Re: [R] how to specify the order of panels with xyplot
On Fri, Nov 20, 2009 at 12:53 PM, Dan Kortschak dan.kortsc...@adelaide.edu.au wrote: I have sorted out how to do this - by much trial an error (a comment from Deepayan in a post some years ago pointed which way to go, though it took a lot of searching to find even where to start with it: I've bound the two sets of data together, making the relevant part an ordered factor. It's probably not the nicest way to do it, but it works. Your example is not reproducible, so it's hard to suggest alternatives. But it seems that your original 'chromosomes' data frame has things in the right order, so a simple fix would be chromosomes$name - with(chromosomes, factor(name, levels = name)) -Deepayan __ 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] symbol in the plot
How about plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta', pch=22, type='o') points(sigma, delta2, col='red', axes=FALSE, type='o') legend(topleft,c(Delta1,Delta2),fill=TRUE,col=c(black,red)) Send runnable example next time. HTH, Joh gcheer3 wrote: TO be specific, here is how I graphed plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1--square delta2--circle', pch=22, type='o') par(new=TRUE) plot(sigma, delta2, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1--square delta2--circle', col='red', axes=FALSE, type='o') Thanks a lot gcheer3 wrote: a graph question. Thanks a lot in advance. I made two scatterplots on one graph (sigma vs. delta1, sigma vs. delta2) (20 observations of delta1, delta2 and corresponding sigma) the x-axis is sigma, the y-axis is either delta1 or delta2. I connected both scatterplots. To seperate them, one curves is a line with circles, the other curve is a line with squares on it. I want to make a notation either on the y-axis or on the graph. The notiaion is delta1--square; delta2--circle. So when people look at the graph, they can easily tell each curve's meaning. The curve with squares on it means the sigma vs. delta1, and the curve with circles on it means sigma vs. delta2. I think I can use 'expression' to write delta1, delta2 and sigma in greek letters, but I am not sure how to denote the square and cirle I graphed. __ 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] Hmisc and Lattice question on gridlines
On Fri, Nov 20, 2009 at 7:47 AM, Joe King j...@joepking.com wrote:
I have been using lattice xyplot and am quite pleased, and I can use the
type=c(b,g) to have it print gridlines into the page, yet if I want to
have a line plot with points on it, how do I get the xYplot to print
gridlines (I use Hmisc xYplot because of its bands method which allows
plotting of confidence intervals). Any suggestions? I have looked at the
panel functions but when I try it I get the gridlines but my data is gone.
So a simple example is below. I want to create the reference lines in the
lattice plot in the xYplot from Hmisc so I can keep the confidence intervals
filled.
x-seq(1,10,1)
y-seq(1,10,1)
ci-y*.10
ciupper-y+ci
cilower-y-ci
xyplot(y~x, type=c(b,g),plot.points = TRUE)#using lattice
xYplot(Cbind(y,cilower,ciupper)~x,col.fill=grey,plot.points =
TRUE,type=c(b),method=filled bands)#using Hmisc
As ?panel.xyplot tells you, type=g is just a shortcut that calls
panel.grid(), so you get the equivalent effect with
xYplot(Cbind(y,cilower,ciupper)~x,col.fill=grey,plot.points = TRUE,
type=b,method=filled bands,
panel = function(...) {
panel.grid(h = -1, v = -1)
panel.xYplot(...)
})
-Deepayan
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[R] different results across versions for glmer/lmer with the quasi-poisson or quasi-binomial families: the lattest version might not be accurate...
Dear R-helpers, this mail is intended to mention a rather trange result and generate potential useful comments on it. I am not aware of another posts on this issue ( RSiteSearch(quasipoisson lmer version dispersion)). MUsing the exemple in the reference of the lmer function (in lme4 library) and turning it into a quasi-poisson or quasi-binomial analysis, we get different results, especially for the dispersion parameter (section 1 in the following; cf. bold passages in the following). For the quasi-poisson, we found even stronger differences with another, bigger database on which we worked (residual variance from approx. 0.7 to 1.2). We also tested the differences between versions for plain likelihood families (poisson and binomial): the differences were slighter, and were actually very small in the case of the poisson family. My first reaction was that the later version should have been better. However, the quasibinomial results of this version are rather strange. Therefore, I simulated a bigger data set corresponding to Poisson and binomial mixed models (section 2 in the following). I actually found out that the later version of lme4 was suspect but not the old one. My temptative conclusion is therefore to use the old versions of lme4 (here: lme4 version 0.99875-9) when using quasi-binomial and quasi-poisson methods. Any comment/insight appreciated. All the best, Frédéric Gosselin Engineer Researcher (PhD) in Forest Ecology Cemagref Domaine des Barres F-45290 Nogent sur Vernisson France ### 1- EXAMPLE FROM LMER HELP # here are the commands for the quasipoisson: library(lme4) gm1 - lmer(incidence ~ period + (1 | herd), family = quasipoisson, data = cbpp) summary(gm1) ## here is the result under R2.5.1 and Package lme4 version 0.99875-9: Generalized linear mixed model fit using Laplace Formula: incidence ~ period + (1 | herd) Data: cbpp Family: quasipoisson(log link) AIC BIC logLik deviance 112.2 122.3 -51.11102.2 Random effects: Groups NameVariance Std.Dev. herd (Intercept) 0.35085 0.59233 Residual 1.40470 1.18520 number of obs: 56, groups: herd, 15 Fixed effects: Estimate Std. Error t value (Intercept) 1.2812 0.2200 5.824 period2 -1.1240 0.3315 -3.391 period3 -1.3203 0.3579 -3.689 period4 -1.9477 0.4808 -4.051 Correlation of Fixed Effects: (Intr) perid2 perid3 period2 -0.339 period3 -0.314 0.219 period4 -0.233 0.163 0.151 # here is the result on R2.7.1 and Package lme4 version 0.999375-26 Generalized linear mixed model fit by the Laplace approximation Formula: incidence ~ period + (1 | herd) Data: cbpp AIC BIC logLik deviance 114.2 126.4 -51.1102.2 Random effects: Groups NameVariance Std.Dev. herd (Intercept) 0.32421 0.56939 Residual 1.29474 1.13786 Number of obs: 56, groups: herd, 15 Fixed effects: Estimate Std. Error t value (Intercept) 1.2762 0.2115 6.035 period2 -1.1249 0.3187 -3.530 period3 -1.3190 0.3438 -3.837 period4 -1.9450 0.4615 -4.215 Correlation of Fixed Effects: (Intr) perid2 perid3 period2 -0.339 period3 -0.314 0.219 period4 -0.233 0.163 0.151 # now the commands for the quasibinomial: library(lme4) toto-as.double(cbpp$incidence0) gm2 - lmer(toto ~ period + (1 | herd), family = quasibinomial, data = cbpp) summary(gm2) ## here is the result under R2.5.1 and Package lme4 version 0.99875-9: Generalized linear mixed model fit using Laplace Formula: toto ~ period + (1 | herd) Data: cbpp Family: quasibinomial(logit link) AIC BIC logLik deviance 72.04 82.17 -31.0262.04 Random effects: Groups NameVariance Std.Dev. herd (Intercept) 5.0259e-10 2.2418e-05 Residual 1.0052e+00 1.0026e+00 number of obs: 56, groups: herd, 15 Fixed effects: Estimate Std. Error t value (Intercept)2.662 1.048 2.540 period2 -2.078 1.188 -1.750 period3 -2.950 1.180 -2.501 period4 -3.135 1.194 -2.626 Correlation of Fixed Effects: (Intr) perid2 perid3 period2 -0.882 period3 -0.888 0.784 period4 -0.878 0.775 0.780 # here is the result on R2.7.1 and Package lme4 version 0.999375-26 Generalized linear mixed model fit by the Laplace approximation Formula: toto ~ period + (1 | herd) Data: cbpp AIC BIC logLik deviance 74.04 86.2 -31.0262.04 Random effects: Groups NameVariance Std.Dev. herd (Intercept) 0.0 0.0 Residual 0.13522 0.36772 Number of obs: 56, groups: herd, 15 Fixed effects: Estimate Std. Error t value (Intercept) 2.6391 0.3806 6.933 period2 -2.0513 0.4324 -4.744 period3 -2.9267 0.4293 -6.817 period4 -3.1091
Re: [R] Problem with sqlSave
On Thu, 19 Nov 2009 04:07:52 -0800 (PST) anna_l lippelanna21 @hotmail.com wrote: Hello, the sqlSave function is used in order to write a dataframe on excel. This function creates worksheets using the attribute tablename and writes the data.frame in it. What I want to do is to create this data.frame but being able in case this worksheet already exists to delete the former datas and write the new ones in it. I used the safer and append attributes. When you set safer to false, from what I understood, it should delete the former datas. Then what I did is setting safer as false and append as true so it can append to the empty dataframe the new dataframe but it didn?t work. Your question doesn't make sense. If you want to delete the older data, you should *not* use append = TRUE, since that is used only in the case that you want to append the new data to the old date. Since you *don't* want to retain the old data, why do you set append = TRUE? -- Karl Ove Hufthammer __ 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] Splitting massive output into multiple text files
try:
capture.output(fit5, file=paste(testperm, i, .txt, sep=), append=T)
Bart
A Singh wrote:
Dear List,
I thought it would be much easier to put a second query into a second
mail.
I need to print 426*1 blocks of variance components data, where 426 is
the number of columns of data that have 1 permutations of variance
generated for each of them.
I have tried printing out a smaller number of permutations for a smaller
number of markers and that has worked.
However, since a text file will not handle 4 million blocks in a single
file (which is what I ultimately need to do), is there a way to tell R to
create a new file for every 10 or so columns?
I tried to use some suggested code that looked like:
for (j in 1:426)
{
write(cbind(modeldf[,j:(j+9)]),file=as.character(j))
j - j+10
}
..but can't figure out how to put it into my own code and make it work.
I did find one example of code for split files, each successive file being
labeled as a series of numbers, but I couldn't figure out how to even
adapt
that to my model.
I cannot figure out what other way there is to conveniently view 4 m.
items
of data without losing some of it somewhere..
Any help will be much much appreciated..
Aditi
--
Code for shorter sample file:
model-read.table(...)
modeldf-data.frame(model)
modeldf[2:13-lapply(modeldf[2:13],factor)
colms-(modeldf)[4:13] ## 10 markers only in this file
se-c(1:1000)
for(f in colms)
{
print(Marker)
{
for( i in 1:1000)
{
print(perm no.)
print(se[i])
{
peg.no.prm-sample(peg.no, length(peg.no))
try(fit5-lmer(data=modeldf, peg.no.prm~1 + (1|family/f)))
print(summary(fit5))
capture.output(fit5, file=testperm5.txt, append=T)
}}}
}
The data files are at:
http://www.4shared.com/file/131980362/460bdafe/Testvcomp10.ht
ml (excel)
http://www.4shared.com/file/131980512/dc7308b/Testvcomp10.html
(txt)
--
--
A Singh
aditi.si...@bristol.ac.uk
School of Biological Sciences
University of Bristol
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Re: [R] advice about R for windows speed
I can only speak for the Windows part, but isn't it possible to test on Windows 7 64bit? (you can download a test version, and use a dual boot setup to try) I always heard about the difficulties with WinXP 64bit, so maybe that is just the problem? Another thing to find out: maybe you can take advantage of the 4 processors of your quadcore by using snow or similar? Bart Carlos Hernandez-7 wrote: Thanks for your reply! I just added some more details below. Our code needs around 1GB of RAM and all machines and R configurations have its default maximum above this number. Our suspicion is that the windows server could run the code in half of its current time (given the apparent factor of 2 between windows and other OS timing). There may be something very important either in the R configuration or in our code that we should take care of? I appreciate a lot any further advice or hints, specially about speeding up the code in the windows xp server with QuadCore Xeon processors. Best regards, Carlos **Server running WinXP 64bit (R 2.10.0 32bit , QuadCore Xeon 2.6GHz 8G Ram) Time per 25 Iterations 6.17 **Dell Latitude running Linux 32bit (R 2.9.2, Intel Core 2 Duo P9500 @ 2.53GHz, 4GB ram) Time per 25 iterations 2.88 **Dell Latitude running Win Vista 32bit (R 2.10.0, Intel Core 2 Duo P9500 @ 2.53GHz, 4GB ram) with New DLL in terminal Time per 25 iterations 5.53 --- **Macbook pro running Snow Leopard (R 2.10.0, 2.16GHz Intel Core 2 Duo 2GB ram) Time per 25 Iterations 4.58 (both R 2.10.0 32bit and 64bit produce almost identical timings) **Macbook pro running WinXp natively (R 2.10.0 32bit, 2.16GHz Intel Core 2 Duo 2GB ram) Time per 25 Iterations 8.23 note: for the Dell and MacBook Pro we replaced the Rblas.dll file of R for Windows with the file available here http://cran.r-project.org/bin/windows/contrib/ATLAS/C2D/ == On Thu, Nov 19, 2009 at 5:06 PM, Marc Schwartz marc_schwa...@me.com wrote: On Nov 19, 2009, at 9:25 AM, Carlos Hernandez wrote: Dear All, I appreciate any advice or hints you could provide about the following. We are running R code in a server (running Windows XP and QuadCore Xeon processors, see details below) and we would like to use the server efficiently. Our code takes a bit more than 6 seconds per 25 iterations in the server using a default R 2.10.0 installation. We tested our code in two other computers, a Dell Latitute and a MacBook Pro, and from the details that i include below you will notice that the code needs almost twice the time when we used R for Windows compared against the time the code needs when we use Linux or MacOSX 10.6.2 in each of these computers. I'm sorry I don't provide details on the code we are using. The code consists of all sort of operations (matrix inverses, random number generation, vectorized functions, a few loops, and so on). I hope I can get some advice from you despite the lack of specific code details. Is there any important R feature we should configure manually in the windows server to speed the code up? Is there an optimized BLAS available somewhere for this type of machine? Is these something else apart of an optimized BLAS that we could do to improve the timing? Best regards, Carlos **Server running WinXP (QuadCore Xeon 2.6GHz 8G Ram) Time per 25 Iterations 6.17 **Dell Latitude running Linux (R 2.9.2, Intel Core 2 Duo P9500 @ 2.53GHz, 4GB ram) Time per 25 iterations 2.88 **Dell Latitude running Win Vista (R 2.10.0, Intel Core 2 Duo P9500 @ 2.53GHz, 4GB ram) with New DLL in terminal Time per 25 iterations 5.53 --- **Macbook pro (2.16GHz Intel Core 2 Duo 2GB ram) Time per 25 Iterations 4.58 **Macbook pro running WinXp (2.16GHz Intel Core 2 Duo 2GB ram) Time per 25 Iterations 8.23 note: for the Dell and MacBook Pro we replaced the Rblas.dll file of R for Windows with the file available here http://cran.r-project.org/bin/windows/contrib/ATLAS/C2D/ Are you running 32 bit R on each platform or are you using 64 bit R on Linux and OSX? On the Dell, you are running two different versions of R and you don't indicate the R versions on the MacBook. The RAM configuration on each computer is different, which will impact the timings to some extent, depending upon how much RAM you may require for your R code, given other processes that are running and before any disk swapping kicks in. You might want to review R Windows FAQ 2.9, if you have not already: http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021 For Windows on the MacBook, are you using Boot Camp to run Windows natively or are you using virtualization (eg. Parallels, VMWare, VirtualBox) to run Windows under OSX? If the latter, some of the time increase will be due to the virtualization overhead. You should be using
Re: [R] 2 functions in xyplot
RICHARD M. HEIBERGER wrote:
Unexpected symbol often means missing punctuation.
In this case, it looks like
panel=function(){panel.xyplot(Kalibrierung$Spannung,Kalibrierung
$Magnetfeld)panel.abline(reg=test)}
this argument is missing a semi-colon ; before panel.abline.
panel=function(){panel.xyplot(Kalibrierung$Spannung,Kalibrierung
$Magnetfeld); panel.abline(reg=test)}
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in addition to Richard:
I would try to write out the function over multiple lines:
panel=function(){
panel.xyplot(Kalibrierung$Spannung,Kalibrierung$Magnetfeld)
panel.abline(reg=test)}
solven the problem you had, as would the semicolon, but in my opinion it
make the command more readable. You can also use '...' in the panel
function:
panel=function(...){
panel.xyplot(...)
panel.abline(reg=test)}
I like this because I don't have think about what to pass on to
panel.xyplot.
hope this helps,
Paul
--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: +3130 274 3113 Mon-Tue
Phone: +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul
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[R] Classification
Hi all, I have got a dataset like the following: 3 5 7 3 9 7 i.e. random numbers with some repeats. I want R to classify them for me. E.g. every row that has a value of 3 will be asigned a value of 1, and every row that has a value will be asigned a value of 2 etc. I want R to return the following, using the example above: 1 2 3 1 4 3 Thanks in advance. Chris -- View this message in context: http://old.nabble.com/Classification-tp26429330p26429330.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] DBFIsRecordDeleted() in read.dbf?
Dear Nicholas Lewin-Koh and Roger Bivand or Frank Warmerdam, I am using read.dbf from the foreign package within my package vegdata. Unfortunately if you delete some data in the primary program the data in the dbase file is not deleted but the line only gets a flag IsDeleted. read.dbf ignores this information but the shapelib C code (http://shapelib.maptools.org/.) provides this information as far as I understood (DBFIsRecordDeleted()). Would it be possible to respect this information during import using read.dbf? All the best, Florian Jansen -- Dr. Florian Jansen Geobotany Nature Conservation Institute of Botany and Landscape Ecology Ernst-Moritz-Arndt-University Grimmer Str. 88 17487 Greifswald Germany +49 (0)3834 86 4147 http://www.botanik.uni-greifswald.de/jansen.html __ 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] Bessel function with large index value
I am looking for a method of dealing with the modified Bessel function K_\nu(x) for large \nu. The besselK function implementation of this allows for dealing with large values of x by allowing for exponential scaling, but there is no facility for dealing with large \nu. What would work for me would be an lbesselK function in the manner of lgamma which returned the log of K_\nu(x) for large \nu. Does anybody have any leads on this? Note that I have trawled through Abramowitz and Stegun and found 9.7.8 which doesn't work for me because of the complication in the definition of the x argument. I have also seen a result of Ismail (1977) reported by Barndorff-Nielsen and Blaesild which has the other problem, the treatment of the x argument is too simple. To do the calculation I am attempting, I need to have the Bessel function in a form that will allow a cancellation with a Gamma function of high order in the denominator. David Scott -- _ David Scott Department of Statistics The University of Auckland, PB 92019 Auckland 1142,NEW ZEALAND Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055 Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018 Director of Consulting, Department of Statistics __ 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] Classification
Hello, x - c(3,5,7,3,9,7) as.numeric(as.factor(x)) [1] 1 2 3 1 4 3 regards, stefan On Fri, Nov 20, 2009 at 12:02:59AM -0800, Chris Li wrote: Hi all, I have got a dataset like the following: 3 5 7 3 9 7 i.e. random numbers with some repeats. I want R to classify them for me. E.g. every row that has a value of 3 will be asigned a value of 1, and every row that has a value will be asigned a value of 2 etc. I want R to return the following, using the example above: 1 2 3 1 4 3 Thanks in advance. Chris -- View this message in context: http://old.nabble.com/Classification-tp26429330p26429330.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] boxplot question
Hi there, I was wondering if anybody can explain to me why the boxplot ends up with different results in the following case: I have some integer data as a vector and I compare the stats of boxplot with the same data divided by a factor. I've attached a csv file with both data present (d1, d2). The factor is 34.16667. If I run the boxplot function on d1 I get the following stats: 0.848... 0.907... 0.936... 0.965... 1.024... For d2 I get these stats: 29 31 32 33 36 If I convert the stats of d1 with the factor, I get 29 31 32 33 35 Obviously different for the upper whisker. But why??? Antje ,d1,d2 1,0.936585365853659,32 2,0.936585365853659,32 3,0.936585365853659,32 4,0.936585365853659,32 5,0.907317073170732,31 6,1.08292682926829,37 7,1.08292682926829,37 8,1.02439024390244,35 9,1.08292682926829,37 10,1.05365853658537,36 11,0.936585365853659,32 12,1.08292682926829,37 13,0.936585365853659,32 14,0.907317073170732,31 15,0.936585365853659,32 16,0.907317073170732,31 17,1.02439024390244,35 18,0.878048780487805,30 19,1.08292682926829,37 20,1.02439024390244,35 21,0.936585365853659,32 22,0.936585365853659,32 23,1.08292682926829,37 24,1.02439024390244,35 25,1.05365853658537,36 26,1.02439024390244,35 27,0.936585365853659,32 28,1.11219512195122,38 29,0.878048780487805,30 30,1.02439024390244,35 31,0.995121951219512,34 32,1.11219512195122,38 33,0.936585365853659,32 34,0.995121951219512,34 35,0.936585365853659,32 36,1.02439024390244,35 37,0.965853658536585,33 38,0.965853658536585,33 39,0.995121951219512,34 40,0.848780487804878,29 41,0.907317073170732,31 42,0.907317073170732,31 43,0.907317073170732,31 44,1.05365853658537,36 45,0.878048780487805,30 46,0.878048780487805,30 47,0.878048780487805,30 48,0.936585365853659,32 49,0.936585365853659,32 50,0.878048780487805,30 51,0.936585365853659,32 52,1.05365853658537,36 53,0.878048780487805,30 54,1.17073170731707,40 55,0.907317073170732,31 56,0.995121951219512,34 57,0.907317073170732,31 58,0.907317073170732,31 59,0.936585365853659,32 60,0.965853658536585,33 61,0.965853658536585,33 62,0.936585365853659,32 63,0.936585365853659,32 64,0.878048780487805,30 65,0.907317073170732,31 66,1.08292682926829,37 67,0.907317073170732,31 68,0.848780487804878,29 69,0.907317073170732,31 70,0.965853658536585,33 71,0.936585365853659,32 72,0.936585365853659,32 73,1.08292682926829,37 74,0.936585365853659,32 75,0.936585365853659,32 76,1.11219512195122,38 77,0.878048780487805,30 78,0.965853658536585,33 79,0.907317073170732,31 80,0.936585365853659,32 81,0.907317073170732,31 82,0.878048780487805,30 83,0.936585365853659,32 84,0.965853658536585,33 85,0.907317073170732,31 86,1.02439024390244,35 87,0.995121951219512,34 88,0.965853658536585,33 89,0.936585365853659,32 90,0.936585365853659,32 91,1.11219512195122,38 92,0.907317073170732,31 93,0.907317073170732,31 94,0.936585365853659,32 95,0.907317073170732,31 96,0.907317073170732,31 97,0.936585365853659,32 98,0.936585365853659,32 99,0.936585365853659,32 100,0.907317073170732,31 101,0.907317073170732,31 102,0.848780487804878,29 103,0.907317073170732,31 104,0.965853658536585,33 105,0.936585365853659,32 106,0.907317073170732,31 107,0.878048780487805,30 108,1.02439024390244,35 109,0.907317073170732,31 110,1.11219512195122,38 111,1.02439024390244,35 112,0.907317073170732,31 113,0.936585365853659,32 114,0.878048780487805,30 115,0.907317073170732,31 116,0.936585365853659,32 117,0.936585365853659,32 118,1.05365853658537,36 119,0.907317073170732,31 120,0.878048780487805,30 121,0.936585365853659,32 122,1.02439024390244,35 123,0.965853658536585,33 124,0.965853658536585,33 125,0.936585365853659,32 126,0.936585365853659,32 127,0.936585365853659,32 128,0.907317073170732,31 129,0.907317073170732,31 130,0.878048780487805,30 131,0.936585365853659,32 132,1.02439024390244,35 133,0.936585365853659,32 134,0.936585365853659,32 135,0.995121951219512,34 136,0.965853658536585,33 137,0.965853658536585,33 138,0.907317073170732,31 139,0.936585365853659,32 140,0.936585365853659,32 141,0.878048780487805,30 142,0.907317073170732,31 143,0.965853658536585,33 144,0.936585365853659,32 145,0.936585365853659,32 146,0.995121951219512,34 147,1.02439024390244,35 148,1.08292682926829,37 149,0.878048780487805,30 150,0.936585365853659,32 151,0.848780487804878,29 152,0.907317073170732,31 153,0.907317073170732,31 154,0.907317073170732,31 155,0.965853658536585,33 156,1.02439024390244,35 157,0.995121951219512,34 158,0.995121951219512,34 159,0.936585365853659,32 160,1.08292682926829,37 161,0.907317073170732,31 162,0.907317073170732,31 163,0.936585365853659,32 164,0.907317073170732,31 165,0.907317073170732,31 166,0.907317073170732,31 167,0.907317073170732,31 168,1.05365853658537,36 169,1.05365853658537,36 170,0.936585365853659,32 171,0.965853658536585,33 172,0.965853658536585,33 173,0.936585365853659,32 174,0.907317073170732,31 175,0.878048780487805,30 176,0.995121951219512,34 177,0.936585365853659,32 178,0.936585365853659,32 179,0.907317073170732,31 180,1.08292682926829,37
[R] barchart problem was: Re: how to specify the order of panels with xyplot
Thank you, that works perfectly and is more elegant - I'm sorry not to
have included complete code/data.
I have another question that I have been having problems with recently,
described by this code:
reads-as.data.frame(cbind(c(1:25),rnorm(25),rnorm(25),rnorm(25),rnorm(25)))
names(reads)-c('id','u','a','b','m')
barchart(cbind(as.vector(reads$u),as.vector(reads$m)),horizontal=FALSE,groups=FALSE,layout=c(1,2))
This is undoubtedly the worst way to do this, and doesn't give me
exactly what I want, though is close: what is desired is the categories
being described by reads$id and the strips holding 'u' or 'm'. I know
this is a result of decontextualising the data as I have.
I have tried to make a data frame that matches the example for barchart
in the help for lattice.
Trying to match the barley data frame:
reads-as.data.frame(rbind(cbind(reads$id,reads$u,'u'),cbind(reads$id,reads$m,'m')))
names(reads)-c('id','freq','type')
barchart(freq ~ id | type, data =
reads,horizontal=FALSE,groups=FALSE,layout=c(1,2))
Does not give anything that is analogous to the naive chart above. Can
you point to where I am going wrong (I have also tried barchart(freq |
type, data = reads,...), but this gives an error)? It looks like the
previously numeric values are being treated as non-numeric on the basis
of the sorting of the categories, but changing this:
reads$id-as.numeric(reads$id)
reads$freq-as.double(reads$freq)
does not fix the problem (except for the categories' order). In fact I'm
not sure how the plot looks the way it does at all from this (the values
of read$freq are completely changed by this cast!).
thanks for your help
Dan
On Fri, 2009-11-20 at 13:53 +0530, Deepayan Sarkar wrote:
Your example is not reproducible, so it's hard to suggest
alternatives. But it seems that your original 'chromosomes' data frame
has things in the right order, so a simple fix would be
chromosomes$name - with(chromosomes, factor(name, levels = name))
-Deepayan
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Re: [R] Classification
On Fri, 20 Nov 2009 10:43:19 +0100 smu m...@z107.de wrote: x - c(3,5,7,3,9,7) as.numeric(as.factor(x)) [1] 1 2 3 1 4 3 While that is my preferred solution too, this may be easier to understand: match(x,sort(unique(x))) (It is basically what 'factor' does.) The question wasn't quite clear, though. Should the first occuring number get the category 1, or should the *lowest* number get this category. I.e., what should be the result of x - c(5,3,7,3,9,7) Should it be 1, 2, 3, 2, 4, 3 or 2, 1, 3, 1, 4, 3? The factor and match methods above give the second solution. To get the first solution, just remove the 'sort': match(x,unique(x)) -- Karl Ove Hufthammer __ 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] problem selecting 330 to 30 longitude
Hello, This is probably very simple but I am trying to select a region from the OIv2 SST dataset that crosses 0 longitude. The longitude variable is arranged from 0 to 360 and I get an error message when trying to go from 330 to 30 for example. The data are from a NOAA netCDF file. *temp = open.ncdf(c:/documents and settings/theoni/desktop/sstoi_v2.nc) print(temp) y1 = get.var.ncdf( temp, latitude) x1 = get.var.ncdf( temp, longitude) t1 = get.var.ncdf( temp, time) z1 = get.var.ncdf( temp, sst) sst = get.var.ncdf( temp, sst, start=c(330,136,313), count=c(56,44,1))* Error message I get is: *Error in get.var.ncdf(temp, sst, start = c(330, 136, 313), count = c(56, : C function R_nc_get_vara_double returned error* I couldn't seem to find any info on this in the help archives but am a new user so apologies if it has been addressed elsewhere. Many thanks, Nora -- Nora Hanson Sea Mammal Research Unit Scottish Oceans Institute University of St. Andrews St. Andrews Fife KY16 8LB Scotland n...@st-andrews.ac.uk tel: 0044 (0)1334 463485 The University of St Andrews is a charity registered in Scotland : No SC013532 [[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] Spatstat, markcorr, max. radius limited??
Hello, could please somebody help me. I want to apply the mark correlation function but for radii up to 75 meters (in 75 individual 1m steps). Unfortunately, There is a sensible default for the values of the argument r at which the mark correlation function kf (r) should be evaluated, so that I do not get results for r 25m. Can I change something in the function to get the required values as written above? Thanks, Rudi -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! __ 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 from sources (ubuntu and x11)
On Thu, Nov 19, 2009 at 11:34:22PM -0600, stephen sefick wrote: am using ubuntu 9.10 and I am getting and x11 lib/headers not found. I have installed libx11-dev. I thought this would solve the problem, but it is not. Any help would be appreciated. Looking at output of the configure script you should be able to know what specific file is missing. Then you can Search the contents of packages at http://packages.ubuntu.com/ to know what package contains the missing file. __ 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] What happen for Negative binomial link in Lmer fonction?
Dear R users, As I have no answer to my las reply i try again. If the binomal negative link has never been implemented in the lmer fonction, and as it was working when I did it some months ago, What kind of result did I get? This is the exemple of the answer of R when i was using lmer with negative binomal family: m1a-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method=Laplace,data=manu) summary(m1a) Generalized linear mixed model fit using Laplace Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) Data: manu Family: Negative Binomial(log link) AIC BIC logLik deviance 125.1 147.6 -54.57109.1 Thank you for your answers, Best Regards Emmanuelle E. Robardet wrote: Thank you for your answers, I have an exemple of that i was using: m1a-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method=Laplace,data=manu) summary(m1a) Generalized linear mixed model fit using Laplace Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) Data: manu Family: Negative Binomial(log link) AIC BIC logLik deviance 125.1 147.6 -54.57109.1 I think It was the version lme4 0.9975-10. Unfortunately, I have this version no more available on my computer.. I wonder if this old results are still valid.. Ben Bolker wrote: ROBARDET Emmanuelle wrote: Dear R users, I'm performing some GLMMs analysis with a negative binomial link. I already performed such analysis some months ago with the lmer() function but when I tried it today I encountered this problem: Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative Binomial' Does anyone know if the negative binomial family has been removed from this function? I really appreciate any response. Emmanuelle I would be extremely surprised if this worked in the past; to the best of my knowledge the negative binomial family has never been implemented in lmer. One could in principle do a glmmPQL fit with the negative binomial family (with a fixed value of the overdispersion parameter). glmmADMB is another option. Can you say which version etc. you were using??? Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org -- View this message in context: http://old.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26439076.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] find data (date) gaps in time series
Dear R users, I have a time series of precipitation data. The time series comprises ~ 20 years and it is supposed to be constant (one value per day), but due to some failure of the measuring device some days or periods are missing. I would like to find these missing days or periods just to get a first idea about the reliability of the measurements. The only function I could find was is.constant(), but of course I only get a true or false statement instead of the dates missing. Google searches and a look at the R help mailing did not reveal an answer. Please find attached a few dates of the time series with missing values from February to April. I would like R to detect those missing dates. Any hints or solutions are highly appreciated. Regards, Stefan Strohmeier 2916 2002-02-17 0.0 2917 2002-02-18 0.3 2918 2002-02-19 3.8 2919 2002-02-20 43.6 2920 2002-02-21 1.0 2921 2002-02-22 5.6 2922 2002-02-23 10.6 2923 2002-02-24 2.8 2924 2002-02-25 19.1 2925 2002-02-26 20.5 2926 2002-03-06 0.0 2927 2002-05-06 0.0 2928 2002-05-07 0.0 2929 2002-05-08 0.0 2930 2002-05-09 0.0 __ 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] Compatibility of AIC values calculated with different link functions?
In a binomial regression analysis I have used the AIC value as a guide for which link function (logit or probit) provides the best fit to my data, but one of the reviewers have questioned this approach. Is AIC values calculated with different link functions within the binomial function in GLM comparable or can AIC values only be used to compare models with the same link? I believe my approach is valid if GLM can be expected to find the true global ML estimate but I do not know if any approximations in the GLM function change this. Kind regards, Søren __ 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 2.10 'memory leak'? on OS X
On 20/11/2009 12:33 AM, Stropharia wrote: Dear R users, I am running R 2.10.0 on OS X 10.5.8. I had been running 2.10 successfully for about a week (and have used previous R versions for 2+ years on the same computer) until 2 days ago it failed to start up for me. Now when I try to start R, the application tries to initiate for several minutes then crashes. Looking at the activity monitor, my memory usage goes from having about 1.6Gb free (out of 2Gb) to 7Mb in the first 10-15 seconds of attempting to start the program. At this point I either have to force quit R (as everything starts to freeze up) or wait several minutes for it to crash. I have erased the application and reinstalled it 4 times now - with exactly the same result. I looked around in the Library and System folders to see if any other files needed to be removed, but couldn't find any. I have also restarted the computer and repaired permissions multiple times - and then reinstalled R, with no luck. The exact same thing happens if I start R64. I did not updated OS X or R, or install any other programs, just prior to this first happening and am at a loss to explain what's going on. I have copied the first part of one of the crash logs below. Does anyone have any ideas for to remedy this? It sounds like one of your user-specific startup files is causing the problem, e.g. .RData, or .Rprofile. Did you try starting R with option --vanilla? That will skip them. Duncan Murdoch best, Steve # Crash log Process: R [231] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: R 2.10.0 GUI 1.30 Leopard build 32-bit (5511) Code Type: X86 (Native) Parent Process: launchd [101] Date/Time: 2009-11-18 23:15:45.570 -0500 OS Version: Mac OS X 10.5.8 (9L31a) Report Version: 6 Anonymous UUID: D86CDCBC-00FD-4AEE-AB50-2EFE0DAE9E1E Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x00067ee2 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0x07c7 __memcpy + 39 (cpu_capabilities.h:246) 1 com.apple.CoreFoundation 0x96a6a0b4 __CFStringEncodeByteStream + 4052 2 com.apple.Foundation 0x94446eb7 -[NSString(NSStringOtherEncodings) getBytes:maxLength:usedLength:encoding:options:range:remainingRange:] + 295 3 com.apple.Foundation 0x94446a1a _NSNewStringByAppendingStrings + 538 4 com.apple.Foundation 0x94446760 -[NSString stringByAppendingString:] + 192 5 org.R-project.R 0x9ce8 -[RController doLoadHistory:] + 808 6 org.R-project.R 0x76df -[RController awakeFromNib] + 2319 7 com.apple.CoreFoundation 0x96ac07f5 -[NSSet makeObjectsPerformSelector:] + 181 8 com.apple.AppKit 0x92efed8e -[NSIBObjectData nibInstantiateWithOwner:topLevelObjects:] + 1533 9 com.apple.AppKit 0x92ef4fba loadNib + 264 10 com.apple.AppKit 0x92ef491c +[NSBundle(NSNibLoading) _loadNibFile:nameTable:withZone:ownerBundle:] + 946 11 com.apple.AppKit 0x92ef455f +[NSBundle(NSNibLoading) loadNibFile:externalNameTable:withZone:] + 171 12 com.apple.AppKit 0x92ef449d +[NSBundle(NSNibLoading) loadNibNamed:owner:] + 391 13 org.R-project.R 0x2538 main + 296 14 org.R-project.R 0x23d6 start + 54 #-- __ 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] Problem with Numerical derivatives (numDeriv) and mvtnorm
I'm trying to obtain numerical derivative of a probability computed
with mvtnorm with respect to its parameters using grad() and
jacobian() from NumDeriv.
To simplify the matter, here is an example:
PP1 - function(p){
thetac - p
thetae - 0.323340333
thetab - -0.280970036
thetao - 0.770768082
ssigma - diag(4)
ssigma[1,2] - 0.229502120
ssigma[1,3] - 0.677949335
ssigma[1,4] - 0.552907745
ssigma[2,3] - 0.784263100
ssigma[2,4] - 0.374065025
ssigma[3,4] - 0.799238700
ssigma[2,1] - ssigma[1,2]
ssigma[3,1] - ssigma[1,3]
ssigma[4,1] - ssigma[1,4]
ssigma[3,2] - ssigma[2,3]
ssigma[4,2] - ssigma[2,4]
ssigma[4,3] - ssigma[3,4]
pp1 -
pmvnorm(lower=c(-Inf,-Inf,-Inf,-Inf),upper=c(thetac,thetae,thetab,thetao),corr=ssigma)
return(pp1)}
xx - -0.6675762
If I compute several times the probability PP1, i obtain some slightly
different numbers but I suppose this is ok:
PP1(xx)
[1] 0.1697787
attr(,error)
[1] 0.000840748
attr(,msg)
[1] Normal Completion
PP1(xx)
[1] 0.1697337
attr(,error)
[1] 0.0009363715
attr(,msg)
[1] Normal Completion
PP1(xx)
[1] 0.1691539
attr(,error)
[1] 0.0006682577
attr(,msg)
[1] Normal Completion
When I now turn to the numerical derivatives of the probability, I
obtain large discrepencies if I repeat the instruction grad:
grad(PP1,xx)
[1] -42.58016
grad(PP1,xx)
[1] 9.297055
grad(PP1,xx)
[1] -6.736725
grad(PP1,xx)
[1] -20.71176
grad(PP1,xx)
[1] 18.51968
The problem is the same if I turn to the jacobian function (when I
want to compute all partial derivatives in one shot)
Someone can help?
Stephane
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[R] HTML help missing?
Hey there, I'm running R 2.10 on Windows XP (Professional) and I was wondering where the HTML help window disappeared? With earlier versions everything was fine. Now I get only this old-fashioned text windows without any links when I type ?some_function Can anybody help me? Antje __ 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] Accessing list names in lapply
Yet another possibility is to iterate on both values and names simultaneously using mapply(): df1 - split( x=rnorm(n=100, sd=seq(from=1, to=10, each=10)), f=letters[seq(from=1, to=10, each=10)] ) mapply(function(x, y) plot(x, ylab=y), df1, names(df1)) Enrique -Original Message- Date: Thu, 19 Nov 2009 13:27:08 +0100 From: Bjarke Christensen bjarke.christen...@sydbank.dk Subject: [R] Accessing list names in lapply To: r-help@r-project.org Message-ID: of5533f0b9.99f78ab0-onc1257673.004273ae-c1257673.00446...@bdpnet.dk Content-Type: text/plain; charset=US-ASCII Hi, When using lapply (or sapply) to loop over a list, can I somehow access the index of the list from inside the function? A trivial example: df1 - split( x=rnorm(n=100, sd=seq(from=1, to=10, each=10)), f=letters[seq(from=1, to=10, each=10)] ) str(df1) #List of 10 # $ a: num [1:10] -0.801 0.418 1.451 -0.554 -0.578 ... # $ b: num [1:10] -2.464 0.279 4.099 -2.483 1.921 ... # $ c: num [1:10] -1.14 -1.773 2.512 -2.072 -0.904 ... # $ d: num [1:10] 2.109 1.243 0.627 -2.343 -6.071 ... #... par(mfcol=c(5,2)) lapply(df1, plot) This plots each element of the list, but the label on the vertical axis is X[[0L]] (as expected from the documentation in ?lapply). I'd like the heading for each plot to be the name of that item in the list. This can be achieved by using a for-loop: for (i in names(df1)) plot(df1[[i]], ylab=i) but can it somehow be achieved bu using lapply? I would be hoping for something like lapply(df1, function(x) plot(x, ylab=parent.index())) or some way to parse the index number out of the call, using match.call() or something like that. Thanks in advance for any comments, Bjarke Christensen __ 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] Problem with sqlSave
Hi Karl, I was setting append=true because safer would delete the former datas when set to false. I must not have understood the purpose of these two attributes right. To be honest I tried all possible combinations and none would work. I am doing all this now with RExcel as I have been advised and it worked very well. Thank you for trying to help. Karl Ove Hufthammer wrote: On Thu, 19 Nov 2009 04:07:52 -0800 (PST) anna_l lippelanna21 @hotmail.com wrote: Hello, the sqlSave function is used in order to write a dataframe on excel. This function creates worksheets using the attribute tablename and writes the data.frame in it. What I want to do is to create this data.frame but being able in case this worksheet already exists to delete the former datas and write the new ones in it. I used the safer and append attributes. When you set safer to false, from what I understood, it should delete the former datas. Then what I did is setting safer as false and append as true so it can append to the empty dataframe the new dataframe but it didn?t work. Your question doesn't make sense. If you want to delete the older data, you should *not* use append = TRUE, since that is used only in the case that you want to append the new data to the old date. Since you *don't* want to retain the old data, why do you set append = TRUE? -- Karl Ove Hufthammer __ 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. - Anna Lippel new in R so be careful I should be asking a lt of questions!:teeth: -- View this message in context: http://old.nabble.com/Problem-with-sqlSave-tp26421303p26441564.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] Compiling from sources (ubuntu and x11)
On 19 November 2009 at 23:34, stephen sefick wrote: | am using ubuntu 9.10 and I am getting and x11 lib/headers not found. | I have installed libx11-dev. I thought this would solve the problem, | but it is not. Any help would be appreciated. You can try 'sudo apt-get build-dep r-base' which will use the package info to get the required packages. You may need deb-src entries for that. Or look at the diff.gz on the mirrors to read the entry: Build-Depends: gcc (= 4:4.1.0), g++ (= 4:4.1.0), gfortran (= 4:4.1.0), libblas-dev, liblapack-dev (= 3.1.1), tcl8.5-dev, tk8.5-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (= 7.2.3), texi2html, texinfo (= 4.1-2), libbz2-dev, libpcre3-dev, xdg-utils, zlib1g-dev, libpng12-dev, libjpeg62-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff4-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, texinfo, texi2html, openjdk-6-jdk [!arm !hppa !kfreebsd-i386 !kfreebsd-amd64 !hurd-i386] so 'libx11-dev, libxt-dev, x11proto-core-dev' are what you need, but you probably also need the headers for devices etc. Or, as suggested, look at the configure output. Or read the 'R Adminstration' manual which details some of this too, and recommends the xorg-dev package on Debian (and Ubuntu should be close). Dirk -- Three out of two people have difficulties with fractions. __ 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] different results across versions for glmer/lmer wi th the quasi-poisson or quasi-binomial families: the lattest version might not be accurate...
Gosselin Frederic frederic.gosselin at cemagref.fr writes: Dear R-helpers, this mail is intended to mention a rather trange result and generate potential useful comments on it. I am not aware of another posts on this issue ( RSiteSearch(quasipoisson lmer version dispersion)). [snip snip] I would definitely forward this to r-sig-mixed-mod...@lists.r-project.org, if I were you. At one point I reported what may be the same bug; http://tinyurl.com/ye3pkve I don't know when it appeared and when it was fixed, so I don't know whether it explains your results or not. __ 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] can R scripts detect signals sent by the task scheduler ?
In general, is it possible to run R scripts through cron jobs ? Is it possible to make the script detect the system interrupt, save its current status and then exit so that next time it is rescheduled it can pick up from where it left ? Examples, if any, are more then welcome. Thank you in advance, Maura tutti i telefonini TIM! [[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] How to do X11 seasonal adjust in R?
Dear All£¬ How to do X-11 seasonal adjustment in R? Thanks£¡ [[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] Bessel function with large index value
This is a reply to my own question. I thought I had found an answer but it seems not so (some analysis follows below). Maybe Martin Maechler or Robin Hankin or Duncan Murdoch may have some ideas---I know the question is a bit specialized. David Scott wrote: I am looking for a method of dealing with the modified Bessel function K_\nu(x) for large \nu. The besselK function implementation of this allows for dealing with large values of x by allowing for exponential scaling, but there is no facility for dealing with large \nu. What would work for me would be an lbesselK function in the manner of lgamma which returned the log of K_\nu(x) for large \nu. Does anybody have any leads on this? Note that I have trawled through Abramowitz and Stegun and found 9.7.8 which doesn't work for me because of the complication in the definition of the x argument. I have also seen a result of Ismail (1977) reported by Barndorff-Nielsen and Blaesild which has the other problem, the treatment of the x argument is too simple. To do the calculation I am attempting, I need to have the Bessel function in a form that will allow a cancellation with a Gamma function of high order in the denominator. David Scott After posting I checked the GNU Scientific Library (http://www.gnu.org/software/gsl/) and found: — Function: double gsl_sf_bessel_lnKnu (double nu, double x) — Function: int gsl_sf_bessel_lnKnu_e (double nu, double x, gsl_sf_result * result) These routines compute the logarithm of the irregular modified Bessel function of fractional order \nu, \ln(K_\nu(x)) for x0, \nu0. I then recalled that Robin Hankin and Duncan Murdoch had made the GSL available. I installed the package gsl and investigated the function bessel_lnKnu. Unfortunately, it appears that this function has *smaller* range than besselK when it comes to the index. The following shows it: library(plyr) library(gsl) ### Check calculations using both methods lnKnu - maply(expand.grid(x = 100*(1:7), nu = 10*(1:100)), bessel_lnKnu) lnKnu Knu - maply(expand.grid(x = 100*(1:7), nu = 10*(1:100)), besselK) Knu lnKnu/log(Knu) I was expecting what happens with gamma and lgamma ### Compare gamma function lgam - lgamma(100*(1:7)) lgam gam - gamma(100*(1:7)) gam lgam/log(gam) It seems that bessel_lnKnu is set up to protect against infinity when x becomes small: ### Does lnKnu protect against Inf when x goes to zero? lnnear0 - maply(expand.grid(x = 0.0001*(1:10), nu = 10*(0:5)), bessel_lnKnu) lnnear0 near0 - maply(expand.grid(x = 0.0001*(1:10), nu = 10*(0:5)), besselK) near0 lnnear0/log(near0) So, I am still in need of a solution: an implementation of log of Bessel K which protects against the index nu becoming large. David Scott -- _ David Scott Department of Statistics The University of Auckland, PB 92019 Auckland 1142,NEW ZEALAND Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055 Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018 Director of Consulting, Department of Statistics __ 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] find data (date) gaps in time series
On Nov 20, 2009, at 6:26 AM, Stefan Strohmeier wrote: Dear R users, I have a time series of precipitation data. The time series comprises ~ 20 years and it is supposed to be constant (one value per day), but due to some failure of the measuring device some days or periods are missing. I would like to find these missing days or periods just to get a first idea about the reliability of the measurements. The only function I could find was is.constant(), but of course I only get a true or false statement instead of the dates missing. Google searches and a look at the R help mailing did not reveal an answer. Please find attached a few dates of the time series with missing values from February to April. I would like R to detect those missing dates. dtdta - read.table(textConnection(2916 2002-02-17 0.0 + 2917 2002-02-18 0.3 + 2918 2002-02-19 3.8 + 2919 2002-02-20 43.6 + 2920 2002-02-21 1.0 + 2921 2002-02-22 5.6 + 2922 2002-02-23 10.6 + 2923 2002-02-24 2.8 + 2924 2002-02-25 19.1 + 2925 2002-02-26 20.5 + 2926 2002-03-06 0.0 + 2927 2002-05-06 0.0 + 2928 2002-05-07 0.0 + 2929 2002-05-08 0.0 + 2930 2002-05-09 0.0) ) dtdta[dtdta$V3 == 0, ] V1 V2 V3 1 2916 2002-02-17 0 11 2926 2002-03-06 0 12 2927 2002-05-06 0 13 2928 2002-05-07 0 14 2929 2002-05-08 0 15 2930 2002-05-09 0 You seem to be using 0 as a missing marker. That's bad practice, but I suppose it's possble you cannot change how your instruments report. You should be using NA and the functions that support proper treatment of missingness. -- David Any hints or solutions are highly appreciated. Regards, Stefan Strohmeier 2916 2002-02-17 0.0 2917 2002-02-18 0.3 2918 2002-02-19 3.8 2919 2002-02-20 43.6 2920 2002-02-21 1.0 2921 2002-02-22 5.6 2922 2002-02-23 10.6 2923 2002-02-24 2.8 2924 2002-02-25 19.1 2925 2002-02-26 20.5 2926 2002-03-06 0.0 2927 2002-05-06 0.0 2928 2002-05-07 0.0 2929 2002-05-08 0.0 2930 2002-05-09 0.0 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list 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] Accessing list names in lapply
Yes, that is it. Or even simpler: mapply(plot, x=df1, ylab=names(df1), col=1:10, main=paste(Plot, names(df1))) Thank you! Bjarke Christensen Bengoechea Bartolomé Enrique (SIES 73) Til enrique.bengoech r-help@r-project.org e...@credit-suisse. cc com bjarke.christen...@sydbank.dk Emne 20-11-2009 13:19 RE: [R] Accessing list names in lapply Yet another possibility is to iterate on both values and names simultaneously using mapply(): df1 - split( x=rnorm(n=100, sd=seq(from=1, to=10, each=10)), f=letters[seq(from=1, to=10, each=10)] ) mapply(function(x, y) plot(x, ylab=y), df1, names(df1)) Enrique -Original Message- Date: Thu, 19 Nov 2009 13:27:08 +0100 From: Bjarke Christensen bjarke.christen...@sydbank.dk Subject: [R] Accessing list names in lapply To: r-help@r-project.org Message-ID: of5533f0b9.99f78ab0-onc1257673.004273ae-c1257673.00446...@bdpnet.dk Content-Type: text/plain; charset=US-ASCII Hi, When using lapply (or sapply) to loop over a list, can I somehow access the index of the list from inside the function? A trivial example: df1 - split( x=rnorm(n=100, sd=seq(from=1, to=10, each=10)), f=letters[seq(from=1, to=10, each=10)] ) str(df1) #List of 10 # $ a: num [1:10] -0.801 0.418 1.451 -0.554 -0.578 ... # $ b: num [1:10] -2.464 0.279 4.099 -2.483 1.921 ... # $ c: num [1:10] -1.14 -1.773 2.512 -2.072 -0.904 ... # $ d: num [1:10] 2.109 1.243 0.627 -2.343 -6.071 ... #... par(mfcol=c(5,2)) lapply(df1, plot) This plots each element of the list, but the label on the vertical axis is X[[0L]] (as expected from the documentation in ?lapply). I'd like the heading for each plot to be the name of that item in the list. This can be achieved by using a for-loop: for (i in names(df1)) plot(df1[[i]], ylab=i) but can it somehow be achieved bu using lapply? I would be hoping for something like lapply(df1, function(x) plot(x, ylab=parent.index())) or some way to parse the index number out of the call, using match.call() or something like that. Thanks in advance for any comments, Bjarke Christensen -- __ 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] find data (date) gaps in time series
On Nov 20, 2009, at 8:04 AM, David Winsemius wrote: On Nov 20, 2009, at 6:26 AM, Stefan Strohmeier wrote: Dear R users, I have a time series of precipitation data. The time series comprises ~ 20 years and it is supposed to be constant (one value per day), but due to some failure of the measuring device some days or periods are missing. I would like to find these missing days or periods just to get a first idea about the reliability of the measurements. The only function I could find was is.constant(), but of course I only get a true or false statement instead of the dates missing. Google searches and a look at the R help mailing did not reveal an answer. Please find attached a few dates of the time series with missing values from February to April. I would like R to detect those missing dates. dtdta - read.table(textConnection(2916 2002-02-17 0.0 + 2917 2002-02-18 0.3 + 2918 2002-02-19 3.8 + 2919 2002-02-20 43.6 + 2920 2002-02-21 1.0 + 2921 2002-02-22 5.6 + 2922 2002-02-23 10.6 + 2923 2002-02-24 2.8 + 2924 2002-02-25 19.1 + 2925 2002-02-26 20.5 + 2926 2002-03-06 0.0 + 2927 2002-05-06 0.0 + 2928 2002-05-07 0.0 + 2929 2002-05-08 0.0 + 2930 2002-05-09 0.0) ) dtdta[dtdta$V3 == 0, ] V1 V2 V3 1 2916 2002-02-17 0 11 2926 2002-03-06 0 12 2927 2002-05-06 0 13 2928 2002-05-07 0 14 2929 2002-05-08 0 15 2930 2002-05-09 0 You seem to be using 0 as a missing marker. That's bad practice, but I suppose it's possble you cannot change how your instruments report. You should be using NA and the functions that support proper treatment of missingness. David, I think that he is actually looking for dates where there is no measurement as opposed to dates where the measurement is 0. Thus: DF V1 V2 V3 1 2916 2002-02-17 0.0 2 2917 2002-02-18 0.3 3 2918 2002-02-19 3.8 4 2919 2002-02-20 43.6 5 2920 2002-02-21 1.0 6 2921 2002-02-22 5.6 7 2922 2002-02-23 10.6 8 2923 2002-02-24 2.8 9 2924 2002-02-25 19.1 10 2925 2002-02-26 20.5 11 2926 2002-03-06 0.0 12 2927 2002-05-06 0.0 13 2928 2002-05-07 0.0 14 2929 2002-05-08 0.0 15 2930 2002-05-09 0.0 # Convert V2 to dates # Default format is %Y-%m-%d # See ?as.Date DF$V2 - as.Date(DF$V2) # Get the range of dates covered DateRange - seq(min(DF$V2), max(DF$V2), by = 1) # Get the dates in DateRange that are not in DF$V2 # See ?%in% DateRange[!DateRange %in% DF$V2] [1] 2002-02-27 2002-02-28 2002-03-01 2002-03-02 2002-03-03 [6] 2002-03-04 2002-03-05 2002-03-07 2002-03-08 2002-03-09 [11] 2002-03-10 2002-03-11 2002-03-12 2002-03-13 2002-03-14 [16] 2002-03-15 2002-03-16 2002-03-17 2002-03-18 2002-03-19 [21] 2002-03-20 2002-03-21 2002-03-22 2002-03-23 2002-03-24 [26] 2002-03-25 2002-03-26 2002-03-27 2002-03-28 2002-03-29 [31] 2002-03-30 2002-03-31 2002-04-01 2002-04-02 2002-04-03 [36] 2002-04-04 2002-04-05 2002-04-06 2002-04-07 2002-04-08 [41] 2002-04-09 2002-04-10 2002-04-11 2002-04-12 2002-04-13 [46] 2002-04-14 2002-04-15 2002-04-16 2002-04-17 2002-04-18 [51] 2002-04-19 2002-04-20 2002-04-21 2002-04-22 2002-04-23 [56] 2002-04-24 2002-04-25 2002-04-26 2002-04-27 2002-04-28 [61] 2002-04-29 2002-04-30 2002-05-01 2002-05-02 2002-05-03 [66] 2002-05-04 2002-05-05 HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] denoting max value in ylim
Have you tried max()? i.e. plot (D10$Part.P ~ D10$Klorofyll,pch=16,log = xy, xlab = (Chla), ylab = (POP), ylim = c (0, max(D10$Klorofyll))) helene frigstad wrote: Hi, is there any way to set the ylim range from zero to whatever is the max value in that dataset? I am plotting many similar plots to the one below, and would like to avoid having to find the max value each time. plot (D10$Part.P ~ D10$Klorofyll,pch=16,log = xy, xlab = (Chla), ylab = (POP), ylim = c (0, ???)) abline(m3, untf=TRUE, lty=1,col=blue) text(5, 0.05,paste(round(glm(D10$Part.P ~ D10$Klorofyll, data = D10, family = Gamma(link = identity))$coef, 2),collapse = )) thank you very much for your time and help. Best regards, Helene Frigstad -- View this message in context: http://old.nabble.com/denoting-max-value-in-ylim-tp26441589p26441703.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] Has anyone had success with RGTK2/rattle and windows 7 64-bit?
I have been unable to get rattle to run in my new Windows7-64 bit configuration. For wither Rgtk2 or rattle, I get an error: Entry point not found The procedure entry point g_assetion_message_expr could not be located in the dynamic link library libglib-2.0-0.dll. Any help is really appreciated. __ 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 do I specify a partially completed survival analysis model?
Sorry for being impatient but is there really no way of doing this at all? It's quite urgent so any help is very much appreciated. Thank you. RWilliam wrote: Hello, I just started using R to do epidemiologic simulation research using the Cox proportional hazard model. I have 2 covariates X1 and X2 which I want to model as h(t,X)=h0(t)*exp(b1*X1+b2*X2). I assume independence of X from t. After I simulate Time and Censor data vectors denoting the censoring time and status respectively, I can call the following function to fit the data into the Cox model (a is a data.frame containing 4 columns X1, X2, Time and Censor): b = coxph (Surv (Time, Censor) ~ X1 + X2, data = a, method = breslow); Now the purpose of me doing simulation is that I have another mechanism to generate the number b2. From the given b2 (say it's 4.3), Cox model can be fit to generate b1 and check how feasible the new model is. Thus, my question is, how do I specify such a model that is partially completed (as in b2 is known). I tried things like Surv(Time,Censor)~X1+4.3*X2, but it's not working. Thanks very much. -- View this message in context: http://old.nabble.com/How-do-I-specify-a-partially-completed-survival-analysis-model--tp26421391p26441878.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] How do I specify a partially completed survival analysis model?
On Nov 20, 2009, at 9:46 AM, RWilliam wrote: Sorry for being impatient but is there really no way of doing this at all? It's quite urgent so any help is very much appreciated. Thank you. The general method with glm's to specify a model with fixed coefficients is to use an offset. I believe that the coxph function also has that facility and seem to remember that Therneau uses offsets in some of the examples he offers in his books and technical reports. Perhaps: cmod - coxph( Surv(Time,Censor)~X1, offset=4.3*X2, data= dfname ) Further requests about specifics should be accompanied (as suggested by the Posting Guide) by some code that sets up a reproducible example. -- David. RWilliam wrote: Hello, I just started using R to do epidemiologic simulation research using the Cox proportional hazard model. I have 2 covariates X1 and X2 which I want to model as h(t,X)=h0(t)*exp(b1*X1+b2*X2). I assume independence of X from t. After I simulate Time and Censor data vectors denoting the censoring time and status respectively, I can call the following function to fit the data into the Cox model (a is a data.frame containing 4 columns X1, X2, Time and Censor): b = coxph (Surv (Time, Censor) ~ X1 + X2, data = a, method = breslow); Now the purpose of me doing simulation is that I have another mechanism to generate the number b2. From the given b2 (say it's 4.3), Cox model can be fit to generate b1 and check how feasible the new model is. Thus, my question is, how do I specify such a model that is partially completed (as in b2 is known). I tried things like Surv(Time,Censor)~X1+4.3*X2, but it's not working. Thanks very much. -- View this message in context: http://old.nabble.com/How-do-I-specify-a-partially-completed-survival-analysis-model--tp26421391p26441878.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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I specify a partially completed survival analysis model?
On Nov 20, 2009, at 9:57 AM, David Winsemius wrote: On Nov 20, 2009, at 9:46 AM, RWilliam wrote: Sorry for being impatient but is there really no way of doing this at all? It's quite urgent so any help is very much appreciated. Thank you. The general method with glm's to specify a model with fixed coefficients is to use an offset. I believe that the coxph function also has that facility and seem to remember that Therneau uses offsets in some of the examples he offers in his books and technical reports. Perhaps: cmod - coxph( Surv(Time,Censor)~X1, offset=4.3*X2, data= dfname ) Or much more likely: cmod - coxph( Surv(Time,Censor)~X1, offset=log(4.3*X2), data= dfname ) I forgot what scale I should be thinking on. Sorry. -- David Further requests about specifics should be accompanied (as suggested by the Posting Guide) by some code that sets up a reproducible example. -- David. RWilliam wrote: Hello, I just started using R to do epidemiologic simulation research using the Cox proportional hazard model. I have 2 covariates X1 and X2 which I want to model as h(t,X)=h0(t)*exp(b1*X1+b2*X2). I assume independence of X from t. After I simulate Time and Censor data vectors denoting the censoring time and status respectively, I can call the following function to fit the data into the Cox model (a is a data.frame containing 4 columns X1, X2, Time and Censor): b = coxph (Surv (Time, Censor) ~ X1 + X2, data = a, method = breslow); Now the purpose of me doing simulation is that I have another mechanism to generate the number b2. From the given b2 (say it's 4.3), Cox model can be fit to generate b1 and check how feasible the new model is. Thus, my question is, how do I specify such a model that is partially completed (as in b2 is known). I tried things like Surv(Time,Censor)~X1+4.3*X2, but it's not working. Thanks very much. -- View this message in context: http://old.nabble.com/How-do-I-specify-a-partially-completed-survival-analysis-model--tp26421391p26441878.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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] can R scripts detect signals sent by the task scheduler ?
On 20 November 2009 at 14:25, mau...@alice.it wrote: | In general, is it possible to run R scripts through cron jobs ? | Is it possible to make the script detect the system interrupt, save its current status and then exit so that next time it is rescheduled it can pick up from where it left ? | Examples, if any, are more then welcome. You are conflating a few things here: i)yes, you can run R from cron or task scheduler -- that is how R updates webpages on the R site, how CRANberries is updated etc pp ii) to a program, it doesn't matter who started it, be it the task scheduler or interactive use (modulo correcly setup PATH et al variables iii) R and its predecessor systems have stopped and resumed for decades, look at help(save.image) or help(save) iv) Snapshotting running applications and resuming them elsewhere is an operating system task -- some OSs do this, but typically not in consumer grade versions. Hope this helps, Dirk -- Three out of two people have difficulties with fractions. __ 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] can R scripts detect signals sent by the task scheduler ?
On Fri, Nov 20, 2009 at 1:25 PM, mau...@alice.it wrote: In general, is it possible to run R scripts through cron jobs ? Yes, the only problem might be if you use anything that needs a graphics window. In the old days you needed an X11 display to create png graphics with the png() function, but not any more. I'm not sure if yo need an X11 system for anything apart from showing graphs. But I don't know everything. Is it possible to make the script detect the system interrupt, save its current status and then exit so that next time it is rescheduled it can pick up from where it left ? ?Signals: Interrupting Execution of R Description: On receiving ‘SIGUSR1’ R will save the workspace and quit. ‘SIGUSR2’ has the same result except that the ‘.Last’ function and ‘on.exit’ expressions will not be called. So if you can send that signal to your process you might be in luck. However if by 'system interrupt' you mean the SIGQUIT signal, then I'm not sure that R can trap interrupts to that extent. You might want to see if your operating system supports 'checkpointing', in which case any process can be saved and restarted. If by 'system interrupt' you mean SIGKILL (signal 9) then you are very stuck. What is going on in your system? Are you trying to checkpoint if the machine is shut down? Barry __ 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] denoting max value in ylim
Hi, is there any way to set the ylim range from zero to whatever is the max value in that dataset? I am plotting many similar plots to the one below, and would like to avoid having to find the max value each time. plot (D10$Part.P ~ D10$Klorofyll,pch=16,log = xy, xlab = (Chla), ylab = (POP), ylim = c (0, ???)) abline(m3, untf=TRUE, lty=1,col=blue) text(5, 0.05,paste(round(glm(D10$Part.P ~ D10$Klorofyll, data = D10, family = Gamma(link = identity))$coef, 2),collapse = )) thank you very much for your time and help. Best regards, Helene Frigstad -- View this message in context: http://old.nabble.com/denoting-max-value-in-ylim-tp26441589p26441589.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] denoting max value in ylim
Hi, is there any way to set the ylim range from zero to whatever is the max value in that dataset? I am plotting many similar plots to the one below, and would like to avoid having to find the max value each time. plot (D10$Part.P ~ D10$Klorofyll,pch=16,log = xy, xlab = (Chla), ylab = (POP), ylim = c (0, ???)) abline(m3, untf=TRUE, lty=1,col=blue) text(5, 0.05,paste(round(glm(D10$Part.P ~ D10$Klorofyll, data = D10, family = Gamma(link = identity))$coef, 2),collapse = )) thank you very much for your time and help. Best regards, Helene Frigstad -- View this message in context: http://old.nabble.com/denoting-max-value-in-ylim-tp26441590p26441590.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] symbol in the plot
Thanks for your reply. It is very helpful. I am sorry I didn't make my queston clearer. I have two concerns about this graph. One thing is denote 'sigma' and 'delta' as greek letters, usually I use 'expression'. But I don't know how to use 'expression' in the 'legend' The other thing is, the graph will also be print out with black and white. I try to use circle and squre to seperate 'delta1's curve and 'delta2's curve. So even someone read the black and white handout, they can tell which graph is which. It will be nice if there is a notation on the graph, next to a square symble, it says 'delta 1', next to a circle symble, it says'delta 2'. I wrote it on the label with phrases, looks not professional. Thank you for any suggestons. my runable code is as follows: sigma=c( 0.00625, 0.06250, 0.12500, 0.18750, 0.25000, 0.31250, 0.37500, 0.43750, 0.5, 0.56250) delta1=c(0.90768, 0.90489, 0.901788,0.898681, 0.8955, 0.89557, 0.892474,0.88936, 0.886262, 0.179959) delta2=c(0.90830, 0.9110998, 0.914203, 0.917308, 0.920412, 0.923517, 0.926623, 1.71524, 1.7153, 1.7154) plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1--square delta2--circle', pch=22, type='o') par(new=TRUE) plot(sigma, delta2, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1--square delta2--circle', col='red', axes=FALSE, type='o') -- View this message in context: http://old.nabble.com/symbol-in-the-plot-tp26422303p26442986.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] denoting max value in ylim
ylim = c(0, max(log10(D10$Part.P))) Make sure you remove any 0s or NAs before computing the max though. --sundar On Fri, Nov 20, 2009 at 6:12 AM, helene frigstad helenefrigs...@hotmail.com wrote: Hi, is there any way to set the ylim range from zero to whatever is the max value in that dataset? I am plotting many similar plots to the one below, and would like to avoid having to find the max value each time. plot (D10$Part.P ~ D10$Klorofyll,pch=16,log = xy, xlab = (Chla), ylab = (POP), ylim = c (0, ???)) abline(m3, untf=TRUE, lty=1,col=blue) text(5, 0.05,paste(round(glm(D10$Part.P ~ D10$Klorofyll, data = D10, family = Gamma(link = identity))$coef, 2),collapse = )) thank you very much for your time and help. Best regards, Helene Frigstad -- View this message in context: http://old.nabble.com/denoting-max-value-in-ylim-tp26441590p26441590.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] find data (date) gaps in time series
On Nov 20, 2009, at 9:21 AM, Marc Schwartz wrote: On Nov 20, 2009, at 8:04 AM, David Winsemius wrote: On Nov 20, 2009, at 6:26 AM, Stefan Strohmeier wrote: Dear R users, I have a time series of precipitation data. The time series comprises ~ 20 years and it is supposed to be constant (one value per day), but due to some failure of the measuring device some days or periods are missing. I would like to find these missing days or periods just to get a first idea about the reliability of the measurements. The only function I could find was is.constant(), but of course I only get a true or false statement instead of the dates missing. Google searches and a look at the R help mailing did not reveal an answer. Please find attached a few dates of the time series with missing values from February to April. I would like R to detect those missing dates. dtdta - read.table(textConnection(2916 2002-02-17 0.0 + 2917 2002-02-18 0.3 + 2918 2002-02-19 3.8 + 2919 2002-02-20 43.6 + 2920 2002-02-21 1.0 + 2921 2002-02-22 5.6 + 2922 2002-02-23 10.6 + 2923 2002-02-24 2.8 + 2924 2002-02-25 19.1 + 2925 2002-02-26 20.5 + 2926 2002-03-06 0.0 + 2927 2002-05-06 0.0 + 2928 2002-05-07 0.0 + 2929 2002-05-08 0.0 + 2930 2002-05-09 0.0) ) dtdta[dtdta$V3 == 0, ] V1 V2 V3 1 2916 2002-02-17 0 11 2926 2002-03-06 0 12 2927 2002-05-06 0 13 2928 2002-05-07 0 14 2929 2002-05-08 0 15 2930 2002-05-09 0 You seem to be using 0 as a missing marker. That's bad practice, but I suppose it's possble you cannot change how your instruments report. You should be using NA and the functions that support proper treatment of missingness. David, I think that he is actually looking for dates where there is no measurement as opposed to dates where the measurement is 0. Thus: DF V1 V2 V3 1 2916 2002-02-17 0.0 2 2917 2002-02-18 0.3 3 2918 2002-02-19 3.8 4 2919 2002-02-20 43.6 5 2920 2002-02-21 1.0 6 2921 2002-02-22 5.6 7 2922 2002-02-23 10.6 8 2923 2002-02-24 2.8 9 2924 2002-02-25 19.1 10 2925 2002-02-26 20.5 11 2926 2002-03-06 0.0 12 2927 2002-05-06 0.0 13 2928 2002-05-07 0.0 14 2929 2002-05-08 0.0 15 2930 2002-05-09 0.0 You're right. I slipped a gear in reading that. # Convert V2 to dates # Default format is %Y-%m-%d # See ?as.Date DF$V2 - as.Date(DF$V2) At this point an alternative approach: # Scan for differences 1 diff(DF$V2) Time differences in days [1] 1 1 1 1 1 1 1 1 1 8 61 1 1 1 #Records at the start of gaps dtdta[diff(dtdta$V2)1, ] V1 V2 V3 10 2925 2002-02-26 20.5 11 2926 2002-03-06 0.0 $Records at the end of gaps dtdta[c(1, diff(dtdta$V2))1, ] V1 V2 V3 11 2926 2002-03-06 0 12 2927 2002-05-06 0 #Gap dataframe dfgaps -data.frame( start= DF[c(1, diff(DF$V2))1, ]$V2, end= DF[diff(DF$V2)1, ]$V2) dfgaps startend 1 2002-03-06 2002-02-26 2 2002-05-06 2002-03-06 # Get the range of dates covered DateRange - seq(min(DF$V2), max(DF$V2), by = 1) # Get the dates in DateRange that are not in DF$V2 # See ?%in% DateRange[!DateRange %in% DF$V2] [1] 2002-02-27 2002-02-28 2002-03-01 2002-03-02 2002-03-03 [6] 2002-03-04 2002-03-05 2002-03-07 2002-03-08 2002-03-09 [11] 2002-03-10 2002-03-11 2002-03-12 2002-03-13 2002-03-14 [16] 2002-03-15 2002-03-16 2002-03-17 2002-03-18 2002-03-19 [21] 2002-03-20 2002-03-21 2002-03-22 2002-03-23 2002-03-24 [26] 2002-03-25 2002-03-26 2002-03-27 2002-03-28 2002-03-29 [31] 2002-03-30 2002-03-31 2002-04-01 2002-04-02 2002-04-03 [36] 2002-04-04 2002-04-05 2002-04-06 2002-04-07 2002-04-08 [41] 2002-04-09 2002-04-10 2002-04-11 2002-04-12 2002-04-13 [46] 2002-04-14 2002-04-15 2002-04-16 2002-04-17 2002-04-18 [51] 2002-04-19 2002-04-20 2002-04-21 2002-04-22 2002-04-23 [56] 2002-04-24 2002-04-25 2002-04-26 2002-04-27 2002-04-28 [61] 2002-04-29 2002-04-30 2002-05-01 2002-05-02 2002-05-03 [66] 2002-05-04 2002-05-05 HTH, Marc Schwartz David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 2.10 'memory leak'? on OS X
Thanks Duncan, I managed to get R to start through the terminal this way. Still no luck getting the R.app to start. Is it possible to directly access (and then trash or modify) the .RData and .RProfile files? I assume they would be recreated if I could then open the R.app. Having searched for them on spotlight and in the /user/library folder, I don't see them anywhere - are they always located in the same place on OS X? thanks, Steve Duncan Murdoch-2 wrote: On 20/11/2009 12:33 AM, Stropharia wrote: Dear R users, I am running R 2.10.0 on OS X 10.5.8. I had been running 2.10 successfully for about a week (and have used previous R versions for 2+ years on the same computer) until 2 days ago it failed to start up for me. Now when I try to start R, the application tries to initiate for several minutes then crashes. Looking at the activity monitor, my memory usage goes from having about 1.6Gb free (out of 2Gb) to 7Mb in the first 10-15 seconds of attempting to start the program. At this point I either have to force quit R (as everything starts to freeze up) or wait several minutes for it to crash. I have erased the application and reinstalled it 4 times now - with exactly the same result. I looked around in the Library and System folders to see if any other files needed to be removed, but couldn't find any. I have also restarted the computer and repaired permissions multiple times - and then reinstalled R, with no luck. The exact same thing happens if I start R64. I did not updated OS X or R, or install any other programs, just prior to this first happening and am at a loss to explain what's going on. I have copied the first part of one of the crash logs below. Does anyone have any ideas for to remedy this? It sounds like one of your user-specific startup files is causing the problem, e.g. .RData, or .Rprofile. Did you try starting R with option --vanilla? That will skip them. Duncan Murdoch best, Steve # Crash log Process: R [231] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: R 2.10.0 GUI 1.30 Leopard build 32-bit (5511) Code Type: X86 (Native) Parent Process: launchd [101] Date/Time: 2009-11-18 23:15:45.570 -0500 OS Version: Mac OS X 10.5.8 (9L31a) Report Version: 6 Anonymous UUID: D86CDCBC-00FD-4AEE-AB50-2EFE0DAE9E1E Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x00067ee2 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0x07c7 __memcpy + 39 (cpu_capabilities.h:246) 1 com.apple.CoreFoundation 0x96a6a0b4 __CFStringEncodeByteStream + 4052 2 com.apple.Foundation 0x94446eb7 -[NSString(NSStringOtherEncodings) getBytes:maxLength:usedLength:encoding:options:range:remainingRange:] + 295 3 com.apple.Foundation 0x94446a1a _NSNewStringByAppendingStrings + 538 4 com.apple.Foundation 0x94446760 -[NSString stringByAppendingString:] + 192 5 org.R-project.R 0x9ce8 -[RController doLoadHistory:] + 808 6 org.R-project.R 0x76df -[RController awakeFromNib] + 2319 7 com.apple.CoreFoundation 0x96ac07f5 -[NSSet makeObjectsPerformSelector:] + 181 8 com.apple.AppKit 0x92efed8e -[NSIBObjectData nibInstantiateWithOwner:topLevelObjects:] + 1533 9 com.apple.AppKit 0x92ef4fba loadNib + 264 10 com.apple.AppKit 0x92ef491c +[NSBundle(NSNibLoading) _loadNibFile:nameTable:withZone:ownerBundle:] + 946 11 com.apple.AppKit 0x92ef455f +[NSBundle(NSNibLoading) loadNibFile:externalNameTable:withZone:] + 171 12 com.apple.AppKit 0x92ef449d +[NSBundle(NSNibLoading) loadNibNamed:owner:] + 391 13 org.R-project.R 0x2538 main + 296 14 org.R-project.R 0x23d6 start + 54 #-- __ 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. -- View this message in context: http://old.nabble.com/R-2.10-%27memory-leak%27--on-OS-X-tp26422775p26443494.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] symbol in the plot
Joh, thank you very much. sorry for confusing you. I didn't make my question clear. I tried your code it looks much better than my original one. Just I prefer I can write the greek letter delta1 and delta 2 instead of words 'delta1' and 'delta2'. Also, it will be nice if there is a square symbol next to delta1 and a circle symbol next to delta 2, since sometimes I have to print the graph in a white and black paper. Thanks for any suggestions. Sorry for not asking question clearly. Johannes Graumann-2 wrote: How about plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta', pch=22, type='o') points(sigma, delta2, col='red', axes=FALSE, type='o') legend(topleft,c(Delta1,Delta2),fill=TRUE,col=c(black,red)) Send runnable example next time. HTH, Joh gcheer3 wrote: TO be specific, here is how I graphed plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1--square delta2--circle', pch=22, type='o') par(new=TRUE) plot(sigma, delta2, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1--square delta2--circle', col='red', axes=FALSE, type='o') Thanks a lot gcheer3 wrote: a graph question. Thanks a lot in advance. I made two scatterplots on one graph (sigma vs. delta1, sigma vs. delta2) (20 observations of delta1, delta2 and corresponding sigma) the x-axis is sigma, the y-axis is either delta1 or delta2. I connected both scatterplots. To seperate them, one curves is a line with circles, the other curve is a line with squares on it. I want to make a notation either on the y-axis or on the graph. The notiaion is delta1--square; delta2--circle. So when people look at the graph, they can easily tell each curve's meaning. The curve with squares on it means the sigma vs. delta1, and the curve with circles on it means sigma vs. delta2. I think I can use 'expression' to write delta1, delta2 and sigma in greek letters, but I am not sure how to denote the square and cirle I graphed. __ 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. -- View this message in context: http://old.nabble.com/symbol-in-the-plot-tp26422303p26443123.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] symbol in the plot
On Nov 20, 2009, at 10:23 AM, gcheer3 wrote: Thanks for your reply. It is very helpful. I am sorry I didn't make my queston clearer. I have two concerns about this graph. One thing is denote 'sigma' and 'delta' as greek letters, usually I use 'expression'. But I don't know how to use 'expression' in the 'legend' The other thing is, the graph will also be print out with black and white. I try to use circle and squre to seperate 'delta1's curve and 'delta2's curve. So even someone read the black and white handout, they can tell which graph is which. It will be nice if there is a notation on the graph, next to a square symble, it says 'delta 1', next to a circle symble, it says'delta 2'. I wrote it on the label with phrases, looks not professional. Thank you for any suggestons. my runable code is as follows: sigma=c( 0.00625, 0.06250, 0.12500, 0.18750, 0.25000, 0.31250, 0.37500, 0.43750, 0.5, 0.56250) delta1=c(0.90768, 0.90489, 0.901788,0.898681, 0.8955, 0.89557, 0.892474,0.88936, 0.886262, 0.179959) delta2=c(0.90830, 0.9110998, 0.914203, 0.917308, 0.920412, 0.923517, 0.926623, 1.71524, 1.7153, 1.7154) plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1-- square delta2--circle', pch=22, type='o') par(new=TRUE) plot(sigma, delta2, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1-- square delta2--circle', col='red', axes=FALSE, type='o') legend(topleft,legend=expression(Delta~1, Delta~2), col=c(black,red), pch=c(22,1) ) (I think I got the order of hte red and circle correct. You should check.) -- David. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Remove leading and trailing white spaces
I have a character string and I would like to remove the leading and
tailing white spaces. The example for 'sub' shows how to remove the
trailing white spaces, but I still can't figure out how to remove both
trailing and leading white spaces because I can't find any documentation
for what +$ means or what \\s+$ means. Maybe its because I don't
have a Unix background. Thanks in advance for any help with this.
str - 'Now is the time '
sub(' +$', '', str) ## spaces only
sub('[[:space:]]+$', '', str) ## white space, POSIX-style
sub('\\s+$', '', str, perl = TRUE) ## Perl-style white space
Thanks,
Roger
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bessel function with large index value
DS == David Scott d.sc...@auckland.ac.nz on Sat, 21 Nov 2009 02:29:38 +1300 writes: DS This is a reply to my own question. I thought I had found an answer but DS it seems not so (some analysis follows below). Maybe Martin Maechler or DS Robin Hankin or Duncan Murdoch may have some ideas---I know the question DS is a bit specialized. Indeed. The good news is that last winter (when in the Swiss Alps, typically after enjoying the sun and snow) I've written an experimental and unpublished R package called 'Bessel' where I've started to collect bessel implementations / approximations that I had collected and partly tested in the past, also looking at what other packages on CRAN had. My 'Bessel' package depends on my new package 'Rmpfr' (for arbitrary precision arithmetic), as I really want to explore the quality of the different Bessel computations, and for that have wanted access to infinite precision arithmetic. Apropos 'Rmpfr': This has been on R-forge for about a year, and now become a CRAN package a couple of weeks ago. Thanks to Brian Ripley and Stefan Theussl, the package is available for Windows from R-forge, but not yet from CRAN. For MacOSX, it has not yet been made available in precompiled form, but there you should be able to build it from the sources, after installing the (GNU) GMP library, and the MPFR library which builds on GMP. Back to Bessel and my experimental code: In there, I have a function, currently only for the Bessel I_[\nu] that uses the Debye polynomial series needed for these cases, and indeed my function has a 'log' argument. DS David Scott wrote: I am looking for a method of dealing with the modified Bessel function K_\nu(x) for large \nu. The besselK function implementation of this allows for dealing with large values of x by allowing for exponential scaling, but there is no facility for dealing with large \nu. What would work for me would be an lbesselK function in the manner of lgamma which returned the log of K_\nu(x) for large \nu. Does anybody have any leads on this? Note that I have trawled through Abramowitz and Stegun and found 9.7.8 which doesn't work for me because of the complication in the definition of the x argument. I have also seen a result of Ismail (1977) reported by Barndorff-Nielsen and Blaesild which has the other problem, the treatment of the x argument is too simple. As my implementation uses A__S 9.3.7 for I_nu, I wonder why you say that that the completely analogous 9.3.8 for K_nu is not appropriate. To do the calculation I am attempting, I need to have the Bessel function in a form that will allow a cancellation with a Gamma function of high order in the denominator. so, working on the log scale saves all problems, right? I think we should further correspond offline on the topic; given your interest, I guess I should probably make my 'Bessel' available from R-forge Martin Maechler, ETH Zurich David Scott DS After posting I checked the GNU Scientific Library DS (http://www.gnu.org/software/gsl/) and found: DS DS — Function: double gsl_sf_bessel_lnKnu (double nu, double x) DS — Function: int gsl_sf_bessel_lnKnu_e (double nu, double x, DS gsl_sf_result * result) DS These routines compute the logarithm of the irregular modified DS Bessel function of fractional order \nu, \ln(K_\nu(x)) for x0, \nu0. DS DS I then recalled that Robin Hankin and Duncan Murdoch had made the GSL DS available. I installed the package gsl and investigated the function DS bessel_lnKnu. DS Unfortunately, it appears that this function has *smaller* range than DS besselK when it comes to the index. The following shows it: DS library(plyr) DS library(gsl) DS ### Check calculations using both methods DS lnKnu - maply(expand.grid(x = 100*(1:7), nu = 10*(1:100)), bessel_lnKnu) DS lnKnu DS Knu - maply(expand.grid(x = 100*(1:7), nu = 10*(1:100)), besselK) DS Knu DS lnKnu/log(Knu) DS I was expecting what happens with gamma and lgamma DS ### Compare gamma function DS lgam - lgamma(100*(1:7)) DS lgam DS gam - gamma(100*(1:7)) DS gam DS lgam/log(gam) DS It seems that bessel_lnKnu is set up to protect against infinity when x DS becomes small: DS ### Does lnKnu protect against Inf when x goes to zero? DS lnnear0 - maply(expand.grid(x = 0.0001*(1:10), nu = 10*(0:5)), DS bessel_lnKnu) DS lnnear0 DS near0 - maply(expand.grid(x = 0.0001*(1:10), nu = 10*(0:5)), besselK) DS near0 DS lnnear0/log(near0) DS So, I am still in need of a solution: an implementation of log of Bessel DS K which protects against the index nu becoming large. DS David Scott DS -- DS
Re: [R] Remove leading and trailing white spaces
try this:
x - ' middle of the string '
sub(^[[:space:]]*(.*?)[[:space:]]*$, \\1, x, perl=TRUE)
[1] middle of the string
On Fri, Nov 20, 2009 at 10:51 AM, Bos, Roger roger@rothschild.com wrote:
I have a character string and I would like to remove the leading and
tailing white spaces. The example for 'sub' shows how to remove the
trailing white spaces, but I still can't figure out how to remove both
trailing and leading white spaces because I can't find any documentation
for what +$ means or what \\s+$ means. Maybe its because I don't
have a Unix background. Thanks in advance for any help with this.
str - ' Now is the time '
sub(' +$', '', str) ## spaces only
sub('[[:space:]]+$', '', str) ## white space, POSIX-style
sub('\\s+$', '', str, perl = TRUE) ## Perl-style white space
Thanks,
Roger
***
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] can R scripts detect signals sent by the task scheduler ?
On Fri, 20 Nov 2009, Barry Rowlingson wrote: On Fri, Nov 20, 2009 at 1:25 PM, mau...@alice.it wrote: In general, is it possible to run R scripts through cron jobs ? Yes, the only problem might be if you use anything that needs a graphics window. In the old days you needed an X11 display to create png graphics with the png() function, but not any more. I'm not sure if yo need an X11 system for anything apart from showing graphs. But I don't know everything. Some package authors assume such a display to install their packages (and a few of those may not have a choice as some graphics libraries seem to need one to be loaded). So my dept's automated package updater scripts run from cron, and start (and stop) a Xvfb X server to get around that. [...] -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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 2.10 'memory leak'? on OS X
On 20/11/2009 10:38 AM, Stropharia wrote: Thanks Duncan, I managed to get R to start through the terminal this way. Still no luck getting the R.app to start. Is it possible to directly access (and then trash or modify) the .RData and .RProfile files? I assume they would be recreated if I could then open the R.app. Having searched for them on spotlight and in the /user/library folder, I don't see them anywhere - are they always located in the same place on OS X? .RProfile won't be recreated: it's where you put your own startup customizations. It sounds as though .RData is a more likely culprit. .RData is created when you quit and reply Yes to the question about saving. I forget if there are special rules on a Mac about where the saving occurs, but on other systems it's in the current working directory. On startup, R will look there and in the user's home directory. You probably want to ask on R-sig-mac for some Mac specific advice. Duncan Murdoch thanks, Steve Duncan Murdoch-2 wrote: On 20/11/2009 12:33 AM, Stropharia wrote: Dear R users, I am running R 2.10.0 on OS X 10.5.8. I had been running 2.10 successfully for about a week (and have used previous R versions for 2+ years on the same computer) until 2 days ago it failed to start up for me. Now when I try to start R, the application tries to initiate for several minutes then crashes. Looking at the activity monitor, my memory usage goes from having about 1.6Gb free (out of 2Gb) to 7Mb in the first 10-15 seconds of attempting to start the program. At this point I either have to force quit R (as everything starts to freeze up) or wait several minutes for it to crash. I have erased the application and reinstalled it 4 times now - with exactly the same result. I looked around in the Library and System folders to see if any other files needed to be removed, but couldn't find any. I have also restarted the computer and repaired permissions multiple times - and then reinstalled R, with no luck. The exact same thing happens if I start R64. I did not updated OS X or R, or install any other programs, just prior to this first happening and am at a loss to explain what's going on. I have copied the first part of one of the crash logs below. Does anyone have any ideas for to remedy this? It sounds like one of your user-specific startup files is causing the problem, e.g. .RData, or .Rprofile. Did you try starting R with option --vanilla? That will skip them. Duncan Murdoch best, Steve # Crash log Process: R [231] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: R 2.10.0 GUI 1.30 Leopard build 32-bit (5511) Code Type: X86 (Native) Parent Process: launchd [101] Date/Time: 2009-11-18 23:15:45.570 -0500 OS Version: Mac OS X 10.5.8 (9L31a) Report Version: 6 Anonymous UUID: D86CDCBC-00FD-4AEE-AB50-2EFE0DAE9E1E Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x00067ee2 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0x07c7 __memcpy + 39 (cpu_capabilities.h:246) 1 com.apple.CoreFoundation 0x96a6a0b4 __CFStringEncodeByteStream + 4052 2 com.apple.Foundation 0x94446eb7 -[NSString(NSStringOtherEncodings) getBytes:maxLength:usedLength:encoding:options:range:remainingRange:] + 295 3 com.apple.Foundation 0x94446a1a _NSNewStringByAppendingStrings + 538 4 com.apple.Foundation 0x94446760 -[NSString stringByAppendingString:] + 192 5 org.R-project.R 0x9ce8 -[RController doLoadHistory:] + 808 6 org.R-project.R 0x76df -[RController awakeFromNib] + 2319 7 com.apple.CoreFoundation 0x96ac07f5 -[NSSet makeObjectsPerformSelector:] + 181 8 com.apple.AppKit 0x92efed8e -[NSIBObjectData nibInstantiateWithOwner:topLevelObjects:] + 1533 9 com.apple.AppKit 0x92ef4fba loadNib + 264 10 com.apple.AppKit 0x92ef491c +[NSBundle(NSNibLoading) _loadNibFile:nameTable:withZone:ownerBundle:] + 946 11 com.apple.AppKit 0x92ef455f +[NSBundle(NSNibLoading) loadNibFile:externalNameTable:withZone:] + 171 12 com.apple.AppKit 0x92ef449d +[NSBundle(NSNibLoading) loadNibNamed:owner:] + 391 13 org.R-project.R 0x2538 main + 296 14 org.R-project.R 0x23d6 start + 54 #-- __ 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] Remove leading and trailing white spaces
See:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/40714.html
There are many packages which have this functionality as well and a
search (??, RSiteSearch, rseek.org) will find them.
The links box on the http://gsubfn.googlecode.com page has links to
regular expression pages on the web.
On Fri, Nov 20, 2009 at 10:51 AM, Bos, Roger roger@rothschild.com wrote:
I have a character string and I would like to remove the leading and
tailing white spaces. The example for 'sub' shows how to remove the
trailing white spaces, but I still can't figure out how to remove both
trailing and leading white spaces because I can't find any documentation
for what +$ means or what \\s+$ means. Maybe its because I don't
have a Unix background. Thanks in advance for any help with this.
str - ' Now is the time '
sub(' +$', '', str) ## spaces only
sub('[[:space:]]+$', '', str) ## white space, POSIX-style
sub('\\s+$', '', str, perl = TRUE) ## Perl-style white space
Thanks,
Roger
***
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and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] symbol in the plot
plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta',pch=22, type='o') points(sigma, delta2, col='red', axes=FALSE, pch=1,type='o') legend(topleft,c(expression(Delta*1),expression(delta*2)),fill=TRUE,col=c(black,red),pch=c(1,22)) See: ?plotmath Still, gimme a easily runnable example next time. HTH, Joh gcheer3 wrote: Joh, thank you very much. sorry for confusing you. I didn't make my question clear. I tried your code it looks much better than my original one. Just I prefer I can write the greek letter delta1 and delta 2 instead of words 'delta1' and 'delta2'. Also, it will be nice if there is a square symbol next to delta1 and a circle symbol next to delta 2, since sometimes I have to print the graph in a white and black paper. Thanks for any suggestions. Sorry for not asking question clearly. Johannes Graumann-2 wrote: How about plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta', pch=22, type='o') points(sigma, delta2, col='red', axes=FALSE, type='o') legend(topleft,c(Delta1,Delta2),fill=TRUE,col=c(black,red)) Send runnable example next time. HTH, Joh gcheer3 wrote: TO be specific, here is how I graphed plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1--square delta2--circle', pch=22, type='o') par(new=TRUE) plot(sigma, delta2, ylim=range(-0.5, 2), xlab='sigma', ylab='delta1--square delta2--circle', col='red', axes=FALSE, type='o') Thanks a lot gcheer3 wrote: a graph question. Thanks a lot in advance. I made two scatterplots on one graph (sigma vs. delta1, sigma vs. delta2) (20 observations of delta1, delta2 and corresponding sigma) the x-axis is sigma, the y-axis is either delta1 or delta2. I connected both scatterplots. To seperate them, one curves is a line with circles, the other curve is a line with squares on it. I want to make a notation either on the y-axis or on the graph. The notiaion is delta1--square; delta2--circle. So when people look at the graph, they can easily tell each curve's meaning. The curve with squares on it means the sigma vs. delta1, and the curve with circles on it means sigma vs. delta2. I think I can use 'expression' to write delta1, delta2 and sigma in greek letters, but I am not sure how to denote the square and cirle I graphed. __ 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] R 2.10 'memory leak'? on OS X
Probably best further discussed on R-SIG-Mac list: https://stat.ethz.ch/mailman/listinfo/r-sig-mac ... since that is where the tricks of convincing MacOSX to display system files is discussed and a semi-regular basis: https://stat.ethz.ch/pipermail/r-sig-mac/2009-November/006768.html https://stat.ethz.ch/pipermail/r-sig-mac/2009-March/005925.html -- David. On Nov 20, 2009, at 10:38 AM, Stropharia wrote: Thanks Duncan, I managed to get R to start through the terminal this way. Still no luck getting the R.app to start. Is it possible to directly access (and then trash or modify) the .RData and .RProfile files? I assume they would be recreated if I could then open the R.app. Having searched for them on spotlight and in the /user/library folder, I don't see them anywhere - are they always located in the same place on OS X? thanks, Steve Duncan Murdoch-2 wrote: On 20/11/2009 12:33 AM, Stropharia wrote: Dear R users, I am running R 2.10.0 on OS X 10.5.8. I had been running 2.10 successfully for about a week (and have used previous R versions for 2+ years on the same computer) until 2 days ago it failed to start up for me. Now when I try to start R, the application tries to initiate for several minutes then crashes. Looking at the activity monitor, my memory usage goes from having about 1.6Gb free (out of 2Gb) to 7Mb in the first 10-15 seconds of attempting to start the program. At this point I either have to force quit R (as everything starts to freeze up) or wait several minutes for it to crash. I have erased the application and reinstalled it 4 times now - with exactly the same result. I looked around in the Library and System folders to see if any other files needed to be removed, but couldn't find any. I have also restarted the computer and repaired permissions multiple times - and then reinstalled R, with no luck. The exact same thing happens if I start R64. I did not updated OS X or R, or install any other programs, just prior to this first happening and am at a loss to explain what's going on. I have copied the first part of one of the crash logs below. Does anyone have any ideas for to remedy this? It sounds like one of your user-specific startup files is causing the problem, e.g. .RData, or .Rprofile. Did you try starting R with option --vanilla? That will skip them. Duncan Murdoch best, Steve # Crash log Process: R [231] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: R 2.10.0 GUI 1.30 Leopard build 32-bit (5511) Code Type: X86 (Native) Parent Process: launchd [101] Date/Time: 2009-11-18 23:15:45.570 -0500 OS Version: Mac OS X 10.5.8 (9L31a) Report Version: 6 Anonymous UUID: D86CDCBC-00FD-4AEE-AB50-2EFE0DAE9E1E Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x00067ee2 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0x07c7 __memcpy + 39 (cpu_capabilities.h:246) 1 com.apple.CoreFoundation 0x96a6a0b4 __CFStringEncodeByteStream + 4052 2 com.apple.Foundation 0x94446eb7 -[NSString(NSStringOtherEncodings) getBytes :maxLength:usedLength:encoding:options:range:remainingRange:] + 295 3 com.apple.Foundation 0x94446a1a _NSNewStringByAppendingStrings + 538 4 com.apple.Foundation 0x94446760 -[NSString stringByAppendingString:] + 192 5 org.R-project.R 0x9ce8 -[RController doLoadHistory:] + 808 6 org.R-project.R 0x76df -[RController awakeFromNib] + 2319 7 com.apple.CoreFoundation 0x96ac07f5 -[NSSet makeObjectsPerformSelector:] + 181 8 com.apple.AppKit 0x92efed8e -[NSIBObjectData nibInstantiateWithOwner:topLevelObjects:] + 1533 9 com.apple.AppKit 0x92ef4fba loadNib + 264 10 com.apple.AppKit 0x92ef491c + [NSBundle(NSNibLoading) _loadNibFile:nameTable:withZone:ownerBundle:] + 946 11 com.apple.AppKit 0x92ef455f + [NSBundle(NSNibLoading) loadNibFile:externalNameTable:withZone:] + 171 12 com.apple.AppKit 0x92ef449d + [NSBundle(NSNibLoading) loadNibNamed:owner:] + 391 13 org.R-project.R 0x2538 main + 296 14 org.R-project.R 0x23d6 start + 54 #-- __ 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. -- View this message in context: http://old.nabble.com/R-2.10-%27memory-leak%27--on-OS-X-tp26422775p26443494.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing
Re: [R] How do I specify a partially completed survival analysis model?
In reply to suggestion by David W., setting an offset parameter doesn't seem to work as R is not recognizing the X2 part of coxph( Surv(Time,Censor)~X1, offset=log(4.3*X2), data= a ). Also, here's some sample data: X1 X2 TimeCensor 1 1 0.40619454 77.00666 0 2 1 0.20717868 100.0 0 3 1 0.77360963 79.03463 1 4 1 0.62221954 100.0 0 5 1 0.32191280 100.0 0 6 1 0.73790704 72.84842 0 7 1 0.65012237 100.0 0 8 1 0.71596105 100.0 0 9 1 0.74787202 84.00172 0 10 1 0.66803790 41.65760 0 11 1 0.79922364 92.41999 0 12 1 0.76433736 90.99983 0 13 1 0.57014524 100.0 0 14 1 0.39642235 100.0 0 15 1 0.55756045 100.0 0 16 0 0.60079340 100.0 0 17 0 0.43630695 100.0 0 18 0 0.09388013 100.0 0 19 0 0.55956791 100.0 0 20 0 0.52491597 97.71884 1 where we set the coefficient of X2 to be 8. RWilliam wrote: Sorry for being impatient but is there really no way of doing this at all? It's quite urgent so any help is very much appreciated. Thank you. RWilliam wrote: Hello, I just started using R to do epidemiologic simulation research using the Cox proportional hazard model. I have 2 covariates X1 and X2 which I want to model as h(t,X)=h0(t)*exp(b1*X1+b2*X2). I assume independence of X from t. After I simulate Time and Censor data vectors denoting the censoring time and status respectively, I can call the following function to fit the data into the Cox model (a is a data.frame containing 4 columns X1, X2, Time and Censor): b = coxph (Surv (Time, Censor) ~ X1 + X2, data = a, method = breslow); Now the purpose of me doing simulation is that I have another mechanism to generate the number b2. From the given b2 (say it's 4.3), Cox model can be fit to generate b1 and check how feasible the new model is. Thus, my question is, how do I specify such a model that is partially completed (as in b2 is known). I tried things like Surv(Time,Censor)~X1+4.3*X2, but it's not working. Thanks very much. -- View this message in context: http://old.nabble.com/How-do-I-specify-a-partially-completed-survival-analysis-model--tp26421391p26443562.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] HTML help missing?
On 20/11/2009 7:11 AM, Antje wrote: Hey there, I'm running R 2.10 on Windows XP (Professional) and I was wondering where the HTML help window disappeared? With earlier versions everything was fine. Now I get only this old-fashioned text windows without any links when I type ?some_function Can anybody help me? Edit the R_HOME/etc/Rprofile.site file to uncomment the line options(help_type=html) (or just install the patched version, this installer bug was discovered after release). 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] How to concatenate expressions
Dear R-users,
I am developing a plotting function, which receives expressions and
character/numerical vectors as part of the many input arguments and
which tries to concatenate them before displaying the result to the
plot. I currently cannot find a way to make this concatenation works. I
have read several posts in the list that solved this problem by pasting
the different elements together before creating the expressions (like in
http://tolstoy.newcastle.edu.au/R/help/02a/4790.html). I cannot
implement this solution because my expressions and numerical/character
vectors are passed to the function and not create inside the function. I
would greatly appreciate any help with the following example code.
Thank you
testplot - function(a,b,c) {
text - as.expression(paste(a,b,c,sep=' '))
dev.new()
plot(-5:5,-5:5,col=0)
for (i in 1:3) {
text(x=i,
y=i,
labels=text[i])
}
}
a - as.expression(c(bquote(alpha),bquote(beta),bquote(gamma)))
b - as.expression(1:3)
c - as.expression(c(bquote('-10'^th),
bquote('-20'^th),
bquote('-30'^th)))
testplot(a,b,c)
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[R] ctree (party) changing font sizes in plots
When plotting Binary Trees (ctree) from the party package, is there a way to adjust the font sizes of the leaves? require(party) irisct - ctree(Species ~ ., data = iris) plot(irisct) I want to adjust the font sizes for Node 2, Node 5, etc. I'd also like to be able to adjust the font sizes for the x-axis and y-axis labels of the histograms. Thanks, Sam Thomas Revelant Technologies, LLC. sam.tho...@revelanttech.com mailto:sam.tho...@revelanttech.com 317-696-9214 [[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] how to draw image of a data distribution? Thanks
I have a file with 3 cols as: xyvalue 110.5000 121.8333 134. 210.7500 220.7500 234 310.7500 321.4167 335.1667 I read them in using p - read.table(data.txt, header=TRUE) My questoin: how to draw a image to show the values at different positions (x, y)? I would like to see different colors for different values. Sorry if it is a naive question, but it is my first week of R and I have been trying for several hours trying to make it. Thank you, -- Senlin Liang [[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] ctree (party) changing font sizes in plots
On Fri, 20 Nov 2009, Sam Thomas wrote: When plotting Binary Trees (ctree) from the party package, is there a way to adjust the font sizes of the leaves? Currently, this is not implemented in party. In interactive usage it is not easy to change the fontsize. If you're printing to PDF, you could easily increase/decrease the height and width which will decrease/increase the relative size of the text, respectively. Not elegant but works. Alternatively, you could obtain the partykit package from R-Forge which has a new implementation of general infrastructure for tree. With that you can do library(partykit) irisct - ctree(Species ~ ., data = iris) plot(irisct, gp = gpar(fontsize = 20)) Note that party and partykit should not be used together, partykit has a slightly enhanced/modified ctree() function. hth, Z require(party) irisct - ctree(Species ~ ., data = iris) plot(irisct) I want to adjust the font sizes for Node 2, Node 5, etc. I'd also like to be able to adjust the font sizes for the x-axis and y-axis labels of the histograms. Thanks, Sam Thomas Revelant Technologies, LLC. sam.tho...@revelanttech.com mailto:sam.tho...@revelanttech.com 317-696-9214 [[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.
Re: [R] how to draw image of a data distribution? Thanks
with(p,plot(x,y,pch=20,col=1+as.integer(value))) -- Clint BowmanINTERNET: cl...@ecy.wa.gov Air Quality Modeler INTERNET: cl...@math.utah.edu Department of Ecology VOICE: (360) 407-6815 PO Box 47600FAX:(360) 407-7534 Olympia, WA 98504-7600 On Fri, 20 Nov 2009, Senlin Liang wrote: I have a file with 3 cols as: xyvalue 110.5000 121.8333 134. 210.7500 220.7500 234 310.7500 321.4167 335.1667 I read them in using p - read.table(data.txt, header=TRUE) My questoin: how to draw a image to show the values at different positions (x, y)? I would like to see different colors for different values. Sorry if it is a naive question, but it is my first week of R and I have been trying for several hours trying to make it. Thank you, __ 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] nlmeODE posthoc
Dear All, I am new to this list, and also to population modeling with R (nlmeODE). Could someone send me a simple example how to do posthoc-type estimate (for example, for the Theoph.nlme model in PKPDmodels library): I have a PK model, and I have a new subject. How to estimate individual parameters for a new subject based on the population model? In general, what would be the best book/tutorial/online resource to learn nlmeODE package (I am a nonmem user, so just need to see examples or clear description of how it needs to be done); I do not want to bother r-help too often but the R-help included into the package is not very detailed. Thanks! Leonid -- -- Leonid Gibiansky, Ph.D. President, QuantPharm LLC web:www.quantpharm.com e-mail: LGibiansky at quantpharm.com tel:(301) 767 5566 __ 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] read a file into a matrix
read.delim gives me a data.frame. Is there a function that can return the result in a matrix rather than data.frame? __ 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] read a file into a matrix
read.delim gives me a data.frame. Is there a function that can return the result in a matrix rather than data.frame? m - as.matrix(read.delim(..)) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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 concatenate expressions
Hi,
You can try this, though I hope to learn of a better way to do it,
a = c(quote(alpha),quote(beta),quote(gamma))
b = lapply(1:3, function(x) as.character(x))
c = c(quote('-10'^th),
quote('-20'^th),
quote('-30'^th))
testplot - function(a,b,c) {
text -
lapply(seq_along(a), function(ii) bquote(.(a[[ii]])*.(b[[ii]])*.(c[[ii]])))
dev.new()
plot(-5:5,-5:5,col=0)
for (i in seq_along(a)) {
text(x=i,
y=i,
labels=text[[i]])
}
}
testplot(a,b,c)
HTH,
baptiste
2009/11/20 Sebastien Bihorel sebastien.biho...@cognigencorp.com:
Dear R-users,
I am developing a plotting function, which receives expressions and
character/numerical vectors as part of the many input arguments and which
tries to concatenate them before displaying the result to the plot. I
currently cannot find a way to make this concatenation works. I have read
several posts in the list that solved this problem by pasting the different
elements together before creating the expressions (like in
http://tolstoy.newcastle.edu.au/R/help/02a/4790.html). I cannot implement
this solution because my expressions and numerical/character vectors are
passed to the function and not create inside the function. I would greatly
appreciate any help with the following example code.
Thank you
testplot - function(a,b,c) {
text - as.expression(paste(a,b,c,sep=' '))
dev.new()
plot(-5:5,-5:5,col=0)
for (i in 1:3) { text(x=i,
y=i,
labels=text[i])
}
}
a - as.expression(c(bquote(alpha),bquote(beta),bquote(gamma)))
b - as.expression(1:3)
c - as.expression(c(bquote('-10'^th),
bquote('-20'^th),
bquote('-30'^th)))
testplot(a,b,c)
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] read a file into a matrix
On Sat, Nov 21, 2009 at 11:55 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: read.delim gives me a data.frame. Is there a function that can return the result in a matrix rather than data.frame? m - as.matrix(read.delim(..)) I knew this approach. But this takes an extra step. Is there a command that read a file directly into a matrix? Regards, Peng __ 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] AKIMA: z values at a set coordinate
Dear all. I am using the akima function to produce 3d contour plots using interp based on irregular data. using the eg in the akima manual library(akima) data(akima) plot(y ~ x, data = akima, main = akima example data) with(akima, text(x, y, formatC(z,dig=2), adj = -0.1)) ## linear interpolation akima.li - interp(akima$x, akima$y, akima$z) image (akima.li, add=TRUE) contour(akima.li, add=TRUE) points (akima, pch = 3) so with this in mind is there a way of obtaining the interpolated value at a particular coordinate eg at (11.25,6.5) I can see that it as an orange and should I look at the contour lines I can see what value it produces. However Is there a way of saying function[11.25,6.5] which provides a value for that coordinate. Hope someone can help [[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] problem with predict from nnet package
Hi,
Im having mayor issues with predict from the nnet package.
Im training a neural network for forecasting. I trained the network with
info from 1995 to 2009 and I want to forecast month by month 2010.(the
network forecasts one month at a time).
Since I have to do iterative forecasting, im using predict several times
including, including the new forecast each time, but for some reason predict
doesnt forecast after the first itereation.
Here is my code:
pronostico4=function(x,rezagosx,muestra, reps, tam, maxi,vo,net){
library(timeSeries)
library(nnet)
library(dummies)
x=as.timeSeries(x)
X=NULL
for (k in 1:length(rezagosx)) {
X=cbind(X, lag(diff(log(x)),rezagosx[k]))
}
pred=predict(net, X,type=raw)
print(sum(is.na(pred)))
pred[muestra]=diff(log(x))[muestra]
pred=exp(diffinv(pred[is.na(pred)==0],xi=log(vo)) )
muestra2=muestra
muestra2[max(which(muestra2==1))+1]=TRUE
print(length(pred))
print(sum(muestra2))
print(sum(is.na(X)))
x[muestra2]=pred[1:sum(muestra2)]
return(x)
}
muestra=(is.na(a[,Precio.Promedio.Bolsa])==0
a[,año]2009)
pred=a[,Precio.Promedio.Bolsa]
pred[muestra==F]=NA
pred=as.timeSeries(pred)
X=NULL
for (k in 1:length(rezagosx)) {
X=cbind(X, lag(diff(log(pred)),rezagosx[k]))
}
net=nnet2(diff(log(pred)),X,muestra,reps,tam,maxi)
for (i in 1:12){
pred=pronostico4(pred,rezagosx,muestra,reps,tam,maxi,vo,net)
muestra[max(which(muestra==1))+1]=TRUE
}
Mauricio Romero
Quantil S.A.
Cel: 3112231150
It is from the earth that we must find our substance; it is on the earth
that we must find solutions to the problems that promise to destroy all life
here
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I specify a partially completed survival analysis model?
On Nov 20, 2009, at 11:07 AM, RWilliam wrote: In reply to suggestion by David W., setting an offset parameter doesn't seem to work as R is not recognizing the X2 part of coxph( Surv(Time,Censor)~X1, offset=log(4.3*X2), data= a ). Also, here's some sample data: The problem, arising as a result of not having a dataset against which to test my memories of syntactic niceties, is that glm and coxph use different methods of supplying offsets. Thereau and Gramsch's book has examples, but if you did not have the book you still had alternatives. A bit of searching with the terms: coxph Therneau offset; produced lots of hits for the occurrence of offset in warning messages so adding -warning to that search then produced a hit to the Google books look at TG's text with a worked example: a$logX2 - log(a$X2) coxph(Surv(Time,Censor)~X1 + offset(logX2), data= a ) Call: coxph(formula = Surv(Time, Censor) ~ X1 + offset(logX2), data = a) coef exp(coef) se(coef) zp X1 -0.885 0.413 1.43 -0.62 0.54 #Or just: coxph(Surv(Time,Censor)~X1 + offset(log(4.3*X2)), data= a ) X1 X2 TimeCensor 1 1 0.40619454 77.00666 0 2 1 0.20717868 100.0 0 3 1 0.77360963 79.03463 1 4 1 0.62221954 100.0 0 5 1 0.32191280 100.0 0 6 1 0.73790704 72.84842 0 7 1 0.65012237 100.0 0 8 1 0.71596105 100.0 0 9 1 0.74787202 84.00172 0 10 1 0.66803790 41.65760 0 11 1 0.79922364 92.41999 0 12 1 0.76433736 90.99983 0 13 1 0.57014524 100.0 0 14 1 0.39642235 100.0 0 15 1 0.55756045 100.0 0 16 0 0.60079340 100.0 0 17 0 0.43630695 100.0 0 18 0 0.09388013 100.0 0 19 0 0.55956791 100.0 0 20 0 0.52491597 97.71884 1 where we set the coefficient of X2 to be 8. RWilliam wrote: Sorry for being impatient but is there really no way of doing this at all? It's quite urgent so any help is very much appreciated. Thank you. RWilliam wrote: Hello, I just started using R to do epidemiologic simulation research using the Cox proportional hazard model. I have 2 covariates X1 and X2 which I want to model as h(t,X)=h0(t)*exp(b1*X1+b2*X2). I assume independence of X from t. After I simulate Time and Censor data vectors denoting the censoring time and status respectively, I can call the following function to fit the data into the Cox model (a is a data.frame containing 4 columns X1, X2, Time and Censor): b = coxph (Surv (Time, Censor) ~ X1 + X2, data = a, method = breslow); Now the purpose of me doing simulation is that I have another mechanism to generate the number b2. From the given b2 (say it's 4.3), Cox model can be fit to generate b1 and check how feasible the new model is. Thus, my question is, how do I specify such a model that is partially completed (as in b2 is known). I tried things like Surv(Time,Censor)~X1+4.3*X2, but it's not working. Thanks very much. -- View this message in context: http://old.nabble.com/How-do-I-specify-a-partially-completed-survival-analysis-model--tp26421391p26443562.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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to: highlight R syntax on webpages ?
My question if in the Subject, but if to extend: I am specifically curious about WordPress blogs. But any solution will give me a lead. Thanks, Tal -- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) [[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] read a file into a matrix
I can't think of anything that is already built in. But you can always: read.as.matrix - function(...) as.matrix(read.delim(...)) and now you get one step only ;-) b On Nov 20, 2009, at 4:01 PM, Peng Yu wrote: On Sat, Nov 21, 2009 at 11:55 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: read.delim gives me a data.frame. Is there a function that can return the result in a matrix rather than data.frame? m - as.matrix(read.delim(..)) I knew this approach. But this takes an extra step. Is there a command that read a file directly into a matrix? Regards, Peng __ 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] How to use results of distribution fitting for further processing?
This is probably simple, but I have a hard time finding the solution. Any help greatly appreciated. I would like to use the results of fitdistr(z,densfun=dweibull,start=list(scale=1,shape=1)) for further processing. How do I assign the values of scale and shape to b and a without manually entering the numbers? TIA __ Looking for the perfect gift? Give the gift of Flickr! [[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: highlight R syntax on webpages ?
take a look at geshi. b On Nov 20, 2009, at 4:26 PM, Tal Galili wrote: My question if in the Subject, but if to extend: I am specifically curious about WordPress blogs. But any solution will give me a lead. Thanks, Tal -- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) [[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.
Re: [R] read a file into a matrix
On Nov 20, 2009, at 1:01 PM, Peng Yu wrote: On Sat, Nov 21, 2009 at 11:55 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: read.delim gives me a data.frame. Is there a function that can return the result in a matrix rather than data.frame? m - as.matrix(read.delim(..)) I knew this approach. But this takes an extra step. Is there a command that read a file directly into a matrix? You can wrap matrix() around a scan() call. An example might prompt more specifics. You also could easily modify read.delim (which is after all a wrapped scan call) to create a matrix rather than a dataframe. -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to use results of distribution fitting for further processing?
Raymond Wong wrote: This is probably simple, but I have a hard time finding the solution. Any help greatly appreciated. I would like to use the results of fitdistr(z,densfun=dweibull,start=list(scale=1,shape=1)) for further processing. How do I assign the values of scale and shape to b and a without manually entering the numbers? fd - fitdistr(z,densfun=dweibull,start=list(scale=1,shape=1)) str(fd) fd$estimate fd$estimate[1] etc Remember the ever useful str(). -Peter Ehlers TIA __ Looking for the perfect gift? Give the gift of Flickr! [[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.
Re: [R] How to concatenate expressions
Thanks a bunch, Baptiste,
Your lapply call works like a charm. BTW, it works also if a, b, and c
are expressions :D
Sebastien
baptiste auguie wrote:
Hi,
You can try this, though I hope to learn of a better way to do it,
a = c(quote(alpha),quote(beta),quote(gamma))
b = lapply(1:3, function(x) as.character(x))
c = c(quote('-10'^th),
quote('-20'^th),
quote('-30'^th))
testplot - function(a,b,c) {
text -
lapply(seq_along(a), function(ii) bquote(.(a[[ii]])*.(b[[ii]])*.(c[[ii]])))
dev.new()
plot(-5:5,-5:5,col=0)
for (i in seq_along(a)) {
text(x=i,
y=i,
labels=text[[i]])
}
}
testplot(a,b,c)
HTH,
baptiste
2009/11/20 Sebastien Bihorel sebastien.biho...@cognigencorp.com:
Dear R-users,
I am developing a plotting function, which receives expressions and
character/numerical vectors as part of the many input arguments and which
tries to concatenate them before displaying the result to the plot. I
currently cannot find a way to make this concatenation works. I have read
several posts in the list that solved this problem by pasting the different
elements together before creating the expressions (like in
http://tolstoy.newcastle.edu.au/R/help/02a/4790.html). I cannot implement
this solution because my expressions and numerical/character vectors are
passed to the function and not create inside the function. I would greatly
appreciate any help with the following example code.
Thank you
testplot - function(a,b,c) {
text - as.expression(paste(a,b,c,sep=' '))
dev.new()
plot(-5:5,-5:5,col=0)
for (i in 1:3) { text(x=i,
y=i,
labels=text[i])
}
}
a - as.expression(c(bquote(alpha),bquote(beta),bquote(gamma)))
b - as.expression(1:3)
c - as.expression(c(bquote('-10'^th),
bquote('-20'^th),
bquote('-30'^th)))
testplot(a,b,c)
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Problem at adding lines on a graphics with lines() function
Hello, I am trying to plot a graphic with many lines with the following command: plot(datas[1:n,1],datas[1:n,2],type=l,main=SP500 Prices and Moving Averages,xlab=Date,ylab=Prices,col=black) lines(datas[1:n,1],datas[1:n,3],type=l,col=green,lty=solid) But I just see the first curve. I have tried it on the console separately and it´s still not working. There is no error message but I can´t see the second curve. Is there a parameter that I need to change with par()? Thank you - Anna Lippel new in R so be careful I should be asking a lt of questions!:teeth: -- View this message in context: http://old.nabble.com/Problem-at-adding-lines-on-a-graphics-with-lines%28%29-function-tp26443627p26443627.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] How to use results of distribution fitting for further processing?
On Nov 20, 2009, at 1:47 PM, Peter Ehlers wrote: Raymond Wong wrote: This is probably simple, but I have a hard time finding the solution. Any help greatly appreciated. I would like to use the results of fitdistr(z,densfun=dweibull,start=list(scale=1,shape=1)) for further processing. How do I assign the values of scale and shape to b and a without manually entering the numbers? library(MASS) fd - fitdistr(z,densfun=dweibull,start=list(scale=1,shape=1)) str(fd) fd$estimate fd$estimate[1] etc Remember the ever useful str(). Agree! You cannot learn R without knowing to use str(). Could also get more self-documenting code with: fd$estimate[c(scale, shape)] -- David -Peter Ehlers David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem at adding lines on a graphics with lines() function
On Nov 20, 2009, at 1:56 PM, anna_l wrote: Hello, I am trying to plot a graphic with many lines with the following command: plot(datas[1:n,1],datas[1:n,2],type=l,main=SP500 Prices and Moving Averages,xlab=Date,ylab=Prices,col=black) lines(datas[1:n,1],datas[1:n,3],type=l,col=green,lty=solid) But I just see the first curve. I have tried it on the console separately and it´s still not working. There is no error message but I can´t see the second curve. Is there a parameter that I need to change with par()? Thank you - Anna Lippel new in R so be careful I should be asking a lt of questions!:teeth: If you are going to be asking a lot of questions, then please take the time to read the Posting Guide and the message at tehend of every r- help reply: and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://old.nabble.com/Problem-at-adding-lines-on-a-graphics-with-lines%28%29-function-tp26443627p26443627.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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] symbol in the plot
Thank you again, Joh Based on your code seems I solved the problem. new code as follows: cs-expression(delta[1], delta[2]) plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta', pch=22, type='o') points(sigma, delta2, col='red', axes=FALSE, type='o') legend(topleft, cs,pch = c(21, 22), lty=1, col=2:1) only concern is there is a waring message in R: Warning message: In plot.xy(xy.coords(x, y), type = type, ...) : axes is not a graphical parameter gcheer3 wrote: a graph question. Thanks a lot in advance. I made two scatterplots on one graph (sigma vs. delta1, sigma vs. delta2) (20 observations of delta1, delta2 and corresponding sigma) the x-axis is sigma, the y-axis is either delta1 or delta2. I connected both scatterplots. To seperate them, one curves is a line with circles, the other curve is a line with squares on it. I want to make a notation either on the y-axis or on the graph. The notiaion is delta1--square; delta2--circle. So when people look at the graph, they can easily tell each curve's meaning. The curve with squares on it means the sigma vs. delta1, and the curve with circles on it means sigma vs. delta2. I think I can use 'expression' to write delta1, delta2 and sigma in greek letters, but I am not sure how to denote the square and cirle I graphed. -- View this message in context: http://old.nabble.com/symbol-in-the-plot-tp26422303p26443550.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] symbol in the plot
Thank you, David. thanks for letting me know how to use expression in legend. It works too. gcheer3 wrote: a graph question. Thanks a lot in advance. I made two scatterplots on one graph (sigma vs. delta1, sigma vs. delta2) (20 observations of delta1, delta2 and corresponding sigma) the x-axis is sigma, the y-axis is either delta1 or delta2. I connected both scatterplots. To seperate them, one curves is a line with circles, the other curve is a line with squares on it. I want to make a notation either on the y-axis or on the graph. The notiaion is delta1--square; delta2--circle. So when people look at the graph, they can easily tell each curve's meaning. The curve with squares on it means the sigma vs. delta1, and the curve with circles on it means sigma vs. delta2. I think I can use 'expression' to write delta1, delta2 and sigma in greek letters, but I am not sure how to denote the square and cirle I graphed. -- View this message in context: http://old.nabble.com/symbol-in-the-plot-tp26422303p26443555.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] How can I remove one of variables which both variables have correlation coefficient more than 0.95 randomly?
http://old.nabble.com/file/p26443595/Edragonr.txt Edragonr.txt
HI all,
I have a 72*495 matrix, and the first column is the response, and the
remaining are independences. Final I want to select some independence to fit
y, but there are so many independences, the fit result is not meaning, so I
want to reduce the independece,now. Which method or R package or algorithms
in R package can deal with this problem?
next question, firstly, I want to check the pair correlation coeficient,and
want to remove one of variables which both variables have correlation
coefficient more than 0.95 randomly? NOTE, This is random. Before I write a
programe that can delete correlation variable onlly the first variable, It
is not scientific.so I hope all friends can help me write a programe to,
randomly,remove one of variables which both variables have correlation
coefficient more than 0.95 ? At last, I use those selected variables to fit
y, and hope the regression result is beter with correlation coefficient (r2)
more than 0.7 at less.
n-0
for(i in 1:(dim.cor[1]-1))
{
for(j in (i+1):(dim.cor[2]))
{
if (mat3.cor[i,j]=0.90)
{
mat3-mat3[,-(i-n)]
n-n+1
break
}
}
} this is my code,but it is not scientific like I said above.
And I upload my file. Hoping all friends can help me.
--
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[R] multivariate type II regressions
Dear all, I am looking for a R package or R code dealing with multivariate type II regressions. I know the lmodel2 and smatr packages, but they just allow to perform bivariate type II regressions. Ideally, I would use the method described by McArdle (1988) called standard minor axis regression, and use the bootstrap to calculate confidence intervals for each coefficient. I would appreciate any help you could provide. Thank you in advance, Angélique McArdle (1988). The structural relationship: regression in biology. Can. J. Zool. 66:2329-2339. -- Angélique Dupuch, PhD Department of Biology Lakehead University 955 Oliver Road Thunder Bay, ON P7B 5E1, CANADA Phone: (807) 343-8732 Fax: (807) 343-7796 [[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] find data (date) gaps in time series
David and Marc, thank you very much for your quick and professional help. Both approaches are doing what I was looking for. Next time I will try to provide an example that is more clearly. Regards, Stefan University of Bayreuth __ 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] Problem at adding lines on a graphics with lines() function
Hi Anna, I guess it happened because the range of datas[1:n, 2] differs from the range of datas[1:n, 3]. A workaround would be either to use the maplot() function as follows or figuring out their ranges and then plug them in as the ylim argument in the plot call. Here is a suggestion using matplot() matplot(datas[1:n,1], cbind(datas[1:n, 2:3]), type=l, main = SP500 Prices and Moving Averages, xlab = Date, ylab = Prices,col = c(black,green), lty = 1) See ?matplot for details. And for what you had before: plot(datas[1:n,1],datas[1:n,2],type=l,main=SP500 Prices and Moving Averages,xlab=Date,ylab=Prices,col=black, ylim = c( min(datas[1:n, 2], datas[1:n, 3]), max(datas[1:n, 2], datas[1:n, 3]))) lines(datas[1:n,1],datas[1:n,3],type=l,col=green,lty=solid) HTH, Jorge On Fri, Nov 20, 2009 at 1:56 PM, anna_l wrote: Hello, I am trying to plot a graphic with many lines with the following command: plot(datas[1:n,1],datas[1:n,2],type=l,main=SP500 Prices and Moving Averages,xlab=Date,ylab=Prices,col=black) lines(datas[1:n,1],datas[1:n,3],type=l,col=green,lty=solid) But I just see the first curve. I have tried it on the console separately and it´s still not working. There is no error message but I can´t see the second curve. Is there a parameter that I need to change with par()? Thank you - Anna Lippel new in R so be careful I should be asking a lt of questions!:teeth: -- View this message in context: http://old.nabble.com/Problem-at-adding-lines-on-a-graphics-with-lines%28%29-function-tp26443627p26443627.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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] symbol in the plot
On Nov 20, 2009, at 10:52 AM, gcheer3 wrote: Thank you again, Joh Based on your code seems I solved the problem. new code as follows: cs-expression(delta[1], delta[2]) plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta', pch=22, type='o') points(sigma, delta2, col='red', axes=FALSE, type='o') legend(topleft, cs,pch = c(21, 22), lty=1, col=2:1) only concern is there is a waring message in R: Warning message: In plot.xy(xy.coords(x, y), type = type, ...) : axes is not a graphical parameter You should not be specifying axis types or flags to a function, [ points() in this case] that is not intended to do anything with the axes. To be Biblical: If thine warning offend thee, pluck it[the argument] out. -- David gcheer3 wrote: a graph question. Thanks a lot in advance. I made two scatterplots on one graph (sigma vs. delta1, sigma vs. delta2) (20 observations of delta1, delta2 and corresponding sigma) the x- axis is sigma, the y-axis is either delta1 or delta2. I connected both scatterplots. To seperate them, one curves is a line with circles, the other curve is a line with squares on it. I want to make a notation either on the y-axis or on the graph. The notiaion is delta1--square; delta2--circle. So when people look at the graph, they can easily tell each curve's meaning. The curve with squares on it means the sigma vs. delta1, and the curve with circles on it means sigma vs. delta2. I think I can use 'expression' to write delta1, delta2 and sigma in greek letters, but I am not sure how to denote the square and cirle I graphed. -- View this message in context: http://old.nabble.com/symbol-in-the-plot-tp26422303p26443550.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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] read a file into a matrix
What is wrong with the extra step? Is it taking too much time (you did not specify that), is it taking too much memory? How many times are you going to be doing it? If not many, then may be it is OK. You have to quantify what you are asking for. It may take longer to send a message to R-Help and get a response than to just read the file in and process it. On Fri, Nov 20, 2009 at 1:01 PM, Peng Yu pengyu...@gmail.com wrote: On Sat, Nov 21, 2009 at 11:55 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: read.delim gives me a data.frame. Is there a function that can return the result in a matrix rather than data.frame? m - as.matrix(read.delim(..)) I knew this approach. But this takes an extra step. Is there a command that read a file directly into a matrix? Regards, Peng __ 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] How to: highlight R syntax on webpages ?
Hi, I am about to release the highlight package which just does that. You would basically do : highlight( some_file, output = some_other_file_or_connection, + renderer = renderer_html() ) If you are in a rush you can grab it from r-forge: http://r-forge.r-project.org/projects/highlight/ Romain On 11/20/2009 07:26 PM, Tal Galili wrote: My question if in the Subject, but if to extend: I am specifically curious about WordPress blogs. But any solution will give me a lead. Thanks, Tal -- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/EAD5 : LondonR slides |- http://tr.im/BcPw : celebrating R commit #5 `- http://tr.im/ztCu : RGG #158:161: examples of package IDPmisc __ 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] nlmeODE
Dear All, One more nlmeODE question: I have a differential equation where one of the parameters depends on time. Values of this parameter at fixed time points are known but need to be interpolated between these known points. Can it be implemented in nlmeODE solver? Thanks Leonid -- Leonid Gibiansky, Ph.D. President, QuantPharm LLC web:www.quantpharm.com e-mail: LGibiansky at quantpharm.com tel:(301) 767 5566 David Winsemius wrote: On Nov 20, 2009, at 10:52 AM, gcheer3 wrote: Thank you again, Joh Based on your code seems I solved the problem. new code as follows: cs-expression(delta[1], delta[2]) plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta', pch=22, type='o') points(sigma, delta2, col='red', axes=FALSE, type='o') legend(topleft, cs,pch = c(21, 22), lty=1, col=2:1) only concern is there is a waring message in R: Warning message: In plot.xy(xy.coords(x, y), type = type, ...) : axes is not a graphical parameter You should not be specifying axis types or flags to a function, [ points() in this case] that is not intended to do anything with the axes. To be Biblical: If thine warning offend thee, pluck it[the argument] out. __ 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 use results of distribution fitting for further processing?
Quite right, David. I forgot to indicate that MASS needs of course to be loaded. It's such a useful package that I usually have it loaded. Raymond: When you ask for help with a function in an add-on package you should indicate that package in your query. -Peter Ehlers David Winsemius wrote: On Nov 20, 2009, at 1:47 PM, Peter Ehlers wrote: Raymond Wong wrote: This is probably simple, but I have a hard time finding the solution. Any help greatly appreciated. I would like to use the results of fitdistr(z,densfun=dweibull,start=list(scale=1,shape=1)) for further processing. How do I assign the values of scale and shape to b and a without manually entering the numbers? library(MASS) fd - fitdistr(z,densfun=dweibull,start=list(scale=1,shape=1)) str(fd) fd$estimate fd$estimate[1] etc Remember the ever useful str(). Agree! You cannot learn R without knowing to use str(). Could also get more self-documenting code with: fd$estimate[c(scale, shape)] __ 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: highlight R syntax on webpages ?
Hello, I wrote a Wordpress blog entry about not only highlighting R syntax, but embedding R commands within an entry and using Sweave to produce the R output, all within Emacs. The output of the process is ready to paste Wordpress HTML, and a few other R blogs have started using it to generate their content. Disclaimer, the following is a link to my blog, but it describes a process you might be interested in: http://blogisticreflections.wordpress.com/2009/09/20/welcome-to-blogistic-reflections/ Best, Erik -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tal Galili Sent: Friday, November 20, 2009 12:27 PM To: r-help@r-project.org Subject: [R] How to: highlight R syntax on webpages ? My question if in the Subject, but if to extend: I am specifically curious about WordPress blogs. But any solution will give me a lead. Thanks, Tal -- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) [[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.
Re: [R] Performance of 'by' and 'ddply' on a large data frame
A faster solution using tapply was sent to me via email:
testtapply = function(p){
df = randomdf(p)
system.time({res = tapply(df$x2,df$x1,min);
res = as.Date(res,origin=as.Date('1970-01-01'));
df$mindate = res[as.character(df$x1)]})
}
Thanks Phil!
Tahir
On Thu, Nov 19, 2009 at 5:19 PM, Tahir Butt tahir.b...@gmail.com wrote:
I've only recently started using R. One of the problems I come up
against is after having extracted a large dataset (5M rows) out of
database, I realize I need another variable. In this case I have data
frame with dates. I want to find the minimum date for each value of x1
and add that minimum date to my data.frame.
randomdf - function(p) {
data.frame(x1=sample(1:10^4, 10^p, replace=T),
x2=sample(seq.Date(Sys.Date() - 356*3,Sys.Date(), by=day), 10^p, replace=T),
y1=sample(1:100, 10^p, replace=T))
}
testby - function(p) {
df - randomdf(p)
system.time(by(df, df$x1, function(dfi) { min(dfi$x2) }))
}
lapply(c(1,2,3,4,5), testby)
[[1]]
user system elapsed
0.006 0.000 0.006
[[2]]
user system elapsed
0.024 0.000 0.025
[[3]]
user system elapsed
0.233 0.000 0.234
[[4]]
user system elapsed
1.996 0.026 2.022
[[5]]
user system elapsed
11.030 0.000 11.032
Strangely enough, not sure why this is, the result of by with the min
function is not date objects but instead integers representing days
from an origin. Is there a min function that would return me a date
instead of an integer? Or is this a result of using by?
I also wanted to see how ddply compares.
testddply - function(p) { pdf - randomdf(p); system.time(ddply(pdf, .(x1),
function(df) { return (data.frame(min(df$x2))) })) }
lapply(c(1,2,3,4,5), testddply)
[[1]]
user system elapsed
0.020 0.000 0.021
[[2]]
user system elapsed
0.119 0.000 0.119
[[3]]
user system elapsed
1.008 0.000 1.008
[[4]]
user system elapsed
8.425 0.001 8.428
[[5]]
user system elapsed
23.070 0.000 23.075
Once the data frame gets above 1M rows, the timings are a bit too long
(on a previous run it went up to 8000s user time). This seems quite a
bit slower than I expected. Maybe there's a better and faster way to
add such variables to a data frame that are derived using some
aggregation.
Also, ddply seems to take twice as long as by. Are these two
operations not equivalent?
Thanks,
Tahir
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Re: [R] nlmeODE
Please, ignore this question (see below): I found the way how to do it Thanks Leonid -- Leonid Gibiansky, Ph.D. President, QuantPharm LLC web:www.quantpharm.com e-mail: LGibiansky at quantpharm.com tel:(301) 767 5566 Leonid Gibiansky wrote: Dear All, One more nlmeODE question: I have a differential equation where one of the parameters depends on time. Values of this parameter at fixed time points are known but need to be interpolated between these known points. Can it be implemented in nlmeODE solver? Thanks Leonid -- Leonid Gibiansky, Ph.D. President, QuantPharm LLC web:www.quantpharm.com e-mail: LGibiansky at quantpharm.com tel:(301) 767 5566 David Winsemius wrote: On Nov 20, 2009, at 10:52 AM, gcheer3 wrote: Thank you again, Joh Based on your code seems I solved the problem. new code as follows: cs-expression(delta[1], delta[2]) plot(sigma, delta1, ylim=range(-0.5, 2), xlab='sigma', ylab='delta', pch=22, type='o') points(sigma, delta2, col='red', axes=FALSE, type='o') legend(topleft, cs,pch = c(21, 22), lty=1, col=2:1) only concern is there is a waring message in R: Warning message: In plot.xy(xy.coords(x, y), type = type, ...) : axes is not a graphical parameter You should not be specifying axis types or flags to a function, [ points() in this case] that is not intended to do anything with the axes. To be Biblical: If thine warning offend thee, pluck it[the argument] out. __ 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] formatting dates in axis labels (ggplot2)
Hi Michael, I'm having trouble figuring out how to format Date variables when used as axis labels in graphs. The particular case here is an attempt to re-create Nightingale's coxcomb graph with ggplot2, where I'd like the months to be labeled as Mar 1885, Apr 1885, using a date format of %b %Y applied to label the dates, or really anything other than 1885-03-01. I know the solution has to do with formatting the dates, while preserving their status as an ordered factor, but I don't know how to do that. Dates are, by their very nature, ordered so you don't need to keep them as an ordered factor. If you don't do that you'll find that the scale_date formatting options will work. Hadley -- http://had.co.nz/ __ 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 2.10 'memory leak'? on OS X
Thanks a lot Duncan and David, the remedy was to delete the files .Rhistory and .RData via the terminal - with rm . Rhistory etc. (By default they are hidden on OS X.) Now R.app opens fine. best, Steve David Winsemius wrote: Probably best further discussed on R-SIG-Mac list: https://stat.ethz.ch/mailman/listinfo/r-sig-mac ... since that is where the tricks of convincing MacOSX to display system files is discussed and a semi-regular basis: https://stat.ethz.ch/pipermail/r-sig-mac/2009-November/006768.html https://stat.ethz.ch/pipermail/r-sig-mac/2009-March/005925.html -- David. On Nov 20, 2009, at 10:38 AM, Stropharia wrote: Thanks Duncan, I managed to get R to start through the terminal this way. Still no luck getting the R.app to start. Is it possible to directly access (and then trash or modify) the .RData and .RProfile files? I assume they would be recreated if I could then open the R.app. Having searched for them on spotlight and in the /user/library folder, I don't see them anywhere - are they always located in the same place on OS X? thanks, Steve Duncan Murdoch-2 wrote: On 20/11/2009 12:33 AM, Stropharia wrote: Dear R users, I am running R 2.10.0 on OS X 10.5.8. I had been running 2.10 successfully for about a week (and have used previous R versions for 2+ years on the same computer) until 2 days ago it failed to start up for me. Now when I try to start R, the application tries to initiate for several minutes then crashes. Looking at the activity monitor, my memory usage goes from having about 1.6Gb free (out of 2Gb) to 7Mb in the first 10-15 seconds of attempting to start the program. At this point I either have to force quit R (as everything starts to freeze up) or wait several minutes for it to crash. I have erased the application and reinstalled it 4 times now - with exactly the same result. I looked around in the Library and System folders to see if any other files needed to be removed, but couldn't find any. I have also restarted the computer and repaired permissions multiple times - and then reinstalled R, with no luck. The exact same thing happens if I start R64. I did not updated OS X or R, or install any other programs, just prior to this first happening and am at a loss to explain what's going on. I have copied the first part of one of the crash logs below. Does anyone have any ideas for to remedy this? It sounds like one of your user-specific startup files is causing the problem, e.g. .RData, or .Rprofile. Did you try starting R with option --vanilla? That will skip them. Duncan Murdoch best, Steve # Crash log Process: R [231] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: R 2.10.0 GUI 1.30 Leopard build 32-bit (5511) Code Type: X86 (Native) Parent Process: launchd [101] Date/Time: 2009-11-18 23:15:45.570 -0500 OS Version: Mac OS X 10.5.8 (9L31a) Report Version: 6 Anonymous UUID: D86CDCBC-00FD-4AEE-AB50-2EFE0DAE9E1E Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x00067ee2 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0x07c7 __memcpy + 39 (cpu_capabilities.h:246) 1 com.apple.CoreFoundation 0x96a6a0b4 __CFStringEncodeByteStream + 4052 2 com.apple.Foundation 0x94446eb7 -[NSString(NSStringOtherEncodings) getBytes :maxLength:usedLength:encoding:options:range:remainingRange:] + 295 3 com.apple.Foundation 0x94446a1a _NSNewStringByAppendingStrings + 538 4 com.apple.Foundation 0x94446760 -[NSString stringByAppendingString:] + 192 5 org.R-project.R 0x9ce8 -[RController doLoadHistory:] + 808 6 org.R-project.R 0x76df -[RController awakeFromNib] + 2319 7 com.apple.CoreFoundation 0x96ac07f5 -[NSSet makeObjectsPerformSelector:] + 181 8 com.apple.AppKit 0x92efed8e -[NSIBObjectData nibInstantiateWithOwner:topLevelObjects:] + 1533 9 com.apple.AppKit 0x92ef4fba loadNib + 264 10 com.apple.AppKit 0x92ef491c + [NSBundle(NSNibLoading) _loadNibFile:nameTable:withZone:ownerBundle:] + 946 11 com.apple.AppKit 0x92ef455f + [NSBundle(NSNibLoading) loadNibFile:externalNameTable:withZone:] + 171 12 com.apple.AppKit 0x92ef449d + [NSBundle(NSNibLoading) loadNibNamed:owner:] + 391 13 org.R-project.R 0x2538 main + 296 14 org.R-project.R 0x23d6 start + 54 #-- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
Re: [R] How to: highlight R syntax on webpages ?
Hi Erik, Interesting blog. I was pleased to see the reference to org-babel, a language-agnostic alternative to Sweave. Org-babel is a software masterpiece that anyone using emacs, LaTeX and R should know about, especially if they also use python, ruby, clojure, etc. All the best, Tom On Nov 20, 2009, at 10:02 AM, Erik Iverson wrote: Hello, I wrote a Wordpress blog entry about not only highlighting R syntax, but embedding R commands within an entry and using Sweave to produce the R output, all within Emacs. The output of the process is ready to paste Wordpress HTML, and a few other R blogs have started using it to generate their content. Disclaimer, the following is a link to my blog, but it describes a process you might be interested in: http://blogisticreflections.wordpress.com/2009/09/20/welcome-to-blogistic-reflections/ Best, Erik -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org ] On Behalf Of Tal Galili Sent: Friday, November 20, 2009 12:27 PM To: r-help@r-project.org Subject: [R] How to: highlight R syntax on webpages ? My question if in the Subject, but if to extend: I am specifically curious about WordPress blogs. But any solution will give me a lead. Thanks, Tal -- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) [[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 with multiple comparisons on a 2-way repeated measures ANOVA
Hi everyone, I'm trying to do a 2-way repeated measures ANOVA with data that looks like this: subject block rep day light response 1 1 1oneL1 5.5 2 1 2oneL1 4.5 3 1 1oneL2 4 4 1 2oneL2 5.1 5 2 1oneL1 5.3 6 2 2oneL1 4.8 7 2 1oneL2 4.6 8 2 2oneL2 4.9 1 1 1twoL1 5.2 2 1 2twoL1 5.0 3 1 1twoL2 3.2 4 1 2twoL2 3.4 5 2 1twoL1 4.6 6 2 2twoL1 4.9 7 2 1twoL2 3.3 8 2 2twoL2 2.9 I'm using lme(): m1-light(buoy~light*day, random=~1|subject/day) summary(m1) and get this output: Linear mixed-effects model fit by REML Data: NULL AIC BIClogLik 24.94574 28.34008 -5.472868 Random effects: Formula: ~1 | subject (Intercept) StdDev: 0.05400619 Formula: ~1 | day %in% subject (Intercept)Residual StdDev: 0.29127730.06415494 Fixed effects: response ~ light * day Value Std.ErrorDF t-value p-value (Intercept) 5.025 0.1515545 6 33.15640 0. lightL2 -0.200 0.2143304 6 -0.93314 0.3868 daytwo -0.100 0.2109008 6 -0.47416 0.6522 lightL2:daytwo -1.525 0.2982588 6 -5.11301 0.0022 Correlation: (Intr) lghtL2 daytwo lightL2 -0.707 daytwo -0.696 0.492 lightL2:daytwo 0.492 -0.696 -0.707 Standardized Within-Group Residuals: MinQ1 MedQ3 Max -0.36863373 -0.15741132 0.03092751 0.14569214 0.32591770 Number of Observations: 16 Number of Groups: subject day %in% subject 816 My FIRST problem is that I'm not quite sure how to analyse the above output. My SECOND problem is when I try to use glht(), to get multiple comparisons: summary(glht(m1,linfct=mcp(day=Tukey))) I get an error message: Error in as.vector(x, mode) : invalid 'mode' argument Im not sure where this comes from. I've tried everything I (and my labmates, we are a bunch of field biologists, not statisticians) can think of, but this keeps coming back. Is it because glht() isn't appropriate for 2-way ANOVAs? If that's the problem, what is the correct way to do this? Or am I going about this completely wrong from the get-go? Thanks for all the help you can provide! K [[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.
