:b
C=1:c
D=1:d
E=1:e

X=matrix(nr=a*b*c*d*e,nc=5)

for(i_a in 1:a-1) {
  for(i_b in 1:b-1) {
for(i_c in 1:c-1) {
  for(i_d in 1:d-1) {
for(i_e in 1:e-1) {
  X[(((i_a * b + i_b) * c + i_c) * d + i_d) * e + i_e + 1, ] =
c(i_a+1, i_b+1, i_c+1, i_d+1, i_e+1)
}
  }
}
  }
}
print(X)

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[R] Repeated measures unbalanced in a split-split design

2009-11-22 Thread Marcelo Laia

Hi,

I have a experiment with block, plots, sub-plots, and sub-sub-plots
with repeated measures and 3 factors (factorial design) when we have
been observed diameter (mm), high (cm) and leaves number (count).
However, we don't have one treatment in one factor, so, my design is
unbalanced.

On a previous message here, a friend tell me that It appears to me
that your design is a split-split plot with repeated measures at the
split-split plot level. Because you have multiple sizes of
experimental unit (blocks, plots and sub-plots), you have a different
random error term at each size of unit, so you have to analyze it as a
mixed-effects model. For the diameter and height measurements, you can
probably get away with using normal errors, but for the counts, you
may well have to use a generalized linear mixed model.

So, I am trying to analyze my data with car package.

I have:
time (days after germination) - 4 levels (38, 53, 73, 85)
Hormone - 2 levels (SH, CH) on sub-plots
Block - 4 blocks
Treatment - 6 levels (1, 2, 3, 4, 5, and 6) on sub-sub-plots
Plant - subjects

I measured Diameter (mm), Height (cm), HD (height/diameter), and
Number of Leaves (count) at each time point. But, plant can be died
and I got NAs.

However, Treatment 6 (control) is only present on SH sub-plots. It
isn't present on CH sub-plots.

I try this model:

idata.Cana - data.frame(Time=factor(c(38,53,73,85)))
idata.Cana

mod.Cana - lm(cbind(Diameter.38, Diameter.53, Diameter.73, Diameter.85)
~  Treatment*Hormone, data=marcelo.subset)
mod.Cana

Call:
lm(formula = cbind(Diameter.38, Diameter.53, Diameter.73, Diameter.85)
~ Treatment * Hormone, data = marcelo.subset)

Coefficients:
  Diameter.38  Diameter.53  Diameter.73  Diameter.85
(Intercept)1.24000  1.35750  1.99375  2.31000
Treatment2-0.31625 -0.14250  0.07500 -0.13875
Treatment3-0.19250 -0.01500 -0.20875 -0.36875
Treatment4-0.35375 -0.08500 -0.22750 -0.27125
Treatment5-0.29125  0.04875 -0.14375 -0.26375
Treatment6-0.00125 -0.25750 -0.81125 -0.77750
HormoneSH -0.30875 -0.08875  0.31500  0.07000
Treatment2:HormoneSH   0.19875  0.11250 -0.44500 -0.24875
Treatment3:HormoneSH   0.15375  0.01875 -0.12125  0.07000
Treatment4:HormoneSH   0.28000 -0.04250 -0.41750 -0.38750
Treatment5:HormoneSH   0.40875 -0.11125 -0.17750 -0.05125
Treatment6:HormoneSHNA   NA   NA   NA

av.Cana - Anova(mod.Cana, idata=idata.Cana, idesign= ~ as.factor(Idade))
Erro em solve.default(crossprod(model.matrix(mod))) :
  rotina Lapack dgesv: sistema é exatamente singular

How I model my data to analyze it with this unbalanced design?

How I could use the block factor on model? Or it is not necessary? And
sub-plots?

Please, here you could find my design
http://www.divshare.com/download/9431636-e0c

and here you could find a subset of my data
http://www.divshare.com/download/9456640-fd7

Thank you very much!

-- 
Marcelo Luiz de Laia
Universidade do Estado de Santa Catarina
UDESC - www.cav.udesc.br
Lages - SC - Brazil
Linux user number 487797

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] MASS loading error




Erin Hodgess wrote:

Dear R People:

I just installed R-2.10.0 on Karmic Koala Ubuntu, via the sudo apt-get
install r-base, etc.

However, when I try to install an Rcmdr Plugin package, I get the following:


install.packages(RcmdrPlugin.qual,depen=TRUE)

Warning in install.packages(RcmdrPlugin.qual, depen = TRUE) :
  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
Warning in install.packages(RcmdrPlugin.qual, depen = TRUE) :
  'lib = /usr/local/lib/R/site-library' is not writable
Would you like to create a personal library
'~/R/i486-pc-linux-gnu-library/2.10'
to install packages into?  (y/n) y
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ‘qcc’

trying URL 'http://cran.opensourceresources.org/src/contrib/qcc_2.0.tar.gz'
Content type 'application/x-gzip' length 163556 bytes (159 Kb)
opened URL
==
downloaded 159 Kb

trying URL 
'http://cran.opensourceresources.org/src/contrib/RcmdrPlugin.qual_0.4.0.tar.gz'
Content type 'application/x-gzip' length 3545 bytes
opened URL
==
downloaded 3545 bytes

* installing *source* package ‘qcc’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (qcc)
* installing *source* package ‘RcmdrPlugin.qual’ ...
** R
** inst
** preparing package for lazy loading
Warning: package 'Rcmdr' was built under R version 2.8.1 and help may
not work correctly
Loading required package: tcltk
Loading Tcl/Tk interface ... done
The Commander GUI is launched only in interactive sessions

Attaching package: 'Rcmdr'


The following object(s) are masked from package:tcltk :

 tclvalue

Warning: package 'rgl' was built under R version 2.8.1 and help may
not work correctly
Warning: package 'abind' was built under R version 2.8.1 and help may
not work correctly
Error : This is R 2.10.0, package 'MASS' needs = 2.9.2
ERROR: lazy loading failed for package ‘RcmdrPlugin.qual’
* removing ‘/home/erin/R/i486-pc-linux-gnu-library/2.10/RcmdrPlugin.qual’

The downloaded packages are in
‘/tmp/RtmpioC2DR/downloaded_packages’
Warning message:
In install.packages(RcmdrPlugin.qual, depen = TRUE) :
  installation of package 'RcmdrPlugin.qual' had non-zero exit status

The line that looks particularly strange is the 'MASS needs = 2.9.2.


Erin,

the MASS you have installed in one of your current libraries needs R = 
2.9.2 (perhaps in /usr/local/lib/R/site-library ?)


Please run
  update.packages(checkBuilt=TRUE)
and packages in your library will be updated.

If the one in /usr/local/lib/R/site-library can't be updated, because 
you do not have write permissions there, please remove it from the 
library path.



Best,
Uwe Ligges






Could that be the problem, please?

Thank you in advance for any help.

Sincerely,
Erin




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[R] How to make the assignment in a for-loop not affect variables outside the loop?

I know that R is a dynamic programming language. But I'm wondering if
there is a way to make the assignment in a for-loop not affect
variables outside the loop.

 n=10
 for(i in 1:n){
+ n=3
+ print(n)
+ }
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3

 print(n)
[1] 3


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Re: [R] How to make a matrix of a number of factors?

2009-11-22 Thread baptiste auguie

Hi,

Try this,

do.call(expand.grid, lapply(7:3, seq, from=1))


HTH,

baptiste


2009/11/22 Peng Yu pengyu...@gmail.com:
 I use the following code to generate a matrix of factors. I'm
 wondering if there is a way to make it more general so that I can have
 any number of factors (not necessarily 5).

 a=3
 b=4
 c=5
 d=6
 e=7

 A=1:a
 B=1:b
 C=1:c
 D=1:d
 E=1:e

 X=matrix(nr=a*b*c*d*e,nc=5)

 for(i_a in 1:a-1) {
  for(i_b in 1:b-1) {
    for(i_c in 1:c-1) {
      for(i_d in 1:d-1) {
        for(i_e in 1:e-1) {
          X[(((i_a * b + i_b) * c + i_c) * d + i_d) * e + i_e + 1, ] =
 c(i_a+1, i_b+1, i_c+1, i_d+1, i_e+1)
        }
      }
    }
  }
 }
 print(X)

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Re: [R] Metaplot Axis Annotation




Ishwar Bridgelal wrote:

Hello,

We are looking to adjust the font size of the axis annotation on the graph
that results from use of the metaplot() function. Metaplot seems to respond
to cex and cex.lab to change those graphical parameters, but it doesn't
respond to cex.axis. Is there a way to work around this by creating a
customized x-axis, and if so, how?



Set the axis' character expansion for the whole device using par() as in:

  par(cex.axis=2)
  metaplot()

And for you next post:
Please provide reproducible code and tell us which package you are 
talking about (here rmeta, I guess).


Best,
Uwe Ligges





Thanks for all your help. Syntax is below.

Best,

Dawn McDaniel
Ishwar Bridgelal
University of Southern California


local({pkg - select.list(sort(.packages(all.available = TRUE)))

+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Loading required package: grid

m1=matrix(scan(file=C:/Users/Roymohan/Desktop/meta.txt), ncol=4,

byrow=TRUE)
Read 208 items

oddsratio=m1[,2]
seinor=m1[,3]
inw=m1[,4]
c1=c(Cross-Drew (1974), Ahlstrom  Havighurst (1982), Litton  Marye

(1981), Gold  Mattick (1974), Willman  Snortum (1982), Leiber 
Mawhorr (1995), Hackler  Hagan (1974), Sadd, Kotkin,  Freidman
(1983), New York State Division for Youth (1972), Spergel (2005),
Bloom et al. (1997), Quigley et al. (1999), Thambidurai (1980,
Schochet et al. (2001), Gruenewald, Laurence,  West (1985), Cave et
al. (1993), Elliot  Knowles (1976), Elliot  Knowles (1976), Porter
(1967), Kawaguchi (1975), Minnesota Governor’s Commission (1973),
Youth Opportunities Upheld (1978), Maynard (1980), Baker  Sadd
(1979), Goldberg  Johnson (1972),Roth (1983),Seckel  Turner
(1967),Zimring (1973),Randall (1973),Anderson  Schumacker
(1986),Lattimore, Witte,  Baker (1990),Weisz, Walter,  Weiss
(1990),Greenwood  Turner (1993),Johnson  Goldberg (1982), Kovacs
(1967),Auerbach (1978),Guthmann (1981),Sullivan  Mandall
(1967),Blew, McGillis,  Bryant (1970)
+ , Custer (1981), Goldberg (1978), Bowker (1977), Zivan (1966),
Massimo  Shore (1966), Killinger (1974), Morris (1970), Bernardo
(1973), Mann  Pratt (1978), Goodwill Industries Vocational Service
(1971), Springfield Massachusetts Goodwill Industries, Inc. (1966),
Walter  Mills (1980), Odell (1974))

metaplot(mn=oddsratio, se=seinor, labels=c1, cex=.65, lwd=2, cex.lab=.65)


[[alternative HTML version deleted]]





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Re: [R] How to make the assignment in a for-loop not affect variables outside the loop?


Either use local as in:

n=10

local(for(i in 1:n){
 n=3
 print(n)
})

print(n)


or write a function that is evaluated in its own environment:

n=10

MyLoopFoo - function(){
for(i in 1:n){
n - 3
print(n)
}
}

MyLoopFoo()

print(n)




Uwe Ligges


Peng Yu wrote:

I know that R is a dynamic programming language. But I'm wondering if
there is a way to make the assignment in a for-loop not affect
variables outside the loop.


n=10
for(i in 1:n){

+ n=3
+ print(n)
+ }
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3
[1] 3

print(n)

[1] 3

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[R] Why F value and Pr are not show in summary() of an aov() result?

I have the following code. I'm wondering why summary() doesn't show F
value and Pr?

Rscript multi_factor.R
 a=3
 b=4
 c=5
 d=6
 e=7

 A=1:a
 B=1:b
 C=1:c
 D=1:d
 E=1:e

 X=matrix(nr=a*b*c*d*e,nc=5)
 colnames(X)=LETTERS[1:5]

 for(i_a in 1:a-1) {
+   for(i_b in 1:b-1) {
+ for(i_c in 1:c-1) {
+   for(i_d in 1:d-1) {
+ for(i_e in 1:e-1) {
+   X[(((i_a * b + i_b) * c + i_c) * d + i_d) * e + i_e + 1, ]
= c(i_a+1, i_b+1, i_c+1, i_d+1, i_e+1)
+ }
+   }
+ }
+   }
+ }

 Y=matrix(nr=a*b*c*d*e,nc=1)
 for(i in 1:(a*b*c*d*e)) {
+   fa=X[i,'A']
+   fb=X[i,'B']
+   fc=X[i,'C']
+   fd=X[i,'D']
+   fe=X[i,'E']
+
+   Y[i,1]= fa +fb +fc +fe +fa*fb +fa*fc +fb*fc +fa*fe +fc*fe
+fa*fb*fc +fa*fc*fe + rnorm(1)
+ }

 aframe = data.frame(
+ A=as.factor(X[,'A'])
+ , B=as.factor(X[,'B'])
+ , C=as.factor(X[,'C'])
+ , D=as.factor(X[,'D'])
+ , E=as.factor(X[,'E'])
+ ,Y)

 afit=aov(Y ~ A * B * C * D * E, aframe)

 summary(afit)
 Df  Sum Sq Mean Sq
A 2 1512240  756120
B 3  453324  151108
C 4 2549895  637474
D 5   2  0.3693
E 6 1451057  241843
A:B   6   338755646
A:C   8  189839   23730
B:C  12   560244669
A:D  10   7   1
B:D  15  25   2
C:D  20  18   1
A:E  12  1075748964
B:E  18  21   1
C:E  24  1804137517
D:E  30  16   1
A:B:C244167 174
A:B:D30  37   1
A:C:D40  42   1
B:C:D60  63   1
A:B:E36  30   1
A:C:E48   13298 277
B:C:E72  62   1
A:D:E60  79   1
B:D:E90  87   1
C:D:E   120 122   1
A:B:C:D 120 140   1
A:B:C:E 144 131   1
A:B:D:E 180 145   1
A:C:D:E 240 225   1
B:C:D:E 360 398   1
A:B:C:D:E   720 713   1

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Re: [R] how to tell if its better to standardize your data matrix first when you do principal


masterinex wrote:



Hi guys , 


Im trying to do principal component analysis in R . There is 2 ways of doing
it , I believe. 
One is doing  principal component analysis right away the other way is 
standardizing the matrix first  using s = scale(m)and then apply principal
component analysis.   
How  do I tell what result is better ? What values in particular should i

look at . I already managed to find the eigenvalues and eigenvectors , the
proportion of  variance for each eigenvector using both methods.



Generally, it is better to standardize. But in some cases, e.g. for the 
same units in your variables indicating also the importance, it might 
make sense not to do so.
You should think about the analysis, you cannot know which result is 
`better' unless you know an interpretation.





I noticed that the proportion of the variance for the first  pca without
standardizing had a larger  value . Is there a meaning to it ? Isnt this
always the case?
 At last , if I am  supposed to predict a variable ie weight should I drop
the variable ie weight from my data matrix when I do principal component
analysis ?



This sounds a bit like homework. If that is the case, please ask your 
teacher rather than this list.
Anyway, it does not make sense to predict weight using a linear 
combination (principle component) that contains weight, does it?


Uwe Ligges

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[R] how do i persuade IT to install R on PCs ?? ...and should I ??

2009-11-22 Thread frenchcr



Please help me persuade IT to install R on my computer!

All suggestions welcome.

Our IT department run scared when you mention software that they have no
working experience of.

I need to know the pros and cons of having R on corporate desktops.

Please no funny stuff, this is quite a serious issue for us.

Pros and cons would be good.

Thanks.
-- 
View this message in context: 
http://old.nabble.com/how-do-i-persuade-IT-to-install-R-on-PCs...and-should-Itp26464163p26464163.html
Sent from the R help mailing list archive at Nabble.com.

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[R] Computing multivariate normal probabilities. Was: Re: Problem with Numerical derivatives (numDeriv) and mvtnorm

2009-11-22 Thread Ravi Varadhan


Hi Torsten,

It would be useful to warn the users that the multivariate normal probability 
calculated by pmvnorm using the GenzBretz algorithm is random, i.e. the 
result can vary between repeated executions of the function.  This would 
prevent inappropriate use of pmvnorm such as computing derivatives of it (see 
this email thread).

It seems that the other algorithm Miwa is deterministic, but not sure how 
reliable it is (I had some trouble with it).

It would also be useful in the help page to provide a link to two other 
functions for evaluating multivariate normal probabilities:

mnormt::sadmvn
mprobit::mvnapp

In particular, the `mvnapp' function of Harry Joe in mprobit package seems to 
be very interesting as it provides very accurate results using asymptotic 
expansions.

Best,
Ravi.


Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University

Ph. (410) 502-2619
email: rvarad...@jhmi.edu


- Original Message -
From: Ravi Varadhan rvarad...@jhmi.edu
Date: Saturday, November 21, 2009 8:15 pm
Subject: Re: [R] Problem with Numerical derivatives (numDeriv) and mvtnorm
To: SL sl...@yahoo.fr
Cc: r-help@r-project.org


 Go back to your calculus text and review the definition of derivative:
 
 f'(x) = lim h - 0  [f(x+h) - f(x)] / h
 
 when f(x) and f(x + h) are random variables, the above limit does not 
 exist.  In fact, f'(x) is also a random variable.
 
 Now, if you want the derivative you have to use a multivariate 
 integration algorithm that yields a deterministic value.  The function 
 `sadmvn' in the package mnormt can do this:
 
 require(mnormt)
 
 PP2 - function(p){
thetac - p
thetae - 0.323340333
thetab - -0.280970036
thetao -  0.770768082
ssigma  - diag(4)
ssigma[1,2] -  0.229502120
ssigma[1,3] -  0.677949335
ssigma[1,4] -  0.552907745
ssigma[2,3] -  0.784263100
ssigma[2,4] -  0.374065025
ssigma[3,4] -  0.799238700
ssigma[2,1] -  ssigma[1,2]
ssigma[3,1] -  ssigma[1,3]
ssigma[4,1] -  ssigma[1,4]
ssigma[3,2] -  ssigma[2,3]
ssigma[4,2] -  ssigma[2,4]
ssigma[4,3] -  ssigma[3,4]
   pp - sadmvn(lower=rep(-Inf, 4), 
 upper=c(thetac,thetae,thetab,thetao), mean=rep(0,4), varcov=ssigma, 
 maxpt=10)
 return(pp)
 }
 
 xx - -0.6675762
 
 P2(xx)
 
 require(numDeriv)
 
 grad(x=xx, func=PP2)
 
 
 I hope this helps,
 Ravi.
 
 
 
 Ravi Varadhan, Ph.D.
 Assistant Professor,
 Division of Geriatric Medicine and Gerontology
 School of Medicine
 Johns Hopkins University
 
 Ph. (410) 502-2619
 email: rvarad...@jhmi.edu
 
 
 - Original Message -
 From: SL sl...@yahoo.fr
 Date: Saturday, November 21, 2009 2:42 pm
 Subject: Re: [R] Problem with Numerical derivatives (numDeriv) and mvtnorm
 To: r-help@r-project.org
 
 
  Thanks for you comment.
  
  There is certainly some Monte Carlo sampling involved in mvtnorm but
  why derivatives could not be computed? In theory, the derivatives
  exist (eg. bivariate probit). Moreover, when used with optim, there
  are some numerical derivatives computed... does it mean that mvtnorm
  cannot be used in an optimisation problem? I think it hard to believe.
  
  One possibility would be to use the analytical derivatives and then 
 a
  do-it-yourself integration but i was looking for something a bit more
  comprehensive. The mvtnorm package uses a specific way to compute
  pmvnorm and I'm far to do a good enough job so that derivatives can
  compare with what mvtnorm can do.
  
  Stef
  
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  and provide commented, minimal, self-contained, reproducible code.
 
 __
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 PLEASE do read the posting guide 
 and provide commented, minimal, self-contained, reproducible code.

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Re: [R] consecutive numbering of elements in a matrix

2009-11-22 Thread Jim Bouldin


Many thanks to Dimitris, William and David for very helpful answers which
solved my problem.  Being a relatve newb, I am confused by something in the
solutions by Dimitris and David.

#Create a matrix A as follows:

 A - matrix(sample(50, 21), 7, 3)
 A[sample(21, 5)] - NA;A

 [,1] [,2] [,3]
[1,]   36   38   24
[2,]6   33   13
[3,]   12   42   10
[4,]7   NA   NA
[5,]   48   NA   NA
[6,]3   NA   47
[7,]   29   234

 B = row(A) - apply(is.na(A), 2, cumsum);B

 [,1] [,2] [,3]
[1,]111
[2,]222
[3,]333
[4,]433
[5,]533
[6,]634
[7,]745

#But:

 B = row(A) - apply(!is.na(A), 2, cumsum);B
 [,1] [,2] [,3]
[1,]000
[2,]000
[3,]000
[4,]011
[5,]022
[6,]032
[7,]032

This seems exactly backwards to me.  The is.na(A) command should be
cumulatively summing the NA values and !is.na(A) should be doing so on the
non-NA values.  But the opposite is the case.  I'm glad I have a solution
but this apparent backwardness of expected logic has me worried.

I do have another, tougher question if anyone has the time, which is, given
a resulting matrix like B below:

 is.na(B) - is.na(A);B

 [,1] [,2] [,3]
[1,]111
[2,]222
[3,]333
[4,]4   NA   NA
[5,]5   NA   NA
[6,]6   NA4
[7,]745

how can I rearrange all the columns so that equal values are in the same
row, i.e. in the case above, the NA values are removed from columns 2 and 3
and all non-NA values that had been below them are moved up to replace them.

Thanks again for your help.

Jim

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Re: [R] Why F value and Pr are not show in summary() of an aov() result?

2009-11-22 Thread Sundar Dorai-Raj

It's hard to read your code, so I won't comment on your specific
example. So when all else fails read the documentation for
?summary.aov:

They have columns ‘Df’, ‘Sum Sq’, ‘Mean
 Sq’, as well as ‘F value’ and ‘Pr(F)’ if there are non-zero
 residual degrees of freedom.

So if you do df.residual(afit), is it 0?

--sundar

On Sun, Nov 22, 2009 at 7:19 AM, Peng Yu pengyu...@gmail.com wrote:
 I have the following code. I'm wondering why summary() doesn't show F
 value and Pr?

 Rscript multi_factor.R
 a=3
 b=4
 c=5
 d=6
 e=7

 A=1:a
 B=1:b
 C=1:c
 D=1:d
 E=1:e

 X=matrix(nr=a*b*c*d*e,nc=5)
 colnames(X)=LETTERS[1:5]

 for(i_a in 1:a-1) {
 +   for(i_b in 1:b-1) {
 +     for(i_c in 1:c-1) {
 +       for(i_d in 1:d-1) {
 +         for(i_e in 1:e-1) {
 +           X[(((i_a * b + i_b) * c + i_c) * d + i_d) * e + i_e + 1, ]
 = c(i_a+1, i_b+1, i_c+1, i_d+1, i_e+1)
 +         }
 +       }
 +     }
 +   }
 + }

 Y=matrix(nr=a*b*c*d*e,nc=1)
 for(i in 1:(a*b*c*d*e)) {
 +   fa=X[i,'A']
 +   fb=X[i,'B']
 +   fc=X[i,'C']
 +   fd=X[i,'D']
 +   fe=X[i,'E']
 +
 +   Y[i,1]= fa +fb +fc +fe +fa*fb +fa*fc +fb*fc +fa*fe +fc*fe
 +fa*fb*fc +fa*fc*fe + rnorm(1)
 + }

 aframe = data.frame(
 +     A=as.factor(X[,'A'])
 +     , B=as.factor(X[,'B'])
 +     , C=as.factor(X[,'C'])
 +     , D=as.factor(X[,'D'])
 +     , E=as.factor(X[,'E'])
 +     ,Y)

 afit=aov(Y ~ A * B * C * D * E, aframe)

 summary(afit)
             Df  Sum Sq Mean Sq
 A             2 1512240  756120
 B             3  453324  151108
 C             4 2549895  637474
 D             5       2  0.3693
 E             6 1451057  241843
 A:B           6   33875    5646
 A:C           8  189839   23730
 B:C          12   56024    4669
 A:D          10       7       1
 B:D          15      25       2
 C:D          20      18       1
 A:E          12  107574    8964
 B:E          18      21       1
 C:E          24  180413    7517
 D:E          30      16       1
 A:B:C        24    4167     174
 A:B:D        30      37       1
 A:C:D        40      42       1
 B:C:D        60      63       1
 A:B:E        36      30       1
 A:C:E        48   13298     277
 B:C:E        72      62       1
 A:D:E        60      79       1
 B:D:E        90      87       1
 C:D:E       120     122       1
 A:B:C:D     120     140       1
 A:B:C:E     144     131       1
 A:B:D:E     180     145       1
 A:C:D:E     240     225       1
 B:C:D:E     360     398       1
 A:B:C:D:E   720     713       1

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[R] scatter plot equation

2009-11-22 Thread Rofizah Mohammad

Hi,

If I have 2D data set say (x,y) and I can do scatter plot by using plot(x,y)
command.
How can I add in this scatter plot the equations curve say

2X2 + 3Y2  6X  7Y + 9 = 0.

Regards

Rofizah

[[alternative HTML version deleted]]

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Re: [R] python

2009-11-22 Thread Peter Ehlers




Stefan Evert wrote:
Sure, badly written R code does not perform as well as well written 
python code or C code. On the other hand badly written python code 
does not perform as well as well written R code.


What happens when you try one of these :

sum - sum( 1:N )


R runs out of memory and crashes. :-)  I didn't tell you how big N is, 
did I?


Really?

 N - 1e30
 sum( 1:N )
 Error in 1:N : result would be too long a vector

 -Peter Ehlers




But this is exactly the point I was trying to make (but perhaps not 
prominently enough).  In many cases, you can vectorize at least parts of 
your code or find a more efficient algorithm, which may be faster in R 
than a brute-force solution in C.  But sometimes, you just cannot avoid 
loops (let's not forget that all the forms of apply() are just loops and 
don't give much of a speed benefit over a for-loop), function calls, 
etc.; in this case, performance differences between interpreted 
languages can matter.


Personally, I'd never switch from R to Perl just for speed, though.

BTW, I also tried a vectorised algorithm in R, which calculates the sum 
above in a small number of chunks:



N1 - 50
N2 - 100
N - N1 * N2
sum - 0

for (i in 1:N1) {
x - as.numeric(i-1) * N2 + 1:N2
sum - sum + sum(x)
}


which gives

R/simple_count_vec.R  31.30 Mops/s  (5000 ops in 1.60 s)

So an interpreted loop in Lua is still faster than this partially 
vectorized code in R:



lua/simple_count.lua 65.78 Mops/s (1 ops in 1.52 s)


As people on the SQLite mailing list always say: there's no general 
answer as to which language/implementation/query/... is faster and 
better.  You just have to test the different options for your specific 
application setting, and be prepared for one or two surprises.


Just in case this isn't obvious: If I rewrote matrix multiplication in C 
and linked this code into R, it would run much slower than if I just 
typed A %*% B.


All the best,
Stefan

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Re: [R] scatter plot equation


On 22/11/2009 11:27 AM, Rofizah Mohammad wrote:

Hi,

If I have 2D data set say (x,y) and I can do scatter plot by using plot(x,y)
command.
How can I add in this scatter plot the equations curve say

2X2 + 3Y2 – 6X – 7Y + 9 = 0.


You could do it using contour(), but you should use an equation that has 
some real solutions.  For example, using a different equation than yours:


x - rnorm(100, sd=1)
y - rnorm(100, sd=1)
xgrid - seq(min(x), max(x), len=100)
ygrid - seq(min(y), max(y), len=120)
grid - expand.grid(x=xgrid, y=ygrid)
LHS - function(x, y) x^2 + y^2 - x - y  - 1
z - apply(grid, 1, function(x) LHS(x[1], x[2]) )
z - matrix(z, 100, 120)
plot(x,y)
contour(xgrid, ygrid, z, levels=0, add=TRUE)

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Re: [R] consecutive numbering of elements in a matrix



On Nov 22, 2009, at 11:11 AM, Jim Bouldin wrote:



Many thanks to Dimitris, William and David for very helpful answers  
which
solved my problem.  Being a relatve newb, I am confused by something  
in the

solutions by Dimitris and David.

#Create a matrix A as follows:


A - matrix(sample(50, 21), 7, 3)
A[sample(21, 5)] - NA;A


[,1] [,2] [,3]
[1,]   36   38   24
[2,]6   33   13
[3,]   12   42   10
[4,]7   NA   NA
[5,]   48   NA   NA
[6,]3   NA   47
[7,]   29   234


B = row(A) - apply(is.na(A), 2, cumsum);B


[,1] [,2] [,3]
[1,]111
[2,]222
[3,]333
[4,]433
[5,]533
[6,]634
[7,]745

#But:


B = row(A) - apply(!is.na(A), 2, cumsum);B

[,1] [,2] [,3]
[1,]000
[2,]000
[3,]000
[4,]011
[5,]022
[6,]032
[7,]032

This seems exactly backwards to me.


Put the individual components together side by side with cbind and it  
will make more sense:


cbind( row(A), apply(is.na(A), 2, cumsum) )

And think about the fact that row(A) and apply(is.na(A), 2, cumsum)  
will be identical in the case where there are no NAs, so their  
difference would be a zero matrix. Double negativism strikes again  
not(is.na) == is



The is.na(A) command should be
cumulatively summing the NA values and !is.na(A) should be doing so  
on the
non-NA values.  But the opposite is the case.  I'm glad I have a  
solution

but this apparent backwardness of expected logic has me worried.

I do have another, tougher question if anyone has the time, which  
is, given

a resulting matrix like B below:


is.na(B) - is.na(A);B


[,1] [,2] [,3]
[1,]111
[2,]222
[3,]333
[4,]4   NA   NA
[5,]5   NA   NA
[6,]6   NA4
[7,]745

how can I rearrange all the columns so that equal values are in the  
same
row, i.e. in the case above, the NA values are removed from columns  
2 and 3
and all non-NA values that had been below them are moved up to  
replace them.


You cannot have unequal length columns in a matrix. Only a list is  
able to handle that task. So we need a more clear description of what  
you expect, preferably typed out in full so we can see it.


--
David.



Thanks again for your help.

Jim


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] scatter plot equation



On Nov 22, 2009, at 11:27 AM, Rofizah Mohammad wrote:


Hi,

If I have 2D data set say (x,y) and I can do scatter plot by using  
plot(x,y)

command.
How can I add in this scatter plot the equations curve say

2X2 + 3Y2  6X  7Y + 9 = 0.



No executable example... so if you are too lazy to construct one, then  
I would suggest looking for worked examples at one of the graphics  
galleries.


Perhaps:

http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=44




Regards

Rofizah

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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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[R] Do you keep an archive of useful R code? and if so - how?

Hello all,

When using R for some time, one comes across more and more useful functions.
 But naturally we can't remember all of them, so I imagine some of you save
these snippets of code.
My question to you is how do you manage that code?
Do you use special software, or archiving system?

Any advice is welcomed.

Tal





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Re: [R] python

2009-11-22 Thread Jean Legeande

Anyway I think it was just a toy example.

Any additionnal information is welcome.

Best,
Jean

2009/11/22 Peter Ehlers ehl...@ucalgary.ca



 Stefan Evert wrote:

 Sure, badly written R code does not perform as well as well written python
 code or C code. On the other hand badly written python code does not perform
 as well as well written R code.

 What happens when you try one of these :

 sum - sum( 1:N )


 R runs out of memory and crashes. :-)  I didn't tell you how big N is, did
 I?


 Really?

  N - 1e30
  sum( 1:N )
  Error in 1:N : result would be too long a vector

  -Peter Ehlers


 


 But this is exactly the point I was trying to make (but perhaps not
 prominently enough).  In many cases, you can vectorize at least parts of
 your code or find a more efficient algorithm, which may be faster in R than
 a brute-force solution in C.  But sometimes, you just cannot avoid loops
 (let's not forget that all the forms of apply() are just loops and don't
 give much of a speed benefit over a for-loop), function calls, etc.; in this
 case, performance differences between interpreted languages can matter.

 Personally, I'd never switch from R to Perl just for speed, though.

 BTW, I also tried a vectorised algorithm in R, which calculates the sum
 above in a small number of chunks:

 N1 - 50
 N2 - 100
 N - N1 * N2
 sum - 0

 for (i in 1:N1) {
x - as.numeric(i-1) * N2 + 1:N2
sum - sum + sum(x)
 }


 which gives

 R/simple_count_vec.R  31.30 Mops/s  (5000 ops in 1.60 s)

 So an interpreted loop in Lua is still faster than this partially
 vectorized code in R:

  lua/simple_count.lua 65.78 Mops/s (1 ops in 1.52 s)


 As people on the SQLite mailing list always say: there's no general answer
 as to which language/implementation/query/... is faster and better.  You
 just have to test the different options for your specific application
 setting, and be prepared for one or two surprises.

 Just in case this isn't obvious: If I rewrote matrix multiplication in C
 and linked this code into R, it would run much slower than if I just typed
 A %*% B.

 All the best,
 Stefan

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Re: [R] how do i persuade IT to install R on PCs ?? ...and should I ??


On Nov 22, 2009, at 5:14 AM, frenchcr wrote:




Please help me persuade IT to install R on my computer!

All suggestions welcome.

Our IT department run scared when you mention software that they  
have no

working experience of.

I need to know the pros and cons of having R on corporate desktops.

Please no funny stuff, this is quite a serious issue for us.

Pros and cons would be good.

Thanks.



You need to define how R will meet and preferably enhance whatever  
functional requirements you have as compared to alternatives that are  
either already installed or that your IT folks are considering. How  
will R enhance your ability to meet the needs of the internal and/or  
external consumers of your analytic services?


Typically, arguments based solely on costs (eg. R is free) will fall  
on deaf ears in IT, since there is the likelihood that your R  
installations will require some level of support from them, thus  
having a real cost in time and money. Are your R installations going  
to need to interface with other platforms such as database servers,  
etc? What security and server/network access implications will it  
have? What other supporting applications will you require to use with  
R (eg. editors, Perl, LaTeX, C/FORTAN compilers and related tools,  
etc.) that will increase support and maintenance requirements?


Who is going to support R as problems occur and updates are needed?  
Most IT departments are used to paying for support to a commercial  
vendor. Somebody that they can call when things go wrong. They may not  
be used to getting support from mailing lists. Yes, there are  
commercial variants of R that address that issue and that may be  
something to consider depending upon the specifics of your situation.


What knowledge does your IT department have of open source development  
and support? Is Linux being used on servers or workstations? Even if  
they are using a commercial Linux installation (eg. Red Hat), they may  
be more comfortable with the general concept of open source, which may  
be part of the battle that you are facing.


Is there an alternative to installing on local desktops versus  
considering a central installation on a server? The former magnifies  
the time and workload requirements to IT for installing and  
maintaining over a larger number of computers. The latter enables a  
more centralized and possibly more efficient IT approach to this.


What, if any, issues are there in converting existing code and  
processes that are implemented using other applications to R? What if  
any code reviews and functional validations will be required,  
resulting in real costs associated with those processes?


There are not only direct costs, but indirect costs and opportunity  
costs associated with moving to and using R. You are going to require  
some level of support from them for R, which means they will have less  
time and resources for other activities.


This becomes a control, political, economic and potentially even a  
legal issue. Over the years, as desktop PC's became common, there was  
a decentralization and dilution of IT involvement from the old  
mainframe/minicomputer days. That trend has been reversing for some  
time in most corporate environments, such that IT is taking a much  
more proactive role in controlling technology decision making, support  
and access across the IT spectrum. That includes driving corporate  
policies regarding applications, hardware, security, mobile platforms  
(laptops, smart phones, etc.) and is influenced by a variety of  
factors, not the least of which can be risk management, regulatory and  
related issues.


An incremental approach is something to consider. Install R on one  
desktop machine or a server and let your IT folks become comfortable  
with it, before moving to a larger scale implementation if you are  
looking beyond just your one desktop.


In addition, sell your manager(s) on R to gain their support and  
influence on the decision making process, therefore helping to  
politically bolster your arguments. It is known as managing up and  
can be an important part of the strategy in gaining IT's support,  
presuming that your managers are in a position of influence with IT.


It would be difficult to provide detailed guidance to you without more  
information on your specific environment, but hopefully the above  
provides food for thought, at least in the abstract.


Cheers,

Marc Schwartz

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[R] contour(): lines labels in different colours?

2009-11-22 Thread Ted Harding

Greetings, All!
I want to draw contour lines in red, using contour(), but also
have the contour labels (for the level-values) in black so that
they will stand out against a coloured background already generated
using filled.contour() (the background shades from green at low
levels of risk to red at high levels).

In any case, contour labels in red are already somewhat inconspicuous
with contour lines in red, regardless of background.

I see nothing in ?contour nor in ?par about this.

One way to approach it could be to first draw the labelled contours
in black, and then overlay by re-drawing (with out labels) in red.
This would sort-of work, but the red contour lines would then cut
through the black numbers, which is somewhat undesirable. Also
(I've tried it) you can get show-through along the contour lines
from the black layer, which is nasty.

Any suggestions?

With thanks,
Ted.


E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 22-Nov-09   Time: 17:06:08
-- XFMail --

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Re: [R] Do you keep an archive of useful R code? and if so - how?


On Nov 22, 2009, at 10:53 AM, Tal Galili wrote:


Hello all,

When using R for some time, one comes across more and more useful  
functions.
But naturally we can't remember all of them, so I imagine some of  
you save

these snippets of code.
My question to you is how do you manage that code?
Do you use special software, or archiving system?

Any advice is welcomed.

Tal



One word:  Subversion (http://subversion.tigris.org/)

A version control system is a critical part of any code management  
process.


If you or other users may not be comfortable at the command line using  
it, there are a plethora of GUI based clients for Subversion available  
depending upon the operating systems you are using.


HTH,

Marc Schwartz

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Re: [R] how do i persuade IT to install R on PCs ?? ...and should I ??

2009-11-22 Thread Ben Bolker

frenchcr frenchcr at btinternet.com writes:

 
 
 Please help me persuade IT to install R on my computer!
 
 All suggestions welcome.
 
 Our IT department run scared when you mention software that they have no
 working experience of.
 
 I need to know the pros and cons of having R on corporate desktops.
 
 Please no funny stuff, this is quite a serious issue for us.
 
 Pros and cons would be good.
 
 Thanks.

  You can probably expect to get some funny stuff along with
any useful advice you do get.

  It is almost impossible to answer this question without
knowing what you want to use R for!

  You could tell your IT department that R is easy to install
and well-behaved (i.e. it is self-contained and doesn't do
nasty things to system libraries etc.), that it doesn't phone
home or need to talk to servers outside your environment
(unless you program it to, or unless you try to download 
install additional packages), that it is used by a very wide
range of reputable companies (see a variety of discussions on
this list, or see http://www.r-project.org/foundation/memberlist.html ),
... but the most important thing should presumably be whether
it helps you do your job ...  The license is unrestrictive,
unless you want to redistribute a modified version, in which
case it requires you to provide source code and allow 
redistribution ...

  Cons: like any software, it takes time and space to
install (although not very much).  R develops rapidly
and there is little support for obsolete versions. 
The software comes without support, but you can pay for 
third-party support.

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Re: [R] scatter plot equation

2009-11-22 Thread Rofizah Mohammad

Many thanks Duncan. I got the plot even I don't really understand the whole
command..
I will study that later..

:-)

Regards



On Sun, Nov 22, 2009 at 4:44 PM, Duncan Murdoch murd...@stats.uwo.cawrote:

  On 22/11/2009 11:27 AM, Rofizah Mohammad wrote:

 Hi,

 If I have 2D data set say (x,y) and I can do scatter plot by using
 plot(x,y)
 command.
 How can I add in this scatter plot the equations curve say

 2X2 + 3Y2  6X  7Y + 9 = 0.


 You could do it using contour(), but you should use an equation that has
 some real solutions.  For example, using a different equation than yours:

 x - rnorm(100, sd=1)
 y - rnorm(100, sd=1)
 xgrid - seq(min(x), max(x), len=100)
 ygrid - seq(min(y), max(y), len=120)
 grid - expand.grid(x=xgrid, y=ygrid)
 LHS - function(x, y) x^2 + y^2 - x - y  - 1
 z - apply(grid, 1, function(x) LHS(x[1], x[2]) )
 z - matrix(z, 100, 120)
 plot(x,y)
 contour(xgrid, ygrid, z, levels=0, add=TRUE)


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Re: [R] AKIMA: z values at a set coordinate

2009-11-22 Thread Rhelp wanted

Dear Dr Hiemstra

Thank you for taking the time to reply to my request. You are a very big
help.

regards and many thanks

Sylvestre

On Sat, Nov 21, 2009 at 10:57 AM, Paul Hiemstra p.hiems...@geo.uu.nlwrote:

 Hi Anonymous, (Maybe next time include your name)

 There are data objects in R that are designed for spatial data, look at the
 sp package. Casting them into this format gives you an enormous increase in
 flexibility with analyzing spatial data. See the example below using your
 example:

 library(akima)
 library(sp)
 data(akima)

 akima.li - interp(akima$x, akima$y, akima$z)
 # Change to sp object
 # Note that we swap the x and y column [1]
 y = rep(akima.li$x, each = length(akima.li$y))
 x = rep(akima.li$y, length(akima.li$x))
 z = as.numeric(akima.li$z)
 akima.sp = data.frame(x, y, z)
 # sp-function, which columns are the coordinates
 coordinates(akima.sp) = ~x+y
 # Tell sp that it is a grid
 gridded(akima.sp) = TRUE

 # Plot and compare
 image (akima.li)
 spplot(akima.sp)

 # Use overlay from sp to get the value
 # at a specific location
 pt = data.frame(x = 11.25, y = 6.5)
 coordinates(pt) = ~x+y
 val = akima...@data[overlay(akima.sp, pt),]
 val
 # [1] 19.14752

 Learning to use sp-objects is really worthwhile. See the spatial Task view
 for more information, or check out the R-wiki [2]. With these kind of
 geographic questions you might want to use the r-sig-geo mailing list
 instead of R-help.

 cheers,
 Paul

 [1] We do this because (from details section of Image):

 Notice that image interprets the z matrix as a table of
 f(x[i], y[j]) values, so that the x axis corresponds to row
 number and the y axis to column number, with column 1 at the
 bottom, i.e. a 90 degree counter-clockwise rotation of the
 conventional printed layout of a matrix.

 [2] http://wiki.r-project.org/rwiki/doku.php?id=tips:spatial-data

 Rhelp wanted wrote:

 Dear all.

 I am using the akima function to produce 3d contour plots using interp
 based
 on irregular data.

 using the eg in the akima manual

 library(akima)
 data(akima)
 plot(y ~ x, data = akima, main = akima example data)
 with(akima, text(x, y, formatC(z,dig=2), adj = -0.1))
 ## linear interpolation
 akima.li - interp(akima$x, akima$y, akima$z)
 image (akima.li, add=TRUE)
 contour(akima.li, add=TRUE)
 points (akima, pch = 3)

 so with this in mind is there a way of obtaining the interpolated value at
 a
 particular coordinate eg at (11.25,6.5) I can see that it as an orange and
 should I look at the contour lines I can see what value it produces.
 However
 Is there a way of saying function[11.25,6.5] which provides a value for
 that
 coordinate.

 Hope someone can help

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 Heidelberglaan 2
 P.O. Box 80.115
 3508 TC Utrecht
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 Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Do you keep an archive of useful R code? and if so - how?

Hello Marc and Jeff,
Thank you for replying.

I am using winXP, and any recommendation for GUI based system will be
welcomed.

However, my initial question was not how to maintain code that I write
and develop, but rather how to keep a filing system for other peoples code
that I find useful.
Here are some simple examples:

   - A code to allow me to start a window with history recording turned
   on.
   - A code to have wider margins so to allow more space for the plot
   labels.
   - A code for creating an ellipse plot of a matrix of correlations.

All of these example are things I wouldn't put into a Subversion system or a
new package.

I hope my question was made more clear, and your answer will be much
appreciated.

Best,
Tal








Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com/ (English)
--




On Sun, Nov 22, 2009 at 7:13 PM, Marc Schwartz marc_schwa...@me.com wrote:

 On Nov 22, 2009, at 10:53 AM, Tal Galili wrote:

  Hello all,

 When using R for some time, one comes across more and more useful
 functions.
 But naturally we can't remember all of them, so I imagine some of you save
 these snippets of code.
 My question to you is how do you manage that code?
 Do you use special software, or archiving system?

 Any advice is welcomed.

 Tal



 One word:  Subversion (http://subversion.tigris.org/)

 A version control system is a critical part of any code management process.

 If you or other users may not be comfortable at the command line using it,
 there are a plethora of GUI based clients for Subversion available depending
 upon the operating systems you are using.

 HTH,

 Marc Schwartz



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Re: [R] Do you keep an archive of useful R code? and if so - how?

2009-11-22 Thread Barry Rowlingson

On Sun, Nov 22, 2009 at 5:45 PM, Tal Galili tal.gal...@gmail.com wrote:
 Hello Marc and Jeff,
 Thank you for replying.

 I am using winXP, and any recommendation for GUI based system will be
 welcomed.

 However, my initial question was not how to maintain code that I write
 and develop, but rather how to keep a filing system for other peoples code
 that I find useful.
 Here are some simple examples:

   - A code to allow me to start a window with history recording turned
   on.
   - A code to have wider margins so to allow more space for the plot
   labels.
   - A code for creating an ellipse plot of a matrix of correlations.

 All of these example are things I wouldn't put into a Subversion system or a
 new package.

I just use plain text files for keeping notes - generally each project
directory I work on has a 'notes.txt' file which is a working log of
what I'm doing. If I think 'how did I do that the other day?' I can
search my text files.

 Recently I've been experimenting with using 'personal' or 'desktop'
wiki systems for this. Like Wikipedia but just for you, and stored as
files on your PC, and edited with a local client program instead of
over the web (although some personal wikis work over the web). I've
found 'zim' to be pretty good for this. It organises notes, lets you
link pages, timestamps things, has various plugins and MOST
importantly it's Open Source so you won't ever have your notes locked
up in a proprietary format that you need to keep paying a license fee
for.

 Not sure if there's a Windows port of it, but I'm certain similar
systems exist for Windows.

 Another idea is to have a public blog for R tips and tricks. That way
not only do you get free storage (from blogspot.com or some other blog
provider) but also it's searchable and other people can find it and
comment and improve on it.

 Or you could contribute to the R-wiki:

http://wiki.r-project.org/rwiki/doku.php?id=tips:tips

Barry

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R-help@r-project.org mailing list
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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.

Re: [R] Do you keep an archive of useful R code? and if so - how?

Tal,

I would still use Subversion.

Think of Subversion as as an electronic filing system. You can  
organize code into project trees, with sub-folders and so forth.

As you come across code snippets that you want to save, copy them to a  
file and commit the file to a project tree or sub-folder, based upon  
the domain of functionality. Add related code snippets to the same  
domains. That way, you have related code snippets in a common area,  
making recall easier.

The advantage of using a VCS is that you can make trackable  
modifications to the code over time, as your functional requirements  
change or as you discover bugs, etc. to existing code.

In terms of a GUI, for Windows, it seems that most use Tortoise SVN:

   http://tortoisesvn.net/

There are cross-platform GUIs such as RapidSVN (http://rapidsvn.tigris.org/ 
), but it all depends upon personal preferences. More links here:

   http://subversion.tigris.org/links.html#all-clients

There are also Subversion extensions for editors, such as Emacs, like  
psvn.el (http://www.xsteve.at/prg/vc_svn/) which enable a blending of  
functionality into environments that you may already be using, such as  
ESS.

Last but not least, there are also commercial variants of Subversion  
clients, which of course have a cost associated with them. These are  
also listed on the clients link above.

An alternative would be to create a local wiki, the implementation  
details, as with a Subversion repo, would be dependent upon whether or  
not you are the only person that needs access or if access and/or  
content modification are to be shared.

HTH,

Marc

On Nov 22, 2009, at 11:45 AM, Tal Galili wrote:

 Hello Marc and Jeff,
 Thank you for replying.

 I am using winXP, and any recommendation for GUI based system will  
 be welcomed.

 However, my initial question was not how to maintain code that I  
 write and develop, but rather how to keep a filing system for  
 other peoples code that I find useful.
 Here are some simple examples:
 A code to allow me to start a window with history recording turned  
 on.
 A code to have wider margins so to allow more space for the plot  
 labels.
 A code for creating an ellipse plot of a matrix of correlations.
 All of these example are things I wouldn't put into a Subversion  
 system or a new package.

 I hope my question was made more clear, and your answer will be much  
 appreciated.

 Best,
 Tal

 On Sun, Nov 22, 2009 at 7:13 PM, Marc Schwartz  
 marc_schwa...@me.com wrote:
 On Nov 22, 2009, at 10:53 AM, Tal Galili wrote:

 Hello all,

 When using R for some time, one comes across more and more useful  
 functions.
 But naturally we can't remember all of them, so I imagine some of  
 you save
 these snippets of code.
 My question to you is how do you manage that code?
 Do you use special software, or archiving system?

 Any advice is welcomed.

 Tal


 One word:  Subversion (http://subversion.tigris.org/)

 A version control system is a critical part of any code management  
 process.

 If you or other users may not be comfortable at the command line  
 using it, there are a plethora of GUI based clients for Subversion  
 available depending upon the operating systems you are using.

 HTH,

 Marc Schwartz




[[alternative HTML version deleted]]

__
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.

Re: [R] Do you keep an archive of useful R code? and if so - how?

Marc and Barry, many thanks for your detailed answers.

Marc -
I thank you for the links and ideas. Thanks to your advice I will look more
into SVN in the future, although it sounds on the surface to require some
learning curve, so It could take me some time to start using it.

Barry -
I am actually a blog builder in my side profession, I already built myself a
blog called:
r-statistics.com
On which I intend to put up good code I will come across.  The problem with
it though is that I don't see blogs as a good information management system.
Since on a blog one is open to the public and doesn't want to leave half
scribles of thoughts (which IS what ends up happening when managing snippets
of code).  Also, blogging is not build for easy hierarchical ordering.

The idea of a wiki is more appealing.
BTW - another suggestion I got was using MS onenote. Although it is not open
source (which is my preference as well), I understood it offers a powerful
solution.

I hope more people will share how they manage their snippets of code.


Best to all of you,
Tal




Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com/ (English)
--




On Sun, Nov 22, 2009 at 8:09 PM, Marc Schwartz marc_schwa...@me.com wrote:

 Tal,

 I would still use Subversion.

 Think of Subversion as as an electronic filing system. You can organize
 code into project trees, with sub-folders and so forth.

 As you come across code snippets that you want to save, copy them to a file
 and commit the file to a project tree or sub-folder, based upon the domain
 of functionality. Add related code snippets to the same domains. That way,
 you have related code snippets in a common area, making recall easier.

 The advantage of using a VCS is that you can make trackable modifications
 to the code over time, as your functional requirements change or as you
 discover bugs, etc. to existing code.

 In terms of a GUI, for Windows, it seems that most use Tortoise SVN:

   http://tortoisesvn.net/

 There are cross-platform GUIs such as RapidSVN (
 http://rapidsvn.tigris.org/), but it all depends upon personal
 preferences. More links here:

   http://subversion.tigris.org/links.html#all-clients

 There are also Subversion extensions for editors, such as Emacs, like
 psvn.el (http://www.xsteve.at/prg/vc_svn/) which enable a blending of
 functionality into environments that you may already be using, such as ESS.

 Last but not least, there are also commercial variants of Subversion
 clients, which of course have a cost associated with them. These are also
 listed on the clients link above.

 An alternative would be to create a local wiki, the implementation details,
 as with a Subversion repo, would be dependent upon whether or not you are
 the only person that needs access or if access and/or content modification
 are to be shared.

 HTH,

 Marc

 On Nov 22, 2009, at 11:45 AM, Tal Galili wrote:

 Hello Marc and Jeff,
 Thank you for replying.

 I am using winXP, and any recommendation for GUI based system will be
 welcomed.

 However, my initial question was not how to maintain code that I write
 and develop, but rather how to keep a filing system for other peoples code
 that I find useful.
 Here are some simple examples:

- A code to allow me to start a window with history recording turned
on.
- A code to have wider margins so to allow more space for the plot
labels.
- A code for creating an ellipse plot of a matrix of correlations.

 All of these example are things I wouldn't put into a Subversion system or
 a new package.

 I hope my question was made more clear, and your answer will be much
 appreciated.

 Best,
 Tal


 On Sun, Nov 22, 2009 at 7:13 PM, Marc Schwartz marc_schwa...@me.comwrote:

 On Nov 22, 2009, at 10:53 AM, Tal Galili wrote:

  Hello all,

 When using R for some time, one comes across more and more useful
 functions.
 But naturally we can't remember all of them, so I imagine some of you
 save
 these snippets of code.
 My question to you is how do you manage that code?
 Do you use special software, or archiving system?

 Any advice is welcomed.

 Tal



 One word:  Subversion (http://subversion.tigris.org/)

 A version control system is a critical part of any code management
 process.

 If you or other users may not be comfortable at the command line using it,
 there are a plethora of GUI based clients for Subversion available depending
 upon the operating systems you are using.

 HTH,

 Marc Schwartz





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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and

[R] serialized plot object (2 years later)

2009-11-22 Thread Jack Tanner


About 2 years ago, Tobias Verbeke asked:

I am looking for a way to capture the binary string that in normal use of 
graphics devices will bewritten to (most commonly) a file connection... Is 
there a way of capturing the binary `jpeg string'
[generated by jpeg()]?

http://tolstoy.newcastle.edu.au/R/e2/devel/07/09/4276.html

Brian Ripley's answer was Nope, unfortunately, they write to files not 
connections and no R object 
is involved.

Is this still the case?
  
_
Hotmail: Trusted email with powerful SPAM protection.

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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.

Re: [R] consecutive numbering of elements in a matrix

2009-11-22 Thread Dimitris Rizopoulos


one approach is the following:

B - cbind(c(1:6, NA), c(1:3, NA,NA,NA, 4), c(1:3, NA,NA, 4,5))
matrix(B[order(col(B), B)], nrow(B), ncol(B))


I hope it helps.

Best,
Dimitris


Jim Bouldin wrote:
And think about the fact that row(A) and apply(is.na(A), 2, cumsum)  
will be identical in the case where there are no NAs, so their  
difference would be a zero matrix. Double negativism strikes again  
not(is.na) == is


OK I see it now--thanks.  I was interpreting the apply function incorrectly
in terms of what it was summing.

You cannot have unequal length columns in a matrix. Only a list is  
able to handle that task. So we need a more clear description of what  
you expect, preferably typed out in full so we can see it.


Given a matrix B like before, which has NAs mixed with integers in all
columns, where those NAs may occur anywhere within the columns, and where
the integers within a column are always consecutive and increasing: 


B

 [,1] [,2] [,3] ...etc
[1,]111
[2,]222
[3,]333
[4,]4   NA   NA
[5,]5   NA   NA
[6,]6   NA4
[7,]NA   45
etc

I would like to create a new matrix, in which all NAs that occur BETWEEN
consecutive integers are removed, and the integers which follow such NAs
are moved up in the column to replace them.  NAs which occur near the
bottom of each column, and are NOT followed by more integers can be
retained without problem.  Empty spaces that might result from this
process, near the column bottoms as the integers are moved up, would need
to be replaced by NAs so that equal numbers of entries are maintained in
each row, hence still allowing a matrix to exist:

If B above were in fact the complete matrix, the desired result would thus be:

 [,1] [,2] [,3] etc
[1,]111
[2,]222
[3,]333
[4,]444
[5,]5   NA5
[6,]6   NA   NA
[7,]NA  NA   NA
etc

In other words, all integers of a particular value in the original matrix
need to be placed on the same row of a new matrix, and all empty values
replaced with NA.  I hope that explains it well enough, but will try again
if not. Thanks again for any help.
Jim

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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.



--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center

Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014

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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.

Re: [R] Do you keep an archive of useful R code? and if so - how?

2009-11-22 Thread Hans-Peter Suter

 Marc -
 I thank you for the links and ideas. Thanks to your advice I will look more
 into SVN in the future, although it sounds on the surface to require some
 learning curve, so It could take me some time to start using it.

If you consider investing time to learn a version control system, I
would recommend looking into a distributed one. - Personally I use
git. http://git-scm.com/ is a good start, http://www.github.com can be
used to store code 'in the cloud'.

Cheers,
Hans-Peter

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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.

Re: [R] Computing multivariate normal probabilities. Was: Re: Problem with Numerical derivatives (numDeriv) and mvtnorm

2009-11-22 Thread stephane Luchini

I'm now making some trials with sadmvn which provides results similar
to pmvnorm for optimization but I know compute my OPG estimator of the
covariance matrix with sadmvn (by the way Ravi, when I was refering to
exist in theory I was refering to the theory not to the computation
- would an appropriate random computation of partial derivative
work?).

Interestingly, mprobit also provides derivatives, exactly what I need.
Unfortunatly it fails to install on mac os X! (I don't want to install
windows in my system and my linux server is off for the moment).

Stephane

2009/11/22 Ravi Varadhan rvarad...@jhmi.edu:

 Hi Torsten,

 It would be useful to warn the users that the multivariate normal 
 probability calculated by pmvnorm using the GenzBretz algorithm is 
 random, i.e. the result can vary between repeated executions of the 
 function.  This would prevent inappropriate use of pmvnorm such as computing 
 derivatives of it (see this email thread).

 It seems that the other algorithm Miwa is deterministic, but not sure how 
 reliable it is (I had some trouble with it).

 It would also be useful in the help page to provide a link to two other 
 functions for evaluating multivariate normal probabilities:

 mnormt::sadmvn
 mprobit::mvnapp

 In particular, the `mvnapp' function of Harry Joe in mprobit package seems 
 to be very interesting as it provides very accurate results using asymptotic 
 expansions.

 Best,
 Ravi.
 

 Ravi Varadhan, Ph.D.
 Assistant Professor,
 Division of Geriatric Medicine and Gerontology
 School of Medicine
 Johns Hopkins University

 Ph. (410) 502-2619
 email: rvarad...@jhmi.edu


 - Original Message -
 From: Ravi Varadhan rvarad...@jhmi.edu
 Date: Saturday, November 21, 2009 8:15 pm
 Subject: Re: [R] Problem with Numerical derivatives (numDeriv) and mvtnorm
 To: SL sl...@yahoo.fr
 Cc: r-help@r-project.org


 Go back to your calculus text and review the definition of derivative:

 f'(x) = lim h - 0  [f(x+h) - f(x)] / h

 when f(x) and f(x + h) are random variables, the above limit does not
 exist.  In fact, f'(x) is also a random variable.

 Now, if you want the derivative you have to use a multivariate
 integration algorithm that yields a deterministic value.  The function
 `sadmvn' in the package mnormt can do this:

 require(mnormt)

 PP2 - function(p){
    thetac - p
    thetae - 0.323340333
    thetab - -0.280970036
    thetao -  0.770768082
    ssigma  - diag(4)
    ssigma[1,2] -  0.229502120
    ssigma[1,3] -  0.677949335
    ssigma[1,4] -  0.552907745
    ssigma[2,3] -  0.784263100
    ssigma[2,4] -  0.374065025
    ssigma[3,4] -  0.799238700
    ssigma[2,1] -  ssigma[1,2]
    ssigma[3,1] -  ssigma[1,3]
    ssigma[4,1] -  ssigma[1,4]
    ssigma[3,2] -  ssigma[2,3]
    ssigma[4,2] -  ssigma[2,4]
    ssigma[4,3] -  ssigma[3,4]
   pp - sadmvn(lower=rep(-Inf, 4),
 upper=c(thetac,thetae,thetab,thetao), mean=rep(0,4), varcov=ssigma, 
 maxpt=10)
 return(pp)
 }

 xx - -0.6675762

 P2(xx)

 require(numDeriv)

 grad(x=xx, func=PP2)


 I hope this helps,
 Ravi.

 

 Ravi Varadhan, Ph.D.
 Assistant Professor,
 Division of Geriatric Medicine and Gerontology
 School of Medicine
 Johns Hopkins University

 Ph. (410) 502-2619
 email: rvarad...@jhmi.edu


 - Original Message -
 From: SL sl...@yahoo.fr
 Date: Saturday, November 21, 2009 2:42 pm
 Subject: Re: [R] Problem with Numerical derivatives (numDeriv) and mvtnorm
 To: r-help@r-project.org


  Thanks for you comment.
 
  There is certainly some Monte Carlo sampling involved in mvtnorm but
  why derivatives could not be computed? In theory, the derivatives
  exist (eg. bivariate probit). Moreover, when used with optim, there
  are some numerical derivatives computed... does it mean that mvtnorm
  cannot be used in an optimisation problem? I think it hard to believe.
 
  One possibility would be to use the analytical derivatives and then
 a
  do-it-yourself integration but i was looking for something a bit more
  comprehensive. The mvtnorm package uses a specific way to compute
  pmvnorm and I'm far to do a good enough job so that derivatives can
  compare with what mvtnorm can do.
 
  Stef
 
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  R-help@r-project.org mailing list
 
  PLEASE do read the posting guide
  and provide commented, minimal, self-contained, reproducible code.

 __
 R-help@r-project.org mailing list

 PLEASE do read the posting guide
 and provide commented, minimal, self-contained, reproducible code.

 __
 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.


__

[R] mac os X: mprobit fails to install

2009-11-22 Thread stephane Luchini

Hi all,

any chance that someone got through the installation problem of
mprobit on mac os X?

Stephane

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R-help@r-project.org mailing list
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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.

Re: [R] Do you keep an archive of useful R code? and if so - how?

2009-11-22 Thread Joe King

I accidentally sent this directly to the author and didn't reply to the
whole list, I am sorry, I need to remember to hit reply all instead of reply
to the R help list, heres my message:

I keep a separate R file of code I commonly use but more generic. So if I am
making contingency tables I say:

ftable(category, category[top])

or if I am wanting to subset data:

subset2$X5-recode(subset2$X5, 6:10=1:5)

things like that, generic code that I can refer to and include my variables
in as necessary (as you can tell the top mark I made in ftable isn't in
the code but reminds me how the table structures itself. Since I am a newbie
at R I am still keeping notes, I do this for importing things, also
graphics:

xyplot(value~X1,data=subset1,groups=factor(X2),
 type=c(b,g),ylim=c(0,1),xlim=c(1,5),lwd=1,cex = 1,
 plot.points = TRUE,auto.key = list(points = TRUE,lines = TRUE, space =
inside),
 label.curves=FALSE,xlab = x axis title, ylab =  y axis title )

so it just lets me organize my codes on my local system. R wiki is ok, but
will be much better as people expand it, I am sure very soon it will grow
exponentially as a good resource. 

(as you can tell some of the code I save includes old variable names instead
of neutral ones, but easy enough to change).

Joe King
206-913-2912
j...@joepking.com
Never throughout history has a man who lived a life of ease left a name
worth remembering. --Theodore Roosevelt


-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Tal Galili
Sent: Sunday, November 22, 2009 10:31 AM
To: Marc Schwartz
Cc: r-help@r-project.org; Barry Rowlingson; jeff.la...@noaa.gov
Subject: Re: [R] Do you keep an archive of useful R code? and if so - how?

Marc and Barry, many thanks for your detailed answers.

Marc -
I thank you for the links and ideas. Thanks to your advice I will look more
into SVN in the future, although it sounds on the surface to require some
learning curve, so It could take me some time to start using it.

Barry -
I am actually a blog builder in my side profession, I already built myself a
blog called:
r-statistics.com
On which I intend to put up good code I will come across.  The problem with
it though is that I don't see blogs as a good information management system.
Since on a blog one is open to the public and doesn't want to leave half
scribles of thoughts (which IS what ends up happening when managing snippets
of code).  Also, blogging is not build for easy hierarchical ordering.

The idea of a wiki is more appealing.
BTW - another suggestion I got was using MS onenote. Although it is not open
source (which is my preference as well), I understood it offers a powerful
solution.

I hope more people will share how they manage their snippets of code.


Best to all of you,
Tal




Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com/ (English)

--




On Sun, Nov 22, 2009 at 8:09 PM, Marc Schwartz marc_schwa...@me.com wrote:

 Tal,

 I would still use Subversion.

 Think of Subversion as as an electronic filing system. You can organize
 code into project trees, with sub-folders and so forth.

 As you come across code snippets that you want to save, copy them to a
file
 and commit the file to a project tree or sub-folder, based upon the domain
 of functionality. Add related code snippets to the same domains. That way,
 you have related code snippets in a common area, making recall easier.

 The advantage of using a VCS is that you can make trackable modifications
 to the code over time, as your functional requirements change or as you
 discover bugs, etc. to existing code.

 In terms of a GUI, for Windows, it seems that most use Tortoise SVN:

   http://tortoisesvn.net/

 There are cross-platform GUIs such as RapidSVN (
 http://rapidsvn.tigris.org/), but it all depends upon personal
 preferences. More links here:

   http://subversion.tigris.org/links.html#all-clients

 There are also Subversion extensions for editors, such as Emacs, like
 psvn.el (http://www.xsteve.at/prg/vc_svn/) which enable a blending of
 functionality into environments that you may already be using, such as
ESS.

 Last but not least, there are also commercial variants of Subversion
 clients, which of course have a cost associated with them. These are also
 listed on the clients link above.

 An alternative would be to create a local wiki, the implementation
details,
 as with a Subversion repo, would be dependent upon whether or not you are
 the only person that needs access or if access and/or content modification
 are to be shared.

 HTH,

 Marc

 On Nov 22, 2009, at 11:45 AM, Tal Galili wrote:

 Hello Marc and Jeff,
 Thank you for replying.

 I am using winXP, and any

Re: [R] Do you keep an archive of useful R code? and if so - how?

2009-11-22 Thread Carlos J. Gil Bellosta


Hello,

I do keep a blog with R and non R related snippets of code.

Besides that, something like Alfresco, Plone or other document 
management systems could be useful. Maybe the solution is too complex 
for a single user, but you can keep tags and other kind of metadata 
attached to your code and you would have an integrated search engine.


Best regards,

Carlos J. Gil Bellosta
http://www.datanalytics.com



Tal Galili wrote:

Hello all,

When using R for some time, one comes across more and more useful functions.
 But naturally we can't remember all of them, so I imagine some of you save
these snippets of code.
My question to you is how do you manage that code?
Do you use special software, or archiving system?

Any advice is welcomed.

Tal





Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com/ (English)
--

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and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list
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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.

Re: [R] mac os X: mprobit fails to install

2009-11-22 Thread Phil Spector


Stephane -
The check log indicated that malloc.h couldn't be found.
Since that header file  is located  in /usr/include/sys on Macs,
you could do the following:

1.  Download mprobit_0.9-2.tar.gz from your local CRAN mirror.
2.  At a terminal, type

  PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL mprobit_0.9-2.tar.gz

They'll be some warning messages, but the package should get built.

- Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 spec...@stat.berkeley.edu

On Sun, 22 Nov 2009, stephane Luchini wrote:


Hi all,

any chance that someone got through the installation problem of
mprobit on mac os X?

Stephane

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Re: [R] how to tell if its better to standardize your data matrix first when you do principal

2009-11-22 Thread masterinex

so under which cases is it better to standardize the data matrix first ?
also is PCA generally used to predict the response variable , should I
keep that variable in my data matrix ?

Uwe Ligges-3 wrote:

masterinex wrote:

Hi guys ,

Im trying to do principal component analysis in R . There is 2 ways of
doing
it , I believe.
One is doing principal component analysis right away the other way is
standardizing the matrix first using s = scale(m)and then apply
principal
component analysis.
How do I tell what result is better ? What values in particular should i
look at . I already managed to find the eigenvalues and eigenvectors ,
the
proportion of variance for each eigenvector using both methods.

Generally, it is better to standardize. But in some cases, e.g. for the
same units in your variables indicating also the importance, it might
make sense not to do so.
You should think about the analysis, you cannot know which result is
`better' unless you know an interpretation.

I noticed that the proportion of the variance for the first pca without
standardizing had a larger value . Is there a meaning to it ? Isnt this
always the case?
At last , if I am supposed to predict a variable ie weight should I
drop
the variable ie weight from my data matrix when I do principal component
analysis ?

This sounds a bit like homework. If that is the case, please ask your
teacher rather than this list.
Anyway, it does not make sense to predict weight using a linear
combination (principle component) that contains weight, does it?

Uwe Ligges

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Re: [R] consecutive numbering of elements in a matrix

2009-11-22 Thread Jim Bouldin


Thank you Dimitris, that solves it exactly!  I continue to be amazed at how
a single line of code can be so powerful in R, containing so much
information.  Hard as hell to interpret though (for me).
Jim

 one approach is the following:
 
 B - cbind(c(1:6, NA), c(1:3, NA,NA,NA, 4), c(1:3, NA,NA, 4,5))
 matrix(B[order(col(B), B)], nrow(B), ncol(B))
 
 
 I hope it helps.
 
 Best,
 Dimitris


Jim Bouldin, PhD
Research Ecologist
Department of Plant Sciences, UC Davis
Davis CA, 95616
530-554-1740

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Re: [R] mac os X: mprobit fails to install

2009-11-22 Thread SL

I have tried your command but without success. Any idea? Here is my log:

Macbook:$ PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL mprobit_0.9-2.tar.gz

* Installing to library ‘/Users/stephaneluchini/Library/R/2.9/library’
* Installing *source* package ‘mprobit’ ...
** libs
** arch - i386
sh: make: command not found
ERREUR : compilation failed pour le package ‘mprobit’
* Removing ‘/Users/stephaneluchini/Library/R/2.9/library/mprobit’

2009/11/22 Phil Spector spec...@stat.berkeley.edu:
 Stephane -
    The check log indicated that malloc.h couldn't be found.
 Since that header file  is located  in /usr/include/sys on Macs,
 you could do the following:

 1.  Download mprobit_0.9-2.tar.gz from your local CRAN mirror.
 2.  At a terminal, type

      PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL mprobit_0.9-2.tar.gz

 They'll be some warning messages, but the package should get built.

                                        - Phil Spector
                                         Statistical Computing Facility
                                         Department of Statistics
                                         UC Berkeley
                                         spec...@stat.berkeley.edu

 On Sun, 22 Nov 2009, stephane Luchini wrote:

 Hi all,

 any chance that someone got through the installation problem of
 mprobit on mac os X?

 Stephane

 __
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 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
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[R] How to get the factor level means with interaction term?

I thought that the last two statements in the following code should
give me the same results (what I want are the factor level means for
factor 'A'). But they don't.

I think that the last statement should give me the correct factor
level means for 'A'. Could somebody let me know what the problems are
with 'afit$coefficients[1:3]'?

set.seed(0)
a=3
b=4

A=1:a
B=1:b

n=4

X=matrix(nr=a*b*n,nc=2)
colnames(X)=LETTERS[1:2]

for(i_a in 1:a-1) {
  for(i_b in 1:b-1) {
for(i_n in 1:n-1) {
  X[(i_a * b + i_b) * n + i_n + 1, ] = c(i_a+1, i_b+1)
}
  }
}

Y=matrix(nr=a*b*n,nc=1)
for(i in 1:(a*b)) {
  for(i_n in 1:n-1) {
print((i-1)*n+i_n+1,1)
Y[(i-1)*n+i_n+1,1]= rnorm(1)
  }
}

aframe = data.frame(
A=as.factor(X[,'A'])
, B=as.factor(X[,'B'])
, Y)

afit=aov(Y ~ A * B - 1, aframe)
summary(afit)
afit$coefficients[1:3]

lapply(split(aframe$Y, aframe$A),mean)

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Re: [R] Do you keep an archive of useful R code? and if so - how?

2009-11-22 Thread Nikhil Kaza

I 've used tiddlywiki a personal notebook for other things but not for  
R. It may be useful to write a css that separates out code from  
description.


http://www.tiddlywiki.com/

On 22 Nov 2009, at 11:53AM, Tal Galili wrote:


Hello all,

When using R for some time, one comes across more and more useful  
functions.
But naturally we can't remember all of them, so I imagine some of  
you save

these snippets of code.
My question to you is how do you manage that code?
Do you use special software, or archiving system?

Any advice is welcomed.

Tal





Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il  
(Hebrew) |

www.r-statistics.com/ (English)
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[R] where is lme() that is referred by aov() help page?

The help page of aov() mentions lme(). Does it refer to lme() in package nlme?

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Re: [R] where is lme() that is referred by aov() help page?


On 22/11/2009 3:38 PM, Peng Yu wrote:

The help page of aov() mentions lme(). Does it refer to lme() in package nlme?


Yes, that's where the link takes you.

Duncan Murdoch

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Re: [R] mac os X: mprobit fails to install

There were quite a few implicit declaration warning messages when I  
followed Phil's advice, but I do seem to get a complete build on a Mac  
10.5.8 running 64 bit R 2.10.0.


Have you installed the Xcode package? The gcc-4.2?

--
David.
On Nov 22, 2009, at 3:15 PM, SL wrote:

I have tried your command but without success. Any idea? Here is my  
log:


Macbook:$ PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL  
mprobit_0.9-2.tar.gz


* Installing to library ‘/Users/stephaneluchini/Library/R/2.9/library’
* Installing *source* package ‘mprobit’ ...
** libs
** arch - i386
sh: make: command not found
ERREUR : compilation failed pour le package ‘mprobit’
* Removing ‘/Users/stephaneluchini/Library/R/2.9/library/mprobit’

2009/11/22 Phil Spector spec...@stat.berkeley.edu:

Stephane -
   The check log indicated that malloc.h couldn't be found.
Since that header file  is located  in /usr/include/sys on Macs,
you could do the following:

1.  Download mprobit_0.9-2.tar.gz from your local CRAN mirror.
2.  At a terminal, type

 PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL mprobit_0.9-2.tar.gz

They'll be some warning messages, but the package should get built.

   - Phil Spector
Statistical Computing  
Facility

Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu

On Sun, 22 Nov 2009, stephane Luchini wrote:


Hi all,

any chance that someone got through the installation problem of
mprobit on mac os X?

Stephane

__
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.





__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] where is lme() that is referred by aov() help page?

On Sun, Nov 22, 2009 at 2:42 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
 On 22/11/2009 3:38 PM, Peng Yu wrote:

 The help page of aov() mentions lme(). Does it refer to lme() in package
 nlme?

 Yes, that's where the link takes you.

Should this information be mentioned in aov() help page? Because ?lme
does not return anything in my system, I think it is better to mention
where lme is from in aov help page.

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Re: [R] Spatstat, markcorr, max. radius limited??

2009-11-22 Thread Rolf Turner



On 21/11/2009, at 12:01 AM, rudi1...@gmx.de wrote:


Hello,

could please somebody help me. I want to apply the mark correlation  
function but for radii up to 75 meters (in 75 individual 1m steps).  
Unfortunately, There is a sensible default for the values of the  
argument r at which the mark correlation function kf (r) should be  
evaluated, so that I do not get results for r  25m. Can I change  
something in the function to get the required values as written above?


Questions about contributed packages should be addressed, in the  
first instance,

to the maintainer(s) of the package rather than to the R-help list.

I am one of the maintainers, but I'm afraid that I don't know/ 
understand a lot about
the mark correlation function, and Adrian --- the other maintainer,  
who does know a lot ---

is off on holidays, and won't be back till 7 December.

In the mean time let me just say that ``There is a sensible default''  
is probably
an understatement.  The default is what you ***should*** use.  Trying  
to set
your own value of ``r'' will probably give you nonsense.  This is my  
understanding

of the situation, anyway.

That being said --- how do you *know* that you do not get results for  
r  25?
Did you just plot the output from markcorr()?  There is also a  
``sensible default''
for the x-axis limits, which is used *unless xlim is specified* in  
your call to
plot().  Did you try specifying xlim to extend to something about r =  
25?


And ***that*** being said, you probably shouldn't!  Given that the  
``sensible
default'' for xlim is c(0,25) then it seems to me very likely that  
***it is simply

not meaningful*** to consider the mark correlation function for r  25.

I cannot explain to you *why* it is not meaningful, but I'm sure that  
were this
not the case Adrian would not have written the function this way.   
When he gets
back from hols Adrian may be able to explain to you just why it is  
not meaningful

to consider r  25 in your setting.

Finally let me draw to your attention a quote from the late great  
John Tukey:



The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from the given
body of data.



The fact that you have an aching desire to know the value of the mark
correlation function at values of r  25 does not guarantee that  
reasonable

estimates of these values can be found from the data that you have
available.

cheers,

Rolf Turner

##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}

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Re: [R] mac os X: mprobit fails to install

2009-11-22 Thread stephane Luchini

Thanks.

I have 10.5.8 with R 2.10.0 now (i still had 2.9 in my previous
messages). I also have gcc-4.2 installed but no Xcode package.

It still fails to install - can it be the Xcode package? Where can I
find it - I don't have my install CDs with me and will not get them
soon?

Stephane

2009/11/22 David Winsemius dwinsem...@comcast.net:
There were quite a few implicit declaration warning messages when I
followed Phil's advice, but I do seem to get a complete build on a Mac
10.5.8 running 64 bit R 2.10.0.

Have you installed the Xcode package? The gcc-4.2?

--
David.
On Nov 22, 2009, at 3:15 PM, SL wrote:

I have tried your command but without success. Any idea? Here is my log:

Macbook:$ PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL mprobit_0.9-2.tar.gz

* Installing to library ‘/Users/stephaneluchini/Library/R/2.9/library’
* Installing *source* package ‘mprobit’ ...
** libs
** arch - i386
sh: make: command not found
ERREUR : compilation failed pour le package ‘mprobit’
* Removing ‘/Users/stephaneluchini/Library/R/2.9/library/mprobit’

2009/11/22 Phil Spector spec...@stat.berkeley.edu:

Stephane -
The check log indicated that malloc.h couldn't be found.
Since that header file is located in /usr/include/sys on Macs,
you could do the following:

1. Download mprobit_0.9-2.tar.gz from your local CRAN mirror.
2. At a terminal, type

PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL mprobit_0.9-2.tar.gz

They'll be some warning messages, but the package should get built.

- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu

On Sun, 22 Nov 2009, stephane Luchini wrote:

Hi all,

any chance that someone got through the installation problem of
mprobit on mac os X?

Stephane

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
R-help@r-project.org mailing list
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Re: [R] where is lme() that is referred by aov() help page?


On 22/11/2009 3:44 PM, Peng Yu wrote:

On Sun, Nov 22, 2009 at 2:42 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:

On 22/11/2009 3:38 PM, Peng Yu wrote:

The help page of aov() mentions lme(). Does it refer to lme() in package
nlme?

Yes, that's where the link takes you.


Should this information be mentioned in aov() help page? Because ?lme
does not return anything in my system, I think it is better to mention
where lme is from in aov help page.


It links to the right page.

Duncan Murdoch

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[R] any equivalent SUM IF statement in R

2009-11-22 Thread ychu066


for example, i want to sum all the row entries if column 1 takes the value
boy. anyone knows ?
-- 
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Re: [R] mac os X: mprobit fails to install



On Nov 22, 2009, at 4:00 PM, stephane Luchini wrote:


Thanks.

I have 10.5.8 with R 2.10.0 now (i still had 2.9 in my previous
messages). I also have gcc-4.2 installed but no Xcode package.

It still fails to install - can it be the Xcode package? Where can I
find it - I don't have my install CDs with me and will not get them
soon?


Xcode is distributed free by Apple through its developer program. All  
you need to do is register, again, free, or at least it used to be so.  
You could also check the tools section of CRAN. I am not sufficient  
UNIXified to be an authoritative source on these issues.


--
David


Stephane


2009/11/22 David Winsemius dwinsem...@comcast.net:

There were quite a few implicit declaration warning messages when I
followed Phil's advice, but I do seem to get a complete build on a  
Mac

10.5.8 running 64 bit R 2.10.0.

Have you installed the Xcode package? The gcc-4.2?

--
David.
On Nov 22, 2009, at 3:15 PM, SL wrote:

I have tried your command but without success. Any idea? Here is  
my log:


Macbook:$ PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL  
mprobit_0.9-2.tar.gz


* Installing to library ‘/Users/stephaneluchini/Library/R/2.9/ 
library’

* Installing *source* package ‘mprobit’ ...
** libs
** arch - i386
sh: make: command not found
ERREUR : compilation failed pour le package ‘mprobit’
* Removing ‘/Users/stephaneluchini/Library/R/2.9/library/mprobit’

2009/11/22 Phil Spector spec...@stat.berkeley.edu:


Stephane -
  The check log indicated that malloc.h couldn't be found.
Since that header file  is located  in /usr/include/sys on Macs,
you could do the following:

1.  Download mprobit_0.9-2.tar.gz from your local CRAN mirror.
2.  At a terminal, type

PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL  
mprobit_0.9-2.tar.gz


They'll be some warning messages, but the package should get built.

  - Phil Spector
   Statistical Computing  
Facility

   Department of Statistics
   UC Berkeley
   spec...@stat.berkeley.edu

On Sun, 22 Nov 2009, stephane Luchini wrote:


Hi all,

any chance that someone got through the installation problem of
mprobit on mac os X?

Stephane

__
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.





__
R-help@r-project.org mailing list
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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.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] any equivalent SUM IF statement in R


On 22/11/2009 3:44 PM, ychu066 wrote:

for example, i want to sum all the row entries if column 1 takes the value
boy. anyone knows ?


Subset then sum:

sum(M[M[,1] == boy, ])

Duncan Murdoch

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Re: [R] any equivalent SUM IF statement in R


Presumably you want all the columns _except_ column 1, right?

Perhaps (no code, no test) :

sum( dta[ dta[,1]==boy , -1 ] )

--  
David.

On Nov 22, 2009, at 3:44 PM, ychu066 wrote:



for example, i want to sum all the row entries if column 1 takes the  
value

boy. anyone knows ?
--
View this message in context: 
http://old.nabble.com/any-equivalent-SUM-IF-statement-in-R-tp26467889p26467889.html
Sent from the R help mailing list archive at Nabble.com.

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Heritage Laboratories
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Re: [R] contour(): lines labels in different colours?

2009-11-22 Thread Peter Ehlers


Hi Ted,

This won't solve your problem, but a small improvement might
be to place the labels over the lines rather than the other
way around. It will definitely avoid putting red lines over
black ones:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2)
contour(z, lty=0, labcex=1, add=TRUE)

Cheers,
Peter


(Ted Harding) wrote:

Greetings, All!
I want to draw contour lines in red, using contour(), but also
have the contour labels (for the level-values) in black so that
they will stand out against a coloured background already generated
using filled.contour() (the background shades from green at low
levels of risk to red at high levels).

In any case, contour labels in red are already somewhat inconspicuous
with contour lines in red, regardless of background.

I see nothing in ?contour nor in ?par about this.

One way to approach it could be to first draw the labelled contours
in black, and then overlay by re-drawing (with out labels) in red.
This would sort-of work, but the red contour lines would then cut
through the black numbers, which is somewhat undesirable. Also
(I've tried it) you can get show-through along the contour lines
from the black layer, which is nasty.

Any suggestions?

With thanks,
Ted.


E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 22-Nov-09   Time: 17:06:08
-- XFMail --

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Re: [R] how do i persuade IT to install R on PCs ?? ...and should I ??

2009-11-22 Thread RICHARD M. HEIBERGER

Please also look at the R document
http://www.r-project.org/doc/R-FDA.pdf
and ask your IT department to read this document

Rich

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Re: [R] how to tell if its better to standardize your data matrix first when you do principal

2009-11-22 Thread hadley wickham

You've asked the same question on stackoverflow.com and received the
same answer. This is rude because it duplicates effort. If you
urgently need a response to a question, perhaps you should consider
paying for it.

Hadley

On Sun, Nov 22, 2009 at 12:04 PM, masterinex xevilgan...@hotmail.com wrote:

so under which cases is it better to standardize the data matrix first ?
also is PCA generally used to predict the response variable , should I
keep that variable in my data matrix ?

Uwe Ligges-3 wrote:

masterinex wrote:

Hi guys ,

Uwe Ligges

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Re: [R] contour(): lines labels in different colours?



On Nov 22, 2009, at 4:57 PM, Peter Ehlers wrote:


Hi Ted,

This won't solve your problem, but a small improvement might
be to place the labels over the lines rather than the other
way around. It will definitely avoid putting red lines over
black ones:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2)
contour(z, lty=0, labcex=1, add=TRUE)


I played around a bit with you example, and can get almost the desired  
color and lack of cutting through labels. There is the possibility of  
plotting empty labels that create a space in the curves for the later  
labels-without-lines overlay:


x - -6:16
z - outer(x,x)
contour(z, labels=, col=2, labcex=1.5, drawlabels=TRUE)
contour(z, lty=0, labcex=1.5, add=TRUE)




Cheers,
Peter


(Ted Harding) wrote:

Greetings, All!
I want to draw contour lines in red, using contour(), but also
have the contour labels (for the level-values) in black so that
they will stand out against a coloured background already generated
using filled.contour() (the background shades from green at low
levels of risk to red at high levels).
In any case, contour labels in red are already somewhat inconspicuous
with contour lines in red, regardless of background.
I see nothing in ?contour nor in ?par about this.
One way to approach it could be to first draw the labelled contours
in black, and then overlay by re-drawing (with out labels) in red.
This would sort-of work, but the red contour lines would then cut
through the black numbers, which is somewhat undesirable. Also
(I've tried it) you can get show-through along the contour lines
from the black layer, which is nasty.
Any suggestions?
With thanks,
Ted.

E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 22-Nov-09   Time: 17:06:08
-- XFMail --
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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[R] how to generate balanced sample from two normal distribution

2009-11-22 Thread gcheer3


Good afternoon,

I have a question on generating simple randomization data. Thanks for any
suggestions.

Two normal distribution N(0,1) and N(1,1)

A: I want to generate 20 data, 10 from N(0,1) and 10 from (1,1). each
observation's indicator (either is from N(0,1) or N(1,1) ) is randomized. I
need use the frist 10 data from the generated 20 dataset. (it is not
necessary 5 from N(0,1) and 5 from N(1,1) for these 10 data, since the
indicator for the 20 data is randomized) . For example, the 10 data's
indicator could be 0 0 0 1 0 1 1 0 0 0  (0 means the observation is from
N(0,1) and 1 indicates the observations is from N(1,1))

B: still the same 20 data generate data above. I want the indictor is forced
to be balanced in the first 10 data. That is, if I use the first 10 data, 5
are from N(0,1) and 5 are from (1,1). For example, the 10 data's indicator
could be 0 1 1 0 0 1 0 1 1 0 

How can I generate the 20 data . Sorry it is a little confusing. I want to
generate the data not the indicator. The dataset I want to generated in A is
not balanced for the frist 10, in B it is balanced in the first 10. I want
to use the same dataset, how can I use to method to randomize it.

Thanks
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Re: [R] mac os X: mprobit fails to install


Xcode is available for download here:

  http://developer.apple.com/technology/xcode.html

As David noted, you do need to register, but it is free. Note also  
that it is a 750 Mb download.


HTH,

Marc Schwartz

On Nov 22, 2009, at 3:11 PM, David Winsemius wrote:



On Nov 22, 2009, at 4:00 PM, stephane Luchini wrote:


Thanks.

I have 10.5.8 with R 2.10.0 now (i still had 2.9 in my previous
messages). I also have gcc-4.2 installed but no Xcode package.

It still fails to install - can it be the Xcode package? Where can I
find it - I don't have my install CDs with me and will not get them
soon?


Xcode is distributed free by Apple through its developer program.  
All you need to do is register, again, free, or at least it used to  
be so. You could also check the tools section of CRAN. I am not  
sufficient UNIXified to be an authoritative source on these issues.


--
David


Stephane


2009/11/22 David Winsemius dwinsem...@comcast.net:
There were quite a few implicit declaration warning messages  
when I
followed Phil's advice, but I do seem to get a complete build on a  
Mac

10.5.8 running 64 bit R 2.10.0.

Have you installed the Xcode package? The gcc-4.2?

--
David.
On Nov 22, 2009, at 3:15 PM, SL wrote:

I have tried your command but without success. Any idea? Here is  
my log:


Macbook:$ PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL  
mprobit_0.9-2.tar.gz


* Installing to library ‘/Users/stephaneluchini/Library/R/2.9/ 
library’

* Installing *source* package ‘mprobit’ ...
** libs
** arch - i386
sh: make: command not found
ERREUR : compilation failed pour le package ‘mprobit’
* Removing ‘/Users/stephaneluchini/Library/R/2.9/library/mprobit’

2009/11/22 Phil Spector spec...@stat.berkeley.edu:


Stephane -
 The check log indicated that malloc.h couldn't be found.
Since that header file  is located  in /usr/include/sys on Macs,
you could do the following:

1.  Download mprobit_0.9-2.tar.gz from your local CRAN mirror.
2.  At a terminal, type

   PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL  
mprobit_0.9-2.tar.gz


They'll be some warning messages, but the package should get  
built.


 - Phil Spector
  Statistical Computing  
Facility

  Department of Statistics
  UC Berkeley
  spec...@stat.berkeley.edu

On Sun, 22 Nov 2009, stephane Luchini wrote:


Hi all,

any chance that someone got through the installation problem of
mprobit on mac os X?

Stephane

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code.






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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] mac os X: mprobit fails to install

2009-11-22 Thread SL

Thanks to all, that was it! Xcode needed to be installed. For those
who did not update to snow Leopard, things could be a bit tricky
because apple did delete links to previous versions in search engines.
On their site, one has to search through their download section.

For snow leopard: version 3.2.1
For leopard : version 3.1.4 did the trick for me.

I now can load mprobit in R - I still have to do some testing.

Thanks again.

Stephane





2009/11/22 Marc Schwartz marc_schwa...@me.com:
 Xcode is available for download here:

  http://developer.apple.com/technology/xcode.html

 As David noted, you do need to register, but it is free. Note also that it
 is a 750 Mb download.

 HTH,

 Marc Schwartz

 On Nov 22, 2009, at 3:11 PM, David Winsemius wrote:


 On Nov 22, 2009, at 4:00 PM, stephane Luchini wrote:

 Thanks.

 I have 10.5.8 with R 2.10.0 now (i still had 2.9 in my previous
 messages). I also have gcc-4.2 installed but no Xcode package.

 It still fails to install - can it be the Xcode package? Where can I
 find it - I don't have my install CDs with me and will not get them
 soon?

 Xcode is distributed free by Apple through its developer program. All you
 need to do is register, again, free, or at least it used to be so. You could
 also check the tools section of CRAN. I am not sufficient UNIXified to be an
 authoritative source on these issues.

 --
 David

 Stephane


 2009/11/22 David Winsemius dwinsem...@comcast.net:

 There were quite a few implicit declaration warning messages when I
 followed Phil's advice, but I do seem to get a complete build on a Mac
 10.5.8 running 64 bit R 2.10.0.

 Have you installed the Xcode package? The gcc-4.2?

 --
 David.
 On Nov 22, 2009, at 3:15 PM, SL wrote:

 I have tried your command but without success. Any idea? Here is my
 log:

 Macbook:$ PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL
 mprobit_0.9-2.tar.gz

 * Installing to library ‘/Users/stephaneluchini/Library/R/2.9/library’
 * Installing *source* package ‘mprobit’ ...
 ** libs
 ** arch - i386
 sh: make: command not found
 ERREUR : compilation failed pour le package ‘mprobit’
 * Removing ‘/Users/stephaneluchini/Library/R/2.9/library/mprobit’

 2009/11/22 Phil Spector spec...@stat.berkeley.edu:

 Stephane -
  The check log indicated that malloc.h couldn't be found.
 Since that header file  is located  in /usr/include/sys on Macs,
 you could do the following:

 1.  Download mprobit_0.9-2.tar.gz from your local CRAN mirror.
 2.  At a terminal, type

   PKG_CFLAGS=-I/usr/include/sys R CMD INSTALL mprobit_0.9-2.tar.gz

 They'll be some warning messages, but the package should get built.

                                     - Phil Spector
                                      Statistical Computing Facility
                                      Department of Statistics
                                      UC Berkeley
                                      spec...@stat.berkeley.edu

 On Sun, 22 Nov 2009, stephane Luchini wrote:

 Hi all,

 any chance that someone got through the installation problem of
 mprobit on mac os X?

 Stephane

 __
 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
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 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
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 David Winsemius, MD
 Heritage Laboratories
 West Hartford, CT

 __
 R-help@r-project.org mailing list
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Re: [R] how do i persuade IT to install R on PCs ?? ...and should I ??

2009-11-22 Thread stephen's mailinglist account

On Sun, Nov 22, 2009 at 11:14 AM, frenchcr frenc...@btinternet.com wrote:

Please help me persuade IT to install R on my computer!

All suggestions welcome.

Our IT department run scared when you mention software that they have no
working experience of.

I need to know the pros and cons of having R on corporate desktops.

Please no funny stuff, this is quite a serious issue for us.

Pros and cons would be good.

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

I requested to have R installed at work.
For me it helped that I have a lot of non-standard technical packages anyway
that are off radar for support from the IT department anyway - they only
support for original install rights anyway.
They wanted to know what the licence was - GPL is recognised and they don't
run a mile.
I did my homework and found some other people on a company research site
were already using R so I could use that as justification.
I had some code ready to run that could produce graphs easily that are very
hard to do in Excel and require a lot of custom code (and even then aren't
good).
We do use some other stats packages anyway and are being encouraged to use
proper packages rather than kludging through in Excel
References like this (below) have been circulated at work which adds weight
to arguments that we should not just accept the 'standard' Office install.
Although I did not use this in my justification.

@ARTICLE{,
author = {B.D. McCullough and David A. Heiser},
title = {On the accuracy of statistical procedures in Microsoft Excel
2007},
journal = {Computational Statistics \ Data Analysis},
year = {2008},
volume = {52},
pages = {4570--4578},
number = {10}
}

( http://dx.doi.org/10.1016/j.csda.2008.03.004)
I use R via TINN-R (http://www.sciviews.org/Tinn-R/) on a Windows desktop.

Stephen

[[alternative HTML version deleted]]

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Re: [R] contour(): lines labels in different colours?


On 22/11/2009 5:21 PM, David Winsemius wrote:

On Nov 22, 2009, at 4:57 PM, Peter Ehlers wrote:


Hi Ted,

This won't solve your problem, but a small improvement might
be to place the labels over the lines rather than the other
way around. It will definitely avoid putting red lines over
black ones:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2)
contour(z, lty=0, labcex=1, add=TRUE)


I played around a bit with you example, and can get almost the desired  
color and lack of cutting through labels. There is the possibility of  
plotting empty labels that create a space in the curves for the later  
labels-without-lines overlay:


x - -6:16
z - outer(x,x)
contour(z, labels=, col=2, labcex=1.5, drawlabels=TRUE)
contour(z, lty=0, labcex=1.5, add=TRUE)


That's a nice solution.  You could probably do a bit better in a couple 
of steps:  1st, figure out what the level labels will be (by default, 
pretty(range(z, finite=TRUE), 10) ), then compute an equivalent number 
of spaces, e.g.


levels - pretty(range(z, finite=TRUE), 10)
strwidth(levels, cex=1.5) / strwidth( , cex=0.5)

Then use the appropriate number of spaces as the labels in the first 
plot, and the numbers in the second one.  Do we have a simple function 
to take input like c(10, 12) and produce two character strings 
containing 10 and 12 spaces?


Duncan Murdoch





Cheers,
Peter


(Ted Harding) wrote:

Greetings, All!
I want to draw contour lines in red, using contour(), but also
have the contour labels (for the level-values) in black so that
they will stand out against a coloured background already generated
using filled.contour() (the background shades from green at low
levels of risk to red at high levels).
In any case, contour labels in red are already somewhat inconspicuous
with contour lines in red, regardless of background.
I see nothing in ?contour nor in ?par about this.
One way to approach it could be to first draw the labelled contours
in black, and then overlay by re-drawing (with out labels) in red.
This would sort-of work, but the red contour lines would then cut
through the black numbers, which is somewhat undesirable. Also
(I've tried it) you can get show-through along the contour lines
from the black layer, which is nasty.
Any suggestions?
With thanks,
Ted.

E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 22-Nov-09   Time: 17:06:08
-- XFMail --
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] contour(): lines labels in different colours?


On 22/11/2009 5:35 PM, Duncan Murdoch wrote:

On 22/11/2009 5:21 PM, David Winsemius wrote:

On Nov 22, 2009, at 4:57 PM, Peter Ehlers wrote:


Hi Ted,

This won't solve your problem, but a small improvement might
be to place the labels over the lines rather than the other
way around. It will definitely avoid putting red lines over
black ones:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2)
contour(z, lty=0, labcex=1, add=TRUE)
I played around a bit with you example, and can get almost the desired  
color and lack of cutting through labels. There is the possibility of  
plotting empty labels that create a space in the curves for the later  
labels-without-lines overlay:


x - -6:16
z - outer(x,x)
contour(z, labels=, col=2, labcex=1.5, drawlabels=TRUE)
contour(z, lty=0, labcex=1.5, add=TRUE)


That's a nice solution.  You could probably do a bit better in a couple 
of steps:  1st, figure out what the level labels will be (by default, 
pretty(range(z, finite=TRUE), 10) ), then compute an equivalent number 
of spaces, e.g.


levels - pretty(range(z, finite=TRUE), 10)
strwidth(levels, cex=1.5) / strwidth( , cex=0.5)

Then use the appropriate number of spaces as the labels in the first 
plot, and the numbers in the second one.  Do we have a simple function 
to take input like c(10, 12) and produce two character strings 
containing 10 and 12 spaces?


Here's a little implementation.  It didn't work using different cex 
values for the spaces and the levels, but this seems okay:


x - -6:16
z - outer(x,x)

levels - pretty(range(z, finite=TRUE), 10)
plot.new() # Might want a throwaway plot instead
reps - round(strwidth(levels, cex=1.5) / strwidth( , cex=1.5))
spaces - sapply(reps, function(x) paste(rep( , round(x)), collapse=))
contour(z, labels=spaces, levels=levels, col=2, labcex=1.5, drawlabels=TRUE)
contour(z, lty=0, labcex=1.5, add=TRUE)

Duncan Murdoch

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Re: [R] contour(): lines labels in different colours?



On Nov 22, 2009, at 5:35 PM, Duncan Murdoch wrote:


On 22/11/2009 5:21 PM, David Winsemius wrote:

On Nov 22, 2009, at 4:57 PM, Peter Ehlers wrote:

Hi Ted,

This won't solve your problem, but a small improvement might
be to place the labels over the lines rather than the other
way around. It will definitely avoid putting red lines over
black ones:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2)
contour(z, lty=0, labcex=1, add=TRUE)
I played around a bit with you example, and can get almost the  
desired  color and lack of cutting through labels. There is the  
possibility of  plotting empty labels that create a space in the  
curves for the later  labels-without-lines overlay:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2, labcex=1.5, drawlabels=TRUE)
contour(z, lty=0, labcex=1.5, add=TRUE)


That's a nice solution.  You could probably do a bit better in a  
couple of steps:  1st, figure out what the level labels will be (by  
default, pretty(range(z, finite=TRUE), 10) ), then compute an  
equivalent number of spaces, e.g.


levels - pretty(range(z, finite=TRUE), 10)
strwidth(levels, cex=1.5) / strwidth( , cex=0.5)

Then use the appropriate number of spaces as the labels in the first  
plot, and the numbers in the second one.  Do we have a simple  
function to take input like c(10, 12) and produce two character  
strings containing 10 and 12 spaces?




Not sure it is simple but this (after more playing around) did the  
trick:


library(R.oo)
vecspaces - function(n) sapply(n, function(x)  
paste(rep(intToChar(32), x), sep=, collapse=) )



 vecspaces(c(10,12) )
[1]  

 vecspaces(1:10)
 [1] 
  

 [8] 

--
David


Duncan Murdoch


Cheers,
Peter


(Ted Harding) wrote:

Greetings, All!
I want to draw contour lines in red, using contour(), but also
have the contour labels (for the level-values) in black so that
they will stand out against a coloured background already generated
using filled.contour() (the background shades from green at low
levels of risk to red at high levels).
In any case, contour labels in red are already somewhat  
inconspicuous

with contour lines in red, regardless of background.
I see nothing in ?contour nor in ?par about this.
One way to approach it could be to first draw the labelled contours
in black, and then overlay by re-drawing (with out labels) in red.
This would sort-of work, but the red contour lines would then cut
through the black numbers, which is somewhat undesirable. Also
(I've tried it) you can get show-through along the contour lines
from the black layer, which is nasty.
Any suggestions?
With thanks,
Ted.

E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 22-Nov-09   Time:  
17:06:08
-- XFMail  
--

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David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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[R] optim(,SANN...)

2009-11-22 Thread lloyd barcza

Hi,

Can anyone please tell me is there a way to view the annealing schedule when 
using SANN is optim. I have tried setting report=1 in the control list, but 
cannot seem to get it to work?

Ant help or suggestions would be appreciated!

Thanks

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[R] Removing + and ? signs

2009-11-22 Thread Steven Kang

Hi all,


I get an error message when trying to replace *+* or *?* signs (with empty
space) from a string.

x - asdf+,jkl?

gsub(?,  , x)


Error message:

Error in
gsub(?,  , x) :
  invalid regular expression '?'
In addition: Warning message:
In gsub(?,  , x) :
  regcomp error:  'Invalid preceding regular expression'

Your expertise in resolving this issue would be appreciated.

Thanks.



Steven

[[alternative HTML version deleted]]

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[R] Missing/Incomplete Data Study

2009-11-22 Thread helpme

Hi, I have a project where unsupervised learning failed to produce rules
using Weka. I wanted to know if there are any tools in R that can be used to
assess how well timestamps of event, task, load, and hardware logs for
completeness or missing and incomplete data to be able to know whether it
impacted our unsupervised approach.

Please advise.

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Re: [R] contour(): lines labels in different colours?

2009-11-22 Thread Ted Harding

Wow! (Top-posting for once, since there's no natural other place ...)

Thanks Peter, David and Duuncan for the suggestions. I'll look at the
later ones from David  Duncan later (it's getting late here).
However, as something to work on if you want to, here is a toy
example, based on the same overall methodology as I'm using for
my real plot (though the real one looks quite different):

#
library(MASS)
set.seed(54321)
X - rnorm(100) ; Y - rnorm(100)
h0 - 2.0
W  - kde2d(x=X,y=Y,n=100,h=c(h0,h0),lims=c(-3,3,-3,3))
Wmax - max(W$z)
W$z  - 10*(W$z/Wmax)
Palette - colorRampPalette(c(lightgreen,red),
interpolate=spline )
Levels - (1.0*(0:10))
filled.contour(x=W$x,y=W$y,z=W$z,levels=Levels,
   xlim=c(-3,3),ylim=c(-3,3),
   color.palette=Palette,
  plot.axes={axis(1);axis(2);points(X,Y,pch=+,col=blue);
 points(X,Y,pch=+,col=blue);
 contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
 col=red,add=TRUE, labels= , method=flattest
);
 contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
 lty=0,col=black,add=TRUE, method=flattest
);
}
)
#

I've incorporated here the first two suggestiong from Peter and
David, though not (yet) any of the later ones. One thing that emerges
is that the two contour() plots don't quite match up as to where
(or whether) the space from 'labels= ' in the first are made,
and the placing of the labels in the second.

I'll try the other suggestions and see what happens -- but I may
end up doing the first plot (red) without labels, so that there's
no break in the contours. Better, I think, to have the black labels
simply stuck onto the red contours, than have some of them misaligned
with bvreaks in the contours.

Thank you all!
Ted.


On 22-Nov-09 22:53:03, David Winsemius wrote:
 
 On Nov 22, 2009, at 5:35 PM, Duncan Murdoch wrote:
 
 On 22/11/2009 5:21 PM, David Winsemius wrote:
 On Nov 22, 2009, at 4:57 PM, Peter Ehlers wrote:
 Hi Ted,

 This won't solve your problem, but a small improvement might
 be to place the labels over the lines rather than the other
 way around. It will definitely avoid putting red lines over
 black ones:

 x - -6:16
 z - outer(x,x)
 contour(z, labels=, col=2)
 contour(z, lty=0, labcex=1, add=TRUE)
 I played around a bit with you example, and can get almost the  
 desired  color and lack of cutting through labels. There is the  
 possibility of  plotting empty labels that create a space in the  
 curves for the later  labels-without-lines overlay:
 x - -6:16
 z - outer(x,x)
 contour(z, labels=, col=2, labcex=1.5, drawlabels=TRUE)
 contour(z, lty=0, labcex=1.5, add=TRUE)

 That's a nice solution.  You could probably do a bit better in a  
 couple of steps:  1st, figure out what the level labels will be (by  
 default, pretty(range(z, finite=TRUE), 10) ), then compute an  
 equivalent number of spaces, e.g.

 levels - pretty(range(z, finite=TRUE), 10)
 strwidth(levels, cex=1.5) / strwidth( , cex=0.5)

 Then use the appropriate number of spaces as the labels in the first  
 plot, and the numbers in the second one.  Do we have a simple  
 function to take input like c(10, 12) and produce two character  
 strings containing 10 and 12 spaces?

 
 Not sure it is simple but this (after more playing around) did the  
 trick:
 
 library(R.oo)
 vecspaces - function(n) sapply(n, function(x)  
 paste(rep(intToChar(32), x), sep=, collapse=) )
 
 
   vecspaces(c(10,12) )
 [1]  
 
   vecspaces(1:10)
   [1]
   
   [8] 
 
 -- 
 David
 
 Duncan Murdoch

 Cheers,
 Peter


 (Ted Harding) wrote:
 Greetings, All!
 I want to draw contour lines in red, using contour(), but also
 have the contour labels (for the level-values) in black so that
 they will stand out against a coloured background already generated
 using filled.contour() (the background shades from green at low
 levels of risk to red at high levels).
 In any case, contour labels in red are already somewhat  
 inconspicuous
 with contour lines in red, regardless of background.
 I see nothing in ?contour nor in ?par about this.
 One way to approach it could be to first draw the labelled contours
 in black, and then overlay by re-drawing (with out labels) in red.
 This would sort-of work, but the red contour lines would then cut
 through the black numbers, which is somewhat undesirable. Also
 (I've tried it) you can get show-through along the contour lines
 from the black layer, which is nasty.
 Any suggestions?
 With thanks,
 Ted.
 
 E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
 Fax-to-email: +44 (0)870 094 0861
 Date: 22-Nov-09   Time:  
 17:06:08
 -- XFMail

Re: [R] how do i persuade IT to install R on PCs ?? ...and should I ??

On Nov 22, 2009, at 4:45 PM, stephen's mailinglist account wrote:

On Sun, Nov 22, 2009 at 11:14 AM, frenchcr frenc...@btinternet.com
wrote:

Please help me persuade IT to install R on my computer!

All suggestions welcome.

Our IT department run scared when you mention software that they
have no

working experience of.

I need to know the pros and cons of having R on corporate desktops.

Please no funny stuff, this is quite a serious issue for us.

Pros and cons would be good.

Thanks.
--
View this message in context:
http://old.nabble.com/how-do-i-persuade-IT-to-install-R-on-PCs...and-should-Itp26464163p26464163.html
Sent from the R help mailing list archive at Nabble.com.

I requested to have R installed at work.
For me it helped that I have a lot of non-standard technical
packages anyway
that are off radar for support from the IT department anyway - they
only

support for original install rights anyway.
They wanted to know what the licence was - GPL is recognised and
they don't

run a mile.
I did my homework and found some other people on a company research
site

were already using R so I could use that as justification.
I had some code ready to run that could produce graphs easily that
are very
hard to do in Excel and require a lot of custom code (and even then
aren't

good).
We do use some other stats packages anyway and are being encouraged
to use

proper packages rather than kludging through in Excel
References like this (below) have been circulated at work which adds
weight
to arguments that we should not just accept the 'standard' Office
install.

Although I did not use this in my justification.

@ARTICLE{,
author = {B.D. McCullough and David A. Heiser},

I'm not surprised to see McCollough and Heiser's names on such an
article. They have both a long track record of pointing out Excel's
statistical deficiencies. (I don't they did so together in the past.)
MS has turned a deaf ear to their efforts to point the way to correct
methods. It is truly amazing that MS continues to ignore constrictive
criticism and that such arrogance is compounded by corporate policies
encouraging reliance on demonstrably faulty tools. The full list of
articles documenting MS's resistance to statistical corrections would
be much longer that just this one article and extends back more than a
decade.

title = {On the accuracy of statistical procedures in Microsoft Excel
2007},
journal = {Computational Statistics \ Data Analysis},
year = {2008},
volume = {52},
pages = {4570--4578},
number = {10}
}

( http://dx.doi.org/10.1016/j.csda.2008.03.004)
I use R via TINN-R (http://www.sciviews.org/Tinn-R/) on a Windows
desktop.

Stephen

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] Removing + and ? signs

2009-11-22 Thread jim holtman

'?' is a metacharacter in a regular expression.  You have to escape it:

 x - asdf+,jkl?

 gsub(?,  , x)
Error in gsub(?,  , x) : invalid regular expression '?'
In addition: Warning message:
In gsub(?,  , x) :
  regcomp error:  'Invalid preceding regular expression'
 # escape it
 gsub(\\?,  , x)
[1] asdf+,jkl 


On Sun, Nov 22, 2009 at 6:01 PM, Steven Kang stochastick...@gmail.com wrote:
 Hi all,


 I get an error message when trying to replace *+* or *?* signs (with empty
 space) from a string.

 x - asdf+,jkl?

 gsub(?,  , x)


 Error message:

 Error in
 gsub(?,  , x) :
  invalid regular expression '?'
 In addition: Warning message:
 In gsub(?,  , x) :
  regcomp error:  'Invalid preceding regular expression'

 Your expertise in resolving this issue would be appreciated.

 Thanks.



 Steven

        [[alternative HTML version deleted]]

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-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

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Re: [R] Removing + and ? signs

2009-11-22 Thread Linlin Yan

Try this:
gsub([?],  , x)

On Mon, Nov 23, 2009 at 7:01 AM, Steven Kang stochastick...@gmail.com wrote:
 Hi all,


 I get an error message when trying to replace *+* or *?* signs (with empty
 space) from a string.

 x - asdf+,jkl?

 gsub(?,  , x)


 Error message:

 Error in
 gsub(?,  , x) :
  invalid regular expression '?'
 In addition: Warning message:
 In gsub(?,  , x) :
  regcomp error:  'Invalid preceding regular expression'

 Your expertise in resolving this issue would be appreciated.

 Thanks.



 Steven

        [[alternative HTML version deleted]]

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 https://stat.ethz.ch/mailman/listinfo/r-help
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 and provide commented, minimal, self-contained, reproducible code.


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Re: [R] Removing + and ? signs

2009-11-22 Thread Jorge Ivan Velez

Dear Steven,

You were almost there:

 x - asdf+,jkl?
 gsub(\\?, , x)
[1] asdf+,jkl

 gsub(\\+, , x)
[1] asdf,jkl?

Take a look at the Basic Regular Expressions section in ?regex for more
details.

HTH,
Jorge


On Sun, Nov 22, 2009 at 6:01 PM, Steven Kang  wrote:

 Hi all,


 I get an error message when trying to replace *+* or *?* signs (with empty
 space) from a string.

 x - asdf+,jkl?

 gsub(?,  , x)


 Error message:

 Error in
 gsub(?,  , x) :
  invalid regular expression '?'
 In addition: Warning message:
 In gsub(?,  , x) :
  regcomp error:  'Invalid preceding regular expression'

 Your expertise in resolving this issue would be appreciated.

 Thanks.



 Steven

[[alternative HTML version deleted]]

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 https://stat.ethz.ch/mailman/listinfo/r-help
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 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


[[alternative HTML version deleted]]

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Re: [R] Removing + and ? signs

2009-11-22 Thread Rolf Turner



On 23/11/2009, at 12:01 PM, Steven Kang wrote:


Hi all,


I get an error message when trying to replace *+* or *?* signs  
(with empty

space) from a string.

x - asdf+,jkl?

gsub(?,  , x)


Error message:

Error in
gsub(?,  , x) :
  invalid regular expression '?'
In addition: Warning message:
In gsub(?,  , x) :
  regcomp error:  'Invalid preceding regular expression'

Your expertise in resolving this issue would be appreciated.


(a) That's funny.  I don't get an error message when I try your example.
I get

[1]  a s d f + , j k l ? 

Of course that's not what you want, though.

(b) You need to escape the question mark:

  gsub(\\?,  , x)

yields

[1] asdf+,jkl 

which I think *is* what you want.

cheers,

Rolf Turner



##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}

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Re: [R] Removing + and ? signs

2009-11-22 Thread Jorge Ivan Velez

And if you want to replace both + and ?, here is a suggestion:

x - asdf+,jkl?
gsub([?]|[+], , x)
# [1] asdf,jkl

HTH,
Jorge


On Sun, Nov 22, 2009 at 6:46 PM, Jorge Ivan Velez  wrote:

 Dear Steven,

 You were almost there:

  x - asdf+,jkl?
  gsub(\\?, , x)
 [1] asdf+,jkl

  gsub(\\+, , x)
 [1] asdf,jkl?

 Take a look at the Basic Regular Expressions section in ?regex for more
 details.

 HTH,
 Jorge


 On Sun, Nov 22, 2009 at 6:01 PM, Steven Kang  wrote:

 Hi all,


 I get an error message when trying to replace *+* or *?* signs (with empty
 space) from a string.

 x - asdf+,jkl?

 gsub(?,  , x)


 Error message:

 Error in
 gsub(?,  , x) :
  invalid regular expression '?'
 In addition: Warning message:
 In gsub(?,  , x) :
  regcomp error:  'Invalid preceding regular expression'

 Your expertise in resolving this issue would be appreciated.

 Thanks.



 Steven

[[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.




[[alternative HTML version deleted]]

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Re: [R] Removing + and ? signs



On Nov 22, 2009, at 6:01 PM, Steven Kang wrote:


Hi all,


I get an error message when trying to replace *+* or *?* signs (with  
empty

space) from a string.

x - asdf+,jkl?

gsub(?,  , x)


Since both ? and + are special regex characters, to do both the  
substitutions at once you need to use double backslashes and an or


 gsub(\\?|\\+,  , x)
[1] asdf ,jkl 

--
David




Error message:

Error in
gsub(?,  , x) :
 invalid regular expression '?'
In addition: Warning message:
In gsub(?,  , x) :
 regcomp error:  'Invalid preceding regular expression'

Your expertise in resolving this issue would be appreciated.

Thanks.



Steven

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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[R] How to change line width in heatmap.2()?

I don't see an option to tune linewdith in heatmap.2(). Could somebody
let me know how to tune the dendrogram line width?

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Re: [R] how to prevent lattic barchart from drawing bar completely to the bottom/left of the chart

2009-11-22 Thread RICHARD M. HEIBERGER

?panel.barchart

use the argument

origin=0

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Re: [R] contour(): lines labels in different colours?


On 22/11/2009 6:28 PM, (Ted Harding) wrote:

Wow! (Top-posting for once, since there's no natural other place ...)

Thanks Peter, David and Duuncan for the suggestions. I'll look at the
later ones from David  Duncan later (it's getting late here).
However, as something to work on if you want to, here is a toy
example, based on the same overall methodology as I'm using for
my real plot (though the real one looks quite different):

#
library(MASS)
set.seed(54321)
X - rnorm(100) ; Y - rnorm(100)
h0 - 2.0
W  - kde2d(x=X,y=Y,n=100,h=c(h0,h0),lims=c(-3,3,-3,3))
Wmax - max(W$z)
W$z  - 10*(W$z/Wmax)
Palette - colorRampPalette(c(lightgreen,red),
interpolate=spline )
Levels - (1.0*(0:10))
filled.contour(x=W$x,y=W$y,z=W$z,levels=Levels,
   xlim=c(-3,3),ylim=c(-3,3),
   color.palette=Palette,
  plot.axes={axis(1);axis(2);points(X,Y,pch=+,col=blue);
 points(X,Y,pch=+,col=blue);
 contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
 col=red,add=TRUE, labels= , method=flattest
);
 contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
 lty=0,col=black,add=TRUE, method=flattest
);
}
)
#

I've incorporated here the first two suggestiong from Peter and
David, though not (yet) any of the later ones. One thing that emerges
is that the two contour() plots don't quite match up as to where
(or whether) the space from 'labels= ' in the first are made,
and the placing of the labels in the second.

I'll try the other suggestions and see what happens -- but I may
end up doing the first plot (red) without labels, so that there's
no break in the contours. Better, I think, to have the black labels
simply stuck onto the red contours, than have some of them misaligned
with bvreaks in the contours.


Here's a version of the last one I posted:

filled.contour(x=W$x,y=W$y,z=W$z,levels=Levels,
   xlim=c(-3,3),ylim=c(-3,3),
   color.palette=Palette,
  plot.axes={axis(1);axis(2);points(X,Y,pch=+,col=blue);
 points(X,Y,pch=+,col=blue);
 reps - round(strwidth(Levels, cex=1.5) / strwidth( , 
cex=1.5))
	   spaces - sapply(reps, function(x) paste(rep( , round(x)), 
collapse=))


contour(x=W$x,y=W$y,z=W$z,labels=spaces,levels=Levels,labcex=1.5,
 col=red,add=TRUE, method=flattest, drawlabels=TRUE
);
 contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
 lty=0,col=black,add=TRUE, method=flattest
);
}
)

Duncan Murdoch



Thank you all!
Ted.


On 22-Nov-09 22:53:03, David Winsemius wrote:

On Nov 22, 2009, at 5:35 PM, Duncan Murdoch wrote:


On 22/11/2009 5:21 PM, David Winsemius wrote:

On Nov 22, 2009, at 4:57 PM, Peter Ehlers wrote:

Hi Ted,

This won't solve your problem, but a small improvement might
be to place the labels over the lines rather than the other
way around. It will definitely avoid putting red lines over
black ones:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2)
contour(z, lty=0, labcex=1, add=TRUE)
I played around a bit with you example, and can get almost the  
desired  color and lack of cutting through labels. There is the  
possibility of  plotting empty labels that create a space in the  
curves for the later  labels-without-lines overlay:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2, labcex=1.5, drawlabels=TRUE)
contour(z, lty=0, labcex=1.5, add=TRUE)
That's a nice solution.  You could probably do a bit better in a  
couple of steps:  1st, figure out what the level labels will be (by  
default, pretty(range(z, finite=TRUE), 10) ), then compute an  
equivalent number of spaces, e.g.


levels - pretty(range(z, finite=TRUE), 10)
strwidth(levels, cex=1.5) / strwidth( , cex=0.5)

Then use the appropriate number of spaces as the labels in the first  
plot, and the numbers in the second one.  Do we have a simple  
function to take input like c(10, 12) and produce two character  
strings containing 10 and 12 spaces?


Not sure it is simple but this (after more playing around) did the  
trick:


library(R.oo)
vecspaces - function(n) sapply(n, function(x)  
paste(rep(intToChar(32), x), sep=, collapse=) )



  vecspaces(c(10,12) )
[1]  

  vecspaces(1:10)
  [1]
  

  [8] 

--
David


Duncan Murdoch


Cheers,
Peter


(Ted Harding) wrote:

Greetings, All!
I want to draw contour lines in red, using contour(), but also
have the contour labels (for the level-values) in black so that
they will stand out against a coloured background already generated
using filled.contour() (the background shades from green at low
levels of risk to red at high levels).
In any case, contour labels in red are already somewhat  
inconspicuous

with contour lines in red,

[R] Help about stability analysis in R software!!!

2009-11-22 Thread lugobueno


   Â

   Hello  people!! I'm trying to make a statistical analysis of stability
   through to package 'Agricolae', and procedure 'stability.par', but I don't
   get conclude the analysis. The problem is in my data set, that have missing
   value, and I didn't manage interpret the 'NA' used to assign missing value.
   Someone have any suggestion to solve the problem?
   I thank from now on!
   Regards,
   LuÃce.
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Re: [R] contour(): lines labels in different colours?



On Nov 22, 2009, at 8:01 PM, Duncan Murdoch wrote:


On 22/11/2009 6:28 PM, (Ted Harding) wrote:

Wow! (Top-posting for once, since there's no natural other place ...)
Thanks Peter, David and Duuncan for the suggestions. I'll look at the
later ones from David  Duncan later (it's getting late here).
However, as something to work on if you want to, here is a toy
example, based on the same overall methodology as I'm using for
my real plot (though the real one looks quite different):
#
library(MASS)
set.seed(54321)
X - rnorm(100) ; Y - rnorm(100)
h0 - 2.0
W  - kde2d(x=X,y=Y,n=100,h=c(h0,h0),lims=c(-3,3,-3,3))
Wmax - max(W$z)
W$z  - 10*(W$z/Wmax)
Palette - colorRampPalette(c(lightgreen,red),
   interpolate=spline )
Levels - (1.0*(0:10))
filled.contour(x=W$x,y=W$y,z=W$z,levels=Levels,
  xlim=c(-3,3),ylim=c(-3,3),
  color.palette=Palette,
 plot.axes={axis(1);axis(2);points(X,Y,pch=+,col=blue);
points(X,Y,pch=+,col=blue);
contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
col=red,add=TRUE, labels= , method=flattest
   );
contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
lty=0,col=black,add=TRUE, method=flattest
   );
   }
)
#
I've incorporated here the first two suggestiong from Peter and
David, though not (yet) any of the later ones. One thing that emerges
is that the two contour() plots don't quite match up as to where
(or whether) the space from 'labels= ' in the first are made,
and the placing of the labels in the second.
I'll try the other suggestions and see what happens -- but I may
end up doing the first plot (red) without labels, so that there's
no break in the contours. Better, I think, to have the black labels
simply stuck onto the red contours, than have some of them misaligned
with bvreaks in the contours.


Here's a version of the last one I posted:

filled.contour(x=W$x,y=W$y,z=W$z,levels=Levels,
  xlim=c(-3,3),ylim=c(-3,3),
  color.palette=Palette,
 plot.axes={axis(1);axis(2);points(X,Y,pch=+,col=blue);
points(X,Y,pch=+,col=blue);
reps - round(strwidth(Levels, cex=1.5) / strwidth( ,  
cex=1.5))
	   spaces - sapply(reps, function(x) paste(rep( , round(x)),  
collapse=))

contour(x=W$x,y=W$y,z=W$z,labels=spaces,levels=Levels,labcex=1.5,
col=red,add=TRUE, method=flattest,  
drawlabels=TRUE

   );
contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
lty=0,col=black,add=TRUE, method=flattest
   );
   }
)

I thought the code was good, although there is a duplicated points ()  
call, but the offered colorPallete would be improved by going to  
lightyellow to blue and the points to orange. Also got bold labels  
to work. Still takes a bit of experimentation with the width of the  
space string when you vary the number of points for some reason:


library(MASS)
set.seed(54321)
X - rnorm(500) ; Y - rnorm(500)
h0 - 2.0
W  - kde2d(x=X,y=Y,n=100,h=c(h0,h0),lims=c(-3,3,-3,3))
Wmax - max(W$z)
W$z  - 10*(W$z/Wmax)
Palette - colorRampPalette(c(lightyellow,blue),
   interpolate=spline )
Levels - (1.0*(0:10))
filled.contour(x=W$x,y=W$y,z=W$z,levels=Levels,
  xlim=c(-3,3),ylim=c(-3,3),
  color.palette=Palette,
 plot.axes={axis(1);axis(2);
points(X,Y,pch=+,col=orange, cex=.8);
contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
col=red,add=TRUE, labels=  , method=flattest
   );
contour(x=W$x,y=W$y,z=W$z,levels=Levels,labcex=1.5,
lty=0,col=black,vfont=c(sans serif, bold),  
add=TRUE, method=flattest

   );
   }
)



Duncan Murdoch


Thank you all!
Ted.
On 22-Nov-09 22:53:03, David Winsemius wrote:

On Nov 22, 2009, at 5:35 PM, Duncan Murdoch wrote:


On 22/11/2009 5:21 PM, David Winsemius wrote:

On Nov 22, 2009, at 4:57 PM, Peter Ehlers wrote:

Hi Ted,

This won't solve your problem, but a small improvement might
be to place the labels over the lines rather than the other
way around. It will definitely avoid putting red lines over
black ones:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2)
contour(z, lty=0, labcex=1, add=TRUE)
I played around a bit with you example, and can get almost the   
desired  color and lack of cutting through labels. There is the   
possibility of  plotting empty labels that create a space in  
the  curves for the later  labels-without-lines overlay:

x - -6:16
z - outer(x,x)
contour(z, labels=, col=2, labcex=1.5, drawlabels=TRUE)
contour(z, lty=0, labcex=1.5, add=TRUE)
That's a nice solution.  You could probably do a bit better in a   
couple of steps:  1st, figure out what the level labels will be  
(by  default, pretty(range(z, finite=TRUE), 10) ), then compute  
an  equivalent number of

Re: [R] how to tell if its better to standardize your data matrix first when you do principal

2009-11-22 Thread masterinex

Hi Hadley ,

I really apreciate the suggestions you gave, It was helpful , but I still
didnt quite get it all. and I really want to do a good job , so any
comments would sure come helpful, please understand me .

hadley wrote:

Hadley

On Sun, Nov 22, 2009 at 12:04 PM, masterinex xevilgan...@hotmail.com
wrote:

so under which cases is it better to standardize the data matrix first
?
also is PCA generally used to predict the response variable , should I
keep that variable in my data matrix ?

Uwe Ligges-3 wrote:

masterinex wrote:

Hi guys ,

Im trying to do principal component analysis in R . There is 2 ways of
doing
it , I believe.
One is doing principal component analysis right away the other way is
standardizing the matrix first using s = scale(m)and then apply
principal
component analysis.
How do I tell what result is better ? What values in particular should
i
look at . I already managed to find the eigenvalues and eigenvectors ,
the
proportion of variance for each eigenvector using both methods.

I noticed that the proportion of the variance for the first pca
without
standardizing had a larger value . Is there a meaning to it ? Isnt
this
always the case?
At last , if I am supposed to predict a variable ie weight should I
drop
the variable ie weight from my data matrix when I do principal
component
analysis ?

Uwe Ligges

--
http://had.co.nz/

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Re: [R] how to generate balanced sample from two normal distribution

2009-11-22 Thread gcheer3

Thank you, Dennis.

It really helps. That is what I want, for the first 10 obs in A, it is not
necessary balanced. for the first 10 obs in B, it is balanced.

But there is one thing I need maybe I didn't say it clear. I generate 20
observations first, I want permutation in these 20 then select the first
ten. For the SAME 20 observation, I want permutation happens among the first
ten and also the second ten. How can I use the same dataset (generated 20
observations) to do two kinds of permutations? Thanks a lot.

gcheer3 wrote:

Good afternoon,

I have a question on generating simple randomization data. Thanks for any
suggestions.

Two normal distribution N(0,1) and N(1,1)

A: I want to generate 20 data, 10 from N(0,1) and 10 from (1,1). each
observation's indicator (either is from N(0,1) or N(1,1) ) is randomized.
I need use the frist 10 data from the generated 20 dataset. (it is not
necessary 5 from N(0,1) and 5 from N(1,1) for these 10 data, since the
indicator for the 20 data is randomized) . For example, the 10 data's
indicator could be 0 0 0 1 0 1 1 0 0 0 (0 means the observation is from
N(0,1) and 1 indicates the observations is from N(1,1))

B: still the same 20 data generate data above. I want the indictor is
forced to be balanced in the first 10 data. That is, if I use the first 10
data, 5 are from N(0,1) and 5 are from (1,1). For example, the 10 data's
indicator could be 0 1 1 0 0 1 0 1 1 0

How can I generate the 20 data . Sorry it is a little confusing. I want to
generate the data not the indicator. The dataset I want to generated in A
is not balanced for the frist 10, in B it is balanced in the first 10. I
want to use the same dataset, how can I use to method to randomize it.

Thanks

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Re: [R] How do I change the colour and format for the trelli plot ?

2009-11-22 Thread ychu066


NICE!!! thanks 

Deepayan Sarkar wrote:
 
 On Thu, Nov 19, 2009 at 6:03 AM, ychu066 ychu...@aucklanduni.ac.nz
 wrote:

 http://old.nabble.com/file/p26418382/hist1.png hist1.png  i want three
 plots
 along on the side , how to i do that ?

  and I also want to change the colour of the bars for each plot, how do i
 do
 that ?

 i got the code here to draw that ..
 
 This code did not produce the plot you have linked to. The answer to
 your question depends on how you created the plot, so you have to tell
 us that. Changing the color in all panels is easy:
 
 histogram(rnorm(100), col = goldenrod)
 
 Different colors in different panels is a little more work:
 
 histogram(~rnorm(100) | gl(3, 1, 100),
   mycolors = sample(colors(), 3),
   panel = function(..., col, mycolors) {
   panel.histogram(..., col = mycolors[panel.number()])
   })
 
 -Deepayan
 
 columns - 8:153
 plots - vector(list, length(columns))
 j - 0
 for (i in columns)
 {
  plots[[ j - j+1 ]] -
    histogram( ~ data[,i],
      ylab = Frequency, xlab = Score,
      xlim = c(1,5), ylim = c(0,100),
      main = colnames(data)[i]
    )
 }

 print(plots[[1]])

 # or export

 for (i in seq_along(plots))
 {
  png(paste(hist, i, .png, sep = ))
  print(plots[[i]])
  dev.off()
 }
 --
 View this message in context:
 http://old.nabble.com/How-do-I-change-the-colour-and-format-for-the-trelli-plot---tp26418382p26418382.html
 Sent from the R help mailing list archive at Nabble.com.

 __
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 http://www.R-project.org/posting-guide.html
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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
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-- 
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Re: [R] How do I change the colour and format for the trelli plot ?

2009-11-22 Thread ychu066


anyone know how to add some text on the panel ??? for example 2.5, 50 and
1000 are mearsured in Litre, and i want to put the units beside the
measurements.  How could i do that? 




ychu066 wrote:
 
 NICE!!! thanks 
 
 Deepayan Sarkar wrote:
 
 On Thu, Nov 19, 2009 at 6:03 AM, ychu066 ychu...@aucklanduni.ac.nz
 wrote:

 http://old.nabble.com/file/p26418382/hist1.png hist1.png  i want three
 plots
 along on the side , how to i do that ?

  and I also want to change the colour of the bars for each plot, how do
 i do
 that ?

 i got the code here to draw that ..
 
 This code did not produce the plot you have linked to. The answer to
 your question depends on how you created the plot, so you have to tell
 us that. Changing the color in all panels is easy:
 
 histogram(rnorm(100), col = goldenrod)
 
 Different colors in different panels is a little more work:
 
 histogram(~rnorm(100) | gl(3, 1, 100),
   mycolors = sample(colors(), 3),
   panel = function(..., col, mycolors) {
   panel.histogram(..., col = mycolors[panel.number()])
   })
 
 -Deepayan
 
 columns - 8:153
 plots - vector(list, length(columns))
 j - 0
 for (i in columns)
 {
  plots[[ j - j+1 ]] -
    histogram( ~ data[,i],
      ylab = Frequency, xlab = Score,
      xlim = c(1,5), ylim = c(0,100),
      main = colnames(data)[i]
    )
 }

 print(plots[[1]])

 # or export

 for (i in seq_along(plots))
 {
  png(paste(hist, i, .png, sep = ))
  print(plots[[i]])
  dev.off()
 }
 --
 View this message in context:
 http://old.nabble.com/How-do-I-change-the-colour-and-format-for-the-trelli-plot---tp26418382p26418382.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 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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 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
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http://old.nabble.com/file/p26471713/hist1.png hist1.png 
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Re: [R] Help about stability analysis in R software!!!