date:20120618


Hello,

Have you tried what I wrote in my last post?
Revised:

# Make a copy first, and operate on the copy.
dep - departures
names(dep) - NULL
dep - data.frame(dep)


Rui Barradas

Em 18-06-2012 11:09, capital_P escreveu:


David Winsemius wrote


That's going to remove a lot of rows.

Since you are not telling us what columns correspond to those
concepts, I'm going to use the terms you are. Something along the
lines of:

require(lattice)
histogram( ~ hours | bird,  data=dat2, nint =24 , xlim=c(0,24))
histogram( ~ hours ,data=dat2,  nint =24 , xlim=c(0,24))

The result on that example was just a list with one element, a
dataframe.

   str(departures)
List of 1
   $ 121.3:'data.frame':1 obs. of  4 variables:
..$ device_info_serial: int 121
..$ hour  : int 10
..$ time  : POSIXct[1:1], format: 2009-05-21 04:59:24
..$ tripID: int 3

So to get what you might have expected

   dep - departures[[1]]
   dep
device_info_serial hourtime tripID
1121   10 2009-05-21 04:59:24  3

But since you didn't actually describe what you did want (or if you
did you left upthread), its only a guess.



I'll try to explain my goals more clearly.

The columns are:

dat2$device_info_serial: The 'number' of the bird, ranging from 121 to 542.
There are 34 different birds, each with their own number.

dat2$tripID: The number of the trip. Every bird has a trip 1, 2, 3, etc.
(some birds have as much as 265 trips, many have less). Every trip has many
measurements, as trips take hours and measurements were taken every 15
minutes.

dat2$time: The time at which a measurement was taken.

dat2$hour: The 'hour' part of dat2$time; the hour in which a measurement was
taken



From my dataset, I need to gather only the first measurement of every trip

of every bird. This way, I can make (circular) graphs of the departure-times
for each trip of each bird. I think that I am very close after using:

departures - lapply(split(dat2, list(dat2$device_info_serial,
dat2$tripID)), function(x) x[x$time == min(x$time),])

But it is in the wrong format. I need it to be in a format so that I can use
commands such as departures$hour and departures$device_info_serial. I need
this so that I can circulise (circularise?) dat2$hour and so that I can make
graphs for each bird seperately.

Making the graphs etc. shouldn't be a problem if I have a dataset that I can
use like this:

d121 - departures[which(departures$device_info_serial == 121),]
d130 - departures[which(departures$device_info_serial == 130),]
d132 - departures[which(departures$device_info_serial == 132),]
d133 - departures[which(departures$device_info_serial == 133),]

and

cdAll - circular(departures$hour, units='hours', template='clock24')
cd121 - circular(d121$hour, units='hours', template='clock24')
cd130 - circular(d130$hour, units='hours', template='clock24')
cd132 - circular(d132$hour, units='hours', template='clock24')

So, if I'm not mistaken, I only need your help with transforming the
'departures' that I have now into something with $hour and
$device_info_serial. I hope this is possible.

I hope my ignorance isn't frustrating you too much. I'm trying my best to
understand and learn how to work with R in the short timespan that I have.

Peter

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Re: [R] noob requesting help

2012-06-18 Thread capital_P


Rui Barradas wrote
 
 Try
 
 names(departures) - NULL
 dep - data.frame(departures[ !sapply(departures, is.null) ])
 
 You now have data.frame 'dep'.
 

dep - data.frame(departures[ !sapply(departures, is.null) ])
Error in data.frame(`121.1` = list(device_info_serial = integer(0), hour =
integer(0),  : 
  arguments imply differing number of rows: 0, 1, 2

 dep - departures
 names(dep) - NULL
 dep - data.frame(dep)
Error in data.frame(list(device_info_serial = integer(0), hour = integer(0), 
: 
  arguments imply differing number of rows: 0, 1, 2

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Re: [R] some help to improve hist to plot relative frequencies

2012-06-18 Thread Deepayan Sarkar

On Fri, Jun 15, 2012 at 9:22 PM, gianni lavaredo
gianni.lavar...@gmail.com wrote:
 Dear Researches,

 sorry for disturb. I wish to improve my figure in R plotting the relative
 frequencies of my data set.

 library(lattice)
 a - c(0,0,0,1,1,2,4,5,6,7,7,7,7,7,8,8,8,8,9,9,9,9,10,10,11)
 histogram(a, xlab=myData)

 what i wish to do is:

 1) invert the order of X and Y (eg: Precent of Total on X-axis and MyData
 on X-axis)
 2) plot not the bar of histogram but a line (i tried with
 lines(density(a)) but the result is not what i wish)

Take your pick:

ta - table(a)

dotplot(ta, type = h, lwd = 2, origin = 0)

dotplot(100 * prop.table(ta), type = h, lwd = 2, origin = 0,
xlab = Percent of total)

xyplot(as.numeric(names(ta)) ~ 100 * prop.table(ta),
   type = h, lwd = 2, origin = 0, horizontal = TRUE,
   xlab = Percent of total, ylab = myData,
   xlim = c(-1, NA))

-Deepayan

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Re: [R] How to specify newdata in a Cox-Modell with a time dependent interaction term?

2012-06-18 Thread Terry Therneau

I've been out for a week, with one more to go.  I'll look at this in 
earnest when I return.
  Terry T

On 06/17/2012 04:07 AM, Jürgen Biedermann wrote:
 Dear John,

 Thank you very much for your help! It was very important for getting 
 along further.

 I found out some additional things which I want to give back to you as 
 feedback (maybe other persons will have the same problems).

 It's also possible to leave away the individual=T argument.
 Instead you can use:

 newdata.1- 
 data.frame(unique(Rossi.2[c(start,stop)]),fin=0,age=30,prio=5,Id=1,arrest.time=0)
 fit - survfit(mod.allison.5, newdata.1, id=Id) *but not* fit - 
 survfit(mod.allison.5, newdata.1, id=Id)

 so you have to leave away the  in specifying the id variable -- 
 maybe the help file could be more precise here.

 Additionally I found out some more things while dealing with my 
 original data.

 It's very important to specify the Surv object and the formula 
 directly in the coxph function, *so don't do this:*

 SurvO - Surv(Rossi.2$start, Rossi.2$stop, Rossi.2$arrest.time)
 form - as.formula(SurvO ~ fin + age + age:stop + prio)
 mod.allison.5- coxph(form,
   data=Rossi.2)
 mod.allison.5

 newdata.1- 
 data.frame(unique(Rossi.2[c(start,stop)]),fin=0,age=30,prio=5,arrest.time=0)
 fit - survfit(mod.allison.5, newdata.1, individual=T)
  Fehler in model.frame.default(data = newdata.1, formula = SurvO ~ 
 fin +  :
   Variablenlängen sind unterschiedlich (gefunden für 'fin')
 -- Error, length of variables are different

 I think the error message is not optimal here, anyway.

 The problem obviously consists in the survfit-function not recognizing 
 the names of the variables anymore.
 It seems completely logic, but anyway, it took me many hours.

 Thanks again,
 Jürgen



 - Korrespondenz --

 Betreff: Re: How to specify newdata in a Cox-Modell with a time 
 dependent interaction term?
 Von: John Fox j...@mcmaster.ca
 An: J?rgen Biedermann juergen.biederm...@googlemail.com
 Datum: 16.06.2012 17:22
 Dear Jurgen,

 fit- survfit(mod.allison.5, newdata.1, individual=TRUE)
 fit
 Call: survfit(formula = mod.allison.5, newdata = newdata.1, individual = 
 TRUE)

 records   n.max n.start  events  median 0.95LCL 0.95UCL
19809 432 432 114  NA  NA  NA

 plot(fit)  # shows one survival curve

 See ?survfit.coxph.

 Best,
   John


 On Sat, 16 Jun 2012 16:23:41 +0200
   Jürgen Biedermannjuergen.biederm...@googlemail.com  wrote:
 Dear John,

 Thank you very much for the quick answer. I will use the mentioned citation 
 of your book in the future.

 However:
 The Id argument is necessary for the function to know that the different 
 rows belong to one individual.

 Or how the Help-File says:

 id:
 optional variable name of subject identifiers. If this is present, then 
 each group
 of rows with the same subject id represents the covariate path through time 
 of
 a single subject, and the result will contain one curve per subject. If the 
 coxph
 fit had strata then that must also be specified in newdata. If missing, 
 then each
 individual row of newdata is presumed to represent a distinct subject and 
 there
 will be nrow(newdata) times the number of strata curves in the result (one 
 for
 each strata/subject combination).

 I tried your proposal anyway, but, as expected, fifty different survival 
 curves appeared.

 So, there is still no solution.

 Best regards
 Jürgen

 -- 
 ---
 Jürgen Biedermann
 Bergmannstraße 3
 10961 Berlin-Kreuzberg
 Mobil: +49 176 247 54 354
 Home: +49 30 940 53 044
 e-mail:juergen.biederm...@gmail.com


 - Korrespondenz --

 Betreff: Re: How to specify newdata in a Cox-Modell with a time dependent 
 interaction term?
 Von: John Foxj...@mcmaster.ca
 An: J?rgen Biedermannjuergen.biederm...@googlemail.com
 Datum: 16.06.2012 15:55
 Dear Jürgen,

 All the values of your Id variable are equal to 1; how can that make 
 sense? Removing the argument Id=id may get you what you want.

 By the way, the document to which you refer was an appendix to a 2002 book 
 that has been superseded by Fox and Weisberg, An R Companion to Applied 
 Regression, Second Edition (Sage, 2011). Appendices for that book are 
 available 
 athttp://socserv.socsci.mcmaster.ca/jfox/Books/Companion/appendix.html.

 I hope this helps,
John

 
 John Fox
 Sen. William McMaster Prof. of Social Statistics
 Department of Sociology
 McMaster University
 Hamilton, Ontario, Canada
 http://socserv.mcmaster.ca/jfox/

 On Sat, 16 Jun 2012 15:04:48 +0200
Jürgen Biedermannjuergen.biederm...@googlemail.com   wrote:
 Dear Mr. Therneau, Mr. Fox, or to whoever, who has some time...

 I don't find a solution to use the survfit function (package: survival) 
  for a defined pattern of covariates with a Cox-Model including a time 
 dependent interaction term. Somehow the definition of my newdata 
 argument seems to be erroneous.
 I

Re: [R] Loop Help

2012-06-18 Thread jim holtman

What do you mean by only the last j?  write.csv writes to a file you
specify and I assume that you are changing the file name if you are
making successive writes.  You need to provide more detail.

On Mon, Jun 18, 2012 at 5:47 AM, @ngel aggelopou...@gmail.com wrote:
 I think that for now I'll keep it as is and try to clean the data in excel.
 Could someone please tell me how can I export the result to csv, since
 write.csv exports only the last j?
 Thank you so much in advance!

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Re: [R] Loop Help

2012-06-18 Thread @ngel

Hello Jim
thank you so much for your response.
When I use write.csv, on the csv file is saved only the last loop
So when I write 

results.matrix - apply(degree_w(net.static[[i]]), 2, mean)
write.csv(results.matrix, file = results.csv)

instead of getting a 550 line document with all loop results, I only get the
last one!
Could you please help me?
Thank you so much in advance

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Re: [R] Loop Help

2012-06-18 Thread Jeff Newmiller

Then don't do that.

write.csv is designed to write a complete matrix or data frame in one call.  
Combine your list of matrices into one (e.g. using sapply) and write that in 
one call afterward rather than piecewise as you do the calculations.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

@ngel aggelopou...@gmail.com wrote:

Hello Jim
thank you so much for your response.
When I use write.csv, on the csv file is saved only the last loop
So when I write 

results.matrix - apply(degree_w(net.static[[i]]), 2, mean)
write.csv(results.matrix, file = results.csv)

instead of getting a 550 line document with all loop results, I only
get the
last one!
Could you please help me?
Thank you so much in advance

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Re: [R] Efficient distance calculation on big matrix

2012-06-18 Thread Boel Brynedal

Stefan, that looks wonderful! I am most certainly going to try to
download and use your 'wordspace', even though I am unsure on how to
even download it at this point. Many thanks! But yes, I need the
Canberra distance unfortunately. But decreasing the time by more than
60% will save me days! If I can get there.

2012/6/17 Stefan Evert stefa...@collocations.de:

 I'm working on analyzing a large data set, lets asume that
 dim(Data)=c(1000,8700). I want to calculate the canberra distance
 between the columns of this matrix, and using a toy example ('test' is
 a matrix filled with random numbers 0-1):

 system.time(d-as.matrix(dist(t(test), method = canberra, diag = FALSE, 
 upper = FALSE, p = 2)))
    user   system  elapsed
 1417.713 3.219 1421.144
 The system.time results also confuse me a bit, since 99% of the time
 is not system time but user time. What does that mean?

 User time is the time that R spends working on your problem; system time 
 refers to tasks done by the operating system, e.g. disk access, managing 
 locks and, most importantly, swapping when you run out of RAM.  With 
 multi-threading, system time can be much larger than the time that has 
 actually elapsed.


 Is there any way to calculate the distance which would take less time?

 Well, one thing you can do is to get a faster computer. :-)  The command 
 above takes only 670 seconds on my MacBook Pro (without multi-threading).

 Calculating a distance matrix is an expensive computation.  In your example, 
 R has to carry out (8700 * 8700 * 1000) / 2 = 37.8 billion floating point 
 divisions.  With approx. 27 clock cycles per division (according to tables 
 I've found on the Web), this takes at least 340 seconds even on a 3GHz CPU 
 (and ignoring memory access, addition/subtraction, loops, etc.).

 You can shave off some of the time if you implement the distance calculation 
 in C, inline the code to avoid callback functions in loops, operate on 
 columns of the matrix directly (which should be more cache-friendly than 
 rows) and don't check for NA's, NaN's and other degenerate cases.

 I've done just that in my experimental R package wordspace, which isn't on 
 CRAN yet:

 library(wordspace)
 A - matrix(runif(8.7e6), 1000, 8700)

 system.time(d1 - as.matrix(dist(t(A), method=canberra)))
   user  system elapsed
 669.207 2.724 669.305

 system.time(d2 - dist.matrix(A, method=canberra, byrow=FALSE))
   user  system elapsed
 250.534 0.784 250.301

 all(d1 == d2)
 [1] TRUE

 If you aren't tied to Canberra distance, you can use a less expensive metric 
 such as the Manhattan distance for an additional, more substantial speed 
 boost:

 system.time(d3 - dist.matrix(A, method=manhattan, byrow=FALSE))
   user  system elapsed
  42.488   0.999  43.569

 This is still single-threaded, so you can run multiple of these calculations 
 in parallel depending on how many cores your server has.

 Hope this helps,
 Stefan


 PS: In case you'd like to give it a try yourself and aren't daunted by a 
 complete lack of documentation:

        svn checkout svn://scm.r-forge.r-project.org/svnroot/wordspace/pkg


 [ ev...@linglit.tu-darmstadt.de | http://purl.org/stefan.evert ]


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Re: [R] Using Sub

Hi Duncan,

That's right but I want to be able to use this to replace back slashes with 
front slashes when I copy and paste file paths. How can I make this work so I 
don't get this error?

Thanks.
Dan

-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Sent: Friday, June 15, 2012 12:04 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

On 12-06-14 6:23 PM, Lopez, Dan wrote:
 Hi,

 I have been trying to get the sub function to work but can't for the life of 
 me figure it out. I tried looking at ?sub but I think there is something that 
 I am just not understanding.

 Example failed attempts
 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: '\C' is an unrecognized escape in character string starting G:\C

This isn't anything to do with sub(), it's the third string that's the problem. 
 When you say G:\Comp... it thinks you've escaped the C, but there's no such 
escape.

Duncan Murdoch


 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=TRUE)
 Error: '\C' is an unrecognized escape in character string starting G:\C

 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=FALSE)
 Error: '\C' is an unrecognized escape in character string starting 
 G:\C)

 sub(/,\,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: unexpected symbol in sub(/,\,G

 Thanks.
 Dan

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 http://www.R-project.org/posting-guide.html
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Re: [R] out put of loop in list

2012-06-18 Thread jim holtman

I would be good if you showed us what you are doing now.  There are
ways of drawing samples and storing in a list, but we have to see what
you are trying to accomplish.  You could use 'lapply' or do it in a
loop, but the solution would depend on how you are doing things now
and what is the problem you are trying to solve.

On Mon, Jun 18, 2012 at 5:38 AM, solafah bh solafa...@yahoo.com wrote:
 Hello
 I have a loop to draw few samples and I want to but this samples in one list, 
 how I can make this? when I use it , the list show just the last sample. I 
 want to know the correct way to put all samples in one list.

 Regards
 Sulafah
        [[alternative HTML version deleted]]


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Tell me what you want to do, not how you want to do it.

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Re: [R] aligning axis labels in a colorkey from levelplot

2012-06-18 Thread Deepayan Sarkar

On Sat, Jun 16, 2012 at 1:41 PM, Stephen Eglen
s.j.eg...@damtp.cam.ac.uk wrote:
 R does a great job with the fine details regarding plots.  e.g in the
 following:

 library(lattice)
 y - -4:4/10
 xyplot(y~1, las=1)

 the y axis is labelled with numbers -0.4, -0.2, 0.0, 0.2, 0.4 with the
 numbers aligned on the decimal point.

 How do I get the same behaviour in the colorkey of a levelplot?  e.g.

 levelplot(matrix(y,3,3))

 the numbers in the colorkey seem left-aligned, and because of the minus
 sign, the numbers now do not align on the decimal point.  Likewise when
 the number of digits changes:

 levelplot(matrix(4:12,3,3))

Justification is hard-coded, and that's not easy to change. This is
not only for the colorkey; e.g.,

  xyplot(y~1, scales = list(alternating = 3))

will also give you left-aligned axes on the right.

My only suggestion (other than custom labels as suggested by ilai) is

 levelplot(matrix(4:12,3,3), colorkey = list(space = left))

-Deepayan

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Re: [R] Error while installing R on RHEL 6

2012-06-18 Thread manish gupta

I used it but still same error.

Regards

On Mon, Jun 18, 2012 at 7:14 PM, Pascal Oettli kri...@ymail.com wrote:

Hello,

The error message gives you the solution.

Regards

Le 18/06/2012 18:26, Manish Gupta a écrit :

Hi,

I am trying to install R from source and using configure command but
gettting one error message.

*configure: error: --with-readline=yes (default) and headers/libs are not
available*

I am installing on server which is not connected by net so can install by
source only. Can u pls suggest me how to rectify such pblm.

Regards

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--
Manish Gupta (M.Sc Bioinformatics)
Bioinformatics Software Developer (Scientist)
MSC Status company
KL-59200
Malaysia

[[alternative HTML version deleted]]

Re: [R] out put of loop in list


Hello,

Please read the posting guide: to draw samples from what? A vector? 
Matrix? Etc...


Anyway, here it goes. In all cases the result is a list with 4 elements.

# Draw 4 samples of integers from 1 to 10
x - rep(10, 4)

# without replacement
set.seed(1)
lapply(x, sample, size=6)

# with replacement
set.seed(12)
lapply(x, sample, size=6, replace=TRUE)

#

# Draw 4 samples from a vector
# Make up a vector
set.seed(123)
(y - sample(LETTERS, 10))
lapply(1:4, function(i) sample(y, size=6, replace=TRUE))


Hope this helps,

Rui Barradas

Em 18-06-2012 10:38, solafah bh escreveu:

Hello
I have a loop to draw few samples and I want to but this samples in one list, 
how I can make this? when I use it , the list show just the last sample. I want 
to know the correct way to put all samples in one list.

Regards
Sulafah
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[R] making svm work harder

2012-06-18 Thread luiceur

Hi all,

I am working on an optimization of the svm classification function based on
the package e1071. So far we have not been able to find any dataset that
really slows down the application. However, from R users surveys seem that
svm would be a good function to speed up.
Is there any one working with this package and has experienced long time
simulations? Do you know a dataset that could help us to properly profile
the svm? Could you give me an example of how to read it and apply it to svm?

Please, any help would be much appreciated!!!

Best,
L

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Re: [R] checking the validity of the expressions

What does any of this mean?

Can you give a concrete example of the transformation you hope to accomplish?

Michael

On Mon, Jun 18, 2012 at 3:10 AM, arunkumar akpbond...@gmail.com wrote:
 hi

 I have a data and have to convert it into the given expression

 like

 data=1000:2000 and expression is exp()

 The code should be checking the validity of the expressions and give out the
 result that it is valid expression or invalid expression.

 can any one help

 -
 Thanks in Advance
        Arun
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[R] Installation problems in Pander from Github

2012-06-18 Thread avinash barnwal

Hello all,

I was trying to create nice tables in HTML on windows and then got to know
about Pander. I have installed Pandoc, devtools, Rtools (which has same
path as of R ) . I have also gone through the depends of Pander and fixed
it all. Still i am not able to install and getting a conflicting error
of *cannot
cd to directory 'C:/Program' *where i have installed my R , Rtools and
Pandoc.

Please guide me through this installation.

-- 
Avinash Barnwal
Statistics and informatics
Department of Mathematics
IIT Kharagpur

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Re: [R] Package of EM and MI for IRT in R

Possibly Amelia: http://cran.r-project.org/web/packages/Amelia/index.html

Best,
Michael

On Mon, Jun 18, 2012 at 3:19 AM, Kamontip Srihaset
kamonti...@student.chula.ac.th wrote:


 Dear all members,

 I am Phd. candidate student at Chulalongkorn U., Thailand. I am interested in 
 expectation maximization algorithm (EM) and multiple imputation (MI) for 
 imputation missing values(missing at random(MAR) and missing not at random 
 (MNAR)) in IRT (3-PL). So, I want to know about package in R or function of 
 EM and MI for simulate this problem

 I am looking forward your answer.

 sincerely yours,

 Kamontip Srihaset



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[R] Need to append vector to all levels of nested list WITHOUT a loop

2012-06-18 Thread Johannes Reichl

Hi everyone,
 
I have a list betaMoments with 2 levels, e.g.
 
 beta1 = list(
+m = 4,
+v = 5
+)
 beta2 = list(
+m = 6,
+v = 7
+)
 
 betaMoments = list()
 betaMoments[[1]] =  beta1
 betaMoments[[2]] =  beta2

and I have a matrix Names which has the same number of lines as the
list has first level elements (here 2; beta1 and beta2). Now I need to
make every line of Names (e.g. Names[1,] = c(2,3,4)) to become an
element of the corresponding list element. For example, calling
betaMoments[[1]] shall return 
 
 betaMoments[[1]]
$m
[1] 4
 
$v
[1] 5
 
$line
[1] c(2,3,4) ... thats Names[1,]
 
I can not do it with a loop since I need to execute this list
construction way too often. So I need a speedy solution.
 
Would be great if someone could help me, this really keeps me away from
resolving the true issues.
 
Regards, Johannes 
 
 
 


Dr. Johannes Reichl
Project Manager 
Energy Institute at the Johannes Kepler University Linz
Altenberger Straße 69
A-4040 Linz
Tel.: +43-732-2468-5652
Fax: +43-732-2468-5651
Email: rei...@energieinstitut-linz.at 
Web: www.energieinstitut-linz.at
 www.energyefficiency.at

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[R] Error w/ Start up Script

I noticed about a couple weeks ago that my R start up script starting showing 
the below errors, following the line Type 'q()' to quit R

Not sure what I did different and so far it hasn't caused major problems but 
kind of fear that it will.

Can you please help?
I also posted my Rprofile below.

Attempting to load the environment 'package:R.utils'
R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object(s) are masked from 'package:R.methodsS3':

throw.default

The following object(s) are masked from 'package:methods':

getClass, getClasses, getMethods

The following object(s) are masked from 'package:base':

attach, detach, gc, load, save

R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object(s) are masked from 'package:utils':

timestamp

The following object(s) are masked from 'package:base':

cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
warnings

And here is my Rprofile.site file specs:
# Things you might want to change
# options(papersize=a4)
# options(editor=notepad)
# options(pager=internal)

# set the default help type
# options(help_type=text)
options(help_type=html)

# set a site library
# .Library.site - file.path(chartr(\\, /, R.home()), site-library)

# set a CRAN mirror
 local({r - getOption(repos)
   r[CRAN] - http://cran.cnr.Berkeley.edu;
   options(repos=r)})

# Give a fortune cookie, but only to interactive sessions
# (This would need the fortunes package to be installed.)
#  if (interactive())
#fortunes::fortune()


Daniel Lopez
Workforce Analytics  Metrics Team




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Re: [R] How do anova() and Anova(type=III) handle incomplete designs?

2012-06-18 Thread Justin Montemarano

Thanks for your response, John.  That was helpful.

I was using Type III from Anova() as a comparison to some results I had
obtained JMP, which I've lost access to and have moved on to R, and I was
confused by the error.  Given that I do have a continuous covariate, the
analyses are not likely comparable, considering your response.

I am still confused about interpretation of interactions within an anova()
with an incomplete design, as mine is.  Is the interaction term still
informative?

-
Justin Montemarano
Graduate Student
Kent State University - Biological Sciences

http://www.montegraphia.com


On Sat, Jun 16, 2012 at 9:20 PM, John Fox j...@mcmaster.ca wrote:

 Dear Justin,

 anova() and Anova() are entirely different functions; the former is part
 of the standard R distribution and the second part of the car package. By
 default, Anova() produces an error for type-III tests conducted on
 rank-deficient models because the hypotheses tested aren't generally
 sensible.

 From ?Anova:

 singular.ok
 defaults to TRUE for type-II tests, and FALSE for type-III tests (where
 the tests for models with aliased coefficients will not be
 straightforwardly interpretable); if FALSE, a model with aliased
 coefficients produces an error.

 and

 The designations type-II and type-III are borrowed from SAS, but the
 definitions used here do not correspond precisely to those employed by SAS.
 Type-II tests are calculated according to the principle of marginality,
 testing each term after all others, except ignoring the term's higher-order
 relatives; so-called type-III tests violate marginality, testing each term
 in the model after all of the others. This definition of Type-II tests
 corresponds to the tests produced by SAS for analysis-of-variance models,
 where all of the predictors are factors, but not more generally (i.e., when
 there are quantitative predictors). Be very careful in formulating the
 model for type-III tests, or the hypotheses tested will not make sense.

 I hope this helps,
  John

 
 John Fox
 Sen. William McMaster Prof. of Social Statistics
 Department of Sociology
 McMaster University
 Hamilton, Ontario, Canada
 http://socserv.mcmaster.ca/jfox/


 On Fri, 15 Jun 2012 15:01:27 -0400
  Justin Montemarano jmont...@kent.edu wrote:
  Hello all:
 
  I am confused about the output from a lm() model with an incomplete
  design/missing level.
 
  I have two categorical predictors and a continuous covariate (day) that
  I am using to model larval mass (l.mass):
 
  leaf.species has three levels - map, syc, and oak
 
  cond.time has two levels - 30 and 150.
 
  There are no response values for Map-150, so that entire, two-way, level
  is missing.
 
  When running anova() on the model with Type I SS, the full factorial
  design does not return errors; however, using package:car Anova() and
  Type III SS, I receive an singularity error unless I used the argument
  'singular.ok = T' (it is defaulted to F).
 
  So, why don't I receive an error with anova() when I do with Anova(type
  = III)?  How do anova() and Anova() handle incomplete designs, and how
  can interactions of variables with missing levels be interpreted?
 
  I realize these are fairly broad questions, but any insight would be
  helpful. Thanks, all.
 
  Below is code to illustrate my question(s):
 
lmMass - lm(log(l.mass) ~ day*leaf.species + cond.time, data =
  growth.data) #lm() without cond.time interactions
lmMassInt - lm(log(l.mass) ~ day*leaf.species*cond.time, data =
  growth.data) #lm() with cond.time interactions
anova(lmMass); anova(lmMassInt) #ANOVA summary of both models
  with Type I SS
  Analysis of Variance Table
 
  Response: log(l.mass)
 Df  Sum Sq Mean Sq F valuePr(F)
  day1  51.373  51.373 75.7451 2.073e-15
  leaf.species   2   0.340   0.170  0.25060.7786
  cond.time  1   0.161   0.161  0.23690.6271
  day:leaf.species   2   1.296   0.648  0.95510.3867
  Residuals179 121.404   0.678
  Analysis of Variance Table
 
  Response: log(l.mass)
   Df  Sum Sq Mean Sq F value  Pr(F)
  day  1  51.373  51.373 76.5651 1.693e-15
  leaf.species 2   0.340   0.170  0.2533 0.77654
  cond.time1   0.161   0.161  0.2394 0.62523
  day:leaf.species 2   1.296   0.648  0.9655 0.38281
  day:cond.time1   0.080   0.080  0.1198 0.72965
  leaf.species:cond.time   1   1.318   1.318  1.9642 0.16282
  day:leaf.species:cond.time   1   1.915   1.915  2.8539 0.09293
  Residuals  176 118.091   0.671
Anova(lmMass, type = 'III'); Anova(lmMassInt, type = 'III')
  #ANOVA summary of both models with Type III SS
  Anova Table (Type III tests)
 
  Response: log(l.mass)

[R] Obtaining r-squared values from phylogenetic autoregression in ape

2012-06-18 Thread Louise Mair

Hello,

I am trying to carry out a phylogenetic autoregression to test whether my
data show a phylogenetic signal, but I keep calculating bizzare R-squared
values.

My script is:

 library(ape)

 x -
R:1,GK:1)d:1,(MW:1,G:1)n:1)a:1,SPW:1)a:1,WB:1)b:1,(((SPBF:1,PBF:1)n:1,(HBF:1,SWF:1)c:1)i:1,(PE:1,((P:1,C:1)w:1,(MF:1,HF:1)l:1)b:1)c:1)x:1)a:1,((CHB:1,AD:1)a:1,BA:1,SSB:1)i:1,(HB:1,SB:1)b:1)x:1,SC:1)x:1,((BRH:1,PH:1)e:1,(WLH:1,GH:1)b:1)d:1)x:1,DBF:1)a:1)a:1,((WW:1,(OT:1,SW:1)v:1)b:1,B:1)z:1)a:1,((DS:1,GS:1)j:1,(SSS:1,LS:1,(ES:1,SS:1)a:1)b:1)e:1)a;
 treeX - read.tree(text=x)
 treeX - compute.brlen(treeX, method = Grafen)

 data -  c(4.854185,  6.008532,  6.221286,  4.369945, 10.044475,
5.801292,  5.128374,  5.540995,  4.566704, 10.188250,  7.121077,
4.469329,  4.815972,  7.798617,  5.892205,  4.853027,  5.080509,
7.982360,  7.518022,  5.675702, 11.989929,  6.760587,  7.433313,
7.906303,  7.235088,  7.131338,  5.582816, 6.769775, 11.886225,  5.589256,
5.626147,  4.714369,  6.040151,  9.098583,  5.194043,  8.830687, 6.231105)
 species - c( AD,   B,BA,   BRH , C,CHB,  DBF,
DS,   ES,  G,GH,   GK,   GS,  HB,   HBF,  HF,
LS,   MF,  MW,   OT,   P,PBF,  PE,   PH,  R,
SB,SC,   SPBF, SPW,  SS,   SSB, SSS,  SW,   SWF,  WB,
WLH,  WW)
 names(data) - species

 cor.mat - vcv.phylo(treeX, cor=TRUE)
 regr - compar.cheverud(data, cor.mat)

 regr$rhohat
[1] 5.541462

 1 - var(regr$residuals)/var(data)
  [,1]
[1,] -1.333095


I don't understand why the autoregression coefficient falls outside the
interval -1 to 1, or why the calculation for obtaining an R-squared
produces a value that doesn't make sense.

Have I made a mistake in the application of this method, or have I
misunderstood when it is appropriate to use phylogenetic autoregression?

Thanks for your help.

Louise

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Re: [R] Loop Help



On Jun 18, 2012, at 5:47 AM, @ngel wrote:


I think that for now I'll keep it


There is no it in this message. Users of Nabble often fail to read  
the POsitng Guide where it is requested that you include context.




as is and try to clean the data in excel.
Could someone please tell me how can I export the result to csv, since
write.csv exports only the last j?


You are probably not changing the name of the output file as you, in  
some entirely unspecified manner,  loop over arguments to write.csv.



Thank you so much in advance!

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The archive of Rhelp is not at Nabble. And Rhelp is a mailing list,  
not a website.


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Re: [R] noob requesting help


Hello,

Ok, sorry about the misleading tip.
This should do it.


do.call(rbind, dep)


Rui Barradas

Em 18-06-2012 13:32, capital_P escreveu:


Rui Barradas wrote


Try

names(departures) - NULL
dep - data.frame(departures[ !sapply(departures, is.null) ])

You now have data.frame 'dep'.



dep - data.frame(departures[ !sapply(departures, is.null) ])
Error in data.frame(`121.1` = list(device_info_serial = integer(0), hour =
integer(0),  :
   arguments imply differing number of rows: 0, 1, 2


dep - departures
names(dep) - NULL
dep - data.frame(dep)

Error in data.frame(list(device_info_serial = integer(0), hour = integer(0),
:
   arguments imply differing number of rows: 0, 1, 2

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Re: [R] Using Sub

Hi A.K.,

That works but when I copy and paste from Window explorer it will have a single 
backslashes and not double.  It works with double as what you have in your 
example below but not with single as what I would end up passing.

Do you have any other suggestions or methods to accomplish this?

Thanks.
Dan


-Original Message-
From: arun [mailto:smartpink...@yahoo.com] 
Sent: Monday, June 18, 2012 8:59 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

Hi,

I guess you need something like this:

 str1-G:\\Compensation Audits_Reports\\Step Audit\\Steps off Step.accdb
 gsub('','/',str1)
[1] G:/Compensation Audits_Reports/Step Audit/Steps off Step.accdb


A.K.




- Original Message -
From: Lopez, Dan lopez...@llnl.gov
To: Duncan Murdoch murdoch.dun...@gmail.com
Cc: R help r-help@r-project.org
Sent: Monday, June 18, 2012 10:37 AM
Subject: Re: [R] Using Sub

Hi Duncan,

That's right but I want to be able to use this to replace back slashes with 
front slashes when I copy and paste file paths. How can I make this work so I 
don't get this error?

Thanks.
Dan

-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Sent: Friday, June 15, 2012 12:04 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

On 12-06-14 6:23 PM, Lopez, Dan wrote:
 Hi,

 I have been trying to get the sub function to work but can't for the life of 
 me figure it out. I tried looking at ?sub but I think there is something that 
 I am just not understanding.

 Example failed attempts
 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: '\C' is an unrecognized escape in character string starting G:\C

This isn't anything to do with sub(), it's the third string that's the 
problem.  When you say G:\Comp... it thinks you've escaped the C, but there's 
no such escape.

Duncan Murdoch


 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=TRUE)
 Error: '\C' is an unrecognized escape in character string starting G:\C

 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=FALSE)
 Error: '\C' is an unrecognized escape in character string starting 
 G:\C)

 sub(/,\,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: unexpected symbol in sub(/,\,G

 Thanks.
 Dan

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Re: [R] Efficient distance calculation on big matrix

2012-06-18 Thread luke-tierney


It so happens I have been looking at very similar changes, as well as
adding multi-threading support for dist(); these should make it into
R-devel later this summer.

Best,

luke

On Sun, 17 Jun 2012, Stefan Evert wrote:




I'm working on analyzing a large data set, lets asume that
dim(Data)=c(1000,8700). I want to calculate the canberra distance
between the columns of this matrix, and using a toy example ('test' is
a matrix filled with random numbers 0-1):


system.time(d-as.matrix(dist(t(test), method = canberra, diag = FALSE, upper 
= FALSE, p = 2)))

   user   system  elapsed
1417.7133.219 1421.144
The system.time results also confuse me a bit, since 99% of the time
is not system time but user time. What does that mean?


User time is the time that R spends working on your problem; system time refers 
to tasks done by the operating system, e.g. disk access, managing locks and, 
most importantly, swapping when you run out of RAM.  With multi-threading, 
system time can be much larger than the time that has actually elapsed.



Is there any way to calculate the distance which would take less time?


Well, one thing you can do is to get a faster computer. :-)  The command above 
takes only 670 seconds on my MacBook Pro (without multi-threading).

Calculating a distance matrix is an expensive computation.  In your example, R 
has to carry out (8700 * 8700 * 1000) / 2 = 37.8 billion floating point 
divisions.  With approx. 27 clock cycles per division (according to tables I've 
found on the Web), this takes at least 340 seconds even on a 3GHz CPU (and 
ignoring memory access, addition/subtraction, loops, etc.).

You can shave off some of the time if you implement the distance calculation in 
C, inline the code to avoid callback functions in loops, operate on columns of 
the matrix directly (which should be more cache-friendly than rows) and don't 
check for NA's, NaN's and other degenerate cases.

I've done just that in my experimental R package wordspace, which isn't on 
CRAN yet:


library(wordspace)
A - matrix(runif(8.7e6), 1000, 8700)



system.time(d1 - as.matrix(dist(t(A), method=canberra)))

  user  system elapsed
669.207   2.724 669.305


system.time(d2 - dist.matrix(A, method=canberra, byrow=FALSE))

  user  system elapsed
250.534   0.784 250.301


all(d1 == d2)

[1] TRUE

If you aren't tied to Canberra distance, you can use a less expensive metric 
such as the Manhattan distance for an additional, more substantial speed boost:


system.time(d3 - dist.matrix(A, method=manhattan, byrow=FALSE))

  user  system elapsed
42.488   0.999  43.569

This is still single-threaded, so you can run multiple of these calculations in 
parallel depending on how many cores your server has.

Hope this helps,
Stefan


PS: In case you'd like to give it a try yourself and aren't daunted by a 
complete lack of documentation:

svn checkout svn://scm.r-forge.r-project.org/svnroot/wordspace/pkg


[ ev...@linglit.tu-darmstadt.de | http://purl.org/stefan.evert ]

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--
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Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
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Re: [R] SAP ABAP Consultant available

2012-06-18 Thread Q

Please DO NOT put ads for your services on this site. This is a violation
of the R forum terms. I will be forwarding this issue to the appropriate
moderator to take further action.

On Tue, Jun 12, 2012 at 1:37 PM, Kanna ka...@silverxis.com wrote:

[1]Click here to unsubscribe if you no longer wish to receive our emails

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Re: [R] Cholesky decomposition error

2012-06-18 Thread Kjetil Halvorsen

see inline!

On Mon, Jun 18, 2012 at 12:38 AM,  nata...@orchidpharma.com wrote:
 Thanks Kjetil for your detailed code for log-Cholesky but my situation is 
 like optimization of the variables inside the matrix.

But you must of course call my function makemat inside the call
to optim() or whatever function you use for optimization!


Here is an extended example, assuming the functions I have defined earlier:

library(MASS) # for mvrnorm
library(mvtnorm) # for dmvnorm

Let us simulate a multinorma sample with expectation zero (to simplify
the example)
and covariance matrix Sigma:

 Sigma
 [,1] [,2] [,3]
[1,]311
[2,]131
[3,]113


 testdat - mvrnorm(n=100, rep(0, 3), Sigma)

We can calculate the usual maxlik estimator of Sigma:

 (t(testdat) %*% testdat) /100
  [,1]  [,2] [,3]
[1,] 3.2424618 0.9670133 1.673897
[2,] 0.9670133 2.9447654 1.289127
[3,] 1.6738970 1.2891268 3.084106

 objective - function(Sigma) {
sum(apply(testdat, 1, FUN=function(x) dmvnorm(x, rep(0, 3),
Sigma, log=TRUE)))
}
 objective(Sigma)

 start
$diag
[1] 0.5493061 0.4904146 0.4581454

$upper
[1] 0.5773503 0.5773503 0.4082483

 startSigma - c(start$diag, start$upper)
 startSigma
[1] 0.5493061 0.4904146 0.4581454 0.5773503 0.5773503 0.4082483

 objective(Sigma)
[1] -571.5945
 objective(Sigma/3)
[1] -699.0552
 objective(3*Sigma)
[1] -638.9688



Finally:

 optim(startSigma, fn=function(parvec) {
R - makemat(parvec[1:3], parvec[4:6])
S - t(R) %*% R
print(S)   # remove this when works!
   obj - -objective(S)
   obj
}, control=list(REPORT=1))

# with method=BFGS dopes not work well,  because takes too long
# steps! default Nelder-Mead is slow,  but works.


Giving the following output:
  much removed ...
$par
[1] 0.5811796 0.4969062 0.3485920 0.5469560 0.9248746 0.4896758

$value
[1] 567.648

$counts
function gradient
 501   NA

$convergence
[1] 1

$message
NULL

  res - .Last.value
 res$par
[1] 0.5811796 0.4969062 0.3485920 0.5469560 0.9248746 0.4896758
 makemat(res$par[1:3], res$par[4:6])
 [,1] [,2]  [,3]
[1,] 1.788146 0.546956 0.9248746
[2,] 0.00 1.643628 0.4896758
[3,] 0.00 0.00 1.4170710
 R -makemat(res$par[1:3], res$par[4:6])
 t(R) %*% R
  [,1]  [,2] [,3]
[1,] 3.1974676 0.9780374 1.653811
[2,] 0.9780374 3.0006752 1.310711
[3,] 1.6538112 1.3107108 3.103266
 Sigma
 [,1] [,2] [,3]
[1,]311
[2,]131
[3,]113



¿Easy?



 Let me change your own example matrix to explain the problem.

  A martrix is      [,1]         [,2]            [,3]
                [1,]    3*Vs+Vn    1*Vs         1*Vs
                [2,]    1*Vs     3*Vs+Vn    1*Vs
                [3,]    1*Vs     1*Vs       3*Vs+Vn

So make your own makemat function specific to this problem!
which you then use inside the call to optim.

kjetil

 So I have to optimize two variables Vs and Vn using the maximum 
 likelihood function, which need the determinant and inverse of the matrix A 
 to compute the value.

 Isn't it logically correct that I have to seed some initial values for the Vs 
 and Vn and use it for predicting the value of the matrix and check for its 
 positive definite condition,

If you construct the matrix by above method, it will automatically be
posdef, so no need to check!
(except as check on programming ... )

if the condition fulfill, then I have to compute the determinant value
and inverse of the matrix in order to use them in the maximum
likelihood function and the optimization iteration to be carried out
further until parameters converges.

 I sincerely believe that you have points to implements log-Cholesky in my 
 situation, but I am simply not able to see where is the Choleksy 
 decomposition to be implemented in this my workflow.

 Regards,
 B.Nataraj




 -Original Message-
 From: Kjetil Halvorsen [mailto:kjetilbrinchmannhalvor...@gmail.com]
 Sent: Sunday, June 17, 2012 4:10 AM
 To: Nataraj B (ORLL-Biotech)
 Cc: r-help@r-project.org
 Subject: Re: [R] Cholesky decomposition error

 see below.

 On Fri, Jun 15, 2012 at 11:53 PM,  nata...@orchidpharma.com wrote:
 Dear Mr.Kjetil,

 Thanks for your comment. You have already pointed me the article in reply to 
 one of my earlier post to this list and I am following the paper. Now I am 
 checking for condition for positive definiteness for original matrix using a 
 simple script (got from earlier posting in the list) and if the condition 
 passed then the optimization function perform decomposition of the matrix 
 using chol() function.

 I believe all 5 parameterization techniques listed in the paper weigh each 
 other based on its performance and not on accuracy, please correct me if I 
 am wrong. Since I am novice, I just want to start with the easiest method 
 Cholesky for my purpose.

 Are you recommending log-Cholesky function , if so could you please tell me 
 the name of the function which does log-Cholesky

Re: [R] Loop Help

2012-06-18 Thread Özgür Asar

@angel,

You can try append option in write.table

for e.g.

for(i in 1:20)
write.table(i,out.txt,append=T,sep=\t,row.names=F,col.names=F)

This will help you save your all results by writing each results on
subsequent rows.

Hope this helps
Ozgur

Hello Jim
thank you so much for your response.
When I use write.csv, on the csv file is saved only the last loop
So when I write

results.matrix - apply(degree_w(net.static[[i]]), 2, mean)
write.csv(results.matrix, file = results.csv)

instead of getting a 550 line document with all loop results, I only get
the last one!
Could you please help me?
Thank you so much in advance 

--
View this message in context: 
http://r.789695.n4.nabble.com/Loop-Help-tp4633558p4633722.html
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] Package of EM and MI for IRT in R

SEARCH!

Go to rseek.org

Type missing data imputation .

You will bring up several alternatives.

-- Bert

On Mon, Jun 18, 2012 at 8:04 AM, R. Michael Weylandt 
michael.weyla...@gmail.com wrote:

 Possibly Amelia: http://cran.r-project.org/web/packages/Amelia/index.html

 Best,
 Michael

 On Mon, Jun 18, 2012 at 3:19 AM, Kamontip Srihaset
 kamonti...@student.chula.ac.th wrote:
 
 
  Dear all members,
 
  I am Phd. candidate student at Chulalongkorn U., Thailand. I am
 interested in expectation maximization algorithm (EM) and multiple
 imputation (MI) for imputation missing values(missing at random(MAR) and
 missing not at random (MNAR)) in IRT (3-PL). So, I want to know about
 package in R or function of EM and MI for simulate this problem
 
  I am looking forward your answer.
 
  sincerely yours,
 
  Kamontip Srihaset
 
 
 
 [[alternative HTML version deleted]]
 
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] Using Sub

2012-06-18 Thread Jeff Newmiller

Please study how escapes work. The representation you see in the source code is 
not the same as what is actually stored in memory.

As to your problems with the clipboard, I recommend writing scripts that do not 
interact with the clipboard directly. Violating this rule puts an error-prone 
human in the loop for repeating the script, and will eventually lead to 
irreproducible results.

That said, using the clipboard to create the script itself is fine. I usually 
just edit Windows paths in scripts to have forward slashes or double 
backslashes, and I use relative paths liberally. You can also play with 
file.choose() or readLines(clipboard) to get source-compatible paths.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Lopez, Dan lopez...@llnl.gov wrote:

Hi A.K.,

That works but when I copy and paste from Window explorer it will have
a single backslashes and not double.  It works with double as what you
have in your example below but not with single as what I would end up
passing.

Do you have any other suggestions or methods to accomplish this?

Thanks.
Dan


-Original Message-
From: arun [mailto:smartpink...@yahoo.com] 
Sent: Monday, June 18, 2012 8:59 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

Hi,

I guess you need something like this:

 str1-G:\\Compensation Audits_Reports\\Step Audit\\Steps off
Step.accdb
 gsub('','/',str1)
[1] G:/Compensation Audits_Reports/Step Audit/Steps off Step.accdb


A.K.




- Original Message -
From: Lopez, Dan lopez...@llnl.gov
To: Duncan Murdoch murdoch.dun...@gmail.com
Cc: R help r-help@r-project.org
Sent: Monday, June 18, 2012 10:37 AM
Subject: Re: [R] Using Sub

Hi Duncan,

That's right but I want to be able to use this to replace back slashes
with front slashes when I copy and paste file paths. How can I make
this work so I don't get this error?

Thanks.
Dan

-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Sent: Friday, June 15, 2012 12:04 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

On 12-06-14 6:23 PM, Lopez, Dan wrote:
 Hi,

 I have been trying to get the sub function to work but can't for the
life of me figure it out. I tried looking at ?sub but I think there is
something that I am just not understanding.

 Example failed attempts
 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: '\C' is an unrecognized escape in character string starting
G:\C

This isn't anything to do with sub(), it's the third string that's the
problem.  When you say G:\Comp... it thinks you've escaped the C, but
there's no such escape.

Duncan Murdoch


 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=TRUE)
 Error: '\C' is an unrecognized escape in character string starting
G:\C

 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=FALSE)
 Error: '\C' is an unrecognized escape in character string starting 
 G:\C)

 sub(/,\,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: unexpected symbol in sub(/,\,G

 Thanks.
 Dan

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

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Re: [R] Using Sub

2012-06-18 Thread William Dunlap

The parser (the part of R that interprets text as R code) interprets things like
\t as the tab character and there is no way to avoid that.  However, when
the functions readLines(), scan(), and readline() handle input they do not 
assign any special
meanings to backslashes.  Hence, if you want to be able to copy and paste
entries from other Windows applications to R you can do it by using scan(), etc.
E.g.,
   readline(prompt=File path? )
  File path? C:\Documents and Settings\Bill Dunlap\My Documents\the data.csv
  [1] C:\\Documents and Settings\\Bill Dunlap\\My Documents\\the data.csv
   gsub(, /, .Last.value)
  [1] C:/Documents and Settings/Bill Dunlap/My Documents/the data.csv
It is not terribly convenient, but it is possible.
 
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf
 Of Jeff Newmiller
 Sent: Monday, June 18, 2012 10:29 AM
 To: Daniel Lopez; arun
 Cc: R help
 Subject: Re: [R] Using Sub
 
 Please study how escapes work. The representation you see in the source code 
 is not the
 same as what is actually stored in memory.
 
 As to your problems with the clipboard, I recommend writing scripts that do 
 not interact
 with the clipboard directly. Violating this rule puts an error-prone human in 
 the loop for
 repeating the script, and will eventually lead to irreproducible results.
 
 That said, using the clipboard to create the script itself is fine. I usually 
 just edit Windows
 paths in scripts to have forward slashes or double backslashes, and I use 
 relative paths
 liberally. You can also play with file.choose() or readLines(clipboard) to 
 get source-
 compatible paths.
 ---
 Jeff NewmillerThe .   .  Go Live...
 DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
   Live:   OO#.. Dead: OO#..  Playing
 Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
 /Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
 ---
 Sent from my phone. Please excuse my brevity.
 
 Lopez, Dan lopez...@llnl.gov wrote:
 
 Hi A.K.,
 
 That works but when I copy and paste from Window explorer it will have
 a single backslashes and not double.  It works with double as what you
 have in your example below but not with single as what I would end up
 passing.
 
 Do you have any other suggestions or methods to accomplish this?
 
 Thanks.
 Dan
 
 
 -Original Message-
 From: arun [mailto:smartpink...@yahoo.com]
 Sent: Monday, June 18, 2012 8:59 AM
 To: Lopez, Dan
 Cc: R help
 Subject: Re: [R] Using Sub
 
 Hi,
 
 I guess you need something like this:
 
  str1-G:\\Compensation Audits_Reports\\Step Audit\\Steps off
 Step.accdb
  gsub('','/',str1)
 [1] G:/Compensation Audits_Reports/Step Audit/Steps off Step.accdb
 
 
 A.K.
 
 
 
 
 - Original Message -
 From: Lopez, Dan lopez...@llnl.gov
 To: Duncan Murdoch murdoch.dun...@gmail.com
 Cc: R help r-help@r-project.org
 Sent: Monday, June 18, 2012 10:37 AM
 Subject: Re: [R] Using Sub
 
 Hi Duncan,
 
 That's right but I want to be able to use this to replace back slashes
 with front slashes when I copy and paste file paths. How can I make
 this work so I don't get this error?
 
 Thanks.
 Dan
 
 -Original Message-
 From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
 Sent: Friday, June 15, 2012 12:04 AM
 To: Lopez, Dan
 Cc: R help
 Subject: Re: [R] Using Sub
 
 On 12-06-14 6:23 PM, Lopez, Dan wrote:
  Hi,
 
  I have been trying to get the sub function to work but can't for the
 life of me figure it out. I tried looking at ?sub but I think there is
 something that I am just not understanding.
 
  Example failed attempts
  sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off
  Step.accdb)
  Error: '\C' is an unrecognized escape in character string starting
 G:\C
 
 This isn't anything to do with sub(), it's the third string that's the
 problem.  When you say G:\Comp... it thinks you've escaped the C, but
 there's no such escape.
 
 Duncan Murdoch
 
 
  sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off
  Step.accdb,fixed=TRUE)
  Error: '\C' is an unrecognized escape in character string starting
 G:\C
 
  sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off
  Step.accdb,fixed=FALSE)
  Error: '\C' is an unrecognized escape in character string starting
  G:\C)
 
  sub(/,\,G:\Compensation Audits_Reports\Step Audit\Steps off
  Step.accdb)
  Error: unexpected symbol in sub(/,\,G
 
  Thanks.
  Dan
 
  __
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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,

Re: [R] Process XML files

2012-06-18 Thread Santosh

Please ignore my previous request for clarification. I was able to resolve
my problem using getNodeSet.

Thanks,
Santosh

On Thu, Jun 14, 2012 at 10:54 AM, Santosh santosh2...@gmail.com wrote:

 Dear Rxperts,
 I am back to favoRite! I would need your favoR, please!

 Is there a way to use read format arguments for POSIXct or strptime
 from  the xml file without specifying format=... in these functions? The
 format of data-time values are present in the xml file as shown below.

 Please see below am example section of XML code:
 ?xml version=1.0??mso-application progid=Excel.Sheet?Workbook
 xmlns=urn:schemas-microsoft-com:office:spreadsheet
 xmlns:o=urn:schemas-microsoft-com:office:office
 xmlns:x=urn:schemas-microsoft-com:office:excel
 xmlns:ss=urn:schemas-microsoft-com:office:spreadsheet xmlns:html=
 http://www.w3.org/TR/REC-html40;StylesStyle ss:ID=s11NumberFormat
 ss:Format=/mm/dd\ hh:mm;@//StyleStyle ss:ID=s21Font
 ss:Color=White ss:Bold=1/Interior ss:Color=Black
 ss:Pattern=Solid//StyleStyle ss:ID=s31BordersBorder
 ss:Position=Bottom ss:LineStyle=Double
 ss:Weight=3//Borders/StyleStyle ss:ID=s41Font
 ss:Size=20//StyleStyle ss:ID=s12NumberFormat
 ss:Format=hh:mm:ss.000//Style/StylesWorksheet
 ss:Name=StartTable ss:DefaultColumnWidth=80RowCellData
 ss:Type=StringID/Data/CellCellData
 ss:Type=String1/Data/Cell/RowRowCellData
 ss:Type=StringStart/Data/CellCell ss:StyleID=s11*Data
 ss:Type=DateTime2012-06-14T09:16:16.512/Data*/Cell/Row/Table
 /Worksheet/Workbook



 On Fri, Jun 8, 2012 at 8:08 AM, Uwe Ligges 
 lig...@statistik.tu-dortmund.de wrote:



 On 06.06.2012 22:44, Santosh wrote:

 Hello experts,

 Sorry for posting the SPlus related question here.. I have not found any
 solution yet after some attempts and hence, sending it to a wider
 spectrum
 of users! I was successful in processing files uing R's XML librariy.


 Not that we know, we just know about an R *package* called XML.



  Thank
 you, Rxperts!

 I know there are libraries like XML and SPXML available in S-Plus. Could
 anyone please share examples of reading an xml file and save the contents
 in a data frame?

 Are there Splus equivalents of getNodeSet,  xmlSApply and xmlValue?



 Most of us do not have S-PLUS available to check (actually, we do have a
 13 year old copy S-PLUS 4.5 at our department). You do, obviously, hence
 why not check it yourself? And if you can't, why not ask the vendor of your
 statistics software?

 Best,
 Uwe Ligges



 Thanks so much!
 Santosh


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 posting-guide.html http://www.R-project.org/posting-guide.html
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Re: [R] Using Sub

Jeff - Thanks. I think I'll just stick to using file.choose().

Dan

-Original Message-
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us] 
Sent: Monday, June 18, 2012 10:29 AM
To: Lopez, Dan; arun
Cc: R help
Subject: Re: [R] Using Sub

Please study how escapes work. The representation you see in the source code is 
not the same as what is actually stored in memory.

As to your problems with the clipboard, I recommend writing scripts that do not 
interact with the clipboard directly. Violating this rule puts an error-prone 
human in the loop for repeating the script, and will eventually lead to 
irreproducible results.

That said, using the clipboard to create the script itself is fine. I usually 
just edit Windows paths in scripts to have forward slashes or double 
backslashes, and I use relative paths liberally. You can also play with 
file.choose() or readLines(clipboard) to get source-compatible paths.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
---
Sent from my phone. Please excuse my brevity.

Lopez, Dan lopez...@llnl.gov wrote:

Hi A.K.,

That works but when I copy and paste from Window explorer it will have 
a single backslashes and not double.  It works with double as what you 
have in your example below but not with single as what I would end up 
passing.

Do you have any other suggestions or methods to accomplish this?

Thanks.
Dan

-Original Message-
From: arun [mailto:smartpink...@yahoo.com]
Sent: Monday, June 18, 2012 8:59 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

Hi,

I guess you need something like this:

 str1-G:\\Compensation Audits_Reports\\Step Audit\\Steps off
Step.accdb
 gsub('','/',str1)
[1] G:/Compensation Audits_Reports/Step Audit/Steps off Step.accdb

A.K.

- Original Message -
From: Lopez, Dan lopez...@llnl.gov
To: Duncan Murdoch murdoch.dun...@gmail.com
Cc: R help r-help@r-project.org
Sent: Monday, June 18, 2012 10:37 AM
Subject: Re: [R] Using Sub

Hi Duncan,

That's right but I want to be able to use this to replace back slashes 
with front slashes when I copy and paste file paths. How can I make 
this work so I don't get this error?

Thanks.
Dan

-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Friday, June 15, 2012 12:04 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

On 12-06-14 6:23 PM, Lopez, Dan wrote:
 Hi,

 I have been trying to get the sub function to work but can't for the
life of me figure it out. I tried looking at ?sub but I think there is 
something that I am just not understanding.

 Example failed attempts
 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off
 Step.accdb)
 Error: '\C' is an unrecognized escape in character string starting
G:\C

This isn't anything to do with sub(), it's the third string that's the 
problem.  When you say G:\Comp... it thinks you've escaped the C, but 
there's no such escape.

Duncan Murdoch

 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off
 Step.accdb,fixed=TRUE)
 Error: '\C' is an unrecognized escape in character string starting
G:\C

 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off
 Step.accdb,fixed=FALSE)
 Error: '\C' is an unrecognized escape in character string starting
 G:\C)

 sub(/,\,G:\Compensation Audits_Reports\Step Audit\Steps off
 Step.accdb)
 Error: unexpected symbol in sub(/,\,G

 Thanks.
 Dan

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

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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] multiplicative error model

2012-06-18 Thread Özgür Asar

What do you mean by using the package?

Aren't the examples in the package manual at 

http://cran.r-project.org/web/packages/dynamo/dynamo.pdf

enough for you?

Ozgur

--
View this message in context: 
http://r.789695.n4.nabble.com/multiplicative-error-model-tp4633730p4633732.html
Sent from the R help mailing list archive at Nabble.com.

__
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] How do anova() and Anova(type=III) handle incomplete designs?

2012-06-18 Thread John Fox

Dear Justin,

On Mon, 18 Jun 2012 11:24:33 -0400
 Justin Montemarano jmont...@kent.edu wrote:
 Thanks for your response, John.  That was helpful.
 
 I was using Type III from Anova() as a comparison to some results I had
 obtained JMP, which I've lost access to and have moved on to R, and I was
 confused by the error.  Given that I do have a continuous covariate, the
 analyses are not likely comparable, considering your response.

If you look more carefully, you'll see that the reference here was to type-II 
tests. I believe that the definition used by Anova() is more sensible.

 
 I am still confused about interpretation of interactions within an anova()
 with an incomplete design, as mine is.  Is the interaction term still
 informative?

I don't think that these matters are easily discussed on an email list. 
Briefly, I'd argue that the type-II tests (as defined by Anova) still have a 
straightforward interpretation since the test for a (say, two-way) interaction 
represent a contrast to a model that's additive with respect to the predictors 
involved in the interaction.

Best,
 John

 
 -
 Justin Montemarano
 Graduate Student
 Kent State University - Biological Sciences
 
 http://www.montegraphia.com
 
 
 On Sat, Jun 16, 2012 at 9:20 PM, John Fox j...@mcmaster.ca wrote:
 
  Dear Justin,
 
  anova() and Anova() are entirely different functions; the former is part
  of the standard R distribution and the second part of the car package. By
  default, Anova() produces an error for type-III tests conducted on
  rank-deficient models because the hypotheses tested aren't generally
  sensible.
 
  From ?Anova:
 
  singular.ok
  defaults to TRUE for type-II tests, and FALSE for type-III tests (where
  the tests for models with aliased coefficients will not be
  straightforwardly interpretable); if FALSE, a model with aliased
  coefficients produces an error.
 
  and
 
  The designations type-II and type-III are borrowed from SAS, but the
  definitions used here do not correspond precisely to those employed by SAS.
  Type-II tests are calculated according to the principle of marginality,
  testing each term after all others, except ignoring the term's higher-order
  relatives; so-called type-III tests violate marginality, testing each term
  in the model after all of the others. This definition of Type-II tests
  corresponds to the tests produced by SAS for analysis-of-variance models,
  where all of the predictors are factors, but not more generally (i.e., when
  there are quantitative predictors). Be very careful in formulating the
  model for type-III tests, or the hypotheses tested will not make sense.
 
  I hope this helps,
   John
 
  
  John Fox
  Sen. William McMaster Prof. of Social Statistics
  Department of Sociology
  McMaster University
  Hamilton, Ontario, Canada
  http://socserv.mcmaster.ca/jfox/
 
 
  On Fri, 15 Jun 2012 15:01:27 -0400
   Justin Montemarano jmont...@kent.edu wrote:
   Hello all:
  
   I am confused about the output from a lm() model with an incomplete
   design/missing level.
  
   I have two categorical predictors and a continuous covariate (day) that
   I am using to model larval mass (l.mass):
  
   leaf.species has three levels - map, syc, and oak
  
   cond.time has two levels - 30 and 150.
  
   There are no response values for Map-150, so that entire, two-way, level
   is missing.
  
   When running anova() on the model with Type I SS, the full factorial
   design does not return errors; however, using package:car Anova() and
   Type III SS, I receive an singularity error unless I used the argument
   'singular.ok = T' (it is defaulted to F).
  
   So, why don't I receive an error with anova() when I do with Anova(type
   = III)?  How do anova() and Anova() handle incomplete designs, and how
   can interactions of variables with missing levels be interpreted?
  
   I realize these are fairly broad questions, but any insight would be
   helpful. Thanks, all.
  
   Below is code to illustrate my question(s):
  
 lmMass - lm(log(l.mass) ~ day*leaf.species + cond.time, data =
   growth.data) #lm() without cond.time interactions
 lmMassInt - lm(log(l.mass) ~ day*leaf.species*cond.time, data =
   growth.data) #lm() with cond.time interactions
 anova(lmMass); anova(lmMassInt) #ANOVA summary of both models
   with Type I SS
   Analysis of Variance Table
  
   Response: log(l.mass)
  Df  Sum Sq Mean Sq F valuePr(F)
   day1  51.373  51.373 75.7451 2.073e-15
   leaf.species   2   0.340   0.170  0.25060.7786
   cond.time  1   0.161   0.161  0.23690.6271
   day:leaf.species   2   1.296   0.648  0.95510.3867
   Residuals179 121.404   0.678
   Analysis of Variance Table
  
   Response: log(l.mass)
Df  Sum Sq Mean Sq F value  Pr(F)
   day

Re: [R] Error w/ Start up Script



On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:

I noticed about a couple weeks ago that my R start up script  
starting showing the below errors, following the line Type 'q()' to  
quit R




I didn't see any errors reported. I didn't see any warnings, either.

--
David.

Not sure what I did different and so far it hasn't caused major  
problems but kind of fear that it will.


Can you please help?
I also posted my Rprofile below.

Attempting to load the environment 'package:R.utils'
R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ? 
R.methodsS3 for help.

R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object(s) are masked from 'package:R.methodsS3':

   throw.default

The following object(s) are masked from 'package:methods':

   getClass, getClasses, getMethods

The following object(s) are masked from 'package:base':

   attach, detach, gc, load, save

R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for  
help.


Attaching package: 'R.utils'

The following object(s) are masked from 'package:utils':

   timestamp

The following object(s) are masked from 'package:base':

   cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
   warnings

And here is my Rprofile.site file specs:
# Things you might want to change
# options(papersize=a4)
# options(editor=notepad)
# options(pager=internal)

# set the default help type
# options(help_type=text)
options(help_type=html)

# set a site library
# .Library.site - file.path(chartr(\\, /, R.home()), site- 
library)


# set a CRAN mirror
local({r - getOption(repos)
  r[CRAN] - http://cran.cnr.Berkeley.edu;
  options(repos=r)})

# Give a fortune cookie, but only to interactive sessions
# (This would need the fortunes package to be installed.)
#  if (interactive())
#fortunes::fortune()


Daniel Lopez
Workforce Analytics  Metrics Team




[[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.


David Winsemius, MD
West Hartford, CT

__
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] Error w/ Start up Script

David,

Sorry I should have been more specific. They are not as much errors as they are 
extra script that is running at startup after Type q() to quit R. It wasn't 
there before. And am thinking eventually it could become a problem.

Thanks.
Dan

Here it is again...what it looks like when I first startup R (partial copy and 
paste):


...
..
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Attempting to load the environment 'package:R.utils'
R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object(s) are masked from 'package:R.methodsS3':

throw.default
..
...

-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net] 
Sent: Monday, June 18, 2012 12:12 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.org)
Subject: Re: [R] Error w/ Start up Script


On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:

 I noticed about a couple weeks ago that my R start up script starting 
 showing the below errors, following the line Type 'q()' to quit R


I didn't see any errors reported. I didn't see any warnings, either.

--
David.

 Not sure what I did different and so far it hasn't caused major 
 problems but kind of fear that it will.

 Can you please help?
 I also posted my Rprofile below.

 Attempting to load the environment 'package:R.utils'
 R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ? 
 R.methodsS3 for help.
 R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

 Attaching package: 'R.oo'

 The following object(s) are masked from 'package:R.methodsS3':

throw.default

 The following object(s) are masked from 'package:methods':

getClass, getClasses, getMethods

 The following object(s) are masked from 'package:base':

attach, detach, gc, load, save

 R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for 
 help.

 Attaching package: 'R.utils'

 The following object(s) are masked from 'package:utils':

timestamp

 The following object(s) are masked from 'package:base':

cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
warnings

 And here is my Rprofile.site file specs:
 # Things you might want to change
 # options(papersize=a4)
 # options(editor=notepad)
 # options(pager=internal)

 # set the default help type
 # options(help_type=text)
 options(help_type=html)

 # set a site library
 # .Library.site - file.path(chartr(\\, /, R.home()), site-
 library)

 # set a CRAN mirror
 local({r - getOption(repos)
   r[CRAN] - http://cran.cnr.Berkeley.edu;
   options(repos=r)})

 # Give a fortune cookie, but only to interactive sessions # (This 
 would need the fortunes package to be installed.) #  if 
 (interactive())
 #fortunes::fortune()


 Daniel Lopez
 Workforce Analytics  Metrics Team




   [[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.

David Winsemius, MD
West Hartford, CT

__
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] Interactive Graphics

2012-06-18 Thread MacQueen, Don

As I recall, there is a package that can be used to create interactive svg
files. I don't remember its name, but I seem to recall it was fairly easy
to find on the CRAN packages page.

-Don

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 6/17/12 7:01 PM, Eder David Borges eder...@gmail.com wrote:

Hi,
I'd like to make an interactive graph like this:
http://blog.ggplot2.org/post/25201174009/name-popularity
I believe he was done with the ggplot2 and saved in svg format. if someone
has experience with this subject (graph interactive web) could give me a
help?
Thanks

-- 
Éder David Borges da Silva
eder...@gmail.com
eder...@hotmail.com
Skype: ederdbs
041 96717488
Tudo é Relativo...(Albert Einstein)

   [[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] Error w/ Start up Script

?suppressPackageStartupMessages

Put this into your appropriate startup file.
?Startup  ## for details on starting R and what files are executed at
startup.

-- Bert

On Mon, Jun 18, 2012 at 12:46 PM, Lopez, Dan lopez...@llnl.gov wrote:

 David,

 Sorry I should have been more specific. They are not as much errors as
 they are extra script that is running at startup after Type q() to quit
 R. It wasn't there before. And am thinking eventually it could become a
 problem.

 Thanks.
 Dan

 Here it is again...what it looks like when I first startup R (partial copy
 and paste):

 
 ...
 ..
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.

 Type 'demo()' for some demos, 'help()' for on-line help, or
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.

 Attempting to load the environment 'package:R.utils'
 R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for
 help.
 R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

 Attaching package: 'R.oo'

 The following object(s) are masked from 'package:R.methodsS3':

throw.default
 ..
 ...
 
 -Original Message-
 From: David Winsemius [mailto:dwinsem...@comcast.net]
 Sent: Monday, June 18, 2012 12:12 PM
 To: Lopez, Dan
 Cc: R help (r-help@r-project.org)
 Subject: Re: [R] Error w/ Start up Script


 On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:

  I noticed about a couple weeks ago that my R start up script starting
  showing the below errors, following the line Type 'q()' to quit R
 

 I didn't see any errors reported. I didn't see any warnings, either.

 --
 David.

  Not sure what I did different and so far it hasn't caused major
  problems but kind of fear that it will.
 
  Can you please help?
  I also posted my Rprofile below.
 
  Attempting to load the environment 'package:R.utils'
  R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?
  R.methodsS3 for help.
  R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.
 
  Attaching package: 'R.oo'
 
  The following object(s) are masked from 'package:R.methodsS3':
 
 throw.default
 
  The following object(s) are masked from 'package:methods':
 
 getClass, getClasses, getMethods
 
  The following object(s) are masked from 'package:base':
 
 attach, detach, gc, load, save
 
  R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for
  help.
 
  Attaching package: 'R.utils'
 
  The following object(s) are masked from 'package:utils':
 
 timestamp
 
  The following object(s) are masked from 'package:base':
 
 cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
 warnings
 
  And here is my Rprofile.site file specs:
  # Things you might want to change
  # options(papersize=a4)
  # options(editor=notepad)
  # options(pager=internal)
 
  # set the default help type
  # options(help_type=text)
  options(help_type=html)
 
  # set a site library
  # .Library.site - file.path(chartr(\\, /, R.home()), site-
  library)
 
  # set a CRAN mirror
  local({r - getOption(repos)
r[CRAN] - http://cran.cnr.Berkeley.edu;
options(repos=r)})
 
  # Give a fortune cookie, but only to interactive sessions # (This
  would need the fortunes package to be installed.) #  if
  (interactive())
  #fortunes::fortune()
 
 
  Daniel Lopez
  Workforce Analytics  Metrics Team
 
 
 
 
[[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.

 David Winsemius, MD
 West Hartford, CT

 __
 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.




-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

[[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] Error w/ Start up Script

Hi Bert,

I tried entering: ?suppressPackageStartupMessages and then 
suppressPackageStartupMessages into my Rprofile.site file and the messages 
still came up.

I did however go to the Misc menu and select List search path and got the 
below results. Not exactly sure what it means but I do notice that several of 
the packages that popup at startup as being masked appear  in this list. 
Maybe this is the problem? If so how do you take out what you don't need at 
startup?

 search()
[1] .GlobalEnv  package:stats   package:graphics
package:grDevices   package:datasets
 [6] package:rattle  package:R.utils package:utils   
package:R.oopackage:R.methodsS3
[11] package:methods Autoloads   package:base
 0

Thanks.
Dan

From: Bert Gunter [mailto:gunter.ber...@gene.com]
Sent: Monday, June 18, 2012 1:10 PM
To: Lopez, Dan
Cc: David Winsemius; R help (r-help@r-project.org)
Subject: Re: [R] Error w/ Start up Script

?suppressPackageStartupMessages

Put this into your appropriate startup file.
?Startup  ## for details on starting R and what files are executed at startup.

-- Bert
On Mon, Jun 18, 2012 at 12:46 PM, Lopez, Dan 
lopez...@llnl.govmailto:lopez...@llnl.gov wrote:
David,

Sorry I should have been more specific. They are not as much errors as they are 
extra script that is running at startup after Type q() to quit R. It wasn't 
there before. And am thinking eventually it could become a problem.

Thanks.
Dan

Here it is again...what it looks like when I first startup R (partial copy and 
paste):


...
..
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Attempting to load the environment 'package:R.utils'
R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object(s) are masked from 'package:R.methodsS3':

   throw.default
..
...

-Original Message-
From: David Winsemius 
[mailto:dwinsem...@comcast.netmailto:dwinsem...@comcast.net]
Sent: Monday, June 18, 2012 12:12 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.orgmailto:r-help@r-project.org)
Subject: Re: [R] Error w/ Start up Script


On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:

 I noticed about a couple weeks ago that my R start up script starting
 showing the below errors, following the line Type 'q()' to quit R


I didn't see any errors reported. I didn't see any warnings, either.

--
David.

 Not sure what I did different and so far it hasn't caused major
 problems but kind of fear that it will.

 Can you please help?
 I also posted my Rprofile below.

 Attempting to load the environment 'package:R.utils'
 R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?
 R.methodsS3 for help.
 R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

 Attaching package: 'R.oo'

 The following object(s) are masked from 'package:R.methodsS3':

throw.default

 The following object(s) are masked from 'package:methods':

getClass, getClasses, getMethods

 The following object(s) are masked from 'package:base':

attach, detach, gc, load, save

 R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for
 help.

 Attaching package: 'R.utils'

 The following object(s) are masked from 'package:utils':

timestamp

 The following object(s) are masked from 'package:base':

cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
warnings

 And here is my Rprofile.site file specs:
 # Things you might want to change
 # options(papersize=a4)
 # options(editor=notepad)
 # options(pager=internal)

 # set the default help type
 # options(help_type=text)
 options(help_type=html)

 # set a site library
 # .Library.site - file.path(chartr(\\, /, R.home()), site-
 library)

 # set a CRAN mirror
 local({r - getOption(repos)
   r[CRAN] - http://cran.cnr.Berkeley.edu;
   options(repos=r)})

 # Give a fortune cookie, but only to interactive sessions # (This
 would need the fortunes package to be installed.) #  if
 (interactive())
 #fortunes::fortune()


 Daniel Lopez
 Workforce Analytics  Metrics Team




   [[alternative HTML version deleted]]

 __
 R-help@r-project.orgmailto: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
West Hartford, CT

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PLEASE do read the posting guide

[R] How to average time series data within certain time periods

2012-06-18 Thread Dominik van Pinxteren


Hi,

I am new to R and wondering how I can subset and average time series data  
based on given irregular time periods:


Say I have a time series of a measured variable x (hourly data) in  
values.csv with columns date and x which I would like to average  
within certain irregular time periods (events), given in events.csv  
with columns EventID, start, and stop (where start and stop indicate  
the start and stop dates of the corresponding event).


What I usually do is to load the two csvs into a database and then perform  
an SQL statement like this:


SELECT a.EventID, avg(b.x) from events as a, values as b WHERE b.date  
between a.start and a.stop GROUP BY a.EventID


This gives a table with the EventIDs and the corresponding mean values of  
x as an output.


As my data are not that large I would like to avoid the database and do  
the averaging in R but I cannot find the way of doing this in R.


I would appreciate any advice to set me on track.

Thanks,
Dominik

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Re: [R] Loop Help

2012-06-18 Thread @ngel

Thank you Jeff,
that sounds like the solution to my problem
but how would I do that code-wise?
could you please help?

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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] multiplicative error model

2012-06-18 Thread saraberta

HI, 
i'm trying to estimate a  multiplicative error model in R, i've seen the
dynamo package but it seems that i'm not able to use it. does someone know
how can i do it? 
thanks

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

[R] Changing strip text

2012-06-18 Thread Julie Truman

I'm trying to create a 5-panel xyplot with each strip labelled by treatment. 
The code is as follows:

xyplot(log(pfuml)~Transfer|Treat,groups=Pop,ylab=Log10 Pfu/ml,as.table=T,
type=a,
auto.key=
list(space=right,points=F,lines=T))



I've tried:

strip=strip.custom(factor.levels=c(0,2,4,8,16)

But it's not working, I still only get Treat printed on each strip. Any ideas?

Thank you,

Julie





[[alternative HTML version deleted]]

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

Re: [R] noob requesting help

2012-06-18 Thread capital_P


Rui Barradas wrote
 
 sorry about the misleading tip.
 This should do it.
 
 do.call(rbind, dep)
 

No problem at all. 

That did the trick. Thank you both so much for your help. I am forever in
your debt.

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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] Inconsistency using seq

2012-06-18 Thread hamoreno

Hi all,

Is there any problem of precision when using seq?. For example:

x- seq(0,4,0.1)
x[4]=0.3

BUT:

x[4]-0.3=5.551115e-17

It means when I use this condition within an if clause, it does not find
values with 0.3 for x[4] as it is not precisely 0.3.
Is there any bug in seq() ?


--
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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] Trying to speed up an if/else statement in simulations

2012-06-18 Thread nqf

Dear R-help,

I am trying to write a function to simulate datasets of size n which contain
two time-to-event outcome variables with associated 'Event'/'Censored'
indicator variables (flag1 and flag2 respectively). One of these indicator
variables needs to be dependent on the other, so I am creating the first and
trying to use this to create the second using an if/else statement. 

My data structure needs to follow this algorithm (for each row of the data):
If flag1=1 then flag2 should be 1 with probability 0.95 and zero otherwise
Else if flag1=0 then flag2 should be 1 with probability 0.5 and zero
otherwise

I can set up this example quite simply using if else statements, but this is
incredibly inefficient when running thousands of datasets:
data-as.data.frame(rbinom(10,1,0.5))
colnames(data)-'flag1'
for (i in 1:n) {
  if (data$flag1[i]==1) {data$flag2[i]-rbinom(1,1,0.95)} else
{data$flag2[i]-rbinom(1,1,0.5)}  
 }


I think to speed up the simulations I would be better changing to
vectorisation and using something like:
ifelse(data$flag1==1,rbinom(1,1,0.95),rbinom(1,1,0.5)) 
but the rbinom statements here generate one value and repeat this draw for
every element of flag2 that matches the 'if' statement on flag1.

Is there a way to assign flag2 to a new bernoulli draw for each subject in
the data frame with flag1=1?

I hope my question is clear, and thank you in advance for your help. 

Thanks,
Natalie
PhD student, Reading University

P.S. I am using R 2.12.1 on Windows 7.


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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] Error w/ Start up Script

2012-06-18 Thread R. Michael Weylandt michael.weyla...@gmail.com

I gave you the references you need. It's up to you to read and understand
how to use them. You apparently need to work harder to do so. BTW

?anything

is an alternative way to type

help(anything)

at the command line for R's help pages.

-- Bert

On Mon, Jun 18, 2012 at 1:34 PM, Lopez, Dan lopez...@llnl.gov wrote:

 Hi Bert,

 ** **

 I tried entering: ?suppressPackageStartupMessages and then
 suppressPackageStartupMessages into my Rprofile.site file and the
 messages still came up.

 ** **

 I did however go to the Misc menu and select List search path and got
 the below results. Not exactly sure what it means but I do notice that
 several of the packages that popup at startup as being masked appear  in
 this list. Maybe this is the problem? If so how do you take out what you
 dont need at startup?

 ** **

  search()

 [1] .GlobalEnv  package:stats   package:graphics
 package:grDevices   package:datasets   

  [6] package:rattle  package:R.utils package:utils
  package:R.oopackage:R.methodsS3

 [11] package:methods Autoloads   package:base   

  0

 ** **

 Thanks.

 Dan

 ** **

 *From:* Bert Gunter [mailto:gunter.ber...@gene.com]
 *Sent:* Monday, June 18, 2012 1:10 PM
 *To:* Lopez, Dan
 *Cc:* David Winsemius; R help (r-help@r-project.org)
 *Subject:* Re: [R] Error w/ Start up Script

 ** **

 ?suppressPackageStartupMessages

 Put this into your appropriate startup file.
 ?Startup  ## for details on starting R and what files are executed at
 startup.

 -- Bert

 On Mon, Jun 18, 2012 at 12:46 PM, Lopez, Dan lopez...@llnl.gov wrote:***
 *

 David,

 Sorry I should have been more specific. They are not as much errors as
 they are extra script that is running at startup after Type q() to quit
 R. It wasn't there before. And am thinking eventually it could become a
 problem.

 Thanks.
 Dan

 Here it is again...what it looks like when I first startup R (partial copy
 and paste):

 
 ...
 ..
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.

 Type 'demo()' for some demos, 'help()' for on-line help, or
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.

 Attempting to load the environment 'package:R.utils'
 R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for
 help.
 R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

 Attaching package: 'R.oo'

 The following object(s) are masked from 'package:R.methodsS3':

throw.default
 ..
 ...
 
 -Original Message-
 From: David Winsemius [mailto:dwinsem...@comcast.net]
 Sent: Monday, June 18, 2012 12:12 PM
 To: Lopez, Dan
 Cc: R help (r-help@r-project.org)
 Subject: Re: [R] Error w/ Start up Script


 On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:

  I noticed about a couple weeks ago that my R start up script starting
  showing the below errors, following the line Type 'q()' to quit R
 

 I didn't see any errors reported. I didn't see any warnings, either.

 --
 David.

  Not sure what I did different and so far it hasn't caused major
  problems but kind of fear that it will.
 
  Can you please help?
  I also posted my Rprofile below.
 
  Attempting to load the environment 'package:R.utils'
  R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?
  R.methodsS3 for help.
  R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.
 
  Attaching package: 'R.oo'
 
  The following object(s) are masked from 'package:R.methodsS3':
 
 throw.default
 
  The following object(s) are masked from 'package:methods':
 
 getClass, getClasses, getMethods
 
  The following object(s) are masked from 'package:base':
 
 attach, detach, gc, load, save
 
  R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for
  help.
 
  Attaching package: 'R.utils'
 
  The following object(s) are masked from 'package:utils':
 
 timestamp
 
  The following object(s) are masked from 'package:base':
 
 cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
 warnings
 
  And here is my Rprofile.site file specs:
  # Things you might want to change
  # options(papersize=a4)
  # options(editor=notepad)
  # options(pager=internal)
 
  # set the default help type
  # options(help_type=text)
  options(help_type=html)
 
  # set a site library
  # .Library.site - file.path(chartr(\\, /, R.home()), site-
  library)
 
  # set a CRAN mirror
  local({r - getOption(repos)
r[CRAN] - http://cran.cnr.Berkeley.edu;
options(repos=r)})
 
  # Give a fortune cookie, but only to interactive sessions # (This
  would need the fortunes package to be installed.) #  if
  (interactive())
  #fortunes::fortune()
 
 
  Daniel Lopez
  Workforce Analytics  Metrics Team
 
 
 
 
[[alternative HTML version deleted]]
 
  __

Re: [R] Inconsistency using seq

2012-06-18 Thread Milan Bouchet-Valat

Le lundi 18 juin 2012 à 12:58 -0700, hamoreno a écrit :
 Hi all,
 
 Is there any problem of precision when using seq?. For example:
 
 x- seq(0,4,0.1)
 x[4]=0.3
 
 BUT:
 
 x[4]-0.3=5.551115e-17
 
 It means when I use this condition within an if clause, it does not find
 values with 0.3 for x[4] as it is not precisely 0.3.
 Is there any bug in seq() ?
No. Have a look at the FAQ:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f


Cheers

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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] Inconsistency using seq

2012-06-18 Thread Sarah Goslee

Please read R FAQ 7.31. The problem is with your computer (and
everyone else's), and has nothing to do with seq().

On Mon, Jun 18, 2012 at 3:58 PM, hamoreno hamor...@asu.edu wrote:
 Hi all,

 Is there any problem of precision when using seq?. For example:

 x- seq(0,4,0.1)
 x[4]=0.3

 BUT:

 x[4]-0.3=5.551115e-17

 It means when I use this condition within an if clause, it does not find
 values with 0.3 for x[4] as it is not precisely 0.3.
 Is there any bug in seq() ?


-- 
Sarah Goslee
http://www.functionaldiversity.org

__
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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] Inconsistency using seq

No, this is rather the nature of floating point calculations. 

You may perhaps be looking for ?all.equal or R FAQ 7.31 (I think that's the 
one) which is google-able. It's a complicated subject, but those should get you 
started. 

Best,
Michael

On Jun 18, 2012, at 2:58 PM, hamoreno hamor...@asu.edu wrote:

 Hi all,
 
 Is there any problem of precision when using seq?. For example:
 
 x- seq(0,4,0.1)
 x[4]=0.3
 
 BUT:
 
 x[4]-0.3=5.551115e-17
 
 It means when I use this condition within an if clause, it does not find
 values with 0.3 for x[4] as it is not precisely 0.3.
 Is there any bug in seq() ?
 
 
 --
 View this message in context: 
 http://r.789695.n4.nabble.com/Inconsistency-using-seq-tp4633739.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.

__
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] Error w/ Start up Script

Ouch Bert. Not patience for the newbies, I see.

I know what ?anything means which is why I didn't ask about ?Startup. But being 
that I just recently discovered what Rprofile.site is I thought it might do 
something different within the start-up file and tried it both ways.

Besides I think what I really need is to just figure out as I said:
I did however go to the Misc menu and select List search path and got the 
below results. Not exactly sure what it means but I do notice that several of 
the packages that popup at startup as being masked appear  in this list. 
Maybe this is the problem? If so how do you take out what you don't need at 
startup?

  search()

[1] .GlobalEnv  package:stats   package:graphics
package:grDevices   package:datasets

 [6] package:rattle  package:R.utils package:utils   
package:R.oopackage:R.methodsS3

[11] package:methods Autoloads   package:base



Dan

From: Bert Gunter [mailto:gunter.ber...@gene.com]
Sent: Monday, June 18, 2012 1:50 PM
To: Lopez, Dan
Cc: David Winsemius; R help (r-help@r-project.org)
Subject: Re: [R] Error w/ Start up Script

I gave you the references you need. It's up to you to read and understand how 
to use them. You apparently need to work harder to do so. BTW

?anything

is an alternative way to type

help(anything)

at the command line for R's help pages.

-- Bert
On Mon, Jun 18, 2012 at 1:34 PM, Lopez, Dan 
lopez...@llnl.govmailto:lopez...@llnl.gov wrote:
Hi Bert,

I tried entering: ?suppressPackageStartupMessages and then 
suppressPackageStartupMessages into my Rprofile.site file and the messages 
still came up.

I did however go to the Misc menu and select List search path and got the 
below results. Not exactly sure what it means but I do notice that several of 
the packages that popup at startup as being masked appear  in this list. 
Maybe this is the problem? If so how do you take out what you don't need at 
startup?

 search()
[1] .GlobalEnv  package:stats   package:graphics
package:grDevices   package:datasets
 [6] package:rattle  package:R.utils package:utils   
package:R.oopackage:R.methodsS3
[11] package:methods Autoloads   package:base
 0

Thanks.
Dan

From: Bert Gunter [mailto:gunter.ber...@gene.commailto:gunter.ber...@gene.com]
Sent: Monday, June 18, 2012 1:10 PM
To: Lopez, Dan
Cc: David Winsemius; R help (r-help@r-project.orgmailto:r-help@r-project.org)
Subject: Re: [R] Error w/ Start up Script

?suppressPackageStartupMessages

Put this into your appropriate startup file.
?Startup  ## for details on starting R and what files are executed at startup.

-- Bert
On Mon, Jun 18, 2012 at 12:46 PM, Lopez, Dan 
lopez...@llnl.govmailto:lopez...@llnl.gov wrote:
David,

Sorry I should have been more specific. They are not as much errors as they are 
extra script that is running at startup after Type q() to quit R. It wasn't 
there before. And am thinking eventually it could become a problem.

Thanks.
Dan

Here it is again...what it looks like when I first startup R (partial copy and 
paste):


...
..
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Attempting to load the environment 'package:R.utils'
R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object(s) are masked from 'package:R.methodsS3':

   throw.default
..
...

-Original Message-
From: David Winsemius 
[mailto:dwinsem...@comcast.netmailto:dwinsem...@comcast.net]
Sent: Monday, June 18, 2012 12:12 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.orgmailto:r-help@r-project.org)
Subject: Re: [R] Error w/ Start up Script


On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:

 I noticed about a couple weeks ago that my R start up script starting
 showing the below errors, following the line Type 'q()' to quit R


I didn't see any errors reported. I didn't see any warnings, either.

--
David.

 Not sure what I did different and so far it hasn't caused major
 problems but kind of fear that it will.

 Can you please help?
 I also posted my Rprofile below.

 Attempting to load the environment 'package:R.utils'
 R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?
 R.methodsS3 for help.
 R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

 Attaching package: 'R.oo'

 The following object(s) are masked from 'package:R.methodsS3':

throw.default

 The following object(s) are masked from 'package:methods':

getClass, getClasses, getMethods

 The following object(s) are masked from 'package:base':

attach, detach, gc, load, save

 R.utils v1.12.1 (2012-03-20) successfully loaded.

Re: [R] Inconsistency using seq

2012-06-18 Thread hamoreno

Thanks everyone... Seems that I will have to use round before seq to make
sure everything has the correct precision.

--
View this message in context: 
http://r.789695.n4.nabble.com/Inconsistency-using-seq-tp4633739p4633750.html
Sent from the R help mailing list archive at Nabble.com.

__
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.

[R] How can I declutter/make a biplot less messy in R

2012-06-18 Thread dss

I am doing a principle component analysis on a dataset with a lot of
different variables and have constructed a biplot of the data. 
Unfortunately, as can be seen on the attached image, the biplot is very
messy, cluttered, and hard to read.  I have performed a few modifications
including outlier removal from a few of the variables, which has made the
plot better, however it still is too cluttered to read the variable names. 
Is there any further improvment that can be made to the attached plot and if
so what steps should I take?

Thanks,
Derek


http://r.789695.n4.nabble.com/file/n4633703/biplot.jpg 

--
View this message in context: 
http://r.789695.n4.nabble.com/How-can-I-declutter-make-a-biplot-less-messy-in-R-tp4633703.html
Sent from the R help mailing list archive at Nabble.com.

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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] Using Sub

2012-06-18 Thread arun

Hi,

I guess you need something like this:

 str1-G:\\Compensation Audits_Reports\\Step Audit\\Steps off Step.accdb
 gsub('','/',str1)
[1] G:/Compensation Audits_Reports/Step Audit/Steps off Step.accdb


A.K.




- Original Message -
From: Lopez, Dan lopez...@llnl.gov
To: Duncan Murdoch murdoch.dun...@gmail.com
Cc: R help r-help@r-project.org
Sent: Monday, June 18, 2012 10:37 AM
Subject: Re: [R] Using Sub

Hi Duncan,

That's right but I want to be able to use this to replace back slashes with 
front slashes when I copy and paste file paths. How can I make this work so I 
don't get this error?

Thanks.
Dan

-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Sent: Friday, June 15, 2012 12:04 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

On 12-06-14 6:23 PM, Lopez, Dan wrote:
 Hi,

 I have been trying to get the sub function to work but can't for the life of 
 me figure it out. I tried looking at ?sub but I think there is something that 
 I am just not understanding.

 Example failed attempts
 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: '\C' is an unrecognized escape in character string starting G:\C

This isn't anything to do with sub(), it's the third string that's the 
problem.  When you say G:\Comp... it thinks you've escaped the C, but there's 
no such escape.

Duncan Murdoch


 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=TRUE)
 Error: '\C' is an unrecognized escape in character string starting G:\C

 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=FALSE)
 Error: '\C' is an unrecognized escape in character string starting 
 G:\C)

 sub(/,\,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: unexpected symbol in sub(/,\,G

 Thanks.
 Dan

 __
 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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[R] Installing xlsx package on Mac OS X

2012-06-18 Thread Victoria Xiao

Hi all,

I'm using a Mac port of R on Mac 10.6. I need to install xlsx package but
it does not install. Do any of you know a way to install it? Thanks very
much.

Sincerely,
Victoria Xiao

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Re: [R] Using Sub

2012-06-18 Thread arun

Hi Dan,

I am using linux.  So, not sure whether this will work or you tried it before.  
After you paste the path at (1:), then press enter two times. One more point.  
In your path, there were spaces within slashes.  So, if you do the scan, it 
will return as 5 items, which you have to join again.  I removed the spaces and 
tried this.


But you can try.

 str=scan(what=character,allowEscapes=F)
1: G:\CompensationAudits_Reports\StepAudit\StepsoffStep.accdb
2: 
Read 1 item
 str
[1] G:\\CompensationAudits_Reports\\StepAudit\\StepsoffStep.accdb
 gsub('', '/',str)
[1] G:/CompensationAudits_Reports/StepAudit/StepsoffStep.accdb


A.K.



- Original Message -
From: Lopez, Dan lopez...@llnl.gov
To: arun smartpink...@yahoo.com
Cc: R help r-help@r-project.org
Sent: Monday, June 18, 2012 12:03 PM
Subject: RE: [R] Using Sub

Hi A.K.,

That works but when I copy and paste from Window explorer it will have a single 
backslashes and not double.  It works with double as what you have in your 
example below but not with single as what I would end up passing.

Do you have any other suggestions or methods to accomplish this?

Thanks.
Dan


-Original Message-
From: arun [mailto:smartpink...@yahoo.com] 
Sent: Monday, June 18, 2012 8:59 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

Hi,

I guess you need something like this:

 str1-G:\\Compensation Audits_Reports\\Step Audit\\Steps off Step.accdb
 gsub('','/',str1)
[1] G:/Compensation Audits_Reports/Step Audit/Steps off Step.accdb


A.K.




- Original Message -
From: Lopez, Dan lopez...@llnl.gov
To: Duncan Murdoch murdoch.dun...@gmail.com
Cc: R help r-help@r-project.org
Sent: Monday, June 18, 2012 10:37 AM
Subject: Re: [R] Using Sub

Hi Duncan,

That's right but I want to be able to use this to replace back slashes with 
front slashes when I copy and paste file paths. How can I make this work so I 
don't get this error?

Thanks.
Dan

-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Sent: Friday, June 15, 2012 12:04 AM
To: Lopez, Dan
Cc: R help
Subject: Re: [R] Using Sub

On 12-06-14 6:23 PM, Lopez, Dan wrote:
 Hi,

 I have been trying to get the sub function to work but can't for the life of 
 me figure it out. I tried looking at ?sub but I think there is something that 
 I am just not understanding.

 Example failed attempts
 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: '\C' is an unrecognized escape in character string starting G:\C

This isn't anything to do with sub(), it's the third string that's the 
problem.  When you say G:\Comp... it thinks you've escaped the C, but there's 
no such escape.

Duncan Murdoch


 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=TRUE)
 Error: '\C' is an unrecognized escape in character string starting G:\C

 sub(\\,/,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb,fixed=FALSE)
 Error: '\C' is an unrecognized escape in character string starting 
 G:\C)

 sub(/,\,G:\Compensation Audits_Reports\Step Audit\Steps off 
 Step.accdb)
 Error: unexpected symbol in sub(/,\,G

 Thanks.
 Dan

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Re: [R] Trying to speed up an if/else statement in simulations

2012-06-18 Thread William Dunlap

inline below

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf
 Of nqf
 Sent: Monday, June 18, 2012 10:30 AM
 To: r-help@r-project.org
 Subject: [R] Trying to speed up an if/else statement in simulations
 
 Dear R-help,
 
 I am trying to write a function to simulate datasets of size n which contain
 two time-to-event outcome variables with associated 'Event'/'Censored'
 indicator variables (flag1 and flag2 respectively). One of these indicator
 variables needs to be dependent on the other, so I am creating the first and
 trying to use this to create the second using an if/else statement.
 
 My data structure needs to follow this algorithm (for each row of the data):
 If flag1=1 then flag2 should be 1 with probability 0.95 and zero otherwise
 Else if flag1=0 then flag2 should be 1 with probability 0.5 and zero
 otherwise
 
 I can set up this example quite simply using if else statements, but this is
 incredibly inefficient when running thousands of datasets:
 data-as.data.frame(rbinom(10,1,0.5))
 colnames(data)-'flag1'
 for (i in 1:n) {
   if (data$flag1[i]==1) {data$flag2[i]-rbinom(1,1,0.95)} else
 {data$flag2[i]-rbinom(1,1,0.5)}
  }

Do you mean
   n - 10
   data - data.frame(flag1 = rbinom(n, 1, 0.5))
   for(i in seq_len(n)) {
  if (data$flag1[i]==1) {data$flag2[i]-rbinom(1,1,0.95)} else 
{data$flag2[i]-rbinom(1,1,0.5)}
  }
?

 
 
 I think to speed up the simulations I would be better changing to
 vectorisation and using something like:
 ifelse(data$flag1==1,rbinom(1,1,0.95),rbinom(1,1,0.5))
 but the rbinom statements here generate one value and repeat this draw for
 every element of flag2 that matches the 'if' statement on flag1.

Assuming that n is nrow(data), use
   data$flag2 - ifelse(data$flag1==1, rbinom(n, 1, 0.95), rbinom(n, 1, 0.5))
so you get n independent draws from each distribution instead of 1.  I prefer
to factor out the common arguments as in
   data$flag2 - rbinom(n, 1, ifelse(data$flag1==1, 0.95, 0.5))

   
 
 Is there a way to assign flag2 to a new bernoulli draw for each subject in
 the data frame with flag1=1?
 
 I hope my question is clear, and thank you in advance for your help.
 
 Thanks,
 Natalie
 PhD student, Reading University
 
 P.S. I am using R 2.12.1 on Windows 7.
 
 
 --
 View this message in context: 
 http://r.789695.n4.nabble.com/Trying-to-speed-up-an-if-
 else-statement-in-simulations-tp4633725.html
 Sent from the R help mailing list archive at Nabble.com.
 
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[R] Biplot - how can I make it more readable?

2012-06-18 Thread Derek . Schanze

Hello,
I am doing a principle component analysis on a dataset with a lot of 
different variables and have constructed a biplot of the data. 
 Unfortunately, as can be seen on the attached image, the biplot is very 
messy, cluttered, and hard to read.  I have performed a few modifications 
including outlier removal from a few of the variables, which has made the 
plot better, however it still is too cluttered to read the variable names. 
 Is there any further improvment that can be made to the attached plot and 
if so what steps should I take? 

Thanks, 
Derek 


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[R] S4 into a data frame

2012-06-18 Thread spf385

Greetings,

I'm still very new to R; however I have been tasked with converting an S4
object into a data.frame. We are just trying to learn the basics of S4.
Could anyone offer a 'simple' example of coercing an S4 object (such as
might be stored in a package attribute) into a data.frame? Ultimately, we
would like to do something along the lines of 

mydata - as.data.frame(original S4 object)

Thanks in advance! 

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[R] (1-1e-100)==1 true?

2012-06-18 Thread whf1984911

Hi, 

This problems has bothered me for the lase couple of hours.  

 1e-100==0
[1] FALSE
 (1-1e-100)==1
[1] TRUE

How can I tell R that 1-1e-100 does not equal to 1,  actually, I found out
that
  (1-1e-16)==1
[1] FALSE
 (1-1e-17)==1
[1] TRUE

The reason I care about this is that I was try to use qnorm() in my code,
for example,

 qnorm(1e-100)
[1] -21.27345

and if I want to find qnorm(x) where x is very close to 1, say x=1-1e-100, 
then you would think using
qnorm(1-x, lower.tail=F) would give me something other than INF, but that
does not work since R would recognize x==1 in this case and therefore,
1-x==0, so qnorm(1-x, lower.tail=F) will give me INF which is what I try to
avoid in my code.

How could get around this, any suggestions?

Thanks,
Haifeng Wu
Graduate Student
University of South Carolina




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Re: [R] How can I declutter/make a biplot less messy in R

2012-06-18 Thread Bryan Hanson

Don't do the biplot. Darn hard to make sense of anyway. Plot the scores and
the loadings separately. You can see how to do that in this thread:
http://r.789695.n4.nabble.com/How-to-plot-PCA-output-td4614732.html

Good Luck. Bryan
***
Bryan Hanson
Professor of Chemistry Biochemistry
DePauw University

On Jun 18, 2012, at 10:37 AM, dss wrote:

I am doing a principle component analysis on a dataset with a lot of
different variables and have constructed a biplot of the data.
Unfortunately, as can be seen on the attached image, the biplot is very
messy, cluttered, and hard to read. I have performed a few modifications
including outlier removal from a few of the variables, which has made the
plot better, however it still is too cluttered to read the variable names.
Is there any further improvment that can be made to the attached plot and if
so what steps should I take?

Thanks,
Derek

http://r.789695.n4.nabble.com/file/n4633703/biplot.jpg

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[R] Listing all binary trees of an ordinal set

2012-06-18 Thread elmo

Hi all,

I'm new to R, have been reading books and trying to get started coding too. 
The first thing of substance I've been trying to do is to create a function
to return a list of all binary trees of a list of ordinals.  So, for
example, an input of list(3,1,2,4) would return:

list(list(1, list(2, list(3, 4))),
   list(1, list(list(2, 3), 4)),
   list(list(1, 2), list(3, 4)),
   list(list(1, list(2, 3)), 4),
   list(list(list(1, 2), 3), 4))

I've been trying recursions but nothing I've written has been both complete
and correct in the final formatting, and I'm sort of clueless when it comes
to recursive wrappers.  For example, one function I wrote,

g=function(x) {
  len.x = length(x);
  if (len.x  2)
  {
y=list()
for (i in 1:(len.x-1))
   y[[i]] = list(g(x[1:i]),g(x[-i:-1])) 
return(y)
  }
  else return(x)
}

trim = function(x) {
  for (i in 1:length(x)) {
if ((length(x[[i]]) == 1)  is.list(x[[i]]))
  x[[i]] = x[[i]][[1]]
  }
  return(x)
}

findBinTreesOrd=function(x) {
  x.lst = sort(unlist(x))
  all.bin.trees = g(x.lst)
  trim(all.bin.trees)
}

returns the trees in a compact, recursively nested form that I haven't found
a way to expand to the format that I desire.  Any help in either writing a
wrapper for that or a different approach to achieve what I'm trying to get
would be greatly appreciated--again, I'm quite new to R and am still shaky
with the powers and constraints that come with it.

LM


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Re: [R] How can I declutter/make a biplot less messy in R

2012-06-18 Thread Sarah Goslee

Hi Derek,

It's good form to provide an example with code so that we can see what
functions you're using and what you've tried.

I'm going to assume that you're using princomp(). Here's one way to
reduce the clutter:

pc.cr - princomp(USArrests, cor = TRUE)
biplot(pc.cr, xlabs=rep(x, nrow(USArrests)))

You can also change the colors and the scalings: see
?biplot.princomp
and
?biplot.default
for details.

Outlier removal may not be a good idea.

You also didn't tell us what your intent was: a publication-quality
plot? Something simply for you to look at yourself? Without knowing
that, it's hard to improve it.

Sarah

On Mon, Jun 18, 2012 at 10:37 AM, dss derek.scha...@srnl.doe.gov wrote:
 I am doing a principle component analysis on a dataset with a lot of
 different variables and have constructed a biplot of the data.
 Unfortunately, as can be seen on the attached image, the biplot is very
 messy, cluttered, and hard to read.  I have performed a few modifications
 including outlier removal from a few of the variables, which has made the
 plot better, however it still is too cluttered to read the variable names.
 Is there any further improvment that can be made to the attached plot and if
 so what steps should I take?

 Thanks,
 Derek



-- 
Sarah Goslee
http://www.functionaldiversity.org

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Inconsistency using seq

Nope. round() is not failsafe either. Basically, there is theoretically no
way to guarantee immunity to floating point error in conditional
comparisons. You need to either switch to integers -- which **are** exactly
represented -- or figure out another way.

Of course, practically speaking, sufficient rounding will work. It's just
that it **can** always break. ... and you know Murphy's first law.

-- Bert

On Mon, Jun 18, 2012 at 1:54 PM, hamoreno hamor...@asu.edu wrote:

 Thanks everyone... Seems that I will have to use round before seq to make
 sure everything has the correct precision.

 --
 View this message in context:
 http://r.789695.n4.nabble.com/Inconsistency-using-seq-tp4633739p4633750.html
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] Trying to speed up an if/else statement in simulations

2012-06-18 Thread Peter Alspach

Tena koe Natalie

Does this do what you want?

set.seed(123)
natalie - matrix(NA, nrow=10^5, ncol=2, dimnames=list(NULL, paste0('flag', 
1:2)))
natalie[,'flag1'] - rbinom(nrow(natalie), 1, 0.5)
natalie[natalie[,'flag1']==1, 'flag2'] - rbinom(sum(natalie[,'flag1']), 1, 
0.95)
natalie[natalie[,'flag1']==0, 'flag2'] - 
rbinom(nrow(natalie)-sum(natalie[,'flag1']), 1, 0.5)
tapply(natalie[,'flag2'], natalie[,'flag1'], table)

HTH 

Peter Alspach

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of nqf
Sent: Tuesday, 19 June 2012 5:30 a.m.
To: r-help@r-project.org
Subject: [R] Trying to speed up an if/else statement in simulations

Dear R-help,

I am trying to write a function to simulate datasets of size n which contain
two time-to-event outcome variables with associated 'Event'/'Censored'
indicator variables (flag1 and flag2 respectively). One of these indicator
variables needs to be dependent on the other, so I am creating the first and
trying to use this to create the second using an if/else statement. 

My data structure needs to follow this algorithm (for each row of the data):
If flag1=1 then flag2 should be 1 with probability 0.95 and zero otherwise
Else if flag1=0 then flag2 should be 1 with probability 0.5 and zero
otherwise

I can set up this example quite simply using if else statements, but this is
incredibly inefficient when running thousands of datasets:
data-as.data.frame(rbinom(10,1,0.5))
colnames(data)-'flag1'
for (i in 1:n) {
  if (data$flag1[i]==1) {data$flag2[i]-rbinom(1,1,0.95)} else
{data$flag2[i]-rbinom(1,1,0.5)}  
 }


I think to speed up the simulations I would be better changing to
vectorisation and using something like:
ifelse(data$flag1==1,rbinom(1,1,0.95),rbinom(1,1,0.5)) 
but the rbinom statements here generate one value and repeat this draw for
every element of flag2 that matches the 'if' statement on flag1.

Is there a way to assign flag2 to a new bernoulli draw for each subject in
the data frame with flag1=1?

I hope my question is clear, and thank you in advance for your help. 

Thanks,
Natalie
PhD student, Reading University

P.S. I am using R 2.12.1 on Windows 7.


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Re: [R] Inconsistency using seq

2012-06-18 Thread Jeff Newmiller

actually, you should build your sequences with integers and scale those to get 
floating point sequences.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

hamoreno hamor...@asu.edu wrote:

Thanks everyone... Seems that I will have to use round before seq to
make
sure everything has the correct precision.

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Re: [R] Trying to speed up an if/else statement in simulations

I might try something like:

data[data$flag1 == 1, flag2] - runif(sum(data$flag1 == 1))  0.95

and similarly for the other case.

Hope this helps,
Michael

On Mon, Jun 18, 2012 at 12:29 PM, nqf n.j.frank...@pgr.reading.ac.uk wrote:
 Dear R-help,

 I am trying to write a function to simulate datasets of size n which contain
 two time-to-event outcome variables with associated 'Event'/'Censored'
 indicator variables (flag1 and flag2 respectively). One of these indicator
 variables needs to be dependent on the other, so I am creating the first and
 trying to use this to create the second using an if/else statement.

 My data structure needs to follow this algorithm (for each row of the data):
 If flag1=1 then flag2 should be 1 with probability 0.95 and zero otherwise
 Else if flag1=0 then flag2 should be 1 with probability 0.5 and zero
 otherwise

 I can set up this example quite simply using if else statements, but this is
 incredibly inefficient when running thousands of datasets:
 data-as.data.frame(rbinom(10,1,0.5))
 colnames(data)-'flag1'
 for (i in 1:n) {
  if (data$flag1[i]==1) {data$flag2[i]-rbinom(1,1,0.95)} else
 {data$flag2[i]-rbinom(1,1,0.5)}
  }


 I think to speed up the simulations I would be better changing to
 vectorisation and using something like:
 ifelse(data$flag1==1,rbinom(1,1,0.95),rbinom(1,1,0.5))
 but the rbinom statements here generate one value and repeat this draw for
 every element of flag2 that matches the 'if' statement on flag1.

 Is there a way to assign flag2 to a new bernoulli draw for each subject in
 the data frame with flag1=1?

 I hope my question is clear, and thank you in advance for your help.

 Thanks,
 Natalie
 PhD student, Reading University

 P.S. I am using R 2.12.1 on Windows 7.


 --
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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] Trying to speed up an if/else statement in simulations



On Jun 18, 2012, at 1:29 PM, nqf wrote:


Dear R-help,

I am trying to write a function to simulate datasets of size n which  
contain

two time-to-event outcome variables with associated 'Event'/'Censored'
indicator variables (flag1 and flag2 respectively). One of these  
indicator
variables needs to be dependent on the other, so I am creating the  
first and

trying to use this to create the second using an if/else statement.

My data structure needs to follow this algorithm (for each row of  
the data):
If flag1=1 then flag2 should be 1 with probability 0.95 and zero  
otherwise

Else if flag1=0 then flag2 should be 1 with probability 0.5 and zero
otherwise

I can set up this example quite simply using if else statements, but  
this is

incredibly inefficient when running thousands of datasets:
data-as.data.frame(rbinom(10,1,0.5))
colnames(data)-'flag1'
for (i in 1:n) {
 if (data$flag1[i]==1) {data$flag2[i]-rbinom(1,1,0.95)} else
{data$flag2[i]-rbinom(1,1,0.5)}
}


I think to speed up the simulations I would be better changing to
vectorisation and using something like:
ifelse(data$flag1==1,rbinom(1,1,0.95),rbinom(1,1,0.5))
but the rbinom statements here generate one value and repeat this  
draw for

every element of flag2 that matches the 'if' statement on flag1.

Is there a way to assign flag2 to a new bernoulli draw for each  
subject in

the data frame with flag1=1?


If the parameters for the the Bernoulli draws stay the same, as they  
appear to do then all you need to do is read the help page for  
`rbinom` and use the appropriate call to create vectors that are as  
long as data$flag.



--
David Winsemius, MD
West Hartford, CT

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

Re: [R] Error w/ Start up Script

You are perhaps not using suppressPackageStartupMessages() correctly
if you're getting those warnings: my .Rprofile has these lines:

suppressPackageStartupMessages(library(quantmod))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(lattice))

but produces no warnings (the first does when loading in a clean
session without suppressing)

Best,
Michael

On Mon, Jun 18, 2012 at 4:08 PM, Lopez, Dan lopez...@llnl.gov wrote:
 Ouch Bert. Not patience for the newbies, I see.

 I know what ?anything means which is why I didn't ask about ?Startup. But 
 being that I just recently discovered what Rprofile.site is I thought it 
 might do something different within the start-up file and tried it both ways.

 Besides I think what I really need is to just figure out as I said:
 I did however go to the Misc menu and select List search path and got the 
 below results. Not exactly sure what it means but I do notice that several of 
 the packages that popup at startup as being masked appear  in this list. 
 Maybe this is the problem? If so how do you take out what you don't need at 
 startup?

   search()

 [1] .GlobalEnv          package:stats       package:graphics    
 package:grDevices   package:datasets

  [6] package:rattle      package:R.utils     package:utils       
 package:R.oo        package:R.methodsS3

 [11] package:methods     Autoloads           package:base



 Dan

 From: Bert Gunter [mailto:gunter.ber...@gene.com]
 Sent: Monday, June 18, 2012 1:50 PM
 To: Lopez, Dan
 Cc: David Winsemius; R help (r-help@r-project.org)
 Subject: Re: [R] Error w/ Start up Script

 I gave you the references you need. It's up to you to read and understand how 
 to use them. You apparently need to work harder to do so. BTW

 ?anything

 is an alternative way to type

 help(anything)

 at the command line for R's help pages.

 -- Bert
 On Mon, Jun 18, 2012 at 1:34 PM, Lopez, Dan 
 lopez...@llnl.govmailto:lopez...@llnl.gov wrote:
 Hi Bert,

 I tried entering: ?suppressPackageStartupMessages and then 
 suppressPackageStartupMessages into my Rprofile.site file and the messages 
 still came up.

 I did however go to the Misc menu and select List search path and got the 
 below results. Not exactly sure what it means but I do notice that several of 
 the packages that popup at startup as being masked appear  in this list. 
 Maybe this is the problem? If so how do you take out what you don't need at 
 startup?

 search()
 [1] .GlobalEnv          package:stats       package:graphics    
 package:grDevices   package:datasets
  [6] package:rattle      package:R.utils     package:utils       
 package:R.oo        package:R.methodsS3
 [11] package:methods     Autoloads           package:base
 0

 Thanks.
 Dan

 From: Bert Gunter 
 [mailto:gunter.ber...@gene.commailto:gunter.ber...@gene.com]
 Sent: Monday, June 18, 2012 1:10 PM
 To: Lopez, Dan
 Cc: David Winsemius; R help 
 (r-help@r-project.orgmailto:r-help@r-project.org)
 Subject: Re: [R] Error w/ Start up Script

 ?suppressPackageStartupMessages

 Put this into your appropriate startup file.
 ?Startup  ## for details on starting R and what files are executed at startup.

 -- Bert
 On Mon, Jun 18, 2012 at 12:46 PM, Lopez, Dan 
 lopez...@llnl.govmailto:lopez...@llnl.gov wrote:
 David,

 Sorry I should have been more specific. They are not as much errors as they 
 are extra script that is running at startup after Type q() to quit R. It 
 wasn't there before. And am thinking eventually it could become a problem.

 Thanks.
 Dan

 Here it is again...what it looks like when I first startup R (partial copy 
 and paste):

 
 ...
 ..
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.

 Type 'demo()' for some demos, 'help()' for on-line help, or
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.

 Attempting to load the environment 'package:R.utils'
 R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for 
 help.
 R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

 Attaching package: 'R.oo'

 The following object(s) are masked from 'package:R.methodsS3':

   throw.default
 ..
 ...
 
 -Original Message-
 From: David Winsemius 
 [mailto:dwinsem...@comcast.netmailto:dwinsem...@comcast.net]
 Sent: Monday, June 18, 2012 12:12 PM
 To: Lopez, Dan
 Cc: R help (r-help@r-project.orgmailto:r-help@r-project.org)
 Subject: Re: [R] Error w/ Start up Script


 On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:

 I noticed about a couple weeks ago that my R start up script starting
 showing the below errors, following the line Type 'q()' to quit R


 I didn't see any errors reported. I didn't see any warnings, either.

 --
 David.

 Not sure what I did different and so far it hasn't caused major
 problems but kind of fear that it will.

 Can you please help?
 I also posted my Rprofile below.

[R] Changing many csv files using apply?

2012-06-18 Thread Chang, Emily@OEHHA

Dear all,

I have many csv files whose contents I want to change a bit en masse. So far, 
I've written code that can change them in a for loop, like so:

# Subset of files in the folder I want to change
subset = somestring
# Retrieve list of files to change
filelist=list.files()
filelist = filelist[grep(subset, filelist)]

for(i in 1:length(filelist)){
setwd(readdir)
temp = read.csv(filelist[i],as.is = T, strip.white = T)
whatever I want to do to temp

setwd(writedir)
write.table(temp, file = filelist[i], sep = ,, col.names=NA)
}


It's a little slow though, so I would like to get rid of the for loop but 
preserve its function. Would it be possible to use sapply() or something 
similar? Any insight would be appreciated!

Best regards,
Emily
__
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] Changing strip text

2012-06-18 Thread Peter Ehlers


On 2012-06-18 10:02, Julie Truman wrote:

I'm trying to create a 5-panel xyplot with each strip labelled by treatment. 
The code is as follows:

xyplot(log(pfuml)~Transfer|Treat,groups=Pop,ylab=Log10 Pfu/ml,as.table=T,
type=a,
auto.key=
list(space=right,points=F,lines=T))



I've tried:

strip=strip.custom(factor.levels=c(0,2,4,8,16)

But it's not working, I still only get Treat printed on each strip. Any ideas?


Convert your Treat variable to a factor with appropriate
levels before plotting or (less desirable) use
as.factor(Treat) in place of Treat.

A couple of bits of advice for future posts:
1. We don't have your data, so either provide relevant
   information about it ( str() is useful) or, if
   possible, illustrate your problem with a built-in
   dataset. Or make up some data to illustrate the
   problem.

2. Excise extraneous information from your code;
   here we don't need your ylab, as.table, groups,
   type, auto.key.

Peter Ehlers



Thank you,

Julie





[[alternative HTML version deleted]]

__
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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-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] Error w/ Start up Script

Hi Michael,

I wasn't getting how to actually use it from ?suppressPackageStartupMessages 
example online. 

Thank you very much.
Dan


-Original Message-
From: R. Michael Weylandt [mailto:michael.weyla...@gmail.com] 
Sent: Monday, June 18, 2012 2:53 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.org)
Subject: Re: [R] Error w/ Start up Script

You are perhaps not using suppressPackageStartupMessages() correctly if you're 
getting those warnings: my .Rprofile has these lines:

suppressPackageStartupMessages(library(quantmod))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(lattice))

but produces no warnings (the first does when loading in a clean session 
without suppressing)

Best,
Michael

On Mon, Jun 18, 2012 at 4:08 PM, Lopez, Dan lopez...@llnl.gov wrote:
 Ouch Bert. Not patience for the newbies, I see.

 I know what ?anything means which is why I didn't ask about ?Startup. But 
 being that I just recently discovered what Rprofile.site is I thought it 
 might do something different within the start-up file and tried it both ways.

 Besides I think what I really need is to just figure out as I said:
 I did however go to the Misc menu and select List search path and got the 
 below results. Not exactly sure what it means but I do notice that several of 
 the packages that popup at startup as being masked appear  in this list. 
 Maybe this is the problem? If so how do you take out what you don't need at 
 startup?

   search()

 [1] .GlobalEnv          package:stats       package:graphics    
 package:grDevices   package:datasets

  [6] package:rattle      package:R.utils     package:utils       
 package:R.oo        package:R.methodsS3

 [11] package:methods     Autoloads           package:base



 Dan

 From: Bert Gunter [mailto:gunter.ber...@gene.com]
 Sent: Monday, June 18, 2012 1:50 PM
 To: Lopez, Dan
 Cc: David Winsemius; R help (r-help@r-project.org)
 Subject: Re: [R] Error w/ Start up Script

 I gave you the references you need. It's up to you to read and 
 understand how to use them. You apparently need to work harder to do 
 so. BTW

 ?anything

 is an alternative way to type

 help(anything)

 at the command line for R's help pages.

 -- Bert
 On Mon, Jun 18, 2012 at 1:34 PM, Lopez, Dan 
 lopez...@llnl.govmailto:lopez...@llnl.gov wrote:
 Hi Bert,

 I tried entering: ?suppressPackageStartupMessages and then 
 suppressPackageStartupMessages into my Rprofile.site file and the messages 
 still came up.

 I did however go to the Misc menu and select List search path and got the 
 below results. Not exactly sure what it means but I do notice that several of 
 the packages that popup at startup as being masked appear  in this list. 
 Maybe this is the problem? If so how do you take out what you don't need at 
 startup?

 search()
 [1] .GlobalEnv          package:stats       package:graphics    
 package:grDevices   package:datasets
  [6] package:rattle      package:R.utils     package:utils       
 package:R.oo        package:R.methodsS3
 [11] package:methods     Autoloads           package:base
 0

 Thanks.
 Dan

 From: Bert Gunter 
 [mailto:gunter.ber...@gene.commailto:gunter.ber...@gene.com]
 Sent: Monday, June 18, 2012 1:10 PM
 To: Lopez, Dan
 Cc: David Winsemius; R help 
 (r-help@r-project.orgmailto:r-help@r-project.org)
 Subject: Re: [R] Error w/ Start up Script

 ?suppressPackageStartupMessages

 Put this into your appropriate startup file.
 ?Startup  ## for details on starting R and what files are executed at startup.

 -- Bert
 On Mon, Jun 18, 2012 at 12:46 PM, Lopez, Dan 
 lopez...@llnl.govmailto:lopez...@llnl.gov wrote:
 David,

 Sorry I should have been more specific. They are not as much errors as they 
 are extra script that is running at startup after Type q() to quit R. It 
 wasn't there before. And am thinking eventually it could become a problem.

 Thanks.
 Dan

 Here it is again...what it looks like when I first startup R (partial copy 
 and paste):

 
 ...
 ..
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and 'citation()' on how to 
 cite R or R packages in publications.

 Type 'demo()' for some demos, 'help()' for on-line help, or 
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.

 Attempting to load the environment 'package:R.utils'
 R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for 
 help.
 R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

 Attaching package: 'R.oo'

 The following object(s) are masked from 'package:R.methodsS3':

   throw.default
 ..
 ...
 
 -Original Message-
 From: David Winsemius 
 [mailto:dwinsem...@comcast.netmailto:dwinsem...@comcast.net]
 Sent: Monday, June 18, 2012 12:12 PM
 To: Lopez, Dan
 Cc: R help (r-help@r-project.orgmailto:r-help@r-project.org)
 Subject: Re: [R] Error w/ Start up Script


 On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:

 I noticed about a couple

Re: [R] (1-1e-100)==1 true?

2012-06-18 Thread David Smith

This is standard behaviour for a floating-point computational system
like R. You might like to take a look at this blog post for a
backgrounder on floating-point arithmetic in R.

http://blog.revolutionanalytics.com/2009/03/when-is-a-zero-not-a-zero.html

# David Smith

On Mon, Jun 18, 2012 at 2:26 PM, whf1984911 whf1984...@yahoo.com.cn wrote:

 Hi,

 This problems has bothered me for the lase couple of hours.

  1e-100==0
 [1] FALSE
  (1-1e-100)==1
 [1] TRUE

 How can I tell R that 1-1e-100 does not equal to 1,  actually, I found out
 that
   (1-1e-16)==1
 [1] FALSE
  (1-1e-17)==1
 [1] TRUE

 The reason I care about this is that I was try to use qnorm() in my code,
 for example,

  qnorm(1e-100)
 [1] -21.27345

 and if I want to find qnorm(x) where x is very close to 1, say x=1-1e-100,
 then you would think using
 qnorm(1-x, lower.tail=F) would give me something other than INF, but that
 does not work since R would recognize x==1 in this case and therefore,
 1-x==0, so qnorm(1-x, lower.tail=F) will give me INF which is what I try
 to
 avoid in my code.

 How could get around this, any suggestions?

 Thanks,
 Haifeng Wu
 Graduate Student
 University of South Carolina

--
David M Smith da...@revolutionanalytics.com
VP of Marketing, Revolution Analytics  http://blog.revolutionanalytics.com
Tel: +1 (650) 646-9523 (Palo Alto, CA, USA)
Twitter: @revodavid

__
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] Changing many csv files using apply?

sapply() won't be notably faster.

What you might try (no guarantee) is wrapping things up as if you were
going to use sapply() but instead use mclapply() from the parallel
package -- that will parallelize the results and should be faster by
roughly as many cores as you use. The no guarantee disclaimer comes
from me not being able to guarantee that I/O is nicely parallelized
having never tried it myself

(it probably is though, those R folks are pretty good at what they do)

Michael

On Mon, Jun 18, 2012 at 4:38 PM, Chang, Emily@OEHHA
emily.ch...@oehha.ca.gov wrote:
 Dear all,

 I have many csv files whose contents I want to change a bit en masse. So far, 
 I've written code that can change them in a for loop, like so:

 # Subset of files in the folder I want to change
 subset = somestring
 # Retrieve list of files to change
 filelist=list.files()
 filelist = filelist[grep(subset, filelist)]

 for(i in 1:length(filelist)){
        setwd(readdir)
        temp = read.csv(filelist[i],as.is = T, strip.white = T)
        whatever I want to do to temp

        setwd(writedir)
        write.table(temp, file = filelist[i], sep = ,, col.names=NA)
        }


 It's a little slow though, so I would like to get rid of the for loop but 
 preserve its function. Would it be possible to use sapply() or something 
 similar? Any insight would be appreciated!

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

Re: [R] S4 into a data frame

2012-06-18 Thread Martin Morgan


On 06/18/2012 01:49 PM, spf385 wrote:

Greetings,

I'm still very new to R; however I have been tasked with converting an S4
object into a data.frame. We are just trying to learn the basics of S4.
Could anyone offer a 'simple' example of coercing an S4 object (such as
might be stored in a package attribute) into a data.frame? Ultimately, we
would like to do something along the lines of

mydata- as.data.frame(original S4 object)


see ?setAs for more extensive discussion.

Not sure what 'stored in a package attribute might mean'. Here's a class

 setClass(A, representation(x=numeric, y=numeric))

and how to coerce from A to a data.frame

 setAs(A, data.frame, function(from) data.frame(x=from@x, y=from@y))

and then in action

 a = new(A, x=1:5, y=5:1)
 as(a, data.frame)
  x y
1 1 5
2 2 4
3 3 3
4 4 2
5 5 1

To use as.data.frame(a), you'd have to implement the 'as.data.frame.A' 
S3 method, e.g.,


 as.data.frame.A = function(x) as(x, data.frame)

Also, probably you'd want a validity method (see ?setValidity) on A, 
to ensure that x, y were equal length.


Martin



Thanks in advance!

--
View this message in context: 
http://r.789695.n4.nabble.com/S4-into-a-data-frame-tp4633746.html
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__
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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.



--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Listing all binary trees of an ordinal set



On Jun 18, 2012, at 5:25 PM, elmo wrote:


Hi all,

I'm new to R, have been reading books and trying to get started  
coding too.
The first thing of substance I've been trying to do is to create a  
function

to return a list of all binary trees of a list of ordinals.  So, for
example, an input of list(3,1,2,4) would return:


Please do not cross-post (but DO read the Posting Guide where this was  
is requested). You have already gotten an answer on StackOverflow.


--
David.


list(list(1, list(2, list(3, 4))),
  list(1, list(list(2, 3), 4)),
  list(list(1, 2), list(3, 4)),
  list(list(1, list(2, 3)), 4),
  list(list(list(1, 2), 3), 4))

I've been trying recursions but nothing I've written has been both  
complete
and correct in the final formatting, and I'm sort of clueless when  
it comes

to recursive wrappers.  For example, one function I wrote,

g=function(x) {
 len.x = length(x);
 if (len.x  2)
 {
   y=list()
   for (i in 1:(len.x-1))
  y[[i]] = list(g(x[1:i]),g(x[-i:-1]))
   return(y)
 }
 else return(x)
}

trim = function(x) {
 for (i in 1:length(x)) {
   if ((length(x[[i]]) == 1)  is.list(x[[i]]))
 x[[i]] = x[[i]][[1]]
 }
 return(x)
}

findBinTreesOrd=function(x) {
 x.lst = sort(unlist(x))
 all.bin.trees = g(x.lst)
 trim(all.bin.trees)
}

returns the trees in a compact, recursively nested form that I  
haven't found
a way to expand to the format that I desire.  Any help in either  
writing a
wrapper for that or a different approach to achieve what I'm trying  
to get
would be greatly appreciated--again, I'm quite new to R and am still  
shaky

with the powers and constraints that come with it.

LM


--
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David Winsemius, MD
West Hartford, CT

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] (1-1e-100)==1 true?

2012-06-18 Thread Ted Harding

On 18-Jun-2012 21:26:41 whf1984911 wrote:
 Hi, 
 
 This problems has bothered me for the lase couple of hours.  
 
 1e-100==0
 [1] FALSE
 (1-1e-100)==1
 [1] TRUE
 
 How can I tell R that 1-1e-100 does not equal to 1,  actually,
 I found out that
   (1-1e-16)==1
 [1] FALSE
 (1-1e-17)==1
 [1] TRUE
 
 The reason I care about this is that I was try to use qnorm()
 in my code, for example,
 
 qnorm(1e-100)
 [1] -21.27345
 
 and if I want to find qnorm(x) where x is very close to 1, say
 x=1-1e-100, then you would think using qnorm(1-x, lower.tail=F)
 would give me something other than INF, but that does not work
 since R would recognize x==1 in this case and therefore, 1-x==0,
 so qnorm(1-x, lower.tail=F) will give me INF which is what I try
 to avoid in my code.
 
 How could get around this, any suggestions?
 
 Thanks,
 Haifeng Wu
 Graduate Student
 University of South Carolina

You are working close to, and also beyond, the boundary of what
R can internally represent, so anomalies like this will frequently
turn up.

For the sort of extreme values which you are using, it is better
to make use of asymptotic formulae, and not to use R's standard
functions such as qnorm, pnorm, ...

For example, there is Mills Ratio, for which (in RF notation)

  x*(1 - pnorm(x))/dnorm(x) -- 1 as x -- Inf

So, for large x, proceed as though it was exactly 1.

Then

  log(x) + log(1 - pnorm(x)) = log(dnorm(x))
  = -0.5*log(2*pi) - 0.5*x^2

so, with (e.g.) pnorm(x) = 1-1e-100, you have

  log(x) + 0.5*x^2 = 100 - 0.5*log(2*pi)

More generally, with pnorm(x) = 1-1e-X where X is large,

  log(x) + 0.5*x^2 = X - 0.5*log(2*pi)

so you now need to write a function, say Qnorm(X), which
solves this equation for x, given X.

The above is only a suggestion. Probably others know a better
approach!

Ted.

-
E-Mail: (Ted Harding) ted.hard...@wlandres.net
Date: 19-Jun-2012  Time: 00:07:11
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Re: [R] Inconsistency using seq

2012-06-18 Thread Henrik Bengtsson

FYI,

 isZero - function(x, neps=1, eps=.Machine$double.eps, ...) {
+  (abs(x)  neps * eps)
+ }

 x - seq(from=0, to=4, by=0.1)
 isZero(x[4]-0.3)
[1] TRUE
 isZero(x[4]-0.3, neps=1)
[1] TRUE
 isZero(x[4]-0.3, neps=0.1)
[1] FALSE

You could also have called isZero() isValueSmallEnoughForWhatINeed().

My $.02

/Henrik

On Mon, Jun 18, 2012 at 2:29 PM, Bert Gunter gunter.ber...@gene.com wrote:
 Nope. round() is not failsafe either. Basically, there is theoretically no
 way to guarantee immunity to floating point error in conditional
 comparisons. You need to either switch to integers -- which **are** exactly
 represented -- or figure out another way.

 Of course, practically speaking, sufficient rounding will work. It's just
 that it **can** always break. ... and you know Murphy's first law.

 -- Bert

 On Mon, Jun 18, 2012 at 1:54 PM, hamoreno hamor...@asu.edu wrote:

 Thanks everyone... Seems that I will have to use round before seq to make
 sure everything has the correct precision.

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 View this message in context:
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 Sent from the R help mailing list archive at Nabble.com.

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 --

 Bert Gunter
 Genentech Nonclinical Biostatistics

 Internal Contact Info:
 Phone: 467-7374
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 http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] Trying to speed up an if/else statement in simulations