Re: [R] bigglm() results different from glm()+Another question
That was definitely helpful. if you change your seq to: seq(chunksize, 1-chunksize, chunksize) then you won't get the error messages Even previously, I was not getting any error messages or warnings at all, i.e., update removes the extra NA rows silently, for example: set.seed(1) xx = data.frame(x1=runif(1,0,10), x2=runif(1,0,10), x3=runif(1,0,10)) xx$y = 3 + xx$x1 + 2*xx$x2 + 3*xx$x3 + rnorm(1) fit1 = biglm(y~x1+x2+x3, data=xx[1:7000,]) fit2 = update(fit1, moredata=xx[7001:1,]) fit3 = update(fit2, moredata=xx[7001:14000,]) Here fit2 and fit3 are exactly same. Also if the number of rows is not a multiple of chunksize then your sequence will not accommodate the last small chunk of data . Regards Utkarsh Greg Snow wrote: OK, it appears that the problem is the df.resid component of the biglm object. Everything else is being updated by the update function except the df.resid piece, so it is based solely on the initial fit and the chunksize used there. The df.resid piece is then used in the computation of the AIC and hence the differences that you see. There could also be a difference in the p-values and confidence intervals, but at those high of numbers, the differences are smaller than can be seen at the level of rounding done. This appears to be a bug/overlooked piece to me, Thomas is cc'd on this so he should be able to fix this. A work around in the meantime is to do something like: fit$df.resid - 1-4 Then compute the AIC. Also as an aside, if you change your seq to: seq(chunksize, 1-chunksize, chunksize) then you won't get the error messages. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 *From:* utkarshsinghal [mailto:utkarsh.sing...@global-analytics.com] *Sent:* Wednesday, July 08, 2009 2:24 AM *To:* Greg Snow *Cc:* Thomas Lumley; r help *Subject:* Re: [R] bigglm() results different from glm()+Another question Hi Greg, Many thanks for your precious time. Here is a workable code: set.seed(1) xx = data.frame(x1=runif(1,0,10), x2=runif(1,0,10), x3=runif(1,0,10)) xx$y = 3 + xx$x1 + 2*xx$x2 + 3*xx$x3 + rnorm(1) chunksize = 500 fit = biglm(y~x1+x2+x3, data=xx[1:chunksize,]) for(i in seq(chunksize,1,chunksize)) fit=update(fit, moredata=xx[(i+1):(i+chunksize),]) AIC(fit) [1] 28956.91 And the AIC for other chunksizes: chunksizeAIC 500 28956.91 100027956.91 200025956.91 250024956.91 500019956.91 19956.91 Also I noted that the estimated coefficients are not dependent on chunksize and AIC is exactly a linear function of chunksize. So I guess it is some problem with the calculation of AIC, may be in some degree of freedom or adding some constant somewhere. And my comments below. Regards Utkarsh Greg Snow wrote: How many rows does xx have? Let's look at your example for chunksize 1, you initially fit the first 1 observations, then the seq results in just the value 1 which means that you do the update based on vaues 10001 through 2, if xx only has 1 rows, then this should give at least one error. If xx has 2 or more rows, then only chunksize 1 will ever see the 2^th value, the other chunksizes will use less of the data. Understood your point and apologize that you had to spend time going into the logic inside for loop. I definitely thought of that but my actual problem was the variation in AICs (which I was sure about), so to ignore this loop problem (temporarily), I deliberately chose the chunksizes such that the number of rows is a multiple of chunksize. I knew there is still one extra iteration happening and I checked that it was not causing any problem, the moredata in the last iteration will be all NA's and update does nothing in such a case. For example: Let's say chunksize=5000, even though xx has only 1 rows, fit2 and fit3 below are exactly same. fit1 = biglm(y~x1+x2+x3, data=xx[1:5000,]) fit2 = update(fit1, moredata=xx[5001:1,]) fit3 = update(fit2, moredata=xx[10001:15000,]) AIC(fit1); AIC(fit2); AIC(fit3) [1] 5018.282 [1] 19956.91 [1] 19956.91 (The AIC matches with the table above and no warnings at all) I checked all these things before sending my first mail and dropped the idea of refining the for loop as this will save me a few lines of code and also the loop looks good and easy to understand. Moreover it is neither taking any extra run time nor producing any warnings or errors. Also looking at the help for update.biglm, the 2^nd argument is moredata not data, so if the code below is the code that you actually ran, then the new data chunks are going into the ... argument (and being ignored as that is there for future expansion and does nothing
Re: [R] Extracting a column name in loop?
If df is your dataframe then names(df) contains the column names and so names(df)[i] is the name of i-th column. --- On Thu, 9/7/09, mister_bluesman mister_blues...@hotmail.com wrote: From: mister_bluesman mister_blues...@hotmail.com Subject: [R] Extracting a column name in loop? To: r-help@r-project.org Received: Thursday, 9 July, 2009, 1:41 AM Hi, I am writing a script that will address columns using syntax like: data_set[,1] to extract the data from the first column of my data set, for example. This code will be placed in a loop (where the column reference will be placed by a variable). What I also need to do is extract the column NAME for a given column being processed in the loop. The dataframe has been set so that R knows that the top line refers to column headers. Can anyone help me understand how to do this? Thanks. -- View this message in context: http://www.nabble.com/Extracting-a-column-name-in-loop--tp24393160p24393160.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 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] Cuminc Plot
Dear All,
here is the example for cumulative incidence analysis with cmprsk package:
set.seed(2)
ss - rexp(100)
gg - factor(sample(1:3,100,replace=TRUE),1:3,c('a','b','c'))
cc - sample(0:2,100,replace=TRUE)
strt - sample(1:2,100,replace=TRUE)
print(xx - cuminc(ss,cc,gg,strt))
plot(xx,lty=1,color=1:6)
When I
perform this example, I have 6 curves.
a 1
b 1
c 1
a 2
b 2
c 2
I would
like to plot only 3 first curves of risk cc=1 not all of 6 curves.
a 1
b 1
c 1
How I can
do this with R ?
Many thanks
Jan
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[R] Node colors in pvclust
Is there a way to assign color to nodes as with hclust/as.dendrogram/dendrapply when using pvclust? The problem is that as.dendrogram isn't working on the pvclust objects. library(pvclust) pvc - pvclust(matrix, nboot=1000) plot(pvc) -- View this message in context: http://www.nabble.com/Node-colors-in-pvclust-tp24405329p24405329.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.
Re: [R] print() to file?
One possibility is to use sink (see ?sink). --- On Thu, 9/7/09, Steve Jaffe sja...@riskspan.com wrote: From: Steve Jaffe sja...@riskspan.com Subject: [R] print() to file? To: r-help@r-project.org Received: Thursday, 9 July, 2009, 5:03 AM I'd like to write some objects (eg arrays) to a log file. cat() flattens them out. I'd like them formatted as in 'print' but print only writes to stdout. Is there a simple way to achieve this result? Thanks -- View this message in context: http://www.nabble.com/print%28%29-to-file--tp24397445p24397445.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 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: no such index at level 2
Hi Godmar Back god...@gmail.com napsal dne 08.07.2009 15:28:50: On Wed, Jul 8, 2009 at 4:22 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 07.07.2009 19:06:17: Hi, I am confused about how to select elements from a list. I'm trying to select all rows of a table 'crossRsorted' such that the mean of a related vector is 0. The related vector is accessible as a list element l[[i]] where i is the row index. I thought this would work: crossRsorted[mean(q[[ crossRsorted[,1] ]], na.rm = TRUE) 0, ] Error in q[[crossRsorted[, 1]]] : no such index at level 2 Strange, I got completely different error. Couldn't be that only ***you*** have crossRsorted? Ok, fair enough. I'm still thinking of a language in which the meaning of operators is apparent from their syntactical structure - probably need to read more of The R Inferno. Here's an example that reproduces the problem, I think (though the error message is slightly different): q-list() q[[105]] - as.numeric(c(0,0,1)) q[[104]] - as.numeric(c(1,1,1)) q[[10]] - as.integer(c(3,3,1)) crossRsorted - data.frame(i = c(105, 104,10)) q[[ crossRsorted[,1] ]] Error in q[[crossRsorted[, 1]]] : recursive indexing failed at level 2 for that q[crossRsorted[,1]] works but your real list is much more complicated. Even though the list 'q' has component 105, 104, and 10, the expression q[[ crossRsorted[,1] ]] causes an error. Why? And why does this work: q[[c(105)]] [1] 0 0 1 but not this: q[[c(105,104)]] Error in q[[c(105, 104)]] : subscript out of bounds q[[c(105,104,10)]] Error in q[[c(105, 104, 10)]] : recursive indexing failed at level 2 even though q[[105]], q[[104], and q[[10]] are perfectly legitimate items? Coming back to my question, how to I express select all i in a vector for which q[[i]] meets some predicate, where q is a list? Thank you for the tip about 'str' - that's the typeof function I've been craving. (I thought 'attributes' or 'summary' was all there was...) The output for str in the original problem: In my original problem, the output is: str(crossRsorted) 'data.frame': 15750 obs. of 5 variables: $ i : num 105 104 9 8 10 9 98 97 10 8 ... $ j : num 104 105 8 9 9 10 97 98 8 10 ... $ r : num -0.973 -0.973 0.764 0.764 0.744 ... $ n : num 135 135 138 138 138 138 136 136 138 138 ... $ pvalue: num 2.90e-86 2.90e-86 0.00 0.00 0.00 ... and str(q) List of 165 $ : NULL $ : NULL $ : NULL $ : NULL $ :'data.frame': 138 obs. of 1 variable: ..$ howdidyouhear: chr [1:138] 0 3 3 3 3 ... $ :'data.frame': 138 obs. of 1 variable: ..$ approximatelywhendidyoustart: int [1:138] 0 0 5 1 5 5 1 2 6 0 ... [ main body deleted ] $ :'data.frame': 138 obs. of 1 variable: ..$ revisiontestpage: num [1:138] 0 0 0 0 0 0 0 0 0 0 ... and referring to what you wrote to Henrique This appears to be doing something different. For instance, my 'q' has 165 components, but what you suggest has 15750: length(q) [1] 165 length(q[ crossRsorted[,1] ]) [1] 15750 hardly what I want. but this is what you asked for. crossRsorted has 15750 items and all has been selected from q. length(q[ unique(crossRsorted[,1] ])) could be what you are looking for. However the result is probably a list of data frames not a data frame with rows. Regards Petr basically - a heterogeneous sparse list of NULL and data.frames of types character, num, and int. However - by construction - the q[[i]] for i in crossRsorted[,1] are all non- NULL, as in my small reproducible example above. with data frame and list df1[sapply(list1,mean)0,] selects rows of df1 which correspond to list elements with mean 0 I can't run 'sapply' over my list because sapply will also iterate over the NULLs. I want to access only those components in list1 that occur in df1[1,]. - Godmar __ 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] Mysteriously vanishing LD_LIBRARY_PATH
On Wed, 08-Jul-2009 at 09:40PM -0500, Marc Schwartz wrote:
[]
When I was using Fedora, several years ago I started to add any
paths that I needed for LD_LIBRARY_PATH into /etc/ld.so.conf. Then
run 'sudo ldconfig' to update the configuration.
Since I don't have root access to the CentOS machine, I can't make use
of that suggestion. However, by modifying the ldpaths file in my home
directory where R is instaled, I could make it the same as it was in
the 2.8.1 installation.
Just why that wasn't a problem before R-2.9.0 and only with CentOS,
I'm no closer to understanding, but I know how to get around the
problem.
[]
Thanks for the suggestion and the one from Godmar Back. I have it
working.
best
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) . Eleanor Roosevelt
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Re: [R] Best way to export values from a function?
Hi
r-help-boun...@r-project.org napsal dne 09.07.2009 02:57:33:
On Wed, Jul 8, 2009 at 8:34 PM, Jason Rupertjasonkrup...@yahoo.com
wrote:
Maybe there is a great website out there or white paper that discusses
this
but again my Google skills (or lack there of) let me down.
Yeah, R is difficult to search for - I've had partial success with
rseek.org, though.
I would like to know the best way to export several doubles from a
function,
where the doubles are not an array.
Here is a contrived function similar to my needs:
multipleoutput-function(x)
{
squared-x^2
cubed-x^3
exponentioal-exp(x)
factorialVal-factorial(x)
}
You can always do:
multipleoutput - function (x) { return (c(square = x^2, cube = x^3,
exp = exp(x))) }
But then you'd have to call it like so:
mapply(multipleoutput, c(0,1,2))
[,1] [,2] [,3]
square0 1.00 4.00
cube 0 1.00 8.00
exp 1 2.718282 7.389056
If you call it like so:
multipleoutput(c(0,1,2))
square1 square2 square3cube1cube2cube3 exp1 exp2
0.00 1.00 4.00 0.00 1.00 8.00 1.00 2.718282
exp3
7.389056
then R flattens the result. Weird.
Not so weird. What do you expect from
c(1:5, 10:20, 30:50)
That is basically what your function do. With slight modification you can
get tabular output without mapply
multipleoutput - function (x) {
result.s - x^2
result.c - x^3
result.e - exp(x)
cbind(square=result.s, cube=result.c, exp=result.e)
}
If the output could be mixed type }numeric, character, ...) use data.frame
instead of cbind
Regards
Petr
- Godmar
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[R] IIA test
Dear all, I'am using mlogit to test IIA hypothesis. I'get the test statistique who is negative, a p-value of 1, and a text saying that the IIA hypothesis is rejeted. Does a negative value mean that constraint model is more efficient that that the full model ? what to do in this case ? Sincerly. Justin BEM BP 1917 Yaoundé Tél (237) 76043774 [[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] heatmap.2: question regarding the raw z-score
Thanks a lot..! What exactly the sweep function is doing? Also, is there a
possibility instead of using the mean of the whole row to get only the mean
of a group of the row values? So the values in the matrix (heat map) used in
the comparison are z-scores and not the intensities of the gene expressions,
right?
Also, as I can understand from the code, heatmap is using distfun function
for the clusering. Can I use pearson correlation for the clustering? My main
object of using the heatmap is to examine the expression levels of the
marker genes and to confirm that the marker genes are clearly differentially
expressed in the two subtypes of the disease that I examine.
Many thanks,
Chrysanthi.
2009/7/8 James W. MacDonald jmac...@med.umich.edu
Hi Chrysanthi,
Chrysanthi A. wrote:
Hi,
I am analysing gene expression data using the heatmap.2 function in R and
I
was wondering what is the formula of the raw z-score bar which shows the
colors for each pixel.
According to that post:
https://mailman.stat.ethz.ch/pipermail/r-help/2006-September/113598.html,
it
is the
(actual value - mean of the group) / standard deviation.
But, mean of which group? Mean of the gene vector? And actual value of
that
gene on a sample? I would be grateful if you could give me some more
details about it or even if there is a book/manual that I could address
to..
How about looking at the code?
if (scale == row) {
retval$rowMeans - rm - rowMeans(x, na.rm = na.rm)
x - sweep(x, 1, rm)
retval$rowSDs - sx - apply(x, 1, sd, na.rm = na.rm)
x - sweep(x, 1, sx, /)
}
else if (scale == column) {
retval$colMeans - rm - colMeans(x, na.rm = na.rm)
x - sweep(x, 2, rm)
retval$colSDs - sx - apply(x, 2, sd, na.rm = na.rm)
x - sweep(x, 2, sx, /)
}
So the z-score is calculated on either the row or column (or the default of
none).
I don't see how you can get something saying 'raw z-score'. I get either
'Row Z-Score' or 'Column Z-Score'. So assuming you meant Row Z-Score, then
the rows are centered and scaled by subtracting the mean of the row from
every value and then dividing the resulting values by the standard deviation
of the row.
Best,
Jim
Thanks a lot,
Chrysanthi.
*
*
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--
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Biostatistician
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Department of Human Genetics
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[R] r bug (?) display of data
Hi R Fans, I stumbled across a strange (I think) bug in R 2.9.1. I have read in a data file with 5934 rows and 9 columns with the commands: daten = data.frame(read.table(C:/fussball.dat,header=TRUE)) Then I needed a subset of the data file: newd = daten[daten[,1]!=daten[,2],] -- two values do not meet the logical specification and are dropped. The strange thing about it: When I print the newd in the R Console, the output still shows 5934 rows. When I check the number of rows with NROW(newd) , I get 5932 as output. When I print newd[5934, ], I get NAs. When I print newd[5932, ] I get the row that is listed in line 5934 when I just type in newd. This is totally crazy! Has anyone had the same problem? Thanks for a post. Marc __ 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] Ordering zoo-object by its index
Hello everyone, Say I have zoo object x.Date - as.Date(2003-02-01) + c(1, 3, 7, 9, 14) - 1 x - zoo(rnorm(5), x.Date) y - zoo(rt(5, df=2), x.Date) z - zoo(rt(5, df=5), x.Date) Data - merge(x,y,z) What should I do to make the latest values appear at the top? Thank you for your help! Regards, Sergey __ 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] r bug (?) display of data
Marc Jekel wrote: Hi R Fans, I stumbled across a strange (I think) bug in R 2.9.1. I have read in a data file with 5934 rows and 9 columns with the commands: daten = data.frame(read.table(C:/fussball.dat,header=TRUE)) Then I needed a subset of the data file: newd = daten[daten[,1]!=daten[,2],] -- two values do not meet the logical specification and are dropped. The strange thing about it: When I print the newd in the R Console, the output still shows 5934 rows. When I check the number of rows with NROW(newd) , I get 5932 as output. When I print newd[5934, ], I get NAs. When I print newd[5932, ] I get the row that is listed in line 5934 when I just type in newd. This is totally crazy! Has anyone had the same problem? Thanks for a post. You're confusing row names and row numbers. When you printed newd, did you actually count the number of lines? Thought so... It isn't any stranger than this: data.frame(x=rnorm(6),y=rnorm(6))[-5,] x y 1 0.9457385 -1.1398275 2 -1.1683732 -0.7269941 3 0.9942821 0.9310146 4 -2.0839580 -0.6261567 6 1.7225233 0.2457897 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ 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] r bug (?) display of data
Marc Jekel wrote: Hi R Fans, I stumbled across a strange (I think) bug in R 2.9.1. I have read in a data file with 5934 rows and 9 columns with the commands: daten = data.frame(read.table(C:/fussball.dat,header=TRUE)) Then I needed a subset of the data file: newd = daten[daten[,1]!=daten[,2],] -- two values do not meet the logical specification and are dropped. The strange thing about it: When I print the newd in the R Console, the output still shows 5934 rows. No 5932 rows, but with the original rownames (with 2 of them missing). Uwe Ligges When I check the number of rows with NROW(newd) , I get 5932 as output. When I print newd[5934, ], I get NAs. When I print newd[5932, ] I get the row that is listed in line 5934 when I just type in newd. This is totally crazy! Has anyone had the same problem? Thanks for a post. Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A Lattice Question
Which curve? How do you want to specify it? Where is the reproducible
example (we do not have all your data to quickly test it)?
Best,
Uwe Ligges
Haoda Fu wrote:
To the Lattice expert -
I am new to the lattice package and I would like to add a curve to the
xyplot(). I know that I need to use panel function to add it. But it doesn't work. Is there anyone can help me out on how to transfer the data into the function?
The following is my code and I would like to add lines for xx,yy
xx - seq(0,1,length = 100);
yy - mean(PS$theta)*(1-exp(mean(PS$k)*xx))/(1-exp(mean(PS$k)))
ts1 - xyplot(VCFB ~ Visit , groups = ID, data = CFB_M, type = c('g','l'),strip
= strip.custom(style =4), as.table=TRUE,xlab = 'Time',ylab = 'FBG CFB',main = '3mg
Change from Baseline FBG',panel=function (xx,yy,...) {
panel.xyplot(...);
panel.lines(xx,yy,...);});
Many thanks!!
Best,
Haoda
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Picante package 0.7 on mac
Alfonso Rojas wrote: Hello, I tried to run the package but it shows me the following error: In addition: Warning message: package 'picante' was built under R version 2.10.0 Error in library(picante) : .First.lib failed for 'picante' Try to reinstall a binary version that fits to your version of R (which obviously is not R-devel, but you have not told which one you are using) - or install the package from sources. Best, Uwe Ligges What could I do to run picante in mac R version? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] \dQuote in packages
Rebecca, the attachments have been stripped off by the mailing list. Rebecca Sela wrote: That's good to know. I have attached three Rd files that gave errors (others gave identical errors). I would love to know what is wrong with them. I'm using 2.1.1 because that is what is installed on the Linux computer I have access to. (I haven't bothered figuring out how to assemble a package in Windows.) You should *really* upgrade! That version is outdated for several years now. How to do it on Windows: See the R Installation and Administration manual with its corresponding section. Best, Uwe Thank you for your help! Rebecca - Original Message - From: Uwe Ligges lig...@statistik.tu-dortmund.de To: Rebecca Sela rs...@stern.nyu.edu Cc: r-help r-help@r-project.org Sent: Wednesday, July 8, 2009 6:11:33 PM GMT -05:00 US/Canada Eastern Subject: Re: [R] \dQuote in packages The difference you are experiencing is the new Rd2 parser that is more picky now (but also prevents to produce wrong documentation files). If you make the code of the Rd available, someone might be able to help. Are you really under R-2.1.1 ??? That is really ancient! Best, Uwe Ligges Rebecca Sela wrote: I am in the process of submitting a package to CRAN. R CMD check ran successfully on the package on my local computer, using R version 2.1.1. However, on the computers for CRAN (with version 2.10.0), the following errors occurred: Warning in parse_Rd(./man/predict.Rd, encoding = unknown) : ./man/predict.Rd:28: unknown macro '\dquote' *** error on file ./man/predict.Rd Error : ./man/predict.Rd:28: Unrecognized macro \dquote Warning in parse_Rd(./man/print.Rd, encoding = unknown) : ./man/print.Rd:17: unexpected UNKNOWN '\sideeffects' Warning in parse_Rd(./man/simpleREEMdata.Rd, encoding = unknown) : ./man/simpleREEMdata.Rd:10: unknown macro '\item' Are \dquote, \sideeffects, and \item not supported in newer versions of R? Is there some underlying problem that I should fix that makes these show up? Thank you very much. Rebecca __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Save rgl plot3d Graph as Image
Patrick Gedeon wrote: Dear Users: I wish to save 3d scatter plots I have generated using the plot3d command in the rgl package. Any image format such as .tiff would work. Can anyone tell me how to do this? Try snapshot3d(), or rgl.postscript(). The postscript conversion is somewhat limited, but produces better quality when it works, because it's not just a bitmap. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Bug in package.skeleton, R 2.9.0?
Dear all, I am using package.skeleton to build a small packages of misc function for personal use. I have recently discovered that the option force=TRUE doesn't seem to do what is meant to do. Here's what I'm doing: setwd(/Users/danielk/Documents/R/packages/dk) files - paste(codebase, dir(codebase, pattern=.R), sep=/) package.skeleton(name=dk, force=TRUE, code_files=files) Creating directories ... Creating DESCRIPTION ... Creating Read-and-delete-me ... Copying code files ... Making help files ... Done. Further steps are described in './dk/Read-and-delete-me'. Now, everything seems fine, but changes to files in me codebase folder, doesn't come along if the folder dk/R already contains the files, even though I use force=TRUE. If I remove the dk/R folder or the dk folder altogether, the changes come along so to me it seems that it's the overwrite part that doesn't work as it should - or am I doing something wrong here? See below for sessionInfo. Thanks a bunch Daniel sessionInfo() R version 2.9.0 (2009-04-17) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.9.0 -- Contact information: Daniel Klevebring M. Sc. Eng., Ph.D. Student Dept of Gene Technology Royal Institute of Technology, KTH SE-106 91 Stockholm, Sweden Visiting address: Roslagstullsbacken 21, B3 Delivery address: Roslagsvägen 30B, 104 06, Stockholm Invoice address: KTH Fakturaserice, Ref DAKL KTHBIO, Box 24075, SE-10450 Stockholm E-mail: dan...@biotech.kth.se Phone: +46 8 5537 8337 (Office) Phone: +46 704 71 65 91 (Mobile) Web: http://www.biotech.kth.se/genetech/index.html Fax: +46 8 5537 8481 [[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] R-help Digest, Vol 77, Issue 9
Hi,
This may be due to several reasons. That I can think about:
1) Ensure you close *all* possibly open workbooks:
nBooks - xl[[Workbooks]]$Count();
for (i in seq_len(nBooks))
xl[[Workbooks]]$item(i)$Close(SaveChanges=FALSE);
2) The excel application reference does not seem to be really released until
the garbage collector runs. So this may help:
xl$Quit();
xl - NULL;
gc();
3) Ensure you don't have any hanging reference to the excel application
(sometimes from previous runs of your code that failed). If your code is inside
a function, wrap the code in point 1 and 2 on an on.exit() call to ensure that
excel is properly closed each time.
Hope this helps.
Enrique
--
Date: Wed, 8 Jul 2009 16:06:57 +0300
From: Lauri Nikkinen lauri.nikki...@iki.fi
Subject: [R] RDCOMClient: how to close Excel process?
To: r-h...@stat.math.ethz.ch
Message-ID:
ba8c09910907080606n29b8a537uac5ba1788376f...@mail.gmail.com
Content-Type: text/plain; charset=windows-1252
Hi,
I?m using R package RDCOMClient (http://www.omegahat.org/RDCOMClient/)
to retrieve data from MS Excel workbook. I?m using the code below to
count the number of sheets in the workbook and then loop the data from
sheets in to a list.
# R code ###
library(gdata)
library(RDCOMClient)
xl - COMCreate(Excel.Application)
sh - xl$Workbooks()$Open(normalizePath(sample_file.xls))$Sheets()$Count()
DF.list - list()
for (i in 1:sh) {
DF.list[[i]] - read.xls(sample_file.xls, sheet=i,
stringsAsFactors = FALSE)
}
##
COMCreate opens Excel process and it can be seen from Windows Task
Manager. When I try to open sample_file.xls in Excel, it just flashes
in the screen and shuts down. When I kill (via task manager) the Excel
process COMCreate started, sample_file.xls will open normally.
The question is, how can I close the Excel process COMCreate started.
xl$Close() doesn?t seem to work. The same problem have been presented
in this post to R-help:
http://tolstoy.newcastle.edu.au/R/help/06/04/25990.html
-L
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Re: [R] Population pyramids
Victor Manuel Garcia Guerrero wrote: Hi, I hope somebody can help me with this issue: I am doing population pyramids using the barplot command, so in the left side I have male age structure and in the right side the female age structure. To plot the male age structure I put the data in negative numbers. Now, I want to change the sign in the bar plot in such way that I have no-sign numbers, both in left and right side of the graph. I have been trying all day long and I could not succed. Hi Victor, I can get part of the way there with pyramid.plot and plotCI, but it would take some concentrated hacking to do it properly. If you can't find another solution, let me know. Jim __ 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] Ordering zoo-object by its index
To display that object in reverse time order try this: as.data.frame(Data)[nrow(Data):1, ] On Thu, Jul 9, 2009 at 5:21 AM, Sergey Goriatchevserg...@gmail.com wrote: Hello everyone, Say I have zoo object x.Date - as.Date(2003-02-01) + c(1, 3, 7, 9, 14) - 1 x - zoo(rnorm(5), x.Date) y - zoo(rt(5, df=2), x.Date) z - zoo(rt(5, df=5), x.Date) Data - merge(x,y,z) What should I do to make the latest values appear at the top? Thank you for your help! Regards, Sergey __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ordering zoo-object by its index
Hi, Gabor Thank you! That is exactly what I did, even before your email. :-) Regards, Sergey On Thu, Jul 9, 2009 at 12:52, Gabor Grothendieckggrothendi...@gmail.com wrote: To display that object in reverse time order try this: as.data.frame(Data)[nrow(Data):1, ] On Thu, Jul 9, 2009 at 5:21 AM, Sergey Goriatchevserg...@gmail.com wrote: Hello everyone, Say I have zoo object x.Date - as.Date(2003-02-01) + c(1, 3, 7, 9, 14) - 1 x - zoo(rnorm(5), x.Date) y - zoo(rt(5, df=2), x.Date) z - zoo(rt(5, df=5), x.Date) Data - merge(x,y,z) What should I do to make the latest values appear at the top? Thank you for your help! Regards, Sergey __ 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. -- I'm not young enough to know everything. /Oscar Wilde Experience is one thing you can't get for nothing. /Oscar Wilde When you are finished changing, you're finished. /Benjamin Franklin Tell me and I forget, teach me and I remember, involve me and I learn. /Benjamin Franklin Luck is where preparation meets opportunity. /George Patten __ 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] Best way to export values from a function?
On Thu, Jul 9, 2009 at 4:50 AM, Petr PIKAL petr.pi...@precheza.cz wrote:
Hi
r-help-boun...@r-project.org napsal dne 09.07.2009 02:57:33:
On Wed, Jul 8, 2009 at 8:34 PM, Jason Rupertjasonkrup...@yahoo.com
wrote:
Maybe there is a great website out there or white paper that discusses
this
but again my Google skills (or lack there of) let me down.
Yeah, R is difficult to search for - I've had partial success with
rseek.org, though.
I would like to know the best way to export several doubles from a
function,
where the doubles are not an array.
Here is a contrived function similar to my needs:
multipleoutput-function(x)
{
squared-x^2
cubed-x^3
exponentioal-exp(x)
factorialVal-factorial(x)
}
You can always do:
multipleoutput - function (x) { return (c(square = x^2, cube = x^3,
exp = exp(x))) }
But then you'd have to call it like so:
mapply(multipleoutput, c(0,1,2))
[,1] [,2] [,3]
square0 1.00 4.00
cube 0 1.00 8.00
exp 1 2.718282 7.389056
If you call it like so:
multipleoutput(c(0,1,2))
square1 square2 square3cube1cube2cube3 exp1 exp2
0.00 1.00 4.00 0.00 1.00 8.00 1.00 2.718282
exp3
7.389056
then R flattens the result. Weird.
Not so weird. What do you expect from
c(1:5, 10:20, 30:50)
You mean what I expect personally, with my background?
I'd expect a jagged array of arrays.
1 2 3 4 5
10 11 12 .. 20
30 31 .. 50
If operator c() constructs an array out of its arguments, and if the
sequence operator : constructs an array, then c(1:5) should construct an
array of arrays.
That is basically what your function do. With slight modification you can
get tabular output without mapply
multipleoutput - function (x) {
result.s - x^2
result.c - x^3
result.e - exp(x)
cbind(square=result.s, cube=result.c, exp=result.e)
}
Just for clarification: is there any significance to your using the . in the
names result.s, result.c, etc. like there would be in some other languages
where dot is an operator?
- Godmar
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Re: [R] Ordering zoo-object by its index
One additional thought. If the reason you want to do that is just so that you can see the last few rows more easily then tail(Data) will display the last few rows or tail(Data, 10) will display the last 10 rows. On Thu, Jul 9, 2009 at 7:36 AM, Sergey Goriatchevserg...@gmail.com wrote: Hi, Gabor Thank you! That is exactly what I did, even before your email. :-) Regards, Sergey On Thu, Jul 9, 2009 at 12:52, Gabor Grothendieckggrothendi...@gmail.com wrote: To display that object in reverse time order try this: as.data.frame(Data)[nrow(Data):1, ] On Thu, Jul 9, 2009 at 5:21 AM, Sergey Goriatchevserg...@gmail.com wrote: Hello everyone, Say I have zoo object x.Date - as.Date(2003-02-01) + c(1, 3, 7, 9, 14) - 1 x - zoo(rnorm(5), x.Date) y - zoo(rt(5, df=2), x.Date) z - zoo(rt(5, df=5), x.Date) Data - merge(x,y,z) What should I do to make the latest values appear at the top? Thank you for your help! Regards, Sergey __ 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. -- I'm not young enough to know everything. /Oscar Wilde Experience is one thing you can't get for nothing. /Oscar Wilde When you are finished changing, you're finished. /Benjamin Franklin Tell me and I forget, teach me and I remember, involve me and I learn. /Benjamin Franklin Luck is where preparation meets opportunity. /George Patten __ 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] Best way to export values from a function?
Hi
Godmar Back god...@gmail.com napsal dne 09.07.2009 14:09:42:
On Thu, Jul 9, 2009 at 4:50 AM, Petr PIKAL petr.pi...@precheza.cz
wrote:
Hi
r-help-boun...@r-project.org napsal dne 09.07.2009 02:57:33:
snip
Not so weird. What do you expect from
c(1:5, 10:20, 30:50)
You mean what I expect personally, with my background?
I'd expect a jagged array of arrays.
1 2 3 4 5
10 11 12 .. 20
30 31 .. 50
If operator c() constructs an array out of its arguments, and if the
sequence
operator : constructs an array, then c(1:5) should construct an array of
arrays.
is.array(1:5)
[1] FALSE
is.vector(1:5)
[1] TRUE
Why. Not much is said about arrays in man page for c. The operator
concatenates its arguments. If they are vectors the output is again a
vector. If they are lists the output is list.
try
c(1:5,10:20)
c(1:5, list(10:20)
c(1:5, data.frame(10:20)
and regarding arrays, matrices and vectors - AFAIK arrays and matrices are
just vectors with dim attribute, which is stripped by c
c is sometimes used for its side effect of removing attributes except
names, for example to turn an array into a vector. as.vector is a more
intuitive way to do this, but also drops names. Note too that methods
other than the default are not required to do this (and they will almost
certainly preserve a class attribute).
That is basically what your function do. With slight modification you
can
get tabular output without mapply
multipleoutput - function (x) {
result.s - x^2
result.c - x^3
result.e - exp(x)
cbind(square=result.s, cube=result.c, exp=result.e)
}
Just for clarification: is there any significance to your using the . in
the
names result.s, result.c, etc. like there would be in some other
languages
where dot is an operator?
No. AFAIK one dot does not have any special meaning unless you use it in
the beginning of name. In that case the variable is not listed by ls()
function. See ?ls and argument all.names
Regards
Petr
- Godmar
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[R] RExcel/ RCom
Hi All Apologies if this is not the correct mailing list for this question. I have installed RExcel and RCom from CRAN. R is indicating that I need an additional file/package statconnDCOM from rcom.univie.ac.at I have been trying to access this website over the last 2 days be it appears to be down. Does anyone know when this site is likely to be back up and/or know of an alternative source for the statconnDCOM file? Kind regards Pete This e-mail may contain confidential or proprietary information belonging to the BP group and is intended only for the use of the recipients named above. If you are not the intended recipient, please immediately notify the sender and either delete this email or return to the sender immediately. You may not review, copy or distribute this email. Within the bounds of law, this part of BP retains all emails and IMs and may monitor them to ensure compliance with BP's internal policies and for other legitimate business purposes. [[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] Reading from Google Docs
Thanks for pointing that out. Yes, the link on the package web site was for 0.2-1 and that was the one used to build the binary for Windows. Now updated in both places and the binary repository will give 0.2-2. How to find the version of an installed package? packageDescription(RGoogleDocs) D. Farrel Buchinsky wrote: Dear Duncan On my home computer I was able to use install.packages(RGoogleDocs, repos = http://www.omegahat.org/R;) But, alas it would not read the data in the spreadsheet. It went back to its nasty ways Error in !includeEmpty : invalid argument type That is what I was getting with version 0.2-1.You then sent me link to 0.2-2 (in source code) which is what worked. Is it possible that that the windows binary version you put in omegahat was 0.2-1 and not 0.2-2? I did not know how to tell what version had been installed. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 22:53, Duncan Temple Lang dun...@wald.ucdavis.edu mailto:dun...@wald.ucdavis.edu wrote: Farrel Buchinsky wrote: Boy oh boy that process of getting source to binary was super painful. Now that I have the package as binary I can share the whole folder with my coworker and she is able to use RGoogleDocs. I intend to use the same process for the other two windows machines that I use. I really do not want to go through the same installation and path hassles all over again. Should I post my directory containing the binary files somewhere so that others do not have to experience pain. Does etiquette dictate that I should post the directory to help other or does etiquette dictate that it is Duncan Temple Lang's code and thus it his prerogative to distribute his work as he wishes? Etiquette is one thing and the license another. Both encourage you to help others and make the binary available to others. And indeed, I hope that Windows users do build binaries for others and remove the additional work from those who provide the software in the first place. Having seen this thread today, I did put a binary version of RGoogleDocs on the Omegahat repository so install.packages(RGoogleDocs, repos = http://www.omegahat.org/R;) should install it and, if I had had time earlier, saved you the hardship of building the binary. Sorry to do it so soon after. D. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:59, Farrel Buchinsky fjb...@gmail.com mailto:fjb...@gmail.com wrote: Does changing the path in Windows work in real time or does one need to restart the computer for the changes to take effect. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:04, Gabor Grothendieck ggrothendi...@gmail.com mailto:ggrothendi...@gmail.comwrote: Its safer just to temporarily add it to your path. Unfortunately Rtools has a find command that conflicts with the find command in Windows so if you add the Rtools bin directory to your path permanently then you could find other programs stop working. That actually happened to me once and it took the longest time until I discovered that Rtools was the culprit. If you follow the advice I gave you normally won't have that problem. On Wed, Jul 8, 2009 at 11:21 AM, Duncan Murdochmurd...@stats.uwo.ca mailto:murd...@stats.uwo.ca wrote: On 08/07/2009 10:13 AM, Farrel Buchinsky wrote: Forgive my naivte, but how do I make windows find tar. In other words from where do I issue the command and what is the command. You need to install the toolset, and let the installer set your path. Duncan Murdoch Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 10:09, Duncan Murdoch murd...@stats.uwo.ca mailto:murd...@stats.uwo.ca wrote: On 08/07/2009 10:02 AM, Farrel Buchinsky wrote: I have previously read R Installation and Administration. I read it again. It does not help me The relevant paragraph is below. But I need lower level instructions.
Re: [R] RDCOMClient: how to close Excel process?
Lauri Nikkinen wrote: Thanks again. That did not work either. I get library(RDCOMClient) xl - COMCreate(Excel.Application) wk - xl$Workbooks() sh - wk$Open(normalizePath(sample_file.xls))$Sheets()$Count() wk$Close() [1] TRUE xl$Quit() NULL and there is still Excel process open in the Task manager (and sample_file.xls won't open). -L In my experience, the Excel process will not go away if any Excel-related object has been created but not destroyed. I suggest that you explictly remove all Excel objects with rm() and run gc() at the end to clean up: library(RDCOMClient) xl - COMCreate(Excel.Application) wk - xl$Workbooks() sh-wk$Open(normalizePath(sample_file.xls))$Sheets()$Count() wk$Close() xl$Quit() rm(sh) rm(wk) rm(xl) gc() J. R. M. Hosking __ 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] T.test error help
Hi I am implementing the t.test in a loop and where the data is the same i get
an error message.
Error in t.test.default(Samp3, Samp1, na.rm = TRUE, var.equal = FALSE, :
data are essentially constant
The script i am using is
for (i in 1:length(zz[,1])) {
Samp1 - zz[i,2:17]
Samp2 - zz[i,18:33]
Samp3 - zz[i,34:47]
Samp4 - zz[i,48:63]
TTestResult[i,2] - t.test(Samp2, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
TTestResult[i,3] - t.test(Samp3, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
TTestResult[i,4] - t.test(Samp4, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
}
Is there a way to make my loop ignore this problem and go onto the next
iteration
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and provide commented, minimal, self-contained, reproducible code.
[R] Apply weights to the Efron Approximation
Dear all, I want to apply weights to my sample data set and I am struggling with the Efron Approximation with weights. I have got one sample data shown as below: customerweekarrest fin age raceweight 1weight 2weight 3 1 20 1 1 27 1 2 15 2 2 17 1 0 18 1 2 19 1 3 25 1 1 19 0 2 20 1 4 52 0 1 23 1 2 5 1 5 52 0 0 19 0 2 11 1 6 25 1 0 19 0 2 26 1 I applied four different weighted Efron Formulas (all are derived by myself) to the data set above and have got the following results for 3 weight sets based on those 4 formulas, respectively. weight 1Formula 1 Formula 2 Formula 3 Formula 4 R software replicated by weights fin-0.235912234 -0.530843641 -0.471823965 -0.471823965 -0.4718 -0.5308 age -0.052005981 -0.122613988 -0.104018973 -0.104018973 -0.104 -0.1226 race0.637573013 1.404345693 1.275165398 1.275165398 1.2752 1.4043 weight 2Formula 1 Formula 2 Formula 3 Formula 4 R softwarereplicated by weight fin 0.600334761 -0.32212452 -0.178028949 -0.244162408 -0.25062 -0.32212 age 0.105321888 -0.214932275 -0.112459016 -0.146957807 -0.14607 -0.21493 race5.742146326 2.2589341822.043479975 1.921804334 1.94056 2.25893 weight 3Formula 1 Formula 2Formula 3 Formula 4 R software replicated by weights fin -0.984946984 -0.909980273 -0.333235566-0.80272443-0.802724 -0.90998 age 0.036891147 0.03225069 -0.194126398 -0.004544225 -0.004544 0.03225 race0.962911927 1.3052554251.435340831 1.318038014 1.318038 1.30526 replicated by weights means that I also replicated individuals as many times as indicated by weights and applied unweighted Efron approximation to the replication of the dataset. The formula 4 can give me same results as the unweighted ones if I apply the same weights to each individual and also can give me the close results to the ones calculated by R (efron method+weights) if I apply different weights to each individual. these results are close to the R's but not exactly the same. I don't know why and what the problem is with my formulas. Could anyone give me some help, please? I will really appreciate it. I have attached my four weighted Efron formulas with this message already. Bessy http://www.nabble.com/file/p24410214/Weighted%2BEfron%2BApproximation_Formulas_Examples.pdf Weighted+Efron+Approximation_Formulas_Examples.pdf -- View this message in context: http://www.nabble.com/Apply-weights-to-the-Efron-Approximation-tp24410214p24410214.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.
Re: [R] Converting indices of a matrix subset
Hi Nathan,
On Jul 8, 2009, at 10:20 PM, Nathan S. Watson-Haigh wrote:
I have two matrices:
m1 - matrix(1,4,4)
m1
[,1] [,2] [,3] [,4]
[1,]1111
[2,]1111
[3,]1111
[4,]1111
m2 - matrix(0,3,3)
diag(m2) - 1
m2
[,1] [,2] [,3]
[1,]100
[2,]010
[3,]001
I want to get indicies from m2 such that they match indicies as
though they came
from the lower right of m1. Here's how things work:
ind1 - which(m1 == 1)
ind1
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
ind2 - which(m2 == 1)
ind2
[1] 1 5 9
I would like ind2 to be offset so they look like indicies from the
lower right
of m1:
ind2
[1] 6 11 16
I have written some utility functions I use often[1], and have
sub2ind function that works in a similar fashion to the MATLAB
function of the same name. It's somehow long and convoluted because
you can send in your arguments 12 different ways from sunday, so:
sub2ind - function(x, y, nrow, ncol=NULL) {
## Returns a linear index for the (x,y) coordinates passed in.
if (is.matrix(x) || is.data.frame(x)) {
stopifnot(ncol(x) == 2)
if (!missing(y)) {
if (missing(nrow)) {
nrow - y
} else {
ncol - nrow
nrow - y
}
}
y - x[,2]
x - x[,1]
}
if (is.matrix(nrow)) {
d - dim(nrow)
nrow - d[1]
ncol - d[2]
} else if (is.null(ncol)) {
stop(Dimensions of matrix under-specified)
}
# Sanity check to ensure we got each var doing what it should be
doing
if (length(x) != length(y) || length(nrow) != 1 || length(ncol) !=
1) {
stop(I'm confused)
}
((x - 1) + ((y - 1) * nrow)) + 1
}
R m1 - matrix(1,4,4)
R m2 - matrix(0,3,3)
R ind2 - which(m2 == 1, arr.ind=T) + 1
R ind2
row col
[1,] 2 2
[2,] 3 3
[3,] 4 4
R my.ind2 - sub2ind(ind2, nrow=4, ncol=4)
# my.ind2 - sub2ind(ind2[,1], ind2[,2], 4, 4)
# my.ind2 - sub2ind(ind2[,1], ind2[,2], m1)
# my.ind2 - sub2ind(ind2, m1)
R my.ind2
[1] 6 11 16
I think that gets you to where you want to be :-)
-steve
[1] They can be found here if your intersted, there isn't much
documentation there, but I'll fix that some time later :-)
http://github.com/lianos/ARE.utils/tree/master
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos
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Re: [R] T.test error help
Hi,
On Jul 9, 2009, at 9:19 AM, Amit Patel wrote:
Hi I am implementing the t.test in a loop and where the data is the
same i get an error message.
Error in t.test.default(Samp3, Samp1, na.rm = TRUE, var.equal =
FALSE, :
data are essentially constant
The script i am using is
for (i in 1:length(zz[,1])) {
Samp1 - zz[i,2:17]
Samp2 - zz[i,18:33]
Samp3 - zz[i,34:47]
Samp4 - zz[i,48:63]
TTestResult[i,2] - t.test(Samp2, Samp1, na.rm=TRUE, var.equal =
FALSE, paired=FALSE, conf.level=0.95)$p.value
TTestResult[i,3] - t.test(Samp3, Samp1, na.rm=TRUE, var.equal =
FALSE, paired=FALSE, conf.level=0.95)$p.value
TTestResult[i,4] - t.test(Samp4, Samp1, na.rm=TRUE, var.equal =
FALSE, paired=FALSE, conf.level=0.95)$p.value
}
Is there a way to make my loop ignore this problem and go onto the
next iteration
Yes, see: ?try and ?tryCatch
For example:
R log(10)
[1] 2.302585
R log(a)
Error in log(a) : Non-numeric argument to mathematical function
R a - tryCatch(log(10), error=function(e) {
+ cat(There was an error\n)
+ NA
+ })
R b - tryCatch(log(a), error=function(e) {
+ cat(There was an error\n)
+ NA
+ })
There was an error
R a
[1] 2.302585
R b
[1] NA
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos
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Re: [R] Ordering zoo-object by its index
Hi, Gabor Yes, I am familiar with tail() function. I use it extensively on a day to day basis. In this particular case I needed to order a zoo object by date, after I have created it with RBloomberg. Thank you for your time! Regards, Sergey On Thu, Jul 9, 2009 at 14:36, Gabor Grothendieckggrothendi...@gmail.com wrote: One additional thought. If the reason you want to do that is just so that you can see the last few rows more easily then tail(Data) will display the last few rows or tail(Data, 10) will display the last 10 rows. On Thu, Jul 9, 2009 at 7:36 AM, Sergey Goriatchevserg...@gmail.com wrote: Hi, Gabor Thank you! That is exactly what I did, even before your email. :-) Regards, Sergey On Thu, Jul 9, 2009 at 12:52, Gabor Grothendieckggrothendi...@gmail.com wrote: To display that object in reverse time order try this: as.data.frame(Data)[nrow(Data):1, ] On Thu, Jul 9, 2009 at 5:21 AM, Sergey Goriatchevserg...@gmail.com wrote: Hello everyone, Say I have zoo object x.Date - as.Date(2003-02-01) + c(1, 3, 7, 9, 14) - 1 x - zoo(rnorm(5), x.Date) y - zoo(rt(5, df=2), x.Date) z - zoo(rt(5, df=5), x.Date) Data - merge(x,y,z) What should I do to make the latest values appear at the top? Thank you for your help! Regards, Sergey __ 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. -- I'm not young enough to know everything. /Oscar Wilde Experience is one thing you can't get for nothing. /Oscar Wilde When you are finished changing, you're finished. /Benjamin Franklin Tell me and I forget, teach me and I remember, involve me and I learn. /Benjamin Franklin Luck is where preparation meets opportunity. /George Patten -- I'm not young enough to know everything. /Oscar Wilde Experience is one thing you can't get for nothing. /Oscar Wilde When you are finished changing, you're finished. /Benjamin Franklin Tell me and I forget, teach me and I remember, involve me and I learn. /Benjamin Franklin Luck is where preparation meets opportunity. /George Patten __ 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] clogit comparison between Stata and R
On Wed, 8 Jul 2009, David Hugh-Jones wrote: Hello all I'm moving back and forth between stata and R at the moment - of course, using R whenever possible :-) I'm running conditional logits on some panel data and I get slightly different results and different N in the two programs. That's probably because you are using method=approximate in R. I understand why Stata is dropping the groups with all outcomes the same... this is inevitable in a conditional logit, right? Yes. Is R doing the same? Yes. -thomas __ 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] heatmap.2: question regarding the raw z-score
Hi Chrysanthi,
Chrysanthi A. wrote:
Thanks a lot..! What exactly the sweep function is doing? Also, is there
a possibility instead of using the mean of the whole row to get only the
mean of a group of the row values? So the values in the matrix (heat
map) used in the comparison are z-scores and not the intensities of the
gene expressions, right?
I was trying to give a subtle hint below, but maybe I should be a bit
more blunt. One of the coolest things about R is that it is free, and
there are these sweet listservs where people give advice and help for
free as well.
HOWEVER, there is still a price to pay, and that is with your time. All
of these functions have help pages that the developers spent time
writing, and the code is there for you to peruse. Because of this, there
is some expectation that you would have done so prior to asking
questions. Now I have read the help page for sweep, and quite frankly it
is a bit confusing. The term 'sweep' is used without definition, so if
one doesn't know what that means the help page is less than helpful. But
it doesn't take much time or effort to empirically see what it does:
a - matrix(rnorm(25), ncol=5)
a
[,1] [,2] [,3][,4][,5]
[1,] 0.6841637 -1.0590185 -0.1719887 -0.01916011 -1.61936817
[2,] 0.5707217 1.4790968 1.6736991 -0.72158518 1.22467334
[3,] 0.4440499 -0.3382888 -0.1504191 0.32140022 1.83780859
[4,] -0.6659568 3.0573678 -1.5709904 -1.35618488 -0.01717017
[5,] -0.3182206 2.2777597 -0.2325356 -0.02001414 1.77440090
rm - rowMeans(a)
rm
[1] -0.4370743 0.8453211 0.4229102 -0.1105869 0.6962780
sweep(a, 1, rm, -)
[,1] [,2] [,3] [,4][,5]
[1,] 1.12123808 -0.6219441 0.2650857 0.4179142 -1.18229384
[2,] -0.27459943 0.6337756 0.8283779 -1.5669063 0.37935220
[3,] 0.02113977 -0.7611990 -0.5733293 -0.1015100 1.41489842
[4,] -0.55536988 3.1679546 -1.4604035 -1.2455980 0.09341672
[5,] -1.01449866 1.5814817 -0.9288137 -0.7162922 1.07812286
For your second question:
?heatmap.2
Also, as I can understand from the code, heatmap is using distfun
function for the clusering. Can I use pearson correlation for the
clustering? My main object of using the heatmap is to examine the
expression levels of the marker genes and to confirm that the marker
genes are clearly differentially expressed in the two subtypes of the
disease that I examine.
No, heatmap.2() is not using distfun for the clustering. There isn't a
function by that name in either gplots nor base R. If you look at the
help page, you can see that distfun is an argument to the function, and
the default is to use the dist() function.
You can use Pearson correlation, but in my experience it takes some
work. Again, if you read the help page, you can see that the Rowv and
Colv arguments can be one of TRUE, FALSE, NULL, or a dendrogram. So if
you want to use Pearson correlation, you should supply heatmap.2() with
dendrograms produced using that correlation. So an example:
a - matrix(rnorm(50), ncol=5)
rowv - as.dendrogram(hclust(as.dist(1-cor(t(a)
colv - as.dendrogram(hclust(as.dist(1-cor(a
heatmap.2(a, scale=row, Rowv=rowv, Colv=colv)
Best,
Jim
Many thanks,
Chrysanthi.
2009/7/8 James W. MacDonald jmac...@med.umich.edu
mailto:jmac...@med.umich.edu
Hi Chrysanthi,
Chrysanthi A. wrote:
Hi,
I am analysing gene expression data using the heatmap.2 function
in R and I
was wondering what is the formula of the raw z-score bar which
shows the
colors for each pixel.
According to that post:
https://mailman.stat.ethz.ch/pipermail/r-help/2006-September/113598.html,
it
is the
(actual value - mean of the group) / standard deviation.
But, mean of which group? Mean of the gene vector? And actual
value of that
gene on a sample? I would be grateful if you could give me some
more
details about it or even if there is a book/manual that I could
address
to..
How about looking at the code?
if (scale == row) {
retval$rowMeans - rm - rowMeans(x, na.rm = na.rm)
x - sweep(x, 1, rm)
retval$rowSDs - sx - apply(x, 1, sd, na.rm = na.rm)
x - sweep(x, 1, sx, /)
}
else if (scale == column) {
retval$colMeans - rm - colMeans(x, na.rm = na.rm)
x - sweep(x, 2, rm)
retval$colSDs - sx - apply(x, 2, sd, na.rm = na.rm)
x - sweep(x, 2, sx, /)
}
So the z-score is calculated on either the row or column (or the
default of none).
I don't see how you can get something saying 'raw z-score'. I get
either 'Row Z-Score' or 'Column Z-Score'. So assuming you meant Row
Z-Score, then the rows are centered and scaled by subtracting the
mean of the row from every value and then dividing the resulting
values
Re: [R] Dantzig Selector
There is an experimental version available here:
http://www.econ.uiuc.edu/~roger/research/sparse/sfn.html
that uses the interior point code in the package quantreg. There is
an option to exploit possible sparsity of the X matrix.
Comments would be welcome.
url:www.econ.uiuc.edu/~rogerRoger Koenker
email rkoen...@uiuc.edu Department of Economics
vox:217-333-4558University of Illinois
fax:217-244-6678Champaign, IL 61820
On Jul 8, 2009, at 6:35 PM, tzygmund mcfarlane wrote:
Hi,
I was wondering if there was an R package or routines for the Dantzig
Selector (Candes Tao, 2007). I know Emmanuel Candes has Matlab
routines to do this but I was wondering if someone had ported those to
R.
Thanks,
T
---Reference---
@article{candes2007dantzig,
title={{The Dantzig selector: statistical estimation when p is much
larger than n}},
author={Candes, E. and Tao, T.},
journal={Annals of Statistics},
volume={35},
number={6},
pages={2313--2351},
year={2007},
publisher={Hayward, Calif.[etc] Institute of Mathematical
Statistics [etc]}
}
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Re: [R] RDCOMClient: how to close Excel process?
This solution worked:
nBooks - xl[[Workbooks]]$Count();
for (i in seq_len(nBooks))
xl[[Workbooks]]$item(i)$Close(SaveChanges=FALSE);
from
http://www.mail-archive.com/r-help@r-project.org/msg61498.html
Thanks!
-L
2009/7/9 Lauri Nikkinen lauri.nikki...@iki.fi:
Thanks again. That did not work either. I get
library(RDCOMClient)
xl - COMCreate(Excel.Application)
wk - xl$Workbooks()
sh - wk$Open(normalizePath(sample_file.xls))$Sheets()$Count()
wk$Close()
[1] TRUE
xl$Quit()
NULL
and there is still Excel process open in the Task manager (and
sample_file.xls won't open).
-L
2009/7/8 Henrique Dallazuanna www...@gmail.com:
Then, you can try this:
xl - COMCreate(Excel.Application)
wk - xl$Workbooks()
sh - wk$Open(normalizePath(sample_file.xls))$Sheets()$Count()
wk$Close()
xl$Quit()
On Wed, Jul 8, 2009 at 10:19 AM, Lauri Nikkinen lauri.nikki...@iki.fi
wrote:
Thanks but that did not work. xl$Quit() does not kill the Excel
process and sample_file.xls will not open.
I'm using Windows XP SP2 and R 2.8.1
-L
2009/7/8 Henrique Dallazuanna www...@gmail.com:
Try this:
xl$Quit()
On Wed, Jul 8, 2009 at 10:06 AM, Lauri Nikkinen lauri.nikki...@iki.fi
wrote:
Hi,
I’m using R package RDCOMClient (http://www.omegahat.org/RDCOMClient/)
to retrieve data from MS Excel workbook. I’m using the code below to
count the number of sheets in the workbook and then loop the data from
sheets in to a list.
# R code ###
library(gdata)
library(RDCOMClient)
xl - COMCreate(Excel.Application)
sh -
xl$Workbooks()$Open(normalizePath(sample_file.xls))$Sheets()$Count()
DF.list - list()
for (i in 1:sh) {
DF.list[[i]] - read.xls(sample_file.xls, sheet=i,
stringsAsFactors = FALSE)
}
##
COMCreate opens Excel process and it can be seen from Windows Task
Manager. When I try to open sample_file.xls in Excel, it just flashes
in the screen and shuts down. When I kill (via task manager) the Excel
process COMCreate started, sample_file.xls will open normally.
The question is, how can I close the Excel process COMCreate started.
xl$Close() doesn’t seem to work. The same problem have been presented
in this post to R-help:
http://tolstoy.newcastle.edu.au/R/help/06/04/25990.html
-L
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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[R] naming of columns in R dataframe consisting of mixed data (alphanumeric and numeric)
Hello, I have an r function that creates the following dataframe tresults2. Notice that column 1 does not have a column heading. Tresults2: [,1] estparam 18.0 nullval 20.0 . . . ciWidth 2.04622 HalfInterval 1.02311 pertinent code: results-cbind( estparam, nullval, t, pv_left, pv_right, pv_two_t, estse, df, cc, tbox, llim, ulim, ciWidth, HalfInterval) tresults-round((results),5) tresults2-data.frame(t(tresults)) names(tresults2)-c(Statistic , Value) tresults2 === After transposing my dataframe tresults2 consists of 2 columns. Col1=alphanumeric data (this really is a variable name) and col2=numeric data (this is value of varaiable). how do I name columns when columns are different (alphanumeric and numeric) to avoid the following error: Error in names(tresults2) - c(Statistic , Value) : 'names' attribute [2] must be the same length as the vector [1] Am I to use c( , ) or list( , ) with a dataframe? Thank you for your help. Sincerely, Mary A. Marion [[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.
[R] treating a data symbol like a character
Hi, is there a way to treat a data symbol, e.g. one with pch = 16, as a character? Specifically, I'm interested in creating a line of text as follows using the text() function O alpha O beta O gamma where the O is pch 16 and filled with a specific color. Not sure if this is possible or not. Thanks, Andrew [[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] treating a data symbol like a character
Hi Andrew,
Do you want to put the symbols you described as a legend in a plot? If so,
here is one way:
x - rnorm(3)
plot(x, pch = 16, cex = 1.1, col = 1:3)
legend('topleft', ncol = 3,
c(expression(alpha), expression(beta), expression(gamma)), pch = 16,
cex = 1.1, col = 1:3)
Is you do not want to use legend, but place the symbols in each plot, then:
plot(x, pch = 16, cex = 1.1, col = 1:3)
text(1.05,1.01*x[1], expression(alpha) )
text(2.05,1.01*x[2], expression(beta) )
text(2.95,1.01*x[3], expression(gamma) )
should get you close.
See ?text, ?expression and ?legend for more information.
HTH,
Jorge
On Thu, Jul 9, 2009 at 10:53 AM, Andrew Yee y...@post.harvard.edu wrote:
Hi, is there a way to treat a data symbol, e.g. one with pch = 16, as a
character?
Specifically, I'm interested in creating a line of text as follows using
the
text() function
O alpha O beta O gamma
where the O is pch 16 and filled with a specific color.
Not sure if this is possible or not.
Thanks,
Andrew
[[alternative HTML version deleted]]
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[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] plm Issues
Hi List I'm having difficulty understanding how plm should work with dynamic formulas. See the commands and output below on a standard data set. Notice that the first summary(plm(...)) call returns the same result as the second (it shouldn't if it actually uses the lagged variable requested). The third call results in error (trying to use diff'ed variable in regression) Other info: I'm running R 2.7.2 on WinXP cheers *data(Gasoline,package=Ecdat) Gasoline_plm-plm.data(Gasoline,c(country,year)) pdim(Gasoline_plm) **Balanced Panel: n=18, T=19, N=342 * *summary(plm(lgaspcar~lincomep,data=Gasoline_plm**)) **Oneway (individual) effect Within Model Call: plm(formula = lgaspcar ~ lincomep, data = Gasoline_plm) Balanced Panel: n=18, T=19, N=342 Residuals : Min. 1st Qu. Median 3rd Qu. Max. -0.40100 -0.08410 -0.00858 0.08770 0.73400 Coefficients : Estimate Std. Error t-value Pr(|t|) lincomep -0.761830.03535 -21.551 2.2e-16 *** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Total Sum of Squares: 17.061 Residual Sum of Squares: 6.9981 Multiple R-Squared: 0.58981 F-statistic: 464.442 on 323 and 1 DF, p-value: 0.036981 ** summary(plm(lgaspcar~lag(lincomep),data=Gasoline_plm)) **Oneway (individual) effect Within Model Call: plm(formula = lgaspcar ~ lag(lincomep), data = Gasoline_plm) Balanced Panel: n=18, T=19, N=342 Residuals : Min. 1st Qu. Median 3rd Qu. Max. -0.40100 -0.08410 -0.00858 0.08770 0.73400 Coefficients : Estimate Std. Error t-value Pr(|t|) lag(lincomep) -0.761830.03535 -21.551 2.2e-16 *** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Total Sum of Squares: 17.061 Residual Sum of Squares: 6.9981 Multiple R-Squared: 0.58981 F-statistic: 464.442 on 323 and 1 DF, p-value: 0.036981 * *summary(plm(lgaspcar~diff(lincomep),data=Gasoline_plm))* *Error in model.frame.default(formula = lgaspcar ~ diff(lincomep), data = mydata, : variable lengths differ (found for 'diff(lincomep)') * [[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] treating a data symbol like a character
Thanks for your help.
I should have been more clear in my initial e-mail. I shouldn't have used
'alpha' or 'beta,' to avoid confusion with them as Greek symbols. I should
have stated something like:
O foo O abcd O John
While I'm familiar with using legend to make the filled boxes, I'm
interested in creating a one line legend of sorts, but manually using
text() with both data symbols defined by pch and text on the same line. Or
is this not possible? I guess at the end of the day, I could use both
points() and text().
Thanks,
Andrew
On Thu, Jul 9, 2009 at 11:03 AM, Jorge Ivan Velez
jorgeivanve...@gmail.comwrote:
Hi Andrew,
Do you want to put the symbols you described as a legend in a plot? If so,
here is one way:
x - rnorm(3)
plot(x, pch = 16, cex = 1.1, col = 1:3)
legend('topleft', ncol = 3,
c(expression(alpha), expression(beta), expression(gamma)), pch =
16, cex = 1.1, col = 1:3)
Is you do not want to use legend, but place the symbols in each plot, then:
plot(x, pch = 16, cex = 1.1, col = 1:3)
text(1.05,1.01*x[1], expression(alpha) )
text(2.05,1.01*x[2], expression(beta) )
text(2.95,1.01*x[3], expression(gamma) )
should get you close.
See ?text, ?expression and ?legend for more information.
HTH,
Jorge
On Thu, Jul 9, 2009 at 10:53 AM, Andrew Yee y...@post.harvard.edu wrote:
Hi, is there a way to treat a data symbol, e.g. one with pch = 16, as a
character?
Specifically, I'm interested in creating a line of text as follows using
the
text() function
O alpha O beta O gamma
where the O is pch 16 and filled with a specific color.
Not sure if this is possible or not.
Thanks,
Andrew
[[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.
[[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.
Re: [R] treating a data symbol like a character
Hi Andrew,
If I understand correctly, then
# Data
x - c(3,4,2)
# Collection of text and symbols
Text - c('foo', 'abcd', 'John')
PCH - c('+','O','$')
# Plotting
plot(x, pch = PCH)
legend('topright', pch = PCH, Text, ncol = 3)
should be close to what you want. Note that the text() / points()
combination could be avoided when using legend().
Best,
Jorge
On Thu, Jul 9, 2009 at 11:08 AM, Andrew Yee wrote:
Thanks for your help.
I should have been more clear in my initial e-mail. I shouldn't have used
'alpha' or 'beta,' to avoid confusion with them as Greek symbols. I should
have stated something like:
O foo O abcd O John
While I'm familiar with using legend to make the filled boxes, I'm
interested in creating a one line legend of sorts, but manually using
text() with both data symbols defined by pch and text on the same line. Or
is this not possible? I guess at the end of the day, I could use both
points() and text().
Thanks,
Andrew
On Thu, Jul 9, 2009 at 11:03 AM, Jorge Ivan Velez wrote:
Hi Andrew,
Do you want to put the symbols you described as a legend in a plot? If
so, here is one way:
x - rnorm(3)
plot(x, pch = 16, cex = 1.1, col = 1:3)
legend('topleft', ncol = 3,
c(expression(alpha), expression(beta), expression(gamma)), pch =
16, cex = 1.1, col = 1:3)
Is you do not want to use legend, but place the symbols in each plot,
then:
plot(x, pch = 16, cex = 1.1, col = 1:3)
text(1.05,1.01*x[1], expression(alpha) )
text(2.05,1.01*x[2], expression(beta) )
text(2.95,1.01*x[3], expression(gamma) )
should get you close.
See ?text, ?expression and ?legend for more information.
HTH,
Jorge
On Thu, Jul 9, 2009 at 10:53 AM, Andrew Yee wrote:
Hi, is there a way to treat a data symbol, e.g. one with pch = 16, as a
character?
Specifically, I'm interested in creating a line of text as follows using
the
text() function
O alpha O beta O gamma
where the O is pch 16 and filled with a specific color.
Not sure if this is possible or not.
Thanks,
Andrew
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] treating a data symbol like a character
Great, that's a good starting point.
Andrew
On Thu, Jul 9, 2009 at 11:20 AM, Jorge Ivan Velez
jorgeivanve...@gmail.comwrote:
Hi Andrew,
If I understand correctly, then
# Data
x - c(3,4,2)
# Collection of text and symbols
Text - c('foo', 'abcd', 'John')
PCH - c('+','O','$')
# Plotting
plot(x, pch = PCH)
legend('topright', pch = PCH, Text, ncol = 3)
should be close to what you want. Note that the text() / points()
combination could be avoided when using legend().
Best,
Jorge
On Thu, Jul 9, 2009 at 11:08 AM, Andrew Yee wrote:
Thanks for your help.
I should have been more clear in my initial e-mail. I shouldn't have used
'alpha' or 'beta,' to avoid confusion with them as Greek symbols. I should
have stated something like:
O foo O abcd O John
While I'm familiar with using legend to make the filled boxes, I'm
interested in creating a one line legend of sorts, but manually using
text() with both data symbols defined by pch and text on the same line. Or
is this not possible? I guess at the end of the day, I could use both
points() and text().
Thanks,
Andrew
On Thu, Jul 9, 2009 at 11:03 AM, Jorge Ivan Velez wrote:
Hi Andrew,
Do you want to put the symbols you described as a legend in a plot? If
so, here is one way:
x - rnorm(3)
plot(x, pch = 16, cex = 1.1, col = 1:3)
legend('topleft', ncol = 3,
c(expression(alpha), expression(beta), expression(gamma)), pch =
16, cex = 1.1, col = 1:3)
Is you do not want to use legend, but place the symbols in each plot,
then:
plot(x, pch = 16, cex = 1.1, col = 1:3)
text(1.05,1.01*x[1], expression(alpha) )
text(2.05,1.01*x[2], expression(beta) )
text(2.95,1.01*x[3], expression(gamma) )
should get you close.
See ?text, ?expression and ?legend for more information.
HTH,
Jorge
On Thu, Jul 9, 2009 at 10:53 AM, Andrew Yee wrote:
Hi, is there a way to treat a data symbol, e.g. one with pch = 16, as a
character?
Specifically, I'm interested in creating a line of text as follows using
the
text() function
O alpha O beta O gamma
where the O is pch 16 and filled with a specific color.
Not sure if this is possible or not.
Thanks,
Andrew
[[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.
[[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] How to: initialize, setValidity, copy-constructor
Hello list,
I'm having troubles setting up a basic calss hierarchy with S4.
Here is a simplified schema of what I'd like to do:
- Two classes: A and B that extends A
- Ensure that the slots added by B are consistent with the slots of A
- Let A initialize itself (I'm not supposed to know the internal cooking
of A)
- By default set the slots of B based on the slots that A initialized
Another question is: what is the recommended way of implementing a
copy-constructor in R?
I know that all of this is easily done in C++. The constructor of each
class is called recursively back-up to the root class. Validity checks
can be performed after/during associated initialization.
Copy-constructor are basics in C++.
Here below is a piece of code that I thought would work (but it does
not... therefore my post), what's wrong with it?
I think the main issue is when is the validity check performed: why is
it performed before the end of the initialize method?
Thank you for your help.
Renaud
# define class A with a single numeric slot
setClass('A', representation(a='numeric'))
# define class B that extends class A, adding another numeric slot
setClass('B', representation('A', b='numeric'))
# we want for example to ensure that slots a and b have the same length
setValidity('B',
function(object){
cat(*** B::validate ***\n)
print(object)
cat(*\n)
if( length(obj...@a) != length(obj...@b) ) return('Inconsistent lengths')
TRUE
}
)
# As a default behaviour if b is not provided, we want slot b to be
equal to slot a
setMethod('initialize', 'B',
function(.Object, b, ...){
cat(*** B::initialize ***\n)
print(.Object)
# Let the superclass (A) initialize itself via callNextMethod
# I thought it would only do that: initialize and optionnaly validate
the class A part of the object
#But it generates an ERROR: apparently it calls the validation method of B,
# before leaving me a chance to set slot b to a valid value
.Object - callNextMethod(.Object, ...)
# now deal with the class B part of the object
cat(*** Test missing b ***\n)
if( missing(b) ){
cat(*** b is MISSING ***\n)
b - .obj...@a
}
# set slot b
.obj...@b - b
.Object
}
)
### Testing
# empty A: OK
aObj - new('A')
aObj
# class A with some data: OK
aObj - new('A', a=c(1,2) )
aObj
# empty B: OK
bObj - new('B')
bObj
# initialize B setting the slot of class A: ERROR
bObj - new('B', a=c(1,2))
# initialize B setting only the slot class B: OK!! Whereas it produces a
non valid object.
bObj - new('B', b=c(1,2))
bObj
# RESULTS:
# empty A: OK
aObj - new('A')
aObj
An object of class “A”
Slot a:
numeric(0)
# class A with some data: OK
aObj - new('A', a=c(1,2) )
aObj
An object of class “A”
Slot a:
[1] 1 2
# empty B: OK
bObj - new('B')
*** B::initialize ***
An object of class “B”
Slot b:
numeric(0)
Slot a:
numeric(0)
*** Test missing b ***
*** b is MISSING ***
bObj
An object of class “B”
Slot b:
numeric(0)
Slot a:
numeric(0)
# initialize B setting the slot of class A: ERROR
bObj - new('B', a=c(1,2))
*** B::initialize ***
An object of class “B”
Slot b:
numeric(0)
Slot a:
numeric(0)
*** B::validate ***
An object of class “B”
Slot b:
numeric(0)
Slot a:
[1] 1 2
*
Error in validObject(.Object) :
invalid class B object: Inconsistent lengths
# initialize B setting only the slot class B: OK!! Whereas it creates
a non valid object.
bObj - new('B', b=c(1,2))
*** B::initialize ***
An object of class “B”
Slot b:
numeric(0)
Slot a:
numeric(0)
*** Test missing b ***
bObj
An object of class “B”
Slot b:
[1] 1 2
Slot a:
numeric(0)
-
sessionInfo()
R version 2.9.1 (2009-06-26)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_ZA.UTF-8;LC_NUMERIC=C;LC_TIME=en_ZA.UTF-8;LC_COLLATE=en_ZA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_ZA.UTF-8;LC_PAPER=en_ZA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_ZA.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] Biobase_2.4.1
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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] correct way to subset a vector
Hi, #make example data dat - data.frame(matrix(rnorm(15),ncol=5)) colnames(dat) - c(ab,cd,ef,gh,ij) If I want to get a subset of the data for the middle 3 columns, and I know the names of the start column and the end column, I can do this: mysub - subset(dat,select=c(cd:gh)) If I wanted to do this just on the column names, without subsetting the data, how could I do this? mynames - colnames(dat); #mynames #[1] ab cd ef gh ij Is there an easy way to create the vector c(cd,ef,gh) as I did above using something similar to cd:gh? Thanks, Juliet __ 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] Population pyramids
Victor, use the axes=FALSE option, as you do. Then use the labels and at options in the axis argument to place the tickmark labels in the negative plot manually par(mfrow=c(1,2),bty=n,mai=c(0.5, 0.25, 0.25, 0.25)) x=rgamma(1000,10,0.3) barplot(height=t(-x), width = 0.825, space = NULL, names.arg = NULL, legend.text = c(Inf 95%,Mediana,Sup 95%), beside = FALSE, horiz = TRUE, density = NULL, angle = 0, axes = FALSE, col = c(yellow,Blue,orange), border = par(fg), main = Mujeres, xlim =NULL, ylim = NULL, xpd = TRUE, log = , axisnames = FALSE, axis(1,hadj=NA,padj=NA,cex.axis=0.75,labels=c(0,10,20,30,40,50, 60,70),at=c(0,-10,-20,-30,-40,-50,-60,-70))) barplot(height=t(x), width = 0.825, space = NULL, names.arg = NULL, legend.text = c(Inf 95%,Mediana,Sup 95%), beside = FALSE, axes=FALSE, horiz = TRUE, density = NULL, angle = 0, col = c(yellow,Blue,orange), border = par(fg), main = Mujeres, xlim =NULL, ylim = NULL, xpd = TRUE, log = , axisnames = FALSE, axis(1,cex.axis=0.75)) That should do. Best, Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: Victor Manuel Garcia Guerrero [mailto:vmgar...@colmex.mx] Gesendet: Thursday, July 09, 2009 1:44 AM An: Daniel Malter; r-help@r-project.org Betreff: RE: [R] Population pyramids Yes the code is the next: par(mfrow=c(1,2),bty=n,mai=c(0.5, 0.25, 0.25, 0.25)) barplot(height=t(icNM2005.dat), width = 0.825, space = NULL, names.arg = NULL, legend.text = NULL, beside = FALSE, horiz = TRUE, density = NULL, angle = 0, col = c(yellow,Blue,orange), border = par(fg), main = Hombres, xlim =NULL, ylim = NULL, xpd = TRUE, log = , axes = FALSE, axisnames = FALSE,cex.axis=0.75) axis(1,pretty(c(-1200,0),n=12), hadj=NA,padj=NA,cex.axis=0.75,las=2) barplot(height=t(icNF2005.dat), width = 0.825, space = NULL, names.arg = NULL, legend.text = c(Inf 95%,Mediana,Sup 95%), beside = FALSE, horiz = TRUE, density = NULL, angle = 0, col = c(yellow,Blue,orange), border = par(fg), main = Mujeres, xlim =NULL, ylim = NULL, xpd = TRUE, log = , axes = FALSE, axisnames = FALSE,cex.axis=0.75) axis(2,pretty(c(0:105),n=21),hadj=0.5,padj=0.5,cex.axis=0.75, las=2) axis(1,pretty(c(0:1200),n=5), hadj=NA,padj=NA,cex.axis=0.5,las=1) Víctor Manuel García Guerrero Doctorado en Estudios de Población, CEDUA, COLMEX Camino al Ajusco N° 20, Pedregal de Sta. Teresa C.P.10740, Tlalpan, México, D.F. * : vmgar...@colmex.mx ( : 5617-9016 -Mensaje original- De: Daniel Malter [mailto:dan...@umd.edu] Enviado el: jue 09/07/2009 12:15 Para: Victor Manuel Garcia Guerrero; r-help@r-project.org Asunto: AW: [R] Population pyramids Can you provide a self-contained example of what you did so far (i.e. code for simulating some data and code for the plot)? That would greatly help to help you find a solution. Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: Victor Manuel Garcia Guerrero [mailto:vmgar...@colmex.mx] Gesendet: Thursday, July 09, 2009 12:48 AM An: Daniel Malter; r-help@r-project.org Betreff: RE: [R] Population pyramids Yes, but my issue is because I need to plot a pop pyramid with confidence intervals, and the pyramid function does not work in that way. Thanks Daniel. -Mensaje original- De: Daniel Malter [mailto:dan...@umd.edu] Enviado el: mié 08/07/2009 11:36 Para: Victor Manuel Garcia Guerrero; r-help@r-project.org Asunto: AW: [R] Population pyramids have you tried the pyramid function in the epicalc package? best, daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von Victor Manuel Garcia Guerrero Gesendet: Thursday, July 09, 2009 12:25 AM An: r-help@r-project.org Betreff: [R] Population pyramids Hi, I hope somebody can help me with this issue: I am doing population pyramids using the barplot command, so in the left side I have male age structure and in the right side the female age structure. To plot the male age structure I put the data in negative numbers. Now, I want to change the sign in the bar plot in such way that I have no-sign numbers, both in left and right side of the graph. I have been trying all day long and I could not succed. Thanks... Victor __ 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] T.test error help
put another condition in your loop
if(all.equal(x,y)=TRUE) i=i+1 else t.test...
something in that direction.
best,
daniel
-
cuncta stricte discussurus
-
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im
Auftrag von Amit Patel
Gesendet: Thursday, July 09, 2009 9:20 AM
An: r-help@r-project.org
Betreff: [R] T.test error help
Hi I am implementing the t.test in a loop and where the data is the same i
get an error message.
Error in t.test.default(Samp3, Samp1, na.rm = TRUE, var.equal = FALSE, :
data are essentially constant
The script i am using is
for (i in 1:length(zz[,1])) {
Samp1 - zz[i,2:17]
Samp2 - zz[i,18:33]
Samp3 - zz[i,34:47]
Samp4 - zz[i,48:63]
TTestResult[i,2] - t.test(Samp2, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
TTestResult[i,3] - t.test(Samp3, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
TTestResult[i,4] - t.test(Samp4, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
}
Is there a way to make my loop ignore this problem and go onto the next
iteration
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Re: [R] correct way to subset a vector
Hi, On Jul 9, 2009, at 11:40 AM, Juliet Hannah wrote: Hi, #make example data dat - data.frame(matrix(rnorm(15),ncol=5)) colnames(dat) - c(ab,cd,ef,gh,ij) If I want to get a subset of the data for the middle 3 columns, and I know the names of the start column and the end column, I can do this: mysub - subset(dat,select=c(cd:gh)) If I wanted to do this just on the column names, without subsetting the data, how could I do this? mynames - colnames(dat); #mynames #[1] ab cd ef gh ij Is there an easy way to create the vector c(cd,ef,gh) as I did above using something similar to cd:gh? How about just taking your mynames vector? eg: R mynames[2:4] [1] cd ef gh R dat[, mynames[2:4]] cd ef gh 1 1.7745386 1.0958930 -0.07213304 2 0.7480372 -0.1364458 -0.62848211 3 -0.5477843 1.5811382 -0.74404103 -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos __ 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] wordStem problems in R 2.9, Fedora 11; Linux Kernel 2.6.29.5-191.fc11.i586
Duncan, Thanks for helping. I reinstalled Rstem from source (using the omegahat URL) and this time things are working. :-) RR -Original Message- From: Duncan Temple Lang [mailto:dun...@wald.ucdavis.edu] Sent: Tuesday, July 07, 2009 5:33 PM To: Reitsma, Rene - COB Cc: r-help@r-project.org Subject: Re: [R] wordStem problems in R 2.9, Fedora 11; Linux Kernel 2.6.29.5-191.fc11.i586 Hi Rene Can you tell us the version of the Rstem package you installed. Rstem_0.3-1 from http://www.omegahat.org/Rstem/ or install.packages(Rstem, repos = http://www.omegahat.org/R;) work fine for me. I seem to recall this being a problem with an older version of Rstem. D. Reitsma, Rene - COB wrote: Dear All, I just updated from Fedora 9 to Fedora 11, kernel version 2.6.29.5-191.fc11.i586. I'm running R 2.9. I successfully installed package Rstem from source (it always ran fine for me in F9). However: wordStem(c(This,is,a,test)) Error in wordStem(c(This, is, a, test)) : VECTOR_ELT() can only be applied to a 'list', not a 'character' Any idea what causes this / how I can fix this? RR __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] T.test error help
Daniel Malter wrote:
put another condition in your loop
if(all.equal(x,y)=TRUE) i=i+1 else t.test...
something in that direction.
Sorry, but that's neither valid R code nor sensible in this case.
See my suggestions below.
best,
daniel
-
cuncta stricte discussurus
-
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im
Auftrag von Amit Patel
Gesendet: Thursday, July 09, 2009 9:20 AM
An: r-help@r-project.org
Betreff: [R] T.test error help
Hi I am implementing the t.test in a loop and where the data is the same i
get an error message.
Error in t.test.default(Samp3, Samp1, na.rm = TRUE, var.equal = FALSE, :
data are essentially constant
The script i am using is
for (i in 1:length(zz[,1])) {
for(i in seq_along(zz[,1])){
should be safer.
Samp1 - zz[i,2:17]
Samp2 - zz[i,18:33]
Samp3 - zz[i,34:47]
Samp4 - zz[i,48:63]
TTestResult[i,2] - t.test(Samp2, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
TTestResult[i,3] - t.test(Samp3, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
TTestResult[i,4] - t.test(Samp4, Samp1, na.rm=TRUE, var.equal = FALSE,
paired=FALSE, conf.level=0.95)$p.value
}
Is there a way to make my loop ignore this problem and go onto the next
iteration
yes, you can wrap it in try() and check the object with
if(inherits(object, try-error)) later on in order to do something
different (e.g. assign an NA) in case of an error.
Uwe Ligges
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[R] math symbols in R
Hello, I would like R software to printout a sentence including a statement such as Ho: mu=5 vs Ha: mu ne 5 where ne stands for the math symbol notequal and mu is greek letter for u. How to do? Most of the help questions I have seen have been those involving graphs. Thank you. Sincerely, Mary A. Marion __ 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] Logistic Regression: Likelihoo-Ratio Based Confidence Intervals
Hello! I hope this email finds you all well. I have a rather elementary question. I am interested in obtaining likelihood ratio-based confidence intervals of logistic regression parameter estimates (i.e., the MLE). How do I specify likelihood ratio CIs in the confint() function, or do I need to use some other function? Thank you for your time, Alex [[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] correct way to subset a vector
On Jul 9, 2009, at 10:40 AM, Juliet Hannah wrote:
Hi,
#make example data
dat - data.frame(matrix(rnorm(15),ncol=5))
colnames(dat) - c(ab,cd,ef,gh,ij)
If I want to get a subset of the data for the middle 3 columns, and I
know the names of the start column and the end column, I can do this:
mysub - subset(dat,select=c(cd:gh))
If I wanted to do this just on the column names, without subsetting
the data, how could I do this?
mynames - colnames(dat);
#mynames
#[1] ab cd ef gh ij
Is there an easy way to create the vector c(cd,ef,gh) as I did
above using something similar to cd:gh?
Thanks,
Juliet
Using the same presumption that the desired values are consecutive in
the vector:
# Use which() to get the indices for the start and end of the subset
mynames[which(mynames == cd):which(mynames == gh)]
[1] cd ef gh
You can encapsulate that in a function:
subset.vector - function(x, start, end)
{
x[which(x == start):which(x == end)]
}
subset.vector(mynames, cd, gh)
[1] cd ef gh
Note that you can also do this:
names(subset(dat, select = cd:gh))
[1] cd ef gh
but that actually goes through the process of subsetting the data
frame first, which potentially introduces a lot of overhead and memory
use if the data frame is large. It also presumes that the desired
vector is a subset of the column names of the initial data frame.
To use the same sequence based approach as is used in
subset.data.frame(), you can do what is used internally within that
function:
subset.vector - function(x, select)
{
nl - as.list(1L:length(x))
names(nl) - x
vars - eval(substitute(select), nl)
x[vars]
}
subset.vector(mynames, select = cd:gh)
[1] cd ef gh
BTW, well done on recognizing that you can use the sequence of column
names for the 'select' argument. A lot of folks, even experienced
useRs, don't realize that you can do that... :-)
HTH,
Marc Schwartz
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Re: [R] math symbols in R
?plotmath Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Mary A. Marion Sent: Thursday, July 09, 2009 12:04 PM To: r-help@r-project.org Subject: [R] math symbols in R Hello, I would like R software to printout a sentence including a statement such as Ho: mu=5 vs Ha: mu ne 5 where ne stands for the math symbol notequal and mu is greek letter for u. How to do? Most of the help questions I have seen have been those involving graphs. Thank you. Sincerely, Mary A. Marion __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Creating and Using Objects in R
Dear All, I am not very into object-oriented programming, but I would like to learn the ropes for some R applications. Quoting from the online R language definition (paragraph 5.1) Consider the following simple example. A point in two-dimensional Euclidean space can be specified by its Cartesian (x-y) or polar (r-theta) coordinates. Hence, to store information about the location of the point, we could define two classes, |xypoint| and |rthetapoint|. All the `xypoint' data structures are lists with an x-component and a y-component. All `rthetapoint' objects are lists with an r-component and a theta-component. Now, suppose we want to get the x-position from either type of object. This can easily be achieved through generic functions. We define the generic function |xpos| as follows. xpos - function(x, ...) UseMethod(xpos) Now we can define methods: xpos.xypoint - function(x) x$x xpos.rthetapoint - function(x) x$r * cos(x$theta) The user simply calls the function |xpos| with either representation as the argument. The internal dispatching method finds the class of the object and calls the appropriate methods. I am a bit confused: when calling e.g. xpos.rthetapoint, I understand that x contains the polar representation of a point, so x=(r,theta), but how do I exactly write it to pass it to xpos.rthetapoint? I have made several attempts, but so far none of them works, so I may have misunderstood something. Many thanks Lorenzo __ 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] assigning vector name by increasing index in loop
Hello I have a large data table that I wish to divide in to vectors, as in v1 v2 v3 v4 v5 id11 2 34 5 id26 7 8 9 10 newv1 - c(table[1,1], table[3,1], table [5,1]) newv2-c(table[1,2], table[3,2]. table[5,2]) ...and so forth. How do I do this using a loop? -- View this message in context: http://www.nabble.com/assigning-vector-name-by-increasing-index-in-loop-tp24410532p24410532.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.
Re: [R] Extracting a column name in loop?
Thank you both for that. Much appreciated. mister_bluesman wrote: Hi, I am writing a script that will address columns using syntax like: data_set[,1] to extract the data from the first column of my data set, for example. This code will be placed in a loop (where the column reference will be placed by a variable). What I also need to do is extract the column NAME for a given column being processed in the loop. The dataframe has been set so that R knows that the top line refers to column headers. Can anyone help me understand how to do this? Thanks. -- View this message in context: http://www.nabble.com/Extracting-a-column-name-in-loop--tp24393160p24407422.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] Executing an error prone function without stopping a script
Dear R Users, I've used this a long time ago but have forgotten. Trawling aroung the various sources somehow does not lead me to it. How can I execute an error prone function without stopping a script if it goes wrong ? Thanks in advance, Tolga This email is confidential and subject to important disclaimers and conditions including on offers for the purchase or sale of securities, accuracy and completeness of information, viruses, confidentiality, legal privilege, and legal entity disclaimers, available at http://www.jpmorgan.com/pages/disclosures/email. [[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] How to: initialize, setValidity, copy-constructor
Hi Renaud --
Renaud Gaujoux ren...@mancala.cbio.uct.ac.za writes:
Hello list,
I'm having troubles setting up a basic calss hierarchy with S4.
Here is a simplified schema of what I'd like to do:
- Two classes: A and B that extends A
- Ensure that the slots added by B are consistent with the slots of A
- Let A initialize itself (I'm not supposed to know the internal
cooking of A)
- By default set the slots of B based on the slots that A initialized
Another question is: what is the recommended way of implementing a
copy-constructor in R?
I know that all of this is easily done in C++. The constructor of each
class is called recursively back-up to the root class. Validity checks
can be performed after/during associated
initialization. Copy-constructor are basics in C++.
Here below is a piece of code that I thought would work (but it does
not... therefore my post), what's wrong with it?
I think the main issue is when is the validity check performed: why is
it performed before the end of the initialize method?
loosely, new(B, ...) calls initialize(prototypeOfB, ...).
initialize,B-method uses callNextMethod(), so initialize,A-method sees
as .Object the value prototypeOfB. If initialize,A-method is
well-behaved, it'll call initialize,ANY-method, which also sees
prototypeOfB. You'll see that, when the ... argument is not empty
getMethod(initialize, ANY)
eventually calls validObject, in this case on prototypeOfB. Hence what
you are seeing, an 'early' check on the validity of B.
There are many creative ways around this in initialize,B-method, e.g.,
assigning B slots before callNextMethod(), or explicitly creating a
new instance of A from appropriate supplied arguments (in
initialize,B-method, name arguments meant to initialize B slots and
pass ... to the A constructor) and using that to initialize B, etc.
The approach I find most palatable (not meant to be real code) is to
have a constructor
B - function(x, y, z, ...) {
# do all the work to map x, y, z into slots of A, B (or an
# instance of A and slots of B), then...
new(B, a=, b=, ...) # or new(B, instanceOfA, b=, ...)
}
and avoid writing explicit initialize methods.
Oddly enough, this solution leads to a copy constructor, viz.,
initialize(instanceOfB, b=)
I'm not sure that this really does anything more than move the
'pattern' from the initialize method to the constructor.
Martin
Thank you for your help.
Renaud
# define class A with a single numeric slot
setClass('A', representation(a='numeric'))
# define class B that extends class A, adding another numeric slot
setClass('B', representation('A', b='numeric'))
# we want for example to ensure that slots a and b have the same length
setValidity('B',
function(object){
cat(*** B::validate ***\n)
print(object)
cat(*\n)
if( length(obj...@a) != length(obj...@b) ) return('Inconsistent lengths')
TRUE
}
)
# As a default behaviour if b is not provided, we want slot b to be
equal to slot a
setMethod('initialize', 'B',
function(.Object, b, ...){
cat(*** B::initialize ***\n)
print(.Object)
# Let the superclass (A) initialize itself via callNextMethod
# I thought it would only do that: initialize and optionnaly validate
the class A part of the object
#But it generates an ERROR: apparently it calls the validation method of B,
# before leaving me a chance to set slot b to a valid value
.Object - callNextMethod(.Object, ...)
# now deal with the class B part of the object
cat(*** Test missing b ***\n)
if( missing(b) ){
cat(*** b is MISSING ***\n)
b - .obj...@a
}
# set slot b
.obj...@b - b
.Object
}
)
### Testing
# empty A: OK
aObj - new('A')
aObj
# class A with some data: OK
aObj - new('A', a=c(1,2) )
aObj
# empty B: OK
bObj - new('B')
bObj
# initialize B setting the slot of class A: ERROR
bObj - new('B', a=c(1,2))
# initialize B setting only the slot class B: OK!! Whereas it produces
a non valid object.
bObj - new('B', b=c(1,2))
bObj
# RESULTS:
# empty A: OK
aObj - new('A')
aObj
An object of class “A”
Slot a:
numeric(0)
# class A with some data: OK
aObj - new('A', a=c(1,2) )
aObj
An object of class “A”
Slot a:
[1] 1 2
# empty B: OK
bObj - new('B')
*** B::initialize ***
An object of class “B”
Slot b:
numeric(0)
Slot a:
numeric(0)
*** Test missing b ***
*** b is MISSING ***
bObj
An object of class “B”
Slot b:
numeric(0)
Slot a:
numeric(0)
# initialize B setting the slot of class A: ERROR
bObj - new('B', a=c(1,2))
*** B::initialize ***
An object of class “B”
Slot b:
numeric(0)
Slot a:
numeric(0)
*** B::validate ***
An object of class “B”
Slot b:
numeric(0)
Slot a:
[1] 1 2
*
Error in validObject(.Object) :
invalid class B object: Inconsistent lengths
# initialize B setting only the slot class B: OK!! Whereas it
creates a non valid object.
bObj - new('B',
Re: [R] R-help Digest, Vol 77, Issue 9
Thanks, this worked!!!
nBooks - xl[[Workbooks]]$Count();
for (i in seq_len(nBooks))
xl[[Workbooks]]$item(i)$Close(SaveChanges=FALSE);
-L
2009/7/9 Bengoechea Bartolomé Enrique (SIES 73)
enrique.bengoec...@credit-suisse.com:
Hi,
This may be due to several reasons. That I can think about:
1) Ensure you close *all* possibly open workbooks:
nBooks - xl[[Workbooks]]$Count();
for (i in seq_len(nBooks))
xl[[Workbooks]]$item(i)$Close(SaveChanges=FALSE);
2) The excel application reference does not seem to be really released until
the garbage collector runs. So this may help:
xl$Quit();
xl - NULL;
gc();
3) Ensure you don't have any hanging reference to the excel application
(sometimes from previous runs of your code that failed). If your code is
inside a function, wrap the code in point 1 and 2 on an on.exit() call to
ensure that excel is properly closed each time.
Hope this helps.
Enrique
--
Date: Wed, 8 Jul 2009 16:06:57 +0300
From: Lauri Nikkinen lauri.nikki...@iki.fi
Subject: [R] RDCOMClient: how to close Excel process?
To: r-h...@stat.math.ethz.ch
Message-ID:
ba8c09910907080606n29b8a537uac5ba1788376f...@mail.gmail.com
Content-Type: text/plain; charset=windows-1252
Hi,
I?m using R package RDCOMClient (http://www.omegahat.org/RDCOMClient/)
to retrieve data from MS Excel workbook. I?m using the code below to
count the number of sheets in the workbook and then loop the data from
sheets in to a list.
# R code ###
library(gdata)
library(RDCOMClient)
xl - COMCreate(Excel.Application)
sh - xl$Workbooks()$Open(normalizePath(sample_file.xls))$Sheets()$Count()
DF.list - list()
for (i in 1:sh) {
DF.list[[i]] - read.xls(sample_file.xls, sheet=i,
stringsAsFactors = FALSE)
}
##
COMCreate opens Excel process and it can be seen from Windows Task
Manager. When I try to open sample_file.xls in Excel, it just flashes
in the screen and shuts down. When I kill (via task manager) the Excel
process COMCreate started, sample_file.xls will open normally.
The question is, how can I close the Excel process COMCreate started.
xl$Close() doesn?t seem to work. The same problem have been presented
in this post to R-help:
http://tolstoy.newcastle.edu.au/R/help/06/04/25990.html
-L
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[R] more than one mathematical annotation into a legend
Dear members, Is there a way to put more than one mathematical annotation into a legend together with a calculated value? x = 2 plot(1:10) #Works legend(8, 8, substitute(t[m] == x)) #does not work legend(4,4, c(substitute(t[m] == x), substitute(t[n] == x))) Thanks Thomas Roth __ 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] executing an error prone function without stopping a script
Dear R Users, I've used this a long time ago but have forgotten. Trawling aroung the various sources somehow does not lead me to it. How can I execute an error prone function without stopping a script if it goes wrong ? Thanks in advance, Tolga This email is confidential and subject to important disclaimers and conditions including on offers for the purchase or sale of securities, accuracy and completeness of information, viruses, confidentiality, legal privilege, and legal entity disclaimers, available at http://www.jpmorgan.com/pages/disclosures/email. [[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] Creating and Using Objects in R
Here it is done without S3. Note that UseMethod
is basically just an alternative to an if statement.
Perhaps this makes it more understandable.
x1 - list(x = 1, y = 2)
class(x1) - xypoint
x2 - list(r = 1, theta = pi/2)
class(x2) - rthetapoint
XPOS - function(x) {
if (inherits(x, xypoint)) xpos.xypoint(x)
else if (inherits(x, rthetapoint)) xpos.rthetapoint(x)
else stop(Cannot find appropriate class)
}
XPOS(x1) # without S3
xpos(x1) # using S3
XPOS(x2) # without S3
xpos(x2) # using S3
On Thu, Jul 9, 2009 at 12:24 PM, Lorenzo Isellalorenzo.ise...@gmail.com wrote:
Dear All,
I am not very into object-oriented programming, but I would like to learn
the ropes for some R applications.
Quoting from the online R language definition (paragraph 5.1)
Consider the following simple example. A point in two-dimensional
Euclidean space can be specified by its Cartesian (x-y) or polar (r-theta)
coordinates. Hence, to store information about the location of the point, we
could define two classes, |xypoint| and |rthetapoint|. All the `xypoint'
data structures are lists with an x-component and a y-component. All
`rthetapoint' objects are lists with an r-component and a theta-component.
Now, suppose we want to get the x-position from either type of object.
This can easily be achieved through generic functions. We define the generic
function |xpos| as follows.
xpos - function(x, ...)
UseMethod(xpos)
Now we can define methods:
xpos.xypoint - function(x) x$x
xpos.rthetapoint - function(x) x$r * cos(x$theta)
The user simply calls the function |xpos| with either representation as
the argument. The internal dispatching method finds the class of the object
and calls the appropriate methods.
I am a bit confused: when calling e.g. xpos.rthetapoint, I understand that x
contains the polar representation of a point, so x=(r,theta), but how do I
exactly write it to pass it to xpos.rthetapoint? I have made several
attempts, but so far none of them works, so I may have misunderstood
something.
Many thanks
Lorenzo
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tex fonts in R plots
KARAVASILIS GEORGE wrote: Hello, R users. I would like to display the font of Math Mode of MikTex 2.3, WinEdt 5.4 in R plots, e.g. in xlab, ylab or legend. How can I do that? Thank you in advance. A colleague and I have developed a package called pgfSweave that turns R plots created inside a Sweave document into code that can be interpreted by PGF/TikZ package for LaTeX. The end result of this process is that the text in your figures are typeset with the same fonts used in the rest of your TeX document. The package can be found at: http://r-forge.r-project.org/projects/pgfsweave/ It has been used by the authors to typeset academic papers on windows and produces good results. However we are still classifying it as an alpha product because it has not been tested extensively. Currently the underlying utility that translates R graphics into PGF form is the java utility eps2pgf which may be found at: http://sourceforge.net/projects/eps2pgf/ You may be interested in using this utility by it's self if you just want to prep graphics for LaTeX and don't want to use Sweave. Simply create your graphs in R using the eps() driver and process them using eps2pgf. eps2pgf has some drawbacks- it takes a few seconds to translate a graph and certain R graphics commands, such as setting text size using cex, are not respected. Good luck! -Charlie - Charlie Sharpsteen Undergraduate Environmental Resources Engineering Humboldt State University -- View this message in context: http://www.nabble.com/Tex-fonts-in-R-plots-tp24382492p24414007.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.
Re: [R] executing an error prone function without stopping a script
TU wrote:
Dear R Users,
I've used this a long time ago but have forgotten. Trawling aroung the
various sources somehow does not lead me to it. How can I execute an error
prone function without stopping a script if it goes wrong ?
Thanks in advance,
Tolga
See ?try
Basically, wrapping the function call in the try() function will make it so
that errors do not halt your script:
result - try( function( args ) )
You can then handle errors in your own way:
if( class(result) == 'try-error' ){
# Error handling stuff.
}
-
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
--
View this message in context:
http://www.nabble.com/executing-an-error-prone-function-without-stopping-a-script-tp24413760p24414337.html
Sent from the R help mailing list archive at Nabble.com.
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[R] X-axis labels not displayed when changing ylim
Dear R users, I am encountering a x axis labeling problem on quite basic plots... I use the following code which displays the labels on the x-axis with a 45 degrees angle: p - plot(myobject1, type=b, col=red,cex=1, lwd=2, axes=FALSE, ann=FALSE, ylim=c(0,70)) title(main=title, font.main=4) axis(side=1, lab=F) text(axTicks(1), par(usr)[3] - 2, srt=45, adj=1,labels=mylabels,xpd=T, cex=0.8, font=2) axis(side=2, las=1, cex.axis=0.8, font=2) I set up the ylim from 0 to 70 for plotting that object myobject1 - works well. However, when i try to use the same script with another set of data myobject2 (same number of points, same labels, but different values...) that ranges from 0 to 2 (ylim changed to c(0,2)), the labels on the x axis disappear... When i try to run the same lines for myobject2 but putting the ylim higher c(0,50), the labels on the x axis are displayed. I picked up some pieces of code here and there so i may do an obvious mistake but cannot figure out what it is! I tried to modify the text parameters adj or par(usr)..., unsuccessfully... I hope i made it clear, there must be a scaling problem that i really don't get... I run R 2.8.0 under Windows XP Pro. Thank you for your help! Sarah __ 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] more than one mathematical annotation into a legend
On Thu, Jul 9, 2009 at 9:39 AM, Thomas Roth (geb. Kaliwe)hamstersqu...@web.de wrote: try this: legend(4,4, expression(t[m] == x, t[n] == x)) cheers, Zhiliang Dear members, Is there a way to put more than one mathematical annotation into a legend together with a calculated value? x = 2 plot(1:10) #Works legend(8, 8, substitute(t[m] == x)) #does not work legend(4,4, c(substitute(t[m] == x), substitute(t[n] == x))) Thanks Thomas Roth __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Compiling R-2.9.1 on Mac OS X 10.4
Hello, I am trying to compile R-2.9.1 on Mac OS-X 10.4 using --enable-R-shlib. I am not comfortable with Mac/Linux environments and trying to follow the instructions from CRAN site to every detail. The Mac OS did not have a gcc (gcc -version did not work). So I did the following: ## For gcc 4.2 and Fortran 4.2.4 Compilers Download gcc-4.2-5566-darwin8-all.tar.gz from http://r.research.att.com/tools/#gcc42 unpacked using: sudo tar fvxz gcc-4.2-5566-darwin8-all.tar.gz -C / Made gcc-4.2 default: sudo link gcc-4.2 gcc Made g++-4.2 default: sudo link g++-4.2 g++ I downloaded the source and tried compiling using: ./configure --with-blas='-framework vecLib' --with-lapack --with-ICU \ --with-aqua --enable-R-framework --enable-R-shlib Got the following error: Configure: error: C compiler cannot create executables I have attached the compile.log file. I would really appreciate some help. Raktim Bioinformatics Engineer DFCI, Harvard Med School Boston The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. __ 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] Issues with file.info?
Are there any tricks associated with file.info? I just tried it on a directory folder and it returned NA for all fields for all files. I tried it on a different folder with different files and it still returned NA. I tried it on a specific file and it returned all the proper info correctly. Just wondering if there are any tricks I've overlooked. __ 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] Compiling R-2.9.1 on Mac OS X 10.4
On Jul 9, 2009, at 12:12 PM, Sinha, Raktim, DFCI wrote: Hello, I am trying to compile R-2.9.1 on Mac OS-X 10.4 using --enable-R- shlib. I am not comfortable with Mac/Linux environments and trying to follow the instructions from CRAN site to every detail. The Mac OS did not have a gcc (gcc -version did not work). So I did the following: ## For gcc 4.2 and Fortran 4.2.4 Compilers Download gcc-4.2-5566-darwin8-all.tar.gz from http://r.research.att.com/tools/#gcc42 unpacked using: sudo tar fvxz gcc-4.2-5566-darwin8-all.tar.gz -C / Made gcc-4.2 default: sudo link gcc-4.2 gcc Made g++-4.2 default: sudo link g++-4.2 g++ I downloaded the source and tried compiling using: ./configure --with-blas='-framework vecLib' --with-lapack --with-ICU \ --with-aqua --enable-R-framework --enable-R-shlib Got the following error: Configure: error: C compiler cannot create executables I have attached the compile.log file. I would really appreciate some help. The log file did not survive the list spam filters, but is there a particular reason that you are compiling from source? A universal binary installation package (which is built using --enable- R-shlib) is available from a CRAN mirror such as: http://cran.us.r-project.org/ You might want to review the OSX FAQ as well: http://cran.us.r-project.org/bin/macosx/RMacOSX-FAQ.html If you really need to build from source, which is not for the feint of heart, begin by reviewing section 2 of the FAQ. HTH, Marc Schwartz __ 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] 'scan' in a script?
When I use the scan function in the Rgui console it works as expected. However it seems that when I put the same command in a script file it doesn't wait for input. Is there an option to scan to make it wait for input when used in a script? Or is there possibly a different function that will do in a script the same sort of thing as scan does in the console? Thanks, Mark __ 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] Substituting numerical values using `apply'
Thank you all for your help. SO. Henrique Dallazuanna wrote: Try this: sapply(names(DF), function(n)ifelse(DF[,n] %in% c(1, 2), n, NA)) Where DF is your data.frame On Wed, Jul 8, 2009 at 5:25 PM, Olivella olive...@wustl.edu mailto:olive...@wustl.edu wrote: Hello, I wish to perform a substitution of certain numerical values in a data matrix with the corresponding column name. For instance, if I have a data matrix V1 V2 V3 201 012 150 500 I want to substitute the `1' and the `2' for the corresponding column name, and make everything else `NA' like this V1V2V3 V1NAV3 NAV2V3 V1NANA NANANA I have done this using an explicit `for' loop, but it takes a really long time to finish. Is there any way I can do this using `apply' or some form of implicit looping? Thank you for your help, SO -- View this message in context: http://www.nabble.com/Substituting-numerical-values-using-%60apply%27-tp24398687p24398687.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailto: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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O -- - Santiago Olivella Ph.D. Program in Political Science Washington University in St. Louis solivella.wustl.edu [[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.
[R] Lattice xyplot: same scales within one factor
I am using R 2.8.1 and lattice to produce xyplots conditioned on two factors. What I would like is to have the scales be free between values of one factor, but some within. Thus, in the example: xyplot(mpg ~ disp | factor(gear) + factor(cyl), mtcars, scales=list(x=list(relation=free))) rather than having the x scales be free within a gear as well, I want it to be the same for the gear, but free between cyl (and thus only have x scales below the bottom panels with no scales or white space in the middle between panels). Any help would be greatly appreciated -Orion [[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] Compiling R-2.9.1 on Mac OS X 10.4
I used to build from source on Mac OS X, but I stopped when I found I
could do everything I needed to do from the binary on CRAN. That
includes building my own packages that use fortran, or building the
one or two CRAN packages that use C code and do not have Mac binaries
on CRAN.
In addition to which, if you were to install the Mac binary from
CRAN, there's an optional install of gcc, and that might even be an
easier way to get a gcc on your machine. You can still build R from
sources separately, even if you've already installed the binary.
For further help on building from source, I'd suggest asking again on
R-sig-Mac.
-Don
At 1:12 PM -0400 7/9/09, Sinha, Raktim, DFCI wrote:
Hello,
I am trying to compile R-2.9.1 on Mac OS-X 10.4 using --enable-R-shlib.
I am not comfortable with Mac/Linux environments and trying to follow the
instructions from CRAN site to every detail.
The Mac OS did not have a gcc (gcc -version did not work). So I did the
following:
## For gcc 4.2 and Fortran 4.2.4 Compilers
Download gcc-4.2-5566-darwin8-all.tar.gz from
http://*r.research.att.com/tools/#gcc42
unpacked using: sudo tar fvxz gcc-4.2-5566-darwin8-all.tar.gz -C /
Made gcc-4.2 default: sudo link gcc-4.2 gcc
Made g++-4.2 default: sudo link g++-4.2 g++
I downloaded the source and tried compiling using:
./configure --with-blas='-framework vecLib' --with-lapack --with-ICU \
--with-aqua --enable-R-framework --enable-R-shlib
Got the following error:
Configure: error: C compiler cannot create executables
I have attached the compile.log file.
I would really appreciate some help.
Raktim
Bioinformatics Engineer
DFCI, Harvard Med School
Boston
The information in this e-mail is intended only for the...{{dropped:26}}
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Re: [R] Reading from Google Docs
Gabor Grothendieck ggrothendi...@gmail.com [Wed, Jul 08, 2009 at 10:31:30PM CEST]: [...] [[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. [[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. [[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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Do you think more people will pay attention when you repeat this over and over? -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:johan...@huesing.name from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi) __ 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] naming of columns in R dataframe consisting of mixed data (alphanumeric and numeric)
Mary A. Marion-2 wrote: Hello, I have an r function that creates the following dataframe tresults2. Notice that column 1 does not have a column heading. Tresults2: [,1] estparam 18.0 nullval 20.0 . . . ciWidth 2.04622 HalfInterval 1.02311 pertinent code: results-cbind( estparam, nullval, t, pv_left, pv_right, pv_two_t, estse, df, cc, tbox, llim, ulim, ciWidth, HalfInterval) tresults-round((results),5) tresults2-data.frame(t(tresults)) names(tresults2)-c(Statistic , Value) tresults2 === After transposing my dataframe tresults2 consists of 2 columns. Col1=alphanumeric data (this really is a variable name) and col2=numeric data (this is value of varaiable). how do I name columns when columns are different (alphanumeric and numeric) to avoid the following error: Error in names(tresults2) - c(Statistic , Value) : 'names' attribute [2] must be the same length as the vector [1] You tried to give a name to a column that do not exist (the second one you called value). You can check that using str(tresults2). The name of the columns should not (well, I don't see how) interfere with the type (or class) they contain. You can create a Value column by using tresults2$Value - your_value Am I to use c( , ) or list( , ) with a dataframe? You picked the right one ( c() )... to give the names, I guess this is what you were asking. Cheers, Etienne Thank you for your help. Sincerely, Mary A. Marion -- View this message in context: http://www.nabble.com/naming-of-columns-in-R-dataframe-consisting-of-mixed-data-%28alphanumeric-and-numeric%29-tp24411614p24416676.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.
Re: [R] 'scan' in a script?
Exactly how are you using it? How you executing your script? Are you using cut/paste or source? Have you tried 'readline'? More details on what you mean by it does not work as expected. On Thu, Jul 9, 2009 at 2:24 PM, Mark Knechtmarkkne...@gmail.com wrote: When I use the scan function in the Rgui console it works as expected. However it seems that when I put the same command in a script file it doesn't wait for input. Is there an option to scan to make it wait for input when used in a script? Or is there possibly a different function that will do in a script the same sort of thing as scan does in the console? Thanks, Mark __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] Issues with file.info?
Works fine for me on 2.9.1:
file.info('/jph')
size isdir mode mtime ctime
atime exe
/jph0 TRUE 777 2009-06-29 15:15:13 2008-02-14 09:31:26
2009-07-09 15:57:04 no
On Thu, Jul 9, 2009 at 2:02 PM, Jason Rupertjasonkrup...@yahoo.com wrote:
Are there any tricks associated with file.info?
I just tried it on a directory folder and it returned NA for all fields for
all files. I tried it on a different folder with different files and it
still returned NA.
I tried it on a specific file and it returned all the proper info correctly.
Just wondering if there are any tricks I've overlooked.
__
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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
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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 to Populate List
On 10/07/2009, at 2:55 AM, Gaurav Kumar wrote:
Hi,
I'm new to R and would like to know, how one can populate the list
with array data.
I'm reading a tab separated table in R. The data in the table looks
something like this.
#Table Data
CompABC
Extracellular103268535759
Nucleus4560347783442744
#R code
myData - read.table(table.data,
header=T,
sep=\t,
comment.char = #
);
inp - scan(table.data, what=list(comp= , A=, B=, C=));
n - c(0:length(inp$comp));
myList=list();
for(i in n-1)
{
obj -c(as.numeric(myData$A[i]),as.numeric(myData$B
[i]),as.numeric(myData$C[i]));
}
Need help to know if there is any function in R to push obj to myList
(a) You apparently ``replied'' to an R-help digest, and included
megabytes
of totally irrelevant material in your post. It took me several
minutes to delete it.
STEP ONE: LEARN HOW TO USE EMAIL!!!
(b) Do the following:
myList - list();
for(i in n-1)
{
myList[[i]] -c(as.numeric(myData$A[i]),as.numeric(myData$B
[i]),as.numeric(myData$C[i]));
}
cheers,
Rolf Turner
##
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Issues with file.info?
Issue was with an entire directory/folder or list of files in a directory. It
seemed to work fine for a single file or being sent a single file/folder.
I will try to generate some example code to demonstrate the problem.
Thanks again for all the replies.
--- On Thu, 7/9/09, jim holtman jholt...@gmail.com wrote:
From: jim holtman jholt...@gmail.com
Subject: Re: [R] Issues with file.info?
To: Jason Rupert jasonkrup...@yahoo.com
Cc: R-help@r-project.org
Date: Thursday, July 9, 2009, 3:04 PM
Works fine for me on 2.9.1:
file.info('/jph')
size isdir mode
mtime
ctime
atime exe
/jph 0 TRUE 777 2009-06-29
15:15:13 2008-02-14 09:31:26
2009-07-09 15:57:04 no
On Thu, Jul 9, 2009 at 2:02 PM, Jason Rupertjasonkrup...@yahoo.com
wrote:
Are there any tricks associated with file.info?
I just tried it on a directory folder and it returned
NA for all fields for all files. I tried it on a different
folder with different files and it still returned NA.
I tried it on a specific file and it returned all the
proper info correctly.
Just wondering if there are any tricks I've
overlooked.
__
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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
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] Issues with file.info?
On 10/07/2009, at 6:02 AM, Jason Rupert wrote:
Are there any tricks associated with file.info?
I just tried it on a directory folder and it returned NA for all
fields for all files. I tried it on a different folder with
different files and it still returned NA.
I tried it on a specific file and it returned all the proper info
correctly.
Just wondering if there are any tricks I've overlooked.
Yes. You've overlooked the trick of telling us about the specifics of
your operating system, version of R, etc., and of showing exactly what
commands you ``tried'', i.e. of reading the Posting Guide.
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
__
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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] Lattice xyplot: same scales within one factor
I am using R 2.8.1 and lattice to produce xyplots conditioned on two factors. What I would like is to have the scales be free between values of one factor, but some within. Thus, in this example, xyplot(mpg ~ disp | factor(gear) + factor(cyl), mtcars, scales=list(x=list(relation=free))) rather than having the x scales be free within a gear as well, I want it to be the same for the gear, but free between cyl (and thus only have x scales below the bottom panels with no scales or white space in the middle between panels). Any help would be greatly appreciated! -Orion __ 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] X-axis labels not displayed when changing ylim
On Thu, 09-Jul-2009 at 05:36PM +0200, Sarah Bonnin wrote:
Dear R users,
I am encountering a x axis labeling problem on quite basic plots...
I use the following code which displays the labels on the x-axis with a
45 degrees angle:
p - plot(myobject1, type=b, col=red,cex=1, lwd=2, axes=FALSE,
ann=FALSE, ylim=c(0,70))
title(main=title, font.main=4)
axis(side=1, lab=F)
text(axTicks(1), par(usr)[3] - 2, srt=45, adj=1,labels=mylabels,xpd=T,
I think this part is what's not transferable to a smaller range of
y-values.
par(usr)[3] will be much smaller when ylim goes to only 2 instead of
70. Subtract 2 from that, and you have a very different kettle of
fish.
Without knowing anything about myobject1 and myobject2 I could be
completely ooff the mark, of cours.
HTH
cex=0.8, font=2)
axis(side=2, las=1, cex.axis=0.8, font=2)
I set up the ylim from 0 to 70 for plotting that object myobject1 -
works well.
However, when i try to use the same script with another set of data
myobject2 (same number of points, same labels, but different
values...) that ranges from 0 to 2 (ylim changed to c(0,2)), the
labels on the x axis disappear...
When i try to run the same lines for myobject2 but putting the ylim
higher c(0,50), the labels on the x axis are displayed.
I picked up some pieces of code here and there so i may do an obvious
mistake but cannot figure out what it is! I tried to modify the text
parameters adj or par(usr)..., unsuccessfully...
I hope i made it clear, there must be a scaling problem that i really
don't get...
I run R 2.8.0 under Windows XP Pro.
Thank you for your help!
Sarah
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Re: [R] 'scan' in a script?
Jim, In Rgui there is a feature to create a new script so I open that and get a blank editor. I put these commands in the script MyNames = scan(what=) MyNames Whether I ask Rgui to run the whole script as a script - not sourced - it runs the first command, doesn't wait for input and then runs the second command. I see MyNames character(0) If I right click the first line and ask it to run the selection or line then R waits for the input. If I source the file then the opposite happens. It does the scan correctly, waiting for me to make entries. When I finish it doesn't print what's in MyNames, as shown here where I typed in happy sad test go and hit enter. source(C:\\Users\\Mark\\Documents\\R\\Test Cases\\scan from script.R) 1: happy sad test go 5: Read 4 items Possibly (probably!) this is a misunderstanding on my part, but it's something I need to start looking at as the reason for me checking out R at all was as a potential way to develop a complete program, as opposed to writing it in C, so I need to start looking at how to give it input (file names, directory paths, user requests) other than changing source code. I hope this is clear enough and I appreciate your inputs. Cheers, Mark On Thu, Jul 9, 2009 at 1:02 PM, jim holtmanjholt...@gmail.com wrote: Exactly how are you using it? How you executing your script? Are you using cut/paste or source? Have you tried 'readline'? More details on what you mean by it does not work as expected. On Thu, Jul 9, 2009 at 2:24 PM, Mark Knechtmarkkne...@gmail.com wrote: When I use the scan function in the Rgui console it works as expected. However it seems that when I put the same command in a script file it doesn't wait for input. Is there an option to scan to make it wait for input when used in a script? Or is there possibly a different function that will do in a script the same sort of thing as scan does in the console? Thanks, Mark __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] Strange t-test error: grouping factor must have exactly 2 levels while it does...
Hi, Could anyone tell me what is wrong: length(unique(mydata$myvariable)) [1] 2 and in t-test: (...) Error in t.test.formula(othervariable ~ myvariable, mydata) : grouping factor must have exactly 2 levels I re-checked the code and still don't get what is wrong. Moreover, there is some strange behavior: /1 It seems that the error is vulnerable to NA'a, because it affects some variables in data set with NA's and doesn't affect same ones in dataset with NA's removed. /2 It seems it works differently with different ways of using variables in t.test: eg. it hapends here: t.test(x~y, dataset) and does not here: t.test(dataset[['x']]~dataset[['y']]) Does anyone have any ideas? Greetz, Timo __ 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] How to combine two rows (in a dataframe) into a third row?
Dear R-helpers, I have two rows in my dataframe: IDVALUE 1A10 1B15 and I would like to combine these two rows into a single (new) row in my dataframe: IDVALUE 125 ...simply by specifying a new value for ID and summing the two VALUES. I have been trying to do this with with rbind, but it's not working. I'd appreciate any pointers. Thanks, Mark Na [[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.
[R] SSOAP failure
Hi, Im using R package SSOAP to retrieve data from web services. Im using the code below to # R code ### library(SSOAP) then I call the nwis.R which exists in SSOAP example folder. However system gives me following errors: Error in parse (text=paste(text, collapse=\n)): Unexpected input in function (x ,obj=new( I could not understand why I get this error. I am very appreciate anybody help me. nermin _ [[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.
[R] datadist() in Design library
Hi I got an error message using datadist() from Design package: library(Design,T) dd - datadist(beta.final) options(datadist=dd) lrm(Disease ~ gsct+apcct+rarct, x=TRUE, y=TRUE) Error in eval(expr, envir, enclos) : object Disease not found All variables inclduing response variable Disease are in the data frame beta.final, why then Disease can not be found? I thought with datadist(), all variables are presented to the model fitting functions. maybe I am wrong? thanks John __ 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] Executing an error prone function without stopping a script
Tolga I Uzuner wrote: Dear R Users, I've used this a long time ago but have forgotten. Trawling aroung the various sources somehow does not lead me to it. How can I execute an error prone function without stopping a script if it goes wrong ? See ?try. Duncan Murdoch Thanks in advance, Tolga This email is confidential and subject to important disclaimers and conditions including on offers for the purchase or sale of securities, accuracy and completeness of information, viruses, confidentiality, legal privilege, and legal entity disclaimers, available at http://www.jpmorgan.com/pages/disclosures/email. [[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. __ 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] Stratified data summaries
Hi All, I'm trying to automate a data summary using summary or describe from the HMisc package. I want to stratify my data set by patient_type. I was hoping to do something like: Describe(myDataFrame ~ patient_type) I can create data subsets and run the describe function one at a time, but there's got to be a better way. Any suggestions? Rachel [[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] datadist() in Design library
Dear John, Have you tried it specifying the 'data' argument as suggested in lrm help? Try this: lrm(Disease ~ gsct + apcct + rarct, data = beta.final, x = TRUE, y = TRUE ) HTH, Jorge On Thu, Jul 9, 2009 at 6:46 PM, array chip arrayprof...@yahoo.com wrote: Hi I got an error message using datadist() from Design package: library(Design,T) dd - datadist(beta.final) options(datadist=dd) lrm(Disease ~ gsct+apcct+rarct, x=TRUE, y=TRUE) Error in eval(expr, envir, enclos) : object Disease not found All variables inclduing response variable Disease are in the data frame beta.final, why then Disease can not be found? I thought with datadist(), all variables are presented to the model fitting functions. maybe I am wrong? thanks John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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] How to combine two rows (in a dataframe) into a third row?
Tena koe Mark ?tapply with the index argument some suitable substring of your ID column. HTH Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Mark Na Sent: Friday, 10 July 2009 10:28 a.m. To: r-help@r-project.org Subject: [R] How to combine two rows (in a dataframe) into a third row? Dear R-helpers, I have two rows in my dataframe: IDVALUE 1A10 1B15 and I would like to combine these two rows into a single (new) row in my dataframe: IDVALUE 125 ...simply by specifying a new value for ID and summing the two VALUES. I have been trying to do this with with rbind, but it's not working. I'd appreciate any pointers. Thanks, Mark Na [[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. The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited. __ 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] validate() in Design library
Hi, another question about validate() in Design library. The arugment B of this function is number of repetition for method=bootstrap, which is easy to understand; but for method=crossvalidation, B is the number of groups of omitted observations. This is confusing, I don't understand what it means. Let's say 5-fold cross validation, all samples are divided into 5 groups of equal number of samples, 4 groups will be used as training and the model developed there will be tested in the 1 group left-over. And the process circulate for all 5 groups. What does the B argument mean in this example? B=5? or B=1 because 1 group of samples omitted from model development? Thanks Yi __ 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] datadist() in Design library
Dear Jorge, Yes, with data=beta.final in the lrm(), it worked. But I thought one of the reasons for datadist() is to make it unnecessary to specify the data frame in the lrm(). Maybe I am completely wrong here. Thanks John --- On Thu, 7/9/09, Jorge Ivan Velez jorgeivanve...@gmail.com wrote: From: Jorge Ivan Velez jorgeivanve...@gmail.com Subject: Re: [R] datadist() in Design library To: array chip arrayprof...@yahoo.com Cc: R mailing list r-help@r-project.org Date: Thursday, July 9, 2009, 6:55 PM Dear John, Have you tried it specifying the 'data' argument as suggested in lrm help? Try this: lrm(Disease ~ gsct + apcct + rarct, data = beta.final, x = TRUE, y = TRUE) HTH, Jorge On Thu, Jul 9, 2009 at 6:46 PM, array chip arrayprof...@yahoo.com wrote: Hi I got an error message using datadist() from Design package: library(Design,T) dd - datadist(beta.final) options(datadist=dd) lrm(Disease ~ gsct+apcct+rarct, x=TRUE, y=TRUE) Error in eval(expr, envir, enclos) : object Disease not found All variables inclduing response variable Disease are in the data frame beta.final, why then Disease can not be found? I thought with datadist(), all variables are presented to the model fitting functions. maybe I am wrong? thanks John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 'scan' in a script?
Check out: http://tolstoy.newcastle.edu.au/R/help/03a/6855.html On Thu, Jul 9, 2009 at 2:24 PM, Mark Knechtmarkkne...@gmail.com wrote: When I use the scan function in the Rgui console it works as expected. However it seems that when I put the same command in a script file it doesn't wait for input. Is there an option to scan to make it wait for input when used in a script? Or is there possibly a different function that will do in a script the same sort of thing as scan does in the console? Thanks, Mark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Compiling R-2.9.1 on Mac OS X 10.4
Matt Don -- Thanks a lot for the comments. I think I need to figure out why JRI is not recognizing the R installation as shared library build first, and go from there. I will try post back on r-sig-mac if I need too. Best, Raktim -Original Message- From: Marc Schwartz [mailto:marc_schwa...@me.com] Sent: Thursday, July 09, 2009 3:36 PM To: Sinha, Raktim, DFCI Subject: Re: [R] Compiling R-2.9.1 on Mac OS X 10.4 On Jul 9, 2009, at 2:08 PM, Sinha, Raktim, DFCI wrote: Hi Matt, Marc and please post follow ups back to the list. That way, you get a wider audience of folks who can reply to your query and you don't impose on specific individuals. To your own benefit, you are not waiting for one specific individual, who may not be available to respond to you. Keep in mind, we are all volunteers and most of us have full time jobs which will keep us busy. As Don noted, there is also a specific R list for OSX related queries. More information here: https://stat.ethz.ch/mailman/listinfo/r-sig-mac If the comments below are not helpful, please post follow ups there after subscribing. I am trying to compile JRI(http://www.rforge.net/JRI/) for Mac, Win Linux which loads R dynamic library into Java. I had no problems doing it with Windows as the binary is built using --enable-R-shlib but for Linux and Mac its giving me errors. The specific errors of Mac: /Library/Frameworks/R.framework/Resources/bin/config: line 1: make: command not found /Library/Frameworks/R.framework/Resources/bin/config: line 1: make: command not found R was not built as a library configure: error: R was not compiled with --enable-R-shlib If you are going to compile from source, the first thing that you need to do is to install the XCode Tools package, which is from Apple and available on the OSX install DVD or from Apple, all of which is noted in the OSX FAQ I pointed you to. XCode Tools provides the basic compiling environment and tools, with the exception of a FORTRAN compiler, which is available from the CRAN OSX Tools page as a binary. I don't use JRI, but would suggest that you review the guidance in their FAQ, which points to certain system configuration things that you need to do to get it to work with R. *** You must have libR.so or equivalent in order to use JRI *** I Installed R-2.9.1 from the same location you pointed me too. Also I was following the instructions from the same site you referred to, to compile on Mac. As noted, you should not have to compile R from source, as the result of your compilation will be essentially identical to the binary available from CRAN. If you are not comfortable with low level system operations, I would urge you to steer away from building R from source. Even for most Linux distributions, there are pre-compiled R binaries available via the normal package management tools and they too are typically built with R as a shared library. You should be able to install JRI using the command noted on the JRI web site, after installing the R binary: install.packages(rJava) There is an OSX binary available on the CRAN mirrors. Is there a way I get the log file across? You can try to rename the file with a .txt extension or better, upload it someplace and post the URL to it, which would be a better option, so as not to send a large attachment to the list. HTH, Marc Thanks Raktim -Original Message- From: Marc Schwartz [mailto:marc_schwa...@me.com] Sent: Thursday, July 09, 2009 2:03 PM To: Sinha, Raktim, DFCI Cc: r-help@r-project.org Subject: Re: [R] Compiling R-2.9.1 on Mac OS X 10.4 On Jul 9, 2009, at 12:12 PM, Sinha, Raktim, DFCI wrote: Hello, I am trying to compile R-2.9.1 on Mac OS-X 10.4 using --enable-R- shlib. I am not comfortable with Mac/Linux environments and trying to follow the instructions from CRAN site to every detail. The Mac OS did not have a gcc (gcc -version did not work). So I did the following: ## For gcc 4.2 and Fortran 4.2.4 Compilers Download gcc-4.2-5566-darwin8-all.tar.gz from http://r.research.att.com/tools/#gcc42 unpacked using: sudo tar fvxz gcc-4.2-5566-darwin8-all.tar.gz -C / Made gcc-4.2 default: sudo link gcc-4.2 gcc Made g++-4.2 default: sudo link g++-4.2 g++ I downloaded the source and tried compiling using: ./configure --with-blas='-framework vecLib' --with-lapack --with- ICU \ --with-aqua --enable-R-framework --enable-R-shlib Got the following error: Configure: error: C compiler cannot create executables I have attached the compile.log file. I would really appreciate some help. The log file did not survive the list spam filters, but is there a particular reason that you are compiling from source? A universal binary installation package (which is built using -- enable- R-shlib) is available from a CRAN mirror such as: http://cran.us.r-project.org/ You might want to
Re: [R] Converting indices of a matrix subset
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Hash: SHA1
Hi Steven,
This looks great. Thanks!
Nathan
Steve Lianoglou wrote:
Hi Nathan,
On Jul 8, 2009, at 10:20 PM, Nathan S. Watson-Haigh wrote:
I have two matrices:
m1 - matrix(1,4,4)
m1
[,1] [,2] [,3] [,4]
[1,]1111
[2,]1111
[3,]1111
[4,]1111
m2 - matrix(0,3,3)
diag(m2) - 1
m2
[,1] [,2] [,3]
[1,]100
[2,]010
[3,]001
I want to get indicies from m2 such that they match indicies as
though they came
from the lower right of m1. Here's how things work:
ind1 - which(m1 == 1)
ind1
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
ind2 - which(m2 == 1)
ind2
[1] 1 5 9
I would like ind2 to be offset so they look like indicies from the
lower right
of m1:
ind2
[1] 6 11 16
I have written some utility functions I use often[1], and have
sub2ind function that works in a similar fashion to the MATLAB
function of the same name. It's somehow long and convoluted because
you can send in your arguments 12 different ways from sunday, so:
sub2ind - function(x, y, nrow, ncol=NULL) {
## Returns a linear index for the (x,y) coordinates passed in.
if (is.matrix(x) || is.data.frame(x)) {
stopifnot(ncol(x) == 2)
if (!missing(y)) {
if (missing(nrow)) {
nrow - y
} else {
ncol - nrow
nrow - y
}
}
y - x[,2]
x - x[,1]
}
if (is.matrix(nrow)) {
d - dim(nrow)
nrow - d[1]
ncol - d[2]
} else if (is.null(ncol)) {
stop(Dimensions of matrix under-specified)
}
# Sanity check to ensure we got each var doing what it should be
doing
if (length(x) != length(y) || length(nrow) != 1 || length(ncol) !=
1) {
stop(I'm confused)
}
((x - 1) + ((y - 1) * nrow)) + 1
}
R m1 - matrix(1,4,4)
R m2 - matrix(0,3,3)
R ind2 - which(m2 == 1, arr.ind=T) + 1
R ind2
row col
[1,] 2 2
[2,] 3 3
[3,] 4 4
R my.ind2 - sub2ind(ind2, nrow=4, ncol=4)
# my.ind2 - sub2ind(ind2[,1], ind2[,2], 4, 4)
# my.ind2 - sub2ind(ind2[,1], ind2[,2], m1)
# my.ind2 - sub2ind(ind2, m1)
R my.ind2
[1] 6 11 16
I think that gets you to where you want to be :-)
-steve
[1] They can be found here if your intersted, there isn't much
documentation there, but I'll fix that some time later :-)
http://github.com/lianos/ARE.utils/tree/master
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos
- --
-
Dr. Nathan S. Watson-Haigh
OCE Post Doctoral Fellow
CSIRO Livestock Industries
Queensland Bioscience Precinct
St Lucia, QLD 4067
Australia
Tel: +61 (0)7 3214 2922
Fax: +61 (0)7 3214 2900
Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
-
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[R] Comparing Probit and Logit Coefficients Across Groups
Hi, I want to compare probit coefficients across groups with the method proposed by Allison (1999). The method corrects for unobserved heterogeneity in binary regression models. I can find only a SAS macro on the author's homepage (http://www.ssc.upenn.edu/~allison/glogit.sas). Has anyone of you ever implemented this method in R or knows how to integrate the macro? Thank you very very much for your kind help and any tips! Marius __ Marius Osterfeld Rue Francois Guillimann 5 CH-1700 Fribourg Lehrstuhl für Makroökonomie, Industrie- und Wachstumspolitik Boulevard de Pérolles 90 CH-1700 Fribourg Tel. (Büro): 0041 26 300 93 81 Natel: 0041 79 269 19 26 Tel. (CH): 0041 26 321 15 59 Tel. (D): 0049 2461 1859 [[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.
