Re: [R] modifying factors in a data frame
Kiaora Koe Peter It worked. I hope I am getting my Maori right. -Abhi On Thu, Aug 19, 2010 at 1:50 AM, Peter Alspach peter.alsp...@plantandfood.co.nz wrote: Tena koe Abhi The easiest way is probably data1$sample - as.numeric(data1$sample) If you want it to remain as a factor then data1$sample - as.factor(as.numeric(data1$sample)) HTH Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Abhishek Pratap Sent: Thursday, 19 August 2010 5:41 p.m. To: r-help@r-project.org Subject: [R] modifying factors in a data frame Hi All I have a data frame in which on the columns is a factor with following levels Levels: M006 M0114 M0379 M0432 M0823 M1012 M1096 M1107 SW393 SW708 I want to change all the M006 to 1, M0114 to 2 and so on. What I am trying is not working. data1$sample[data1$sample =='M006'] - 1 Warning message: In `[-.factor`(`*tmp*`, data1$sample == M006, value = 1) : invalid factor level, NAs generated Any slick way to do this ? Thanks! -Abhi [[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] R reports
I don't see much in the way of an ability to write reports in R the way you can with SAS. You basically have to write a program with R in a 3G way unlike SAS with it's 4G proc print and proc report. Are there similar R functions and packages? -- View this message in context: http://r.789695.n4.nabble.com/R-reports-tp2330733p2330733.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] Help with Vectors and conditional functions
Good morning,
I have something like this: names(coint_tests) - apply(b,2,paste,
collapse=_) which prints 15 names like: A_B, C_D, E_F, ...
AA,B,C,D.. Are time series. Then there is a vector called coint_tests of length
15 which yields yes or no.
I need to add a function to plot the time series Ai_Bi if the coint_tests
vectors gives me a YES.
I tried:for (i in 1:(length(coint_tests))
if (coint_tests[[i]]=YES) {plot(coint_tests[i])}
But it does not work. I would most appreciate if someone could give me some
insight as to how to sort this out. Thank you
__
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Re: [R] Rolling window linear regression
The function rollapply() in package zoo can be used to run rolling
regressions. See the examples in the manual page for a worked example.
On Thu, 19 Aug 2010, siddharth.gar...@gmail.com wrote:
Thanks, I will try it.
Regards
Sid
Sent on my BlackBerry? from Vodafone
-Original Message-
From: Dennis Murphy djmu...@gmail.com
Date: Wed, 18 Aug 2010 08:46:49
To: siddharth.gar...@gmail.com
Subject: Re: [R] Rolling window linear regression
This is called kernel-based regression; the most popular version is loess.
Try
library(sos)
findFn('loess')
to see some of the various implementations available, including graphics
functions. The basic function is loess(); the window width is related to the
span = parameter of that function.
HTH,
Dennis
On Wed, Aug 18, 2010 at 2:08 AM, siddharth.gar...@gmail.com wrote:
Hi
Does there exists an efficient way of performing linear regression on
rolling windows in R.
The exact problem is:
We have a dataset of length l. The window size is w.
Now, I perform linear regression on window i to (i+w) . Using this model
can I perform linear regression over window (i+1) to (i+w+1).
Thanks
Sid
Sent on my BlackBerry? from Vodafone
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with Vectors and conditional functions
Hi,
I haven't spent too much time on it, but that might help:
if (coint_tests[[i]]==YES)...
Note the double = which is the operator for equality. The single =
is the assignment operator, especially with arguments.
HTH, Ivan
Le 8/19/2010 09:03, Ferreira, Thiago Alves a écrit :
Good morning,
I have something like this: names(coint_tests)- apply(b,2,paste,
collapse=_) which prints 15 names like: A_B, C_D, E_F, ...
AA,B,C,D.. Are time series. Then there is a vector called coint_tests of
length 15 which yields yes or no.
I need to add a function to plot the time series Ai_Bi if the coint_tests
vectors gives me a YES.
I tried:for (i in 1:(length(coint_tests))
if (coint_tests[[i]]=YES) {plot(coint_tests[i])}
But it does not work. I would most appreciate if someone could give me some
insight as to how to sort this out. Thank you
__
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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.
--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. Säugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de
**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php
[[alternative HTML version deleted]]
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Re: [R] Rolling window linear regression
On Thu, 19 Aug 2010, siddharth.gar...@gmail.com wrote:
Hi
That's right, but that isn't what I am trying to achieve. When we have a
rolling window, the only difference between two neighboring windows is
first and the last point.
Yes, this is what the example does. Consider the following artificial
example:
## artificial bivariate series of length 5
set.seed(1)
z - zoo(matrix(rnorm(10), ncol = 2))
colnames(z) - c(y, x)
## rolling regression of width 4
rollapply(z, width = 4,
function(x) coef(lm(y ~ x, data = as.data.frame(x))),
by.column = FALSE, align = right)
## result is identical to
coef(lm(y ~ x, data = z[1:4,]))
coef(lm(y ~ x, data = z[2:5,]))
First window indexes from i to i+w and second
window from (i+1) to (i+w+1). Is there a efficient way to run regression
on second window if I am given the results of regression on the first
window.
Yes, the above computations are not efficient but use a brute-force
approach. I'm not sure whether there is a rolling regression
implementation that uses an updating algorithm.
Z
Regards
Sid
--Original Message--
From: Achim Zeileis
To: siddharth.gar...@gmail.com
Cc: Dennis Murphy
Cc: R-help@r-project.org
Subject: Re: [R] Rolling window linear regression
Sent: Aug 19, 2010 12:42 PM
The function rollapply() in package zoo can be used to run rolling
regressions. See the examples in the manual page for a worked example.
On Thu, 19 Aug 2010, siddharth.gar...@gmail.com wrote:
Thanks, I will try it.
Regards
Sid
Sent on my BlackBerry? from Vodafone
-Original Message-
From: Dennis Murphy djmu...@gmail.com
Date: Wed, 18 Aug 2010 08:46:49
To: siddharth.gar...@gmail.com
Subject: Re: [R] Rolling window linear regression
This is called kernel-based regression; the most popular version is loess.
Try
library(sos)
findFn('loess')
to see some of the various implementations available, including graphics
functions. The basic function is loess(); the window width is related to the
span = parameter of that function.
HTH,
Dennis
On Wed, Aug 18, 2010 at 2:08 AM, siddharth.gar...@gmail.com wrote:
Hi
Does there exists an efficient way of performing linear regression on
rolling windows in R.
The exact problem is:
We have a dataset of length l. The window size is w.
Now, I perform linear regression on window i to (i+w) . Using this model
can I perform linear regression over window (i+1) to (i+w+1).
Thanks
Sid
Sent on my BlackBerry? from Vodafone
__
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]]
Sent on my BlackBerry® from Vodafone__
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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] reading lmer table
Hi Nicola, In few word: does this row indicate a global effect of the predictor 'cat' or a more specific passage? It indicates a more specific passage. Use anova(m7) for global/omnibus. Check this for yourself by fitting the model with different contrasts. The default contrasts in R are treatment contrasts. ## m7 - lmer(log.second ~ Cond + cat + (1|subjID) + (1|Code), data = march.f, contrasts=list(Cond=contr.treatment, cat=contr.treatment)) m7s - lmer(log.second ~ Cond + cat + (1|subjID) + (1|Code), data = march.f, contrasts=list(Cond=contr.sum, cat=contr.sum)) summary(m7) summary(m7s) anova(m7) anova(m7s) Regards, Mark. -- View this message in context: http://r.789695.n4.nabble.com/reading-lmer-table-tp2329521p2330809.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] AIC in MuMIn
On Thu, 2010-08-19 at 04:42 +0800, elaine kuo wrote: Yes, I tried the example in the ?dredge and agreed that something else caused the mistake. Aside from the cause which takes time to clarify (16 explanatory variables in the model), I would like to ask another question. Please kindly advise if it is possible to show the singular model with only one certain variable using the command subset. (or maybe others) I tried the command subset=X3 but it returned multiple models including X3. The above demand might look unnecessary when visual inspection offers the solution with few exp. variables. However, it is of great importance for recognizing AIC for each variable in the model selection with more than 10 variables. No, there isn't. The object returned by dredge is a data frame so you can subset it to your hearts content, but you'll need to select rows where you specify that all your variables (except the one you are interested in) are missing (NA). Without writing this all out, I don't know of a quick way of doing this sort of subsetting. In effect, you want data(Cement) lm1 - lm(y ~ ., data = Cement) dd - dredge(lm1, subset = X1) want - with(dd, is.na(X) is.na(X2) is.na(X3) is.na(X4)) want ## how many models selected? sum(want) ## OK selected just 1, show it dd[want, , drop = FALSE] Oh, actually, I suppose you could automate this, so it will return all models with single variable: dd - dredge(lm1) parms - !is.na(dd[, -c(1, (ncol(dd) - c(0:7)))]) want - which(rowSums(parms) == 1) dd[want, ] Having said all this, I don't think this is a good way to do model selection. G Please kindly help and thank you in advance. Elaine code library(MuMIn) data(Cement) lm1 - lm(y ~ ., data = Cement) dd - dredge(lm1, beta = FALSE, eval = TRUE, rank = AIC) X3-dredge(lm1, rank = AIC, subset=X3) On Wed, Aug 18, 2010 at 9:18 PM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Wed, 2010-08-18 at 21:11 +0800, elaine kuo wrote: A cause other than data based on standardized regression was identified. It is that the manual command added with target - at the left hand side. C1 did not work but C2 did. C1 target-dredge(mig.stds, subset = temp_max) C2 dredge(mig.stds, subset = temp_max) Glad you have this working, but that can't possibly be the reason for the error. There must be something else going on. The only difference between the two calls is that you are storing the result somewhere, yet the error was coming from within the running of the dredge function. If everything works from within a new, clean R session then great. G Elaine On Wed, Aug 18, 2010 at 5:37 PM, elaine kuo elaine.kuo...@gmail.com wrote: Please suggest how to define subset in my case How would I know? I still haven't seen your data. You seem to be mistaken on what is and is not included in your model and you fitted it. What hope do we have...? However, given the model 'mig.stds' from above in this email: mig.stds -lm(SummerM_ratio ~ temp_max + evi_mean + topo_var + topo_mean + coast + Iso_index_0808, ## now tell R were to find the variables in formula data = datum.std) ## If you are fitting a Gaussian GLM it is better fitted with lm() If you want to consider dredged models containing temp_max, then you would do dredge(mig.stds, subset = temp_max) If you want models that contain temp_max and coast, then you'd do dredge(mig.stds, subset = temp_max coast) or dredge(mig.stds, fixed = ~ temp_max + coast) The bits you include in subset or fixed are the names of your variables that you want in or out of the models. In your
Re: [R] Yet another memory limit problem
Thanks for everyones help - mydat was not what I thought it was. str(mydat) showed: $ Date : Factor w/ 1504 levels ,2002-11-22,..: 295 295 295 295 295 295 295 295 295 295 ... $ Time : Factor w/ 72447 levels ,00:00:00,..: 15423 15470 15509 17112 17136 17159 17209 17239 17266 21527 ... I didn't properly convert date and time using chron. Not sure how R plots factor levels, but obviously it has problems with it! Aloha, Tim Tim Clark Department of Zoology University of Hawaii - Original Message From: Peter Dalgaard pda...@gmail.com To: Tim Clark mudiver1...@yahoo.com Cc: r-help@r-project.org Sent: Wed, August 18, 2010 8:34:56 AM Subject: Re: [R] Yet another memory limit problem On 08/18/2010 11:19 AM, Tim Clark wrote: Dear List, ... I would appreciate some help. I think I set the target field correctly, both memory.size and memory.limit indicate I have over 2G of memory, yet I can't allocate 831.3Mb? It just doesn't make sense to me. That shouldn't by itself cause concern. It is always the _last_ allocation that triggers the message, so it could happen due to allocation of 3 vectors of size 800M. Straw, camel, back... Another matter is that memory.size is the amount _used_, not amount _available_, so you would seem to have more like 1500M left. However, it does look odd that mydat with dimensions 245x9 should generate an 800M memory request. As others have suggested, perhaps mydat is not what you think it should be... -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] Why does Bootstrap work for one of similar models but not for the other?
Dear all, Could anyone help me figure out why bootstrap works for one of similar models but not for the other and how I can solve it? I am using R 2.11.1 in Windows and would like to get confidence intervals for my models A and B by bootstrapping. However, bootstrap gives expected output for the model A but not for B, which I found was puzzling because the structure of the models is similar as I describe below. I had another person running the models in another computer and the same thing happens so this does not seem to be computer-specific. I could not find a clue for a solution in the R archive or in the R book (at least to the extent I understood). Here are the properties of the models A and B and what happens when I run bootstrap. modelA: rA~stA1+ stA2+stA3 model B: rB~stB1+stB2+stB3 The variables for the models A and B are in the same dataset called ?data?. The sample size is 32 for both models and the value range and distribution of the variables in the two models are similar. (Variables from both models are at the end of this enquiry.) [bootstrap of the model A] A.fun-function(data,indices)coefficients(lm(rA~stA1+ stA2+stA3,data=data[indices,])) bootA-boot(data,A.fun,1000);bootA ORDINARY NONPARAMETRIC BOOTSTRAP Call: boot(data = data, statistic = A.fun, R = 1000) Bootstrap Statistics : original biasstd. error t1* 1.00016501 -0.004350842 0.05309877 t2* 0.02343475 0.008501989 0.07638795 t3* -0.01602954 -0.004980400 0.07806805 t4* 0.03601194 -0.005417404 0.08510128 [bootstrap of the model B] B.fun-function(data,indices)coefficients(lm(rB~stB1+stB2+stB3),data=data[indices,]) bootB-boot(data,B.fun,1000);bootB ORDINARY NONPARAMETRIC BOOTSTRAP Call: boot(data = data, statistic = B.fun, R = 1000) Bootstrap Statistics : original biasstd. error t1* 0.99975370 0 0 t2* -0.06091574 0 0 t3* 0.27506203 0 0 t4* -0.03040424 0 0 What am I missing here? I highly appreciate any comments and suggestions. Best Wishes, Reiko Akiyama Uppsala University Sweden [Variables from the model A] rA [1] 0.7100881 1.0406464 1.1100229 0.6182664 0.7345739 1.0577865 0.6856024 [8] 0.5264447 1.5793340 1.1793993 0.6488737 1.0214076 1.3589618 1.0528893 [15] 1.5242409 1.3761019 0.9427032 0.6794809 1.4752693 0.7737512 1.0120797 [22] 0.8692458 1.2079660 1.0610513 0.8570029 0.9794319 1.0957395 0.8243552 [29] 0.4162586 1.4079334 1.0692132 1.1059419 stA1 [1] -0.9126354 -0.8331680 -1.0239203 -0.3721959 -0.5311308 0.7564474 [7] -1.1828933 -1.2146727 -0.8172593 -0.9921410 -0.5152602 -0.9285442 [13] -0.4198840 -0.9444529 -0.4198840 -0.8331680 1.2810163 1.4081718 [19] 1.7102091 2.3460247 1.3806653 1.3127957 1.2333282 1.4240806 [25] -0.1337555 -0.1973142 0.2954372 -0.1337555 -0.4039753 -0.3880665 [31] 0.2795666 -0.2291317 stA2 [1] -0.2292617 -0.4917962 -0.6437899 -1.2241293 -0.3398026 -2.0946384 [7] -1.0721356 -1.2655821 -1.3484877 -1.8873744 -0.7543307 -0.9615948 [13] -0.3674378 0.4483537 0.8761467 -0.8786892 0.5312593 1.1524988 [19] 0.3234425 -0.4088906 0.5102565 1.1945044 1.7748438 0.6827002 [25] 0.6418001 1.1801340 0.4207184 0.8076114 0.9181522 0.6827002 [31] 0.9037819 0.9181522 stA3 [1] 0.86459627 -0.23416149 -2.00372671 0.04161491 0.78881988 -2.50869565 [7] -0.02608696 -0.84161491 -0.95465839 -0.28012422 0.47080745 0.07577640 [13] 0.84223602 0.24472050 2.83975155 0.43043478 -0.75652174 -0.92795031 [19] 0.29192547 -0.78633540 -0.78385093 -0.51242236 0.59627329 0.19068323 [25] 0.02919255 1.17018634 -0.19440994 0.68385093 1.08881988 -0.28385093 [31] -0.71118012 1.06583851 [Variables from the model B] rB [1] 1.5385568 1.5885100 1.3587255 0.8991566 1.4086787 0.3097095 0.9191378 [8] 0.3996252 0.7393065 0.6993440 1.2488286 1.4186693 1.4586318 1.8282851 [15] 0.8991566 0.9790816 1.0889785 1.0090535 0.7792690 0.8991566 0.8791753 [22] 0.7892597 0.6294096 0.9690910 1.0689973 0.5994377 0.6793628 0.7293159 [29] 0.9690910 0.7393065 0.7193253 1.7583507 stB1 [1] -0.67898627 -0.94275552 -1.32045796 0.03417996 -1.18276552 2.01872951 [7] -1.75937865 -1.85016395 -0.70319013 -0.89159673 -0.35055299 -0.38890124 [13] -0.81445562 -0.98941255 -0.95548269 -0.63066192 0.52759406 1.27063302 [19] 1.19746568 1.34424498 0.62679931 1.15103096 1.24195520 0.94395043 [25] 0.20232868 0.71085978 0.53654199 0.67470683 0.41377202 0.38428833 [31] 0.58178180 -0.40626910 stB2 [1] 2.18599646 1.64030436 0.29913150 -0.30874645 2.29052340 -2.13238029 [7] -0.78386750 -0.53233418 -0.96552917 -1.00046883 -0.02227346 -0.71399585 [13] 0.42490201 1.27034048 0.09650296 -0.32970563 -0.23188840 -0.24586119 [19] 0.04061179 -0.07118592 -0.49040812 -0.04323265 -0.06419952 -0.18297594 [25] 0.40393513 -0.73495504 -0.53233418 -0.23188840 0.13144263 -0.21092921 [31] -1.24501576 2.29052340 stB3 [1] -0.368 0.3416667 -1.788 -1.813 -0.617
[R] Slow response from Windows Rgui - caused by Word?
Dear list, I quite often experience a delayed response when I type in the console of the RGui of my computer. When typing a command, the text only appears letter-by-letter on the console if I type rather slow (maximum 1-2 letters per second), otherwise it appears some time after I finished writing the complete command. Moving back and forth in a command with arrows keys are similarly slow if I need to correct something (which I often have to do, given that I cannot read while writing). Although this might sound like a minor problem (thinking takes more time than writing when programming, and writing should anyway take place in a proper text editor), it is quite annoying, especially when I just want to rerun a long command after changing something at the start of the line. Strangely, it seems that this problem starts when I open a Word-document, and it stops when I close all open Word-documents. I do not have any problems with other programs (including other programs from the office package), and computation seems to run as quick as normal. Some info about my system: sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base objects() character(0) And as Word seems to be connected to the problem - I am running Windows 7 Pro with Office 2007, the only Add-In to Word is Endnote (version 9). I have turned off the instant formatting option, as it also caused some other problems. Does anyone have a clue how I can have a Word document open and at the same time work with R without having this delayed response? Best wishes, Jon __ 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] texi2dvi: option clean also deletes the generated pdf file
Dear expeRts,
below are two examples of using texi2dvi. The problem becomes clear from the
second example: on cleaning, texi2dvi also deletes the generated .pdf file.
Is there a solution?
Cheers,
Marius
## Example 1: texi2dvi cleans fine, without deleting the generated .pdf
require(tools)
sink(file=myLaTeXFile1.tex)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(myLaTeXFile1.tex,pdf=TRUE,clean=TRUE,quiet=TRUE)
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] ROCR predictions
Hello everybody, yes I'm sorry. I can see it is not so easy to understand. I'l try to explain a bit more. The experiment was used to compare two (protein domain) data bases and find out whether or not the results founded in one are comparable to the second DB. the first column shows the list of the various inputs in the DB, the second lists the various domains for each gene. the p-value column calculates the probability that the found in column four (Expected) to be found by chance. in column five the expected values was listed. The calculation of the TP,TN,FP,FN was made many times, each time with a different p-value (from p=1,...,p=10E-12) as a threshold to calculate the various values of TP,TN, etc. The goal of this calculation was to find the optimal p-value wit ha maximum of TP and a minimum of FP. To do so I thought about making the column of p-values my predictions and the values in the column Is.Expected (TRUE,FALSE) to my labels. This how I calculated my first ROC curve: pValue - read.delim(file = p=1.txt, as.is= TRUE) desc1 - pValue[[p.value]] label1 - pValue[[Is.Expected]] # after changing the values of TRUE = 0, FALSE = 1 pred - prediction(desc1, label1) perf - performance(pred, tpr, fpr) plot(perf, colorsize = TRUE) my question are as follow: 1. Am I right in my way of thinkning, that the p-values here are predictions? I know you said I need to decided it for myself, but I'm not sure. If they are, than I will have the same predictions for each and every calculation of ROCR. Will it make any difference at the prediction? 2. how can i calculate the other p-values thresholds? Do I need to do each separately, or is there a way of combining them? I hope you can still help we with some hints or further advieces. Thanks Assa On Wed, Aug 18, 2010 at 07:55, Claudia Beleites cbelei...@units.it wrote: Dear Assa, you need to call prediction with continuous predictions and a _binary_ true class label. You are the only one who can tell whether the p-values are actually predictions and what the class labels are. For the list readers p is just the name of whatever variable, and you didn't even vaguely say what you try to classify, nor did you offer any explanation of what the columns are. The only information we get from your table is that p-value has small and continuous values. From what I see the p-values could also be fitting errors of the predictions (e.g. expressed as a probability that the similarity to the predicted class is random). Claudia Assa Yeroslaviz wrote: Dear Claudia, thank you for your fast answer. I add again the table of the data as an example. Protein ID Pfam Domain p-value ExpectedIs Expected True Postive False Negative False Positive True Negative NP_11.2 APH 1.15E-05APH TRUE1 0 0 0 NP_11.2 MutS_V 0.0173 APH FALSE 0 0 1 0 NP_62.1 CBS 9.40E-08CBS TRUE1 0 0 0 NP_66.1 APH 3.83E-06APH TRUE1 0 0 0 NP_66.1 CobU0.009 APH FALSE 0 0 1 0 NP_66.1 FeoA0.3975 APH FALSE 0 0 1 0 NP_66.1 Phage_integr_N 0.0219 APH FALSE 0 0 1 0 NP_000161.2 Beta_elim_lyase 6.25E-12Beta_elim_lyase TRUE1 0 0 0 NP_000161.2 Glyco_hydro_6 0.002 Beta_elim_lyase FALSE 0 0 1 0 NP_000161.2 SurE0.0059 Beta_elim_lyase FALSE 0 0 1 0 NP_000161.2 SapB_2 0.0547 Beta_elim_lyase FALSE 0 0 1 0 NP_000161.2 Runt0.1034 Beta_elim_lyase FALSE 0 0 1 0 NP_000204.3 EGF 0.004666118 EGF TRUE1 0 0 0 NP_000229.1 PAS 3.13E-06PAS TRUE1 0 0 0 NP_000229.1 zf-CCCH 0.2067 PAS FALSE 0 1 1 0 NP_000229.1 E_raikovi_mat 0.0206 PAS FALSE 0 0 0 0 NP_000388.2 NAD_binding_1 8.21E-24NAD_binding_1 TRUE1 0 0 0 NP_000388.2 ABM 1.40E-08NAD_binding_1 FALSE 0 0 1 0 NP_000483.3 MMR_HSR11.98E-05MMR_HSR1TRUE1 0 0 0 NP_000483.3 DEAD2.30E-05MMR_HSR1FALSE 0 0 1 0 NP_000483.3 APS_kinase 1.80E-09MMR_HSR1FALSE 0 0 1 0 NP_000483.3 CbiA0.0003 MMR_HSR1FALSE 0 0 1 0 NP_000483.3 CoaE1.28E-07MMR_HSR1FALSE 0 0 1 0 NP_000483.3 FMN_red 4.61E-08MMR_HSR1FALSE 0 0 1 0 NP_000483.3 Fn_bind 0.3855 MMR_HSR1
Re: [R] R reports
Dear Donald, I'm not sure what the meaning of '3G' and '4G' is. You should take a look at Sweave() which is a very powerfull tool for generating reports in R. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Donald Paul Winston Verzonden: donderdag 19 augustus 2010 8:53 Aan: r-help@r-project.org Onderwerp: [R] R reports I don't see much in the way of an ability to write reports in R the way you can with SAS. You basically have to write a program with R in a 3G way unlike SAS with it's 4G proc print and proc report. Are there similar R functions and packages? -- View this message in context: http://r.789695.n4.nabble.com/R-reports-tp2330733p2330733.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. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reading lmer table
Thank you very much Mark, I'll try. Regards, Nicola Mark Difford ha scritto: Hi Nicola, In few word: does this row indicate a global effect of the predictor 'cat' or a more specific passage? It indicates a more specific passage. Use anova(m7) for global/omnibus. Check this for yourself by fitting the model with different contrasts. The default contrasts in R are treatment contrasts. ## m7 - lmer(log.second ~ Cond + cat + (1|subjID) + (1|Code), data = march.f, contrasts=list(Cond=contr.treatment, cat=contr.treatment)) m7s - lmer(log.second ~ Cond + cat + (1|subjID) + (1|Code), data = march.f, contrasts=list(Cond=contr.sum, cat=contr.sum)) summary(m7) summary(m7s) anova(m7) anova(m7s) Regards, Mark. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R reports
and: - brew - HTMLUtils - ascii - odfWeave - R2HTML - hwriter - ... 2010/8/19 ONKELINX, Thierry thierry.onkel...@inbo.be Dear Donald, I'm not sure what the meaning of '3G' and '4G' is. You should take a look at Sweave() which is a very powerfull tool for generating reports in R. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Donald Paul Winston Verzonden: donderdag 19 augustus 2010 8:53 Aan: r-help@r-project.org Onderwerp: [R] R reports I don't see much in the way of an ability to write reports in R the way you can with SAS. You basically have to write a program with R in a 3G way unlike SAS with it's 4G proc print and proc report. Are there similar R functions and packages? -- View this message in context: http://r.789695.n4.nabble.com/R-reports-tp2330733p2330733.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. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to read ANOVA output
- Original Message From: ted.hard...@manchester.ac.uk ted.hard...@manchester.ac.uk To: r-help@r-project.org Cc: Stephen Liu sati...@yahoo.com Sent: Wed, August 18, 2010 4:41:11 PM Subject: RE: [R] How to read ANOVA output Hi Ted, Thanks for your advice. - snip - You need to understand how that works (basic statistical theory) before even thinking of looking at the Tukey thing (omitted in this reply). I have been googling a while. There were many documents discovered. I wonder where shall I start? Which direction shall I choose? Could you please shed me some hints. TIA I found follows; Basic Inferential Statistics: Theory and Application http://owl.english.purdue.edu/owl/resource/672/05/ Basic Statistics-I http://works.bepress.com/durgesh_chandra_pathak/10/ file download basic_Statistics-I-fulltext.pdf The following is an explanation of your 1-way ANOVA written entirely in R (preceded by a duplicate of your ANOVA output): Performed following steps:- ## anova(lm(values ~ ind, data = tablets)) ## Analysis of Variance Table ## Response: values ## DfSum Sq Mean Sq F value Pr(F) ## ind 2 2.05787 1.0289345.239 2.015e-05 *** ## Residuals 9 0.20470 0.02274 ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 tabA = c(5.67, 5.67, 5.55, 5.57) tabB = c(5.75, 5.47, 5.43, 5.45) tabC = c(4.74, 4.45, 4.65, 4.94) nA - length(tabA) ; nB - length(tabB) ; nC - length(tabC) nG - nA + nB + nC nG [1] 12 mG - mean(c(tabA,tabB,tabC)) mA - mean(tabA) ; mB - mean(tabB) ; mC - mean(tabC) SSres - sum((tabA-mA)^2) + sum((tabB-mB)^2) + sum((tabC-mC)^2) SSres # = 0.2047 [1] 0.2047 ( I suppose - ^2 here means a raised to the power of 2) ?? ( SSres is the sum of squares residual (or sum of squares error it is sometimes called), which is the variation in the dependent variable that is not predicted by the model. Adding the SSreg to the SSres gives the SStotal, which represents how much variation there is in the data overall) ?? SSeff - nA*(mA-mG)^2 + nB*(mB-mG)^2 + nC*(mC-mG)^2 SSeff # = 2.057867 [1] 2.057867 (What does SSeff refer to here)?? ## Number of groups = 3 hence df.groups = (3-1) = 2 (?df Description: Density, distribution function, quantile function and random generation for the F distribution with ‘df1’ and ‘df2’ degrees of freedom (and optional non-centrality parameter ‘ncp’). What does df refer here? ) ?? df.groups - 2 meanSSeff - SSeff/df.groups meanSSeff # = 1.028933 [1] 0.0227 ## df for residuals in each group = (n.group - 1): df.res - (nA-1) + (nB-1) + (nC-1) ## = 3 + 3 + 3 = 9 meanSSres - SSres/df.res meanSSres # = 0.0227 [1] 0.0227 ## Fisher's F-ratio statistic = meanSSeff/meanSSres: F - meanSSeff/meanSSres F # = 45.23889 [1] 45.23889 (Fisher's F-ratio F-test ??? http://en.wikipedia.org/wiki/F-test ) ## P-value for F as test of difference between group means ## relative to within-group residuals (upper tail): Pval - pf(F, df.groups, df.res, lower.tail=FALSE) Pval # = 2.015227e-05 [1] 2.015227e-05 (The P-values for the Popular Distributions http://home.ubalt.edu/ntsbarsh/Business-stat/otherapplets/pvalues.htm ) ?? If I'm wrong please correct me. TIA B.R. Stephen __ 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 read ANOVA output
- Original Message From: Gavin Simpson gavin.simp...@ucl.ac.uk To: Stephen Liu sati...@yahoo.com Cc: r-help@r-project.org Sent: Wed, August 18, 2010 4:13:03 PM Subject: Re: [R] How to read ANOVA output Hi Gavin, Thanks for your advice. tabA = c(5.67, 5.67, 5.55, 5.57) tabB = c(5.75, 5.47, 5.43, 5.45) tabC = c(4.74, 4.45, 4.65, 4.94) tabs = data.frame(tabA, tabB, tabC) tablets = stack(tabs) anova(lm(values ~ ind, data = tablets)) Analysis of Variance Table Response: values Df Sum Sq Mean Sq F value Pr(F) ind 2 2.05787 1.02893 45.239 2.015e-05 *** Residuals 9 0.20470 0.02274 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 That output is designed to look like ANOVA tables from classical text books, so any introductory textbook designed for your particular background or area of knowledge would probably help you understand it. - snip - Could you pls shed me some hints where can I find the relevant online document for my use? Google search brought me tons of output. To go through all it would take lengthy time. Also it may lead me to the wrong direction. TIA B.R. Stephen __ 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] Slow response from Windows Rgui - caused by Word?
Start up perfmon on your system (or the task manager) and then look at who is consuming the CPU and memory. This will provide insight to the problem. You need to determine if it is a CPU problem or possibly memory due to paging. The tools are there for you to trouble shoot the problem since it is probably not being caused by R unless you have some very large objects. The task manager will tell you how much memory a process is consuming. On Thu, Aug 19, 2010 at 4:35 AM, Jon Olav Skoien jon.sko...@jrc.ec.europa.eu wrote: Dear list, I quite often experience a delayed response when I type in the console of the RGui of my computer. When typing a command, the text only appears letter-by-letter on the console if I type rather slow (maximum 1-2 letters per second), otherwise it appears some time after I finished writing the complete command. Moving back and forth in a command with arrows keys are similarly slow if I need to correct something (which I often have to do, given that I cannot read while writing). Although this might sound like a minor problem (thinking takes more time than writing when programming, and writing should anyway take place in a proper text editor), it is quite annoying, especially when I just want to rerun a long command after changing something at the start of the line. Strangely, it seems that this problem starts when I open a Word-document, and it stops when I close all open Word-documents. I do not have any problems with other programs (including other programs from the office package), and computation seems to run as quick as normal. Some info about my system: sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base objects() character(0) And as Word seems to be connected to the problem - I am running Windows 7 Pro with Office 2007, the only Add-In to Word is Endnote (version 9). I have turned off the instant formatting option, as it also caused some other problems. Does anyone have a clue how I can have a Word document open and at the same time work with R without having this delayed response? Best wishes, Jon __ 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] reading a text file, one line at a time
Here is how I would do it to just do character substitution on the data:
inFile - textConnection( V1 V2 V3 V4 V5
+ 1 1 b b a -0.4990719
+ 2 2 b a a 1.5134101
+ 3 3 a b b 1.9375467
+ 4 4 a a b 0.3310612
+ 5 5 a b a 0.2807520
+ 6 6 a a b 0.9646351
+ 7 7 b a b 0.6243979
+ 8 8 a b a -0.8076008
+ 9 9 a b b -1.7645273
+ 10 10 b b a 0.5460802
+ 11 11 c c b 12.300)
output - NULL # initialize output file (just a vector in this case
while(length(input - readLines(inFile, n=3)) 0){
+ # replace 'b' with 'z'
+ for (i in seq_along(input)){
+ input[i] - gsub('b', 'z', input[i])
+ }
+ output - c(output, input) # collect the output
+ }
close(inFile)
print(cbind(output)) # show converted data
output
[1,]V1 V2 V3 V4 V5
[2,] 1 1 z z a -0.4990719
[3,] 2 2 z a a 1.5134101
[4,] 3 3 a z z 1.9375467
[5,] 4 4 a a z 0.3310612
[6,] 5 5 a z a 0.2807520
[7,] 6 6 a a z 0.9646351
[8,] 7 7 z a z 0.6243979
[9,] 8 8 a z a -0.8076008
[10,] 9 9 a z z -1.7645273
[11,] 10 10 z z a 0.5460802
[12,] 11 11 c c z 12.300
On Wed, Aug 18, 2010 at 10:51 PM, Juliet Hannah juliet.han...@gmail.com wrote:
Hi Jim,
I was trying to use your template without success. With the toy data
below, could
you explain how to use this template to change all bs to zs --
just as an exercise, reading
in 3 lines at a time. I need to use this strategy for a larger
problem, but I haven't
been able to get the basics working.
Thanks,
Juliet
myData - structure(list(V1 = 1:11, V2 = structure(c(2L, 2L, 1L, 1L, 1L,
1L, 2L, 1L, 1L, 2L, 3L), .Label = c(a, b, c), class = factor),
V3 = structure(c(2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L,
3L), .Label = c(a, b, c), class = factor), V4 = structure(c(1L,
1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L), .Label = c(a,
b), class = factor), V5 = c(-0.499071939558026, 1.51341011554134,
1.93754671209923, 0.331061227463955, 0.280752001959284, 0.964635079229074,
0.624397908891502, -0.807600774484419, -1.76452730888732,
0.546080229326458, 12.3)), .Names = c(V1, V2, V3, V4,
V5), class = data.frame, row.names = c(NA, -11L))
On Sun, Aug 15, 2010 at 1:06 PM, jim holtman jholt...@gmail.com wrote:
For efficiency of processing, look at reading in several
hundred/thousand lines at a time. One line read/write will probably
spend most of the time in the system calls to do the I/O and will take
a long time. So do something like this:
con - file('yourInputFile', 'r')
outfile - file('yourOutputFile', 'w')
while (length(input - readLines(con, n=1000) 0){
for (i in 1:length(input)){
..your one line at a time processing
}
writeLines(output, con=outfile)
}
On Sun, Aug 15, 2010 at 7:58 AM, Data Analytics Corp.
w...@dataanalyticscorp.com wrote:
Hi,
I have an upcoming project that will involve a large text file. I want to
1. read the file into R one line at a time
2. do some string manipulations on the line
3. write the line to another text file.
I can handle the last two parts. Scan and read.table seem to read the whole
file in at once. Since this is a very large file (several hundred thousand
lines), this is not practical. Hence the idea of reading one line at at
time. The question is, can R read one line at a time? If so, how? Any
suggestions are appreciated.
Thanks,
Walt
Walter R. Paczkowski, Ph.D.
Data Analytics Corp.
44 Hamilton Lane
Plainsboro, NJ 08536
(V) 609-936-8999
(F) 609-936-3733
w...@dataanalyticscorp.com
www.dataanalyticscorp.com
_
--
Walter R. Paczkowski, Ph.D.
Data Analytics Corp.
44 Hamilton Lane
Plainsboro, NJ 08536
(V) 609-936-8999
(F) 609-936-3733
w...@dataanalyticscorp.com
www.dataanalyticscorp.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.
--
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.
--
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,
Re: [R] Adding column to dataframe
I think you are probably paging on your system. Turn on your performance metrics and look at it. If the object you are processing is all numeric, it would seem to require about 3.5GB of space (50% of available memory). Provide and 'str' and 'object.size' of the object so that we can see what you are working with. My rule of thumb is that no single object should take more than 25-30% of memory since copies may be made. So the reasons things are taking 20 minutes is you might be paging. It is always good to break the problem into pieces to see what is happening. Read in only 25% of the data and time it; then 50% and so on. In any performance related problems you need to determine where the knee of the curve it. Never undertake processing the large data file at once; start with some pieces and work up so that you know what to expect. On Wed, Aug 18, 2010 at 9:46 PM, Matt Cooper mattcst...@gmail.com wrote: Two questions: 1) Are there any good R guides/sites with information/techniques for dealing with large datasets in R? (Large being ~2 mil rows and ~200 columns) 2) My specific problem with this dataset. I am essentially trying to convert a date and add it to a data frame. I imagine any 'data manipulation on a column within dataframe into a new column' will present the same issue, be it as.Date or anything else. I have a dataset, size dim(morbidity) [1] 1775683 264 This was read in from a STATA .dta file. The dates have come in as the number of ms from 1960 so I have the following to convert these to usable dates. as.Date(morbidity$adm_date / (100*10*60*60*24), origin=1960-01-01) when I store this as a vector it is near instant, 5 seconds test - as.Date(etc) when I place it over itself it takes ~20 minutes morbidity$adm_date - as.Date(etc) when I place the vector over it (so no computation involved), or place it as a new column it still takes ~20 minutes morbidity$adm_date - test morbidity$new_col - test when I tried a cbind to add it that way it took 20 minutes new_morb - cbind(morbidity,test) Has anyone done something similar or know of a different command that should work faster? I can't get my head around what R is doing, if it can create the vector instantly then the computation is quite simple, I don't understand why then adding it as a column to a dataframe can take that long. R64 bit on mac os x, 2.4 GHz dual core, 8gb ram so more than enough resources. Thanks Matt [[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. -- 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] texi2dvi: option clean also deletes the generated pdf file
Dear Marius,
from reading the texi2dvi man-page and R-help on texi2dvi I suggest to set
'clean=F' and use 'texi2dvi = getOption(texi2dvi --mostly-clean)' instead.
Tim
On Thu, Aug 19, 2010 at 10:36:30AM +0200, Marius Hofert wrote:
Dear expeRts,
below are two examples of using texi2dvi. The problem becomes clear from the
second example: on cleaning, texi2dvi also deletes the generated .pdf file.
Is there a solution?
Cheers,
Marius
## Example 1: texi2dvi cleans fine, without deleting the generated .pdf
require(tools)
sink(file=myLaTeXFile1.tex)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(myLaTeXFile1.tex,pdf=TRUE,clean=TRUE,quiet=TRUE)
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] memory problem
avsha38 wrote: Hi, when i run the following code i get this massege: The instruction at 0x reference memory at 0x###, the memory cannot be read. and then i have to close R. what is the problem and how can i solve it? The problem is a bug in the underlying C (or other) code. To solve it, put together a minimal example that produces it reliably. If it requires the frailtypack package to work, then send your example to the maintainer of that package. If the minimal example uses only standard R packages, then submit an R bug report about it. There's no point reporting it unless someone can reproduce it, and people might not follow up if the example is too complicated, so you should make an effort to simplify as much as you can before reporting. Duncan Murdoch thanks in advance Avi my code # frailtypack library(frailtypack) cgd.ag - read.csv(C:/rfiles/RE/cgd.csv) cgd.nfm -frailtyPenal(Surv(TStart, TStop, Status)~cluster(Center)+subcluster(ID) Treatment,data=cgd.ag,Frailty=TRUE,n.knots=8,kappa1=5, cross.validation=TRUE,recurrentAG=TRUE) __ 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] texi2dvi: option clean also deletes the generated pdf file
Dear Tim,
you mean
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,quiet=TRUE,texi2dvi=getOption(texi2dvi
--mostly-clean))
?
The problem is that this does not work. It produces the same output as my
Example 2 without the clean-option. So it leaves all files in the working
directory.
The reason why I am looking for a clean-up is that I have to compile several
hundred LaTeX files in different directories...
Cheers,
Marius
On 2010-08-19, at 12:33 , Tim Gruene wrote:
Dear Marius,
from reading the texi2dvi man-page and R-help on texi2dvi I suggest to set
'clean=F' and use 'texi2dvi = getOption(texi2dvi --mostly-clean)' instead.
Tim
On Thu, Aug 19, 2010 at 10:36:30AM +0200, Marius Hofert wrote:
Dear expeRts,
below are two examples of using texi2dvi. The problem becomes clear from the
second example: on cleaning, texi2dvi also deletes the generated .pdf file.
Is there a solution?
Cheers,
Marius
## Example 1: texi2dvi cleans fine, without deleting the generated .pdf
require(tools)
sink(file=myLaTeXFile1.tex)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(myLaTeXFile1.tex,pdf=TRUE,clean=TRUE,quiet=TRUE)
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
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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.
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Re: [R] How to read ANOVA output
He's already sent you some good advice. Go to amazon.com and search for basic statistics + your area in Books. Giving you specific recommendations will also take a lot of time, both for us and you, especially seeing as we don't really know what area or subject you're looking for. Any basic book should give you enough knowledge to understand the basics of ANOVA and statistics in general. You should also find a book with basic problems and answers, so you can try them out yourself. Siri. Siterer Stephen Liu sati...@yahoo.com: - Original Message From: Gavin Simpson gavin.simp...@ucl.ac.uk To: Stephen Liu sati...@yahoo.com Cc: r-help@r-project.org Sent: Wed, August 18, 2010 4:13:03 PM Subject: Re: [R] How to read ANOVA output Hi Gavin, Thanks for your advice. tabA = c(5.67, 5.67, 5.55, 5.57) tabB = c(5.75, 5.47, 5.43, 5.45) tabC = c(4.74, 4.45, 4.65, 4.94) tabs = data.frame(tabA, tabB, tabC) tablets = stack(tabs) anova(lm(values ~ ind, data = tablets)) Analysis of Variance Table Response: values Df Sum Sq Mean Sq F value Pr(F) ind 2 2.05787 1.02893 45.239 2.015e-05 *** Residuals 9 0.20470 0.02274 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 That output is designed to look like ANOVA tables from classical text books, so any introductory textbook designed for your particular background or area of knowledge would probably help you understand it. - snip - Could you pls shed me some hints where can I find the relevant online document for my use? Google search brought me tons of output. To go through all it would take lengthy time. Also it may lead me to the wrong direction. TIA B.R. Stephen __ 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 reports
On Thu, 19 Aug 2010, ONKELINX, Thierry wrote: Dear Donald, I'm not sure what the meaning of '3G' and '4G' is. You should take a I think he means 3GL, as in http://en.wikipedia.org/wiki/Third-generation_programming_language (and I've not heard the term used for 20 years now). look at Sweave() which is a very powerfull tool for generating reports in R. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Donald Paul Winston Verzonden: donderdag 19 augustus 2010 8:53 Aan: r-help@r-project.org Onderwerp: [R] R reports I don't see much in the way of an ability to write reports in R the way you can with SAS. You basically have to write a program with R in a 3G way unlike SAS with it's 4G proc print and proc report. Are there similar R functions and packages? -- View this message in context: http://r.789695.n4.nabble.com/R-reports-tp2330733p2330733.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. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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. -- 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.
[R] Math symbols in ylab with vis.gam() or plot.gam()
Hi all, Has anyone tried to plot math symbols with vis.gam() - a function that uses (I think) plot.gam() internally? This is from the package mgcv - I am new to gam(). For example, with the normal plot(), the expression() works fine for Math symbols: plot(xx, ylab=expression(paste(Delta,H,sep=))) # works fine But, with vis.gam(), the same ylab=expression(paste(Delta,H,sep=)) does not plot the symbols - in stead it is 'paste(Delta,H,sep=)'. Do I have an alternative way of specifying the expression() to vis.gam()? Am I not doing this correctly? Thanks, Parthiban. [[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] Help with Vectors and conditional functions
In additiion to Ivan's comment, in this case, you are just plotting
Yes or No. I think thats not what you want.
Nikhil Kaza
Asst. Professor,
City and Regional Planning
University of North Carolina
nikhil.l...@gmail.com
On Aug 19, 2010, at 3:42 AM, Ivan Calandra wrote:
Hi,
I haven't spent too much time on it, but that might help:
if (coint_tests[[i]]==YES)...
Note the double = which is the operator for equality. The single =
is the assignment operator, especially with arguments.
HTH, Ivan
Le 8/19/2010 09:03, Ferreira, Thiago Alves a écrit :
Good morning,
I have something like this: names(coint_tests)- apply(b,2,paste,
collapse=_) which prints 15 names like: A_B, C_D, E_F, ...
AA,B,C,D.. Are time series. Then there is a vector called
coint_tests of length 15 which yields yes or no.
I need to add a function to plot the time series Ai_Bi if the
coint_tests vectors gives me a YES.
I tried:for (i in 1:(length(coint_tests))
if (coint_tests[[i]]=YES)
{plot(coint_tests[i])}
But it does not work. I would most appreciate if someone could give
me some insight as to how to sort this out. Thank you
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Abt. Säugetiere
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[R] 2d kriging with anisotropy on an irregular network (RandomFields Package)
Dear List I am using the RandomFields package, and I have a problem when 2d-kriging, with an anisotropy, some values from an irregular network. It works well when : - 2d-kriging, without any anisotropy, some data from an irregular network - 2d-kriging, with and without anisotropy, some data from a regular network - 3d-kriging, with and without anisotropy, some data from a regular network Here is my script highly inspired by some examples from the package. rm(list=ls()) library(RandomFields) ### # PARAMETERS ### Mean-1 Variance-4.5 Range-1 nbRainG-20 rPoint - 1:nbRainG points1 - rPoint xMax-5 yMax-10 ## #CREATION OF AN IRREGULAR RAINGAUGE NETWORK, DATA SIMULATION ## model=exponential param1 - c(mean=Mean,variance=Variance,nugget=0,scale=Range) RFparameters(PracticalRange=FALSE) data - GaussRF(points1, grid=FALSE, model=model,param=param1) data[which(data0)]-0 xPoint - runif(nbRainG,0,xMax) yPoint - runif(nbRainG,0,yMax) MatCoord-matrix(0,nr=nbRainG,nc=2) MatCoord[,1]-t(xPoint) MatCoord[,2]-t(yPoint) points2-MatCoord dim(data)-NULL ### # PARAMETERS FOR KRIGING ### stepSpace - 0.25 xkrig - seq(0,xMax,stepSpace) ykrig - seq(0,yMax,stepSpace) valuesLim - c(0,3) colour - rainbow(100) ### #2D KRIGING ### #NO ANISOTROPY-It works krige.method - O values - Kriging(krige.method=krige.method, x=xkrig,y=ykrig,grid=TRUE, model=list( list(m=exp, v=Variance,s=Range) ), given=points2,data=data) #ANISOTROPY -doesnt work anisoMatrix-matrix(0,2,2) AnisoS-1 #whatever this value, it doesn't work anisoMatrix[1,1]-1 anisoMatrix[2,2]-AnisoS krige.method - O values - Kriging(krige.method=krige.method, x=xkrig,y=ykrig,grid=TRUE, model=list( list(m=exp, v=Variance,s=Range,a=anisoMatrix) ), given=points2,data=data) ## #END# ## As an error message, R writes : Error: (in PrepareModel) do not mix isotropic definitions with anisotropic ones I don't know why. - The problem comes from adding the anisotropy parameter (a=anisoMatrix, in the function Kriging). When putting the anisotropy coefficient to one (ie isotropy), it doesn't work as well. - I have tested the script for several theoritical model of structure (sph,...), but it doesn't work as well - Even if the dimension of the data set is a vector in the case of irregular network (instead of a matrix in the case of a regular network), the anisotropy matrix has to stay with the dimension 2x2 (for a spatial network), and not a scalar. Does someone has any idea about this error? Some information about my system : sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=Norwegian (Bokmål)_Norway.1252 LC_CTYPE=Norwegian (Bokmål)_Norway.1252 [3] LC_MONETARY=Norwegian (Bokmål)_Norway.1252 LC_NUMERIC=C [5] LC_TIME=Norwegian (Bokmål)_Norway.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RandomFields_1.3.41 Thanks a lot Jean-Marie [[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] texi2dvi: option clean also deletes the generated pdf file
Dear Marius,
yes, that's what I had meant.
I am sorry I had not actually tested my suggestion nor your problem (bad
practice). Now I have and actually in case 2 you describe I only end up
with test/myLaTeXFile2.tex and myLaTeXFile2.pdf.
If, however, I run texi2dvi at least once with option 'clean=F', the auxiliary
files
are generated and left in the path. Also upon a subsequent run with the option
'clean=T', they are not being deleted.
Could this also be the case for you, i.e., that you once used the option
'clean=F' (or not set at all) and now are made believe 'clean=T' does not work
because they are still there but actually left-overs from the old run?
I run R version 2.7.1 (2008-06-23) on Debian stable.
Kind regards, Tim
On Thu, Aug 19, 2010 at 12:41:57PM +0200, Marius Hofert wrote:
Dear Tim,
you mean
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,quiet=TRUE,texi2dvi=getOption(texi2dvi
--mostly-clean))
?
The problem is that this does not work. It produces the same output as my
Example 2 without the clean-option. So it leaves all files in the working
directory.
The reason why I am looking for a clean-up is that I have to compile
several hundred LaTeX files in different directories...
Cheers,
Marius
On 2010-08-19, at 12:33 , Tim Gruene wrote:
Dear Marius,
from reading the texi2dvi man-page and R-help on texi2dvi I suggest to set
'clean=F' and use 'texi2dvi = getOption(texi2dvi --mostly-clean)' instead.
Tim
On Thu, Aug 19, 2010 at 10:36:30AM +0200, Marius Hofert wrote:
Dear expeRts,
below are two examples of using texi2dvi. The problem becomes clear from
the
second example: on cleaning, texi2dvi also deletes the generated .pdf file.
Is there a solution?
Cheers,
Marius
## Example 1: texi2dvi cleans fine, without deleting the generated .pdf
require(tools)
sink(file=myLaTeXFile1.tex)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(myLaTeXFile1.tex,pdf=TRUE,clean=TRUE,quiet=TRUE)
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
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--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Re: [R] R reports
Oops, I meant 4GL. Part of SAS involves more or less declarative coding where SAS figures out how to process the information and you don't have to. Sweave and html generators in R are not what I'm looking for. I'm looking for a function whose arguments are data, column names, grouping variables, summary stats, titles, footnotes, etc. Sort of like what plot does except the function will generate a report. I suppose you could specify an output format or printer device as plain text, rich text, pdf, or html. -- View this message in context: http://r.789695.n4.nabble.com/R-reports-tp2330733p2331037.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] Slow response from Windows Rgui - caused by Word?
Hi, It is certainly not a memory or CPU problem, I should have mentioned in the first email that I already tried to check for that. However, I now tried to disable EndNote 9 from the Add-Ins, and it seems that was the problem. I still dont understand why this happens though. There seems to be some issues with using older versions of EndNote on a 64-bit computer: http://www.endnote.com/support/Faqs/Install/faq28.asp This caused me some trouble in the past, slowing down Windows Explorer, but this got solved by turning off the instant formatting. It is very strange that it apparently only affects R now, and I would prefer if I could use the two programs at the same time... Thanks for the suggestion though, Jon jim holtman wrote: Start up perfmon on your system (or the task manager) and then look at who is consuming the CPU and memory. This will provide insight to the problem. You need to determine if it is a CPU problem or possibly memory due to paging. The tools are there for you to trouble shoot the problem since it is probably not being caused by R unless you have some very large objects. The task manager will tell you how much memory a process is consuming. On Thu, Aug 19, 2010 at 4:35 AM, Jon Olav Skoien jon.sko...@jrc.ec.europa.eu wrote: Dear list, I quite often experience a delayed response when I type in the console of the RGui of my computer. When typing a command, the text only appears letter-by-letter on the console if I type rather slow (maximum 1-2 letters per second), otherwise it appears some time after I finished writing the complete command. Moving back and forth in a command with arrows keys are similarly slow if I need to correct something (which I often have to do, given that I cannot read while writing). Although this might sound like a minor problem (thinking takes more time than writing when programming, and writing should anyway take place in a proper text editor), it is quite annoying, especially when I just want to rerun a long command after changing something at the start of the line. Strangely, it seems that this problem starts when I open a Word-document, and it stops when I close all open Word-documents. I do not have any problems with other programs (including other programs from the office package), and computation seems to run as quick as normal. Some info about my system: sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base objects() character(0) And as Word seems to be connected to the problem - I am running Windows 7 Pro with Office 2007, the only Add-In to Word is Endnote (version 9). I have turned off the instant formatting option, as it also caused some other problems. Does anyone have a clue how I can have a Word document open and at the same time work with R without having this delayed response? Best wishes, Jon __ 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] Different way of aggregating
Phil Spector wrote: For chron objects: aggregate(thedata$value,list(hour=hours(thedata$date)),mean) Ok, thanks, that's what I need. Now it seems so easy... Could you tell me why we write... ? aggregate(thedata$value,list(hour=hours(thedata$date)),mean) instead of just aggregate(thedata$value,hours(thedata$date),mean) thanks -- View this message in context: http://r.789695.n4.nabble.com/Different-way-of-aggregating-tp2330497p2331072.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] texi2dvi: option clean also deletes the generated pdf file
Dear Tim,
if I run ...
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
... on a fresh-and-clean working directory (and also no files in the
subdirectory ./test), I only get the file myLaTeXFile2.tex in ./test, so
*everything* (including the .pdf) is deleted :-(
I work with R version 2.11.1 (2010-05-31) on a MacBook Pro running 10.6.4.
Cheers,
Marius
On 2010-08-19, at 13:38 , Tim Gruene wrote:
Dear Marius,
yes, that's what I had meant.
I am sorry I had not actually tested my suggestion nor your problem (bad
practice). Now I have and actually in case 2 you describe I only end up
with test/myLaTeXFile2.tex and myLaTeXFile2.pdf.
If, however, I run texi2dvi at least once with option 'clean=F', the
auxiliary files
are generated and left in the path. Also upon a subsequent run with the option
'clean=T', they are not being deleted.
Could this also be the case for you, i.e., that you once used the option
'clean=F' (or not set at all) and now are made believe 'clean=T' does not work
because they are still there but actually left-overs from the old run?
I run R version 2.7.1 (2008-06-23) on Debian stable.
Kind regards, Tim
On Thu, Aug 19, 2010 at 12:41:57PM +0200, Marius Hofert wrote:
Dear Tim,
you mean
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,quiet=TRUE,texi2dvi=getOption(texi2dvi
--mostly-clean))
?
The problem is that this does not work. It produces the same output as my
Example 2 without the clean-option. So it leaves all files in the
working directory.
The reason why I am looking for a clean-up is that I have to compile
several hundred LaTeX files in different directories...
Cheers,
Marius
On 2010-08-19, at 12:33 , Tim Gruene wrote:
Dear Marius,
from reading the texi2dvi man-page and R-help on texi2dvi I suggest to set
'clean=F' and use 'texi2dvi = getOption(texi2dvi --mostly-clean)' instead.
Tim
On Thu, Aug 19, 2010 at 10:36:30AM +0200, Marius Hofert wrote:
Dear expeRts,
below are two examples of using texi2dvi. The problem becomes clear from
the
second example: on cleaning, texi2dvi also deletes the generated .pdf file.
Is there a solution?
Cheers,
Marius
## Example 1: texi2dvi cleans fine, without deleting the generated .pdf
require(tools)
sink(file=myLaTeXFile1.tex)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(myLaTeXFile1.tex,pdf=TRUE,clean=TRUE,quiet=TRUE)
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
__
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.
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
__
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 reports
I'm not sure I understand what is 3GL or 4GL, but R is on the list of fourth-generation languages : Data manipulation, analysis, and reporting languageshttp://en.wikipedia.org/wiki/Fourth-generation_programming_language#Some_fourth-generation_languages on wikipedia. I don't know a function like that (nervertheless, I know nothing about proc report, and I don't understand how it works). But if you don't want a Sweave-like process, hwriter can automatically generate (html) reports: # from http://www.ebi.ac.uk/~gpau/hwriter/ library(hwriter) hwrite(iris[1:2,1:2], 'test.html', row.bgcolor='#ffdc98') browseURL(paste(file://, getwd(), /test.html, sep = )) In all case, to generate the report, you must first create the results, and then display it into a report. Or perhaps you're looking for something like rreport package (in development): http://biostat.mc.vanderbilt.edu/wiki/Main/Rreport (never tried) david 2010/8/19 Donald Paul Winston satchwins...@yahoo.com Oops, I meant 4GL. Part of SAS involves more or less declarative coding where SAS figures out how to process the information and you don't have to. Sweave and html generators in R are not what I'm looking for. I'm looking for a function whose arguments are data, column names, grouping variables, summary stats, titles, footnotes, etc. Sort of like what plot does except the function will generate a report. I suppose you could specify an output format or printer device as plain text, rich text, pdf, or html. -- View this message in context: http://r.789695.n4.nabble.com/R-reports-tp2330733p2331037.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] texi2dvi: option clean also deletes the generated pdf file
On 19/08/2010 7:55 AM, Marius Hofert wrote:
Dear Tim,
if I run ...
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
... on a fresh-and-clean working directory (and also no files in the
subdirectory ./test), I only get the file myLaTeXFile2.tex in ./test, so *everything*
(including the .pdf) is deleted :-(
The texi2dvi function has two possible execution paths: in one, it
basically constructs a call to the system texi2dvi command and calls
that, and in the other it emulates the behaviour of texi2dvi. I haven't
checked recently, but I think the second method doesn't do anything with
clean=TRUE, so it looks as though this is a problem with the texi2dvi
command you have installed on your system.
To confirm this, run debug(tools:::.shell_with_capture), and run
texi2dvi. When R breaks in that .shell_with_capture, it will show you
what it is trying to execute. If it is using your system texi2dvi
command, it will call it once with option --help to find out what
options are supported, and then a second call will show you the main
command line. You can use this to report a bug to Apple or whoever
supplied your texi2dvi.
Duncan Murdoch
I work with R version 2.11.1 (2010-05-31) on a MacBook Pro running 10.6.4.
Cheers,
Marius
On 2010-08-19, at 13:38 , Tim Gruene wrote:
Dear Marius,
yes, that's what I had meant.
I am sorry I had not actually tested my suggestion nor your problem (bad
practice). Now I have and actually in case 2 you describe I only end up
with test/myLaTeXFile2.tex and myLaTeXFile2.pdf.
If, however, I run texi2dvi at least once with option 'clean=F', the auxiliary files
are generated and left in the path. Also upon a subsequent run with the option
'clean=T', they are not being deleted.
Could this also be the case for you, i.e., that you once used the option
'clean=F' (or not set at all) and now are made believe 'clean=T' does not work
because they are still there but actually left-overs from the old run?
I run R version 2.7.1 (2008-06-23) on Debian stable.
Kind regards, Tim
On Thu, Aug 19, 2010 at 12:41:57PM +0200, Marius Hofert wrote:
Dear Tim,
you mean
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,quiet=TRUE,texi2dvi=getOption(texi2dvi
--mostly-clean))
?
The problem is that this does not work. It produces the same output as my Example 2 without the clean-option. So it leaves all files in the working directory.
The reason why I am looking for a clean-up is that I have to compile several hundred LaTeX files in different directories...
Cheers,
Marius
On 2010-08-19, at 12:33 , Tim Gruene wrote:
Dear Marius,
from reading the texi2dvi man-page and R-help on texi2dvi I suggest to set
'clean=F' and use 'texi2dvi = getOption(texi2dvi --mostly-clean)' instead.
Tim
On Thu, Aug 19, 2010 at 10:36:30AM +0200, Marius Hofert wrote:
Dear expeRts,
below are two examples of using texi2dvi. The problem becomes clear from the
second example: on cleaning, texi2dvi also deletes the generated .pdf file.
Is there a solution?
Cheers,
Marius
## Example 1: texi2dvi cleans fine, without deleting the generated .pdf
require(tools)
sink(file=myLaTeXFile1.tex)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(myLaTeXFile1.tex,pdf=TRUE,clean=TRUE,quiet=TRUE)
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
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PLEASE do read the posting guide
Re: [R] Finding a scalar value...
Your best option is to read the relevant help files.
A simple (untested) example to find R when P, T and scal.fn=Z is given,
is to do this:
my.fun - function(P, R, T, Z) scal.fn(P, R, T) - Z
uniroot( fn, R=rr, T=tt, Z=zz, lower=-100, upper=100 )$root
You have to make an intelligent guess on the upper and lower ranges for
the parameter R. I have used +/- 1 million as a silly example.
HOWEVER, I do not think this works when P,R,T,Z are scalars. Try it to
be sure. If not, then you may have to write a for or apply loop.
Regards, Adai
On 16/08/2010 13:19, Petar Milin wrote:
Thanks for the answer!
However, if I would have scal.fn() like below, how would I apply
uniroot() or optimize() or the like?
Best,
PM
On 16/08/10 13:24, Adaikalavan Ramasamy wrote:
You probably need to look up on how to write functions.
Try
scal.fn- function(P, R, T){
out- ( 1/R - T ) / ( P - T )
return(out)
}
Here is a fake example:
df- cbind.data.frame( P=rnorm(10), R=rnorm(10), T=rnorm(10) )
scal.fn( df$P, df$R, df$T )
Or are you trying to solve other parameters given scal values? If so,
try having a look at functions like uniroot().
Regards, Adai
On 16/08/2010 11:48, Petar Milin wrote:
Hello!
I need to find a simple scalar value:
Scal = ((1/R) - T) / (P - T),
where R, T, and P are vectors in a data.frame.
Please, can anyone tell me how to solve that in R?
Best,
PM
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] texi2dvi: option clean also deletes the generated pdf file
Dear Marius,
I see. I suppose it's a matter of your version of texi2dvi then - when I do the
same in a freshly created directory (including the test directory), cutting
and pasting your very code into R leaves me only with myLaTeXFile2.pdf and
test/myLaTeXFile2.tex
This is texi2dvi --version
texi2dvi (GNU Texinfo 4.11) 1.104
Tim
On Thu, Aug 19, 2010 at 01:55:06PM +0200, Marius Hofert wrote:
Dear Tim,
if I run ...
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
... on a fresh-and-clean working directory (and also no files in the
subdirectory ./test), I only get the file myLaTeXFile2.tex in ./test, so
*everything* (including the .pdf) is deleted :-(
I work with R version 2.11.1 (2010-05-31) on a MacBook Pro running 10.6.4.
Cheers,
Marius
On 2010-08-19, at 13:38 , Tim Gruene wrote:
Dear Marius,
yes, that's what I had meant.
I am sorry I had not actually tested my suggestion nor your problem (bad
practice). Now I have and actually in case 2 you describe I only end up
with test/myLaTeXFile2.tex and myLaTeXFile2.pdf.
If, however, I run texi2dvi at least once with option 'clean=F', the
auxiliary files
are generated and left in the path. Also upon a subsequent run with the
option
'clean=T', they are not being deleted.
Could this also be the case for you, i.e., that you once used the option
'clean=F' (or not set at all) and now are made believe 'clean=T' does not
work
because they are still there but actually left-overs from the old run?
I run R version 2.7.1 (2008-06-23) on Debian stable.
Kind regards, Tim
On Thu, Aug 19, 2010 at 12:41:57PM +0200, Marius Hofert wrote:
Dear Tim,
you mean
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,quiet=TRUE,texi2dvi=getOption(texi2dvi
--mostly-clean))
?
The problem is that this does not work. It produces the same output as my
Example 2 without the clean-option. So it leaves all files in the
working directory.
The reason why I am looking for a clean-up is that I have to compile
several hundred LaTeX files in different directories...
Cheers,
Marius
On 2010-08-19, at 12:33 , Tim Gruene wrote:
Dear Marius,
from reading the texi2dvi man-page and R-help on texi2dvi I suggest to set
'clean=F' and use 'texi2dvi = getOption(texi2dvi --mostly-clean)'
instead.
Tim
On Thu, Aug 19, 2010 at 10:36:30AM +0200, Marius Hofert wrote:
Dear expeRts,
below are two examples of using texi2dvi. The problem becomes clear from
the
second example: on cleaning, texi2dvi also deletes the generated .pdf
file.
Is there a solution?
Cheers,
Marius
## Example 1: texi2dvi cleans fine, without deleting the generated .pdf
require(tools)
sink(file=myLaTeXFile1.tex)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(myLaTeXFile1.tex,pdf=TRUE,clean=TRUE,quiet=TRUE)
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
__
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.
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
--
--
Re: [R] texi2dvi: option clean also deletes the generated pdf file
Dear all,
many thanks for your help. I totally missed that texi2dvi is also a system
command (I don't use that explicitly to compile my .tex docs). So I checked my
system-texi2dvi. It's quite interesting, if I use the option
--mostly-clean, everthing is removed. However, if I use just --clean, then
the generated pdf file is not removed. So the solution is to call (in the
shell):
texi2dvi --clean --pdf ./test/myLaTeXFile2.tex
I can call this from within system() [or even use pdflatex directly from within
system()]. I guess I don't need R's texi2dvi anymore.
Many thanks
Marius
Ps: Here is the output of what Duncan suggested:
debug(tools:::.shell_with_capture)
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
debugging in: .shell_with_capture(paste(shQuote(texi2dvi), --help))
debug: {
outfile - tempfile(xshell)
errfile - tempfile(xshell)
on.exit(unlink(c(outfile, errfile)))
status - if (.Platform$OS.type == windows)
shell(sprintf(%s %s 2 %s, command, outfile, errfile),
input = input, shell = cmd.exe)
else system(sprintf(%s %s 2 %s, command, outfile, errfile),
input = input)
list(status = status, stdout = readLines(outfile, warn = FALSE),
stderr = readLines(errfile, warn = FALSE))
}
Browse[2]
debug: outfile - tempfile(xshell)
Browse[2]
debug: errfile - tempfile(xshell)
Browse[2]
debug: on.exit(unlink(c(outfile, errfile)))
Browse[2]
debug: status - if (.Platform$OS.type == windows) shell(sprintf(%s %s 2
%s,
command, outfile, errfile), input = input, shell = cmd.exe) else
system(sprintf(%s %s 2 %s,
command, outfile, errfile), input = input)
Browse[2]
debug: system(sprintf(%s %s 2 %s, command, outfile, errfile), input =
input)
Browse[2]
debug: list(status = status, stdout = readLines(outfile, warn = FALSE),
stderr = readLines(errfile, warn = FALSE))
Browse[2]
exiting from: .shell_with_capture(paste(shQuote(texi2dvi), --help))
debugging in: .shell_with_capture(paste(shQuote(texi2dvi), opt_pdf, opt_quiet,
opt_extra, shQuote(file)))
debug: {
outfile - tempfile(xshell)
errfile - tempfile(xshell)
on.exit(unlink(c(outfile, errfile)))
status - if (.Platform$OS.type == windows)
shell(sprintf(%s %s 2 %s, command, outfile, errfile),
input = input, shell = cmd.exe)
else system(sprintf(%s %s 2 %s, command, outfile, errfile),
input = input)
list(status = status, stdout = readLines(outfile, warn = FALSE),
stderr = readLines(errfile, warn = FALSE))
}
Browse[2]
debug: outfile - tempfile(xshell)
Browse[2]
debug: errfile - tempfile(xshell)
Browse[2]
debug: on.exit(unlink(c(outfile, errfile)))
Browse[2]
debug: status - if (.Platform$OS.type == windows) shell(sprintf(%s %s 2
%s,
command, outfile, errfile), input = input, shell = cmd.exe) else
system(sprintf(%s %s 2 %s,
command, outfile, errfile), input = input)
Browse[2]
debug: system(sprintf(%s %s 2 %s, command, outfile, errfile), input =
input)
Browse[2]
debug: list(status = status, stdout = readLines(outfile, warn = FALSE),
stderr = readLines(errfile, warn = FALSE))
Browse[2]
exiting from: .shell_with_capture(paste(shQuote(texi2dvi), opt_pdf, opt_quiet,
opt_extra, shQuote(file)))
On 2010-08-19, at 15:02 , Tim Gruene wrote:
Dear Marius,
I see. I suppose it's a matter of your version of texi2dvi then - when I do
the
same in a freshly created directory (including the test directory), cutting
and pasting your very code into R leaves me only with myLaTeXFile2.pdf and
test/myLaTeXFile2.tex
This is texi2dvi --version
texi2dvi (GNU Texinfo 4.11) 1.104
Tim
On Thu, Aug 19, 2010 at 01:55:06PM +0200, Marius Hofert wrote:
Dear Tim,
if I run ...
## Example 2: texi2dvi also deletes the generated .pdf
require(tools)
filepath - paste(getwd(),/test/myLaTeXFile2.tex,sep=)
sink(file=filepath)
cat(\\documentclass{article}\n)
cat(\\usepackage[T1]{fontenc}\n)
cat(\\usepackage[english]{babel}\n)
cat(\\usepackage{blindtext}\n)
cat(\\begin{document}\n)
cat(\\blindtext[10]\n)
cat(\\end{document}\n)
sink()
texi2dvi(filepath,pdf=TRUE,clean=TRUE,quiet=TRUE)
... on a fresh-and-clean working directory (and also no files in the
subdirectory ./test), I only get the file myLaTeXFile2.tex in ./test, so
*everything* (including the .pdf) is deleted :-(
I work with R version 2.11.1 (2010-05-31) on a MacBook Pro running 10.6.4.
Cheers,
Marius
On 2010-08-19, at 13:38 , Tim Gruene wrote:
Dear Marius,
yes, that's
Re: [R] GLMM random effects
Natasha natasha.lloyd at gmail.com writes: For future reference, you may have better luck *either* on the r-sig-mixed-models help list (for advice about GLMMs) *or* on r-sig-ecology (for advice about ecological studies) [it's not considered polite to cross-post: try looking at the archives of both lists to decide which is more appropriate]. Background information: Our study design: We used mark-recapture trapping to obtain density estimates and demography of prairie dogs. The location of our study sites are nested, we have 6 trapping plots within 3 colonies of prairie dogs. Within each colony 3 plots are treatment (given supplemental food) and 3 are control sites. Therefore, in total we have 18 study plots (9 control and 9 treatment). Our study spans over two years and within each year we trapped prairie dogs twice (Spring 2008, Summer 2008, Spring 2009, Summer 2009) for a total of four trapping sessions. Therefore we also have temporal repeated measures in our sampling design. From the mark-recapture data we estimated density using Program DENSITY for each study plot and for each session (a total of 4 density estimates for each 18 plots over time). We also did vegetation sampling to obtain estimates of the natural food available in each plot, which gave us total biomass and % edible vegetation as covariates. We are using the lme4 package in program R (2.11.1) for analysis: We fitted a GLMM with Laplace restricted maximum likelihood estimation. Since our response variable density is a count with overdispersion we used a corrected poisson distribution with a log link function. (I'm not sure corrected is a technically meaningful term: do Zuur et al use this?) And in order to account for the nested and repeated measures in our design we want to include Plot nested in Colony as random effects. The explanatory variables include Treatment, Session, Total biomass, and/or %Edible food for the fixed effects. (Colony, Plot, Treatment, and Session are all factor variables). And an example of the R code that we started with is: PDmodel_1 - lmer(Density~1+Treatment+Session+Biomass+(1|Colony/Plot), family=quasipoisson, data=DensityPD) (You don't need the 1 in this formula: the intercept is implicitly included.) My main question is: Does this accurately take into account our nested and repeated measures design? Have we accounted for any possible pseudoreplication with this type of analysis? Do I need to also look at type AR-1 error structures (or can I do that in a glmm?) Or is there a simpler way you might suggest? I can also look at the change in density between time intervals instead density at time intervals if that makes anything easier to analyze? I can also split Session into season and year if that is helpful too. This looks reasonable. You're likely to have trouble estimating the among-colony variance, because there are only 3 colonies (try estimating a variance from 3 samples sometime) -- I wouldn't be surprised if the estimate of the among-colony variance is zero, unless the colonies are very different. You might alternatively try Colony as a fixed effect and Colony:Plot as the random effect (or equivalently make sure your plots have 18 distinct labels rather than being numbered 1..6 in each plot). It's a bit tricky to incorporate autoregressive structures in a GLMM -- if your densities are high (means 5) you can try this in MASS::glmmPQL. However, I suspect you're unlikely to be able to resolve AR structure in this data set -- if you're worried, take the residuals and examine the correlation between r(t) and r(t+1) [you'll have 54 points -- one for each plot/session combination, not counting the final session]. If that correlation is small/non-significant, you're off the hook. Quasipoisson fits are a little bit problematic in lme4 -- two alternatives are (1) fitting a lognormal-Poisson model by adding a random effect with a distinct level for each observation (2) fitting a negative binomial model with glmm.admb (glmm.admb only allows a single random effect, but you could do that if you make Colony fixed as suggested above). Also keep in mind the rule of thumb that you need at least 10-20 observations per parameter you want to estimate -- with 72 observations, you're pushing it a little (intercept (1) + treatment (1) + session (3) + biomass (1) + random effects (2)) (it's hard to know exactly how to count random effects, but this is a crude rule of thumb). I certainly wouldn't try to make your model any *more* complicated ... good luck __ 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 reports
What do low level proc print and proc report have on Sweave or http://biostat.mc.vanderbilt.edu/wiki/pub/Main/StatReport/summary.pdf? If proc print and proc report are 4G, let's move back a generation. Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University On Thu, 19 Aug 2010, Donald Paul Winston wrote: I don't see much in the way of an ability to write reports in R the way you can with SAS. You basically have to write a program with R in a 3G way unlike SAS with it's 4G proc print and proc report. Are there similar R functions and packages? -- View this message in context: http://r.789695.n4.nabble.com/R-reports-tp2330733p2330733.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] ifelse command
On Aug 18, 2010, at 10:46 PM, Philip Wong wrote: well to be honest, it is a assignment for the Bayesian statistic paper I wish to take later in the academic year. But I'm a slow learner, so I'm going to try out some of the assignments posted in the university forum hoping to get some practice in advance. Could you please elaborate more on the set.seed() function, I understood from the ?set.seed the general idea of set.seed (if I didn't misunderstood it). I could stimulate a six side dice by set.seed(1:6) with n number of runs using runif(), does that meant if I use set.seed() I don't need to use the prob=c(1,1,2,3,2,1)/10) to create my bias dice? No. set.seed()'s only purpose is to fix the RNG in a predictiable starting state so that the reuslts of one or more simulation runs can be recreated exactly. -- View this message in context: http://r.789695.n4.nabble.com/ifelse-command-tp2329538p2330591.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 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] Correlograms and linear regression
Dear all, I generated a Correlograms and used the panel.ellipse (confidence ellipse and smoothed line) option. Is there a way to get instead of the smoothed line the linear regression? Thanks, As hz -- View this message in context: http://r.789695.n4.nabble.com/Correlograms-and-linear-regression-tp2331071p2331071.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] Linear regression equation and coefficient matrix
Dear Greg, Thanks for the tip. As I am new in R can you please provide me a script how do to so. It will help my learning process. Thanks, Asher -- View this message in context: http://r.789695.n4.nabble.com/Linear-regression-equation-and-coefficient-matrix-tp2329804p2330867.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] Combining means
Hi volunteer statisticians, I want to combine the stdev of 6 populations of means for two different treatments and there seem to be many methods for doing so. It is QPCR data consisting of 3 technical replicates building one mean and 6 biological samples in two treatment groups. Now as an overview I just assumed each value to be a replicate it self within each of the two treatments and calculated an overall mean with overall stdev. But this seems to be a bit of a mistake. Is it? First - I think I need a more robust mean. So I applied the geometric mean. Next I combined the deviations by calculating with the formula for error propagation (wiki german Fehlerfortpflanzung). Isn't this a too complicated way? So: 3 technical replicates build one mean with stdev 6 of these build the population of one treatment 2 treatments Any suggestions which method I should use and how I perform the calculations? Thanks for your help Best Holger __ 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] Little's MCAR test
L.S., Does anyone know if there is an R library which implements Little's MCAR test for completely at random missing values? It is implemented in SPSS and SAS, and widely mentioned in the literature. Thanks in advance! Sander van Kuijk -- View this message in context: http://r.789695.n4.nabble.com/Little-s-MCAR-test-tp2331137p2331137.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] creation package
Dear r-help, I don't use namespace. How can I make asia available? I think my problem in creating the package in this: I have a singleglobal function (RT) in my package, but inside RT I need to call several other function( comb l,earn_comb, nchoo). When I used package.sekeleton, Iput in lists all the functions(comb l,earn_comb, nchoo,RT),but in the 'man' I left only namepackage-package.Rd and RT.Rd. When I did do this, is it true?? Best Regards 2010/8/18, Michael Dewey i...@aghmed.fsnet.co.uk: At 10:27 18/08/2010, anderson nuel wrote: Dear r-help, No, I find errors in the file C:/Rp/namepackage.Rcheck/00check.txt : * using log directory 'C:/Rpackage/namepackage.Rcheck' * using R version 2.10.1 (2009-12-14) * using session charset: ISO8859-1 * checking for file 'namepackage/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'namepackage' version '1.0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking for executable files ... OK * checking whether package 'namepackage' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE comb: no visible global function definition for 'copy_bloc' comb: no visible global function definition for 'copy_interl' * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: comb learn_comb nchoo All user-level objects in a package should have documentation entries. See the chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking examples ... ERROR Running examples in 'namepackage-Ex.R' failed. The error most likely occurred in: ### * RT flush(stderr()); flush(stdout()) ### Name: RT ### Title: RT ### Aliases: RT ### ** Examples data(asia) Warning in data(asia) : data set 'asia' not found RT(asia, c(2,2,2), c(1,2,3),c(a,b,c )) Error in nrow(data) : object 'x' not found Calls: RT - array - nrow Execution halted I think my problem in creating the package in this: I have a singleglobal function (RT) in my package, but inside RT I need to call several other function( comb l,earn_comb, nchoo). When I used package.sekeleton, Iput in lists all the functions(comb l,earn_comb, nchoo,RT),but in the 'man' I left only namepackage-package.Rd and RT.Rd. When I did do this, is it true?? Are you using a namespace? If not I think it may help you with the warnings about documentation. The other warning tells you R cannot find asia. You need to make it available. Best Regards, 2010/8/16, Uwe Ligges lig...@statistik.tu-dortmund.de: On 16.08.2010 18:52, anderson nuel wrote: Dear r-help, the file C:/Rp/namepackage.Rcheck/00install.out : * install options are ' --no-html' * installing *source* package 'namepackage' ... ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** MD5 sums * DONE (namepackage) So it was successful. Uwe Best Regards, 2010/8/14, Uwe Liggeslig...@statistik.tu-dortmund.de: On 14.08.2010 11:21, anderson nuel wrote: Dear r-help, I run R CMD INSTALL : c:\RpR CMD INSTALL namepackage *installing to library'c:/PROGRA~1/R/R-210~1-1/library' *installing *source* 'namepackage'... **R **preparing package for lazy loading **help Avis:./man/namepackage-package.Rd:25:'' inatttendue **installing help indices **building package indices **MD5sums *DONEnamepackage best OK, but strange that checking the package fails now in its installation checks. Can you send us the file C:/Rp/namepackage.Rcheck/00install.out please. Uwe Ligges 2010/8/13, Uwe Liggeslig...@statistik.tu-dortmund.de: In my previous maiul I asked you to run R CMD INSTALL at first (rather than R CMD check). You could also look into the mentioned file C:/Rp/namepackage.Rcheck/00install.out But we really need that file to understand what is going on. Uwe Ligges On 13.08.2010 15:12, anderson nuel wrote: Dear r-help, I try this
[R] zoo. window
Hi, I have a dataset including monthly date from 1971-01-01 to 2009-01-01. The dates are character variables. I want to select the subsample from my original data, so I use mydata3-window(mydata,start=1972-02-01,end=2005-02-01), or mydata3-window(mydata, start=as.date(1972-02-01),end=as.date(2005-02-01)) or mydata3-window(mydata, start=c(1972-02-01),end=c(2005-02-01)) but I constantly receive Error in attr(x, tsp) - c(1, NROW(x), 1) : invalid time series parameters specified I don't know how to fix it in this case. Many thanks YD [[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] error with bitmap, please help
Hi All I still have a problem with “bitmap” function in R, I have downloaded ghostscript 8.71 and added the path to the executable to the path environment variable, by going to the control panel , system, advanced system settings, added C:\Program Files(x86)\gs\gs8.71\bin to the path variable. I have also added the R executable path to the path variable. I have a 64 bit computer with windows 7 as an operating system. When running the following script, I get an error in the system df=read.table(sample.txt,sep=\t) bitmap(file=sample.JPG,type=jpeg,width=5,height=5,res=300,pointsize=10) Error in system(paste(gsexe, -help), intern = TRUE, invisible = TRUE) : gswin32c.exe not found plot(df$V1,df$V2,pch=20,col=blue) is there anything that I am missing?? Thanks for your input -- View this message in context: http://r.789695.n4.nabble.com/error-with-bitmap-please-help-tp2331196p2331196.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] R reports
On Aug 19, 2010, at 3:49 PM, Frank Harrell wrote: What do low level proc print and proc report have on Sweave or http://biostat.mc.vanderbilt.edu/wiki/pub/Main/StatReport/summary.pdf? If proc print and proc report are 4G, let's move back a generation. Er, no... AFAIK, 4GL just means that the end user writes (short) programs to control a (complex) application. (3GL is systems programming languages: fortran, C, Pascal, Algol, 2GL is assembler, 1GL is binary code). So a SAS programming is quite typical 4GL, as is S and R. However, SAS may be more contemporary with the buzzword, which roughly corresponds to the perceived state of the art in computer science anno 1945, 1955, 1965, and 1975. If you try continuing into 1985, 1995, 2005, 2015, you'll realize that languages fell off the avant-garde, and instead we got (say) word processors, internet, handheld devices, ... -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] Does R always insist on sending plot output to a file?
Donald, I was able to 'trick' R into writing plot data to a GNU Linux fifo. I had forgotten that the fifo will block until there is a process at either end (a writer and a reader): At one terminal, create a fifo and set a program to catch output $ mkfifo Rfifo $ cat Rfifo At a second terminal $ R postscript(file=Rfifo) plot(0) dev.off() -Matt On Wed, 2010-08-18 at 23:21 -0400, Matt Shotwell wrote: Donald, At least for the PDF device (I know you asked about png, but I believe they are similar), the answer no. Ultimately, this device calls the standard C function fopen, and writes its data to the resulting file stream. If you're using GNU Linux, you might trick R into writing to a fifo (a named pipe, see 'man fifo'), or some other in-memory device, and read from it with another program. My initial experiments with this, however, were not successful. A better solution here, would be to have the various graphics devices write to an R connection, as do most other R functions that input and output data. In this way, we could write graphics data to a RAW connection (rawConnection()), which is essentially a memory buffer. There are two obvious barriers to this: 1. C level I/O routines (e.g. fprintf) are heavily integrated into the graphics device code. Hence, accommodating R connections would require significant changes. 2. The graphics devices are mostly implemented in C, and there is (at present) no interface to R connections at the C level. -Matt On Wed, 2010-08-18 at 21:49 -0400, Donald Paul Winston wrote: I need to write the output of a R plot to a Java OutputStream. It looks like R insists on sending it's output to a file. Is there anyway to get bytes directly from the output of a plot so I can write it with Java? Writing it to a file is too slow. Is there a parameter in the graphics device function png(..) that directs output to a variable in memory? x - plot(.) would make sense. -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ 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] probabilities from predict.svm
Hi James, I'd like to help you out, but I'm not sure I understand what the problem is. Does the problem lie with building a predictive SVM, or getting the right values (class probabilities) to land in the right place on your map/plot? -steve On Wed, Aug 18, 2010 at 3:09 PM, Watling,James I watli...@ufl.edu wrote: Dear R Community- I am a new user of support vector machines for species distribution modeling and am using package e1071 to run svm() and predict.svm(). Briefly, I want to create an svm model for classification of a factor response (species presence or absence) based on climate predictor variables. I have used a training dataset to train the model, and tested it against a validation data set with good results: AUC is high, and the confusion matrix indicates low commission and omission errors. The code for the best-fit model is: svm.model -svm(as.factor(acutus)~p_feb+p_jan+p_mar+p_sep+t_feb+t_july+t_june+t_mar,cost=1, gamma=1, probability=T) Because ultimately I want to create prediction maps of probabilities of species occurrence under future climate change, I want to use the results of the validated model to predict probability of presence using data describing future conditions. I have created a data frame (predict.data) with new values for the same predictor variables used in the original model; each value corresponds to an observation from a raster grid of the study area. I enabled the probability option when creating the original model, and acquire the probabilities using the predict function: pred.map -predict(svm.model, predict.data, probability=T). However, when I use probs-attr(pred.map, probabilities) to acquire the probabilities for each grid cell, the spatial signature of the probabilities does make sense. I have extracted the column of probabilities for class = 1 (probability of presence), and the resulting map of the study area is spatially accurate (it has the right shape), but the probability values are incorrect, or at least in the wrong place. I am attaching a pdf (SVM prediction maps) of the resulting map using probabilities obtained using the code described above (page 1) and a map of what the prediction map should look like given spatial autocorrelation in climate predictors (page 2, map generated using openmodeller). Note that the openmodeller map was created with the same input data and same svm algorithm (also using code from libsvm) as the model in R, just run using different software. I don't know why the prediction map of probabilities based on the model is so different from what I would expect, and would appreciate any thoughts from the group. All the best James *** James I Watling, PhD Postdoctoral Research Associate University of Florida Ft. Lauderdale Research Education Center 3205 College Avenue Ft Lauderdale, FL 33314 USA 954.577.6316 (phone) 954.475.4125 (fax) *** James I Watling, PhD Postdoctoral Research Associate University of Florida Ft. Lauderdale Research Education Center 3205 College Avenue Ft Lauderdale, FL 33314 USA 954.577.6316 (phone) 954.475.4125 (fax) __ 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. -- 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] R reports
The sos package is designed to search the help pages of all contributed packages and return the results in a data.frame sorted to put first the package with the most matches. It also has a vignette, which appeared in last December's issue of The R Journal. This can be used to search in a variety of ways for whatever you want. It has union capabilities to support combining the results of different searches. Spencer Graves, lead author of sos On 8/19/2010 6:49 AM, Frank Harrell wrote: What do low level proc print and proc report have on Sweave or http://biostat.mc.vanderbilt.edu/wiki/pub/Main/StatReport/summary.pdf? If proc print and proc report are 4G, let's move back a generation. Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University On Thu, 19 Aug 2010, Donald Paul Winston wrote: I don't see much in the way of an ability to write reports in R the way you can with SAS. You basically have to write a program with R in a 3G way unlike SAS with it's 4G proc print and proc report. Are there similar R functions and packages? -- View this message in context: http://r.789695.n4.nabble.com/R-reports-tp2330733p2330733.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. -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ 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] Adding lines to xyplot with abline
Is it kosher to add, say, horizontal lines to a lattice xyplot using abline(h=xxx)? The lines don't appear at the right value, that is, if h=150, the line might appear at h=140? Jeff This communication, including any attachments, is intended solely for the use of the addressee and may contain information which is privileged, confidential, exempt from disclosure under applicable law or subject to copyright. If you are not an intended recipient, any use, disclosure, distribution, reproduction, review or copying is unauthorized and may be unlawful. If you have received this transmission in error, please notify the sender immediately. Thank you. Cette communication,y compris les pieces jointes, est reservee a l'usage exclusif du destinataire et peut contenir des informations privilegiees, confidentielles, exemptees de divulgation selon la loi ou protegees par les droits de publication. Si vous n'etes pas un destinataire, toute utilisation, divulgation, distribution, reproduction, examen ou copie est non-autorisee et peut etre illegale. Si vous avez recu cette communication par erreur, veuillez aviser l'expediteur immediatement. Merci. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] error with bitmap, please help
On Thu, 19 Aug 2010, kayj wrote: Hi All I still have a problem with “bitmap” function in R, I have downloaded ghostscript 8.71 and added the path to the executable to the path environment variable, by going to the control panel , system, advanced system settings, added C:\Program Files(x86)\gs\gs8.71\bin to the path variable. I have also added the R executable path to the path variable. I have a 64 bit computer with windows 7 as an operating system. When running the following script, I get an error in the system df=read.table(sample.txt,sep=\t) bitmap(file=sample.JPG,type=jpeg,width=5,height=5,res=300,pointsize=10) Error in system(paste(gsexe, -help), intern = TRUE, invisible = TRUE) : gswin32c.exe not found plot(df$V1,df$V2,pch=20,col=blue) is there anything that I am missing?? As it says it is not found, so you need to check your paths: do Sys.getenv(PATH) inside R. Note that the help page mentions two environment variables you can set to the path to the gswin32c.exe, which is designed to make this easier for you to set. Please note that it is getting increasingly important to supply 'at a minimum' information asked for in the posting guide. This is the second time that you have not done so, and would-be helpers are put off by the lack of basic information. For example, here we don't know the version or build of R (your OS may be 64-bit, is your R)? Thanks for your input -- View this message in context: http://r.789695.n4.nabble.com/error-with-bitmap-please-help-tp2331196p2331196.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. -- 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.
[R] solution
Hello
I am not sure about your general aim, but from my previous experience on
combination of treatments, it can be more useful to create a matrix or
data.frame, which you can fulfill either with 1s and 0s, or with the values of
treatment, especially if you will need this data later for the analysis.
I can propose a small function, but only for the case of pair selection
treat=function(x,y){
data.frame(Treatment=x[-which(x==y)], Comparator=rep(y,times=length(x)-1))
}
treat(c(t1,t2,t3,t4),t2)
Treatment Comparator
1 t1 t2
2 t3 t2
3 t4 t2
In this case you can define the list of names of treatments ant the comparator
each time you need, and you will get the result as a data frame in the way you
asked.
Good luck
Alex Levitchi
PhD in Genetics,
Bioinformatician at Laboratory of Bioinformatics
CBM, Area Science Park, Trieste, Italy
http://www.cbm.fvg.it/laboratories/bioinformatics_research
scientific researcher,
Center of Molecular Biology,
University of Academy of Sciences of Moldova
www.edu.asm.md
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Re: [R] zoo. window
On Thu, 19 Aug 2010, wyd...@msn.com wrote: Hi, I have a dataset including monthly date from 1971-01-01 to 2009-01-01. The dates are character variables. I would suggest to use a more suitable class for the index, such as yearmon (if you only want to indicate the month anyway) or Date (if you want to use a particular day within the month). From your description, I would recommend yearmon. Also look at the examples on the manual pages and in the vignettes of the package that provide various illustrations of both approaches. I want to select the subsample from my original data, so I use mydata3-window(mydata,start=1972-02-01,end=2005-02-01), or mydata3-window(mydata, start=as.date(1972-02-01),end=as.date(2005-02-01)) or mydata3-window(mydata, start=c(1972-02-01),end=c(2005-02-01)) but I constantly receive Error in attr(x, tsp) - c(1, NROW(x), 1) : invalid time series parameters specified I don't know how to fix it in this case. Many thanks YD [[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] Adding lines to xyplot with abline
On Aug 19, 2010, at 10:31 AM, jeffrey.mor...@sanofipasteur.com wrote: Is it kosher to add, say, horizontal lines to a lattice xyplot using abline(h=xxx)? The lines don't appear at the right value, that is, if h=150, the line might appear at h=140? Correct. The coordinate systems are not shared between lattice and base graphics. ?panel.abline If you have an existing plot on your screen device, you can try what the help pages describe as an experimental method: trellis.focus(panel, 1, 1) panel.abline(h=140) trellis.unfocus() As far as I can tell, it doesn't actually change the lattice object but the plot can be saved as whatever options for Save as your GUI may offer. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Correlograms and linear regression
Just define your own panel function. Here I modified the panel.ellipse
function and called it panel.lm
library(corrgram)
data(baseball)
vars2 - c(Assists,Atbat,Errors,Hits,Homer,logSal,
Putouts,RBI,Runs,Walks,Years)
panel.lm - function(x, y, ...){
dfn - 2
dfd - length(x) - 1
shape - var(cbind(x, y), na.rm = TRUE)
keep - (!is.na(x) !is.na(y))
center - c(mean(x[keep]), mean(y[keep]))
radius - sqrt(dfn * qf(0.68, dfn, dfd))
segments - 75
angles - seq(0, 2 * pi, length = segments)
unit.circle - cbind(cos(angles), sin(angles))
ellipse.pts - t(center + radius * t(unit.circle %*% chol(shape)))
ellx - ellipse.pts[, 1]
elly - ellipse.pts[, 2]
usr - par()$usr
minx - usr[1]
maxx - usr[2]
miny - usr[3]
maxy - usr[4]
ellx - ifelse(ellx minx, minx, ellx)
ellx - ifelse(ellx maxx, maxx, ellx)
elly - ifelse(elly miny, miny, elly)
elly - ifelse(elly maxy, maxy, elly)
lines(ellx, elly, col = gray30, ...)
#ok - is.finite(x) is.finite(y)
#if (any(ok))
# lines(stats::lowess(x[ok], y[ok], f = 2/3, iter = 3),
#col = red, ...)
abline(coef(lm(y~x)), col=red)
}
corrgram(baseball[,vars2], order=TRUE,
main=Baseball correlation ellipses,
panel=panel.lm, text.panel=panel.txt, diag.panel=panel.minmax)
Kevin Wright
On Thu, Aug 19, 2010 at 7:07 AM, ashz a...@walla.co.il wrote:
Dear all,
I generated a Correlograms and used the panel.ellipse (confidence ellipse
and smoothed line) option. Is there a way to get instead of the smoothed
line the linear regression?
Thanks,
As hz
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Re: [R] How to measure correlations in terms of distance and draw them on a 2-dimmentional plot?
Thank you all a lot for all the suggestion! -- View this message in context: http://r.789695.n4.nabble.com/How-to-measure-correlations-in-terms-of-distance-and-draw-them-on-a-2-dimmentional-plot-tp2330413p2331408.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] probabilities from predict.svm
On Thu, Aug 19, 2010 at 10:56 AM, Watling,James I watli...@ufl.edu wrote: Hi Steve-- Thanks for your interest in helping me figure this out. I think the problem has to do with the values of the probabilities returned from the use of the model to predict occurrence in a new dataframe. Ok, so if you're sure this is the problem, and not, say, getting the correct values for the predictor variables at a given point, then I'd be a bit more thorough when building your model. Originally you said: I have used a training dataset to train the model, and tested it against a validation data set with good results: AUC is high, and the confusion matrix indicates low commission and omission errors. Maybe your originally good AUC's was just a function of your train/test split? Why not use all of your data and do something like 10 fold cross validation to find: (1) Your average accuracy over your folds (2) The best value for your cost parameter; (how did you pick cost=1)? (3) or even the best kernel to use. Doing 2 and 3 will likely be time consuming. To help with (2) you might try looking at the svmpath package: http://cran.r-project.org/web/packages/svmpath/index.html It only works on 2-class classification problems, and (I think) using a linear kernel (sorry, don't remember off hand, but it's written in the package help and linked pubs). You don't need to use svmpath, but then you'll need to define a grid of C values (or maybe a 2d grid, if your svm + kernel combo has more params) and train over these values ... takes lots of cpu time, but not too much human time. Does that make sense? -- 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 measure correlations in terms of distance and draw them on a 2-dimmentional plot?
You could also try RSiteSearch(correlation circle) Kjetil On Thu, Aug 19, 2010 at 11:31 AM, weijian21cn wli...@stern.nyu.edu wrote: Thank you all a lot for all the suggestion! -- View this message in context: http://r.789695.n4.nabble.com/How-to-measure-correlations-in-terms-of-distance-and-draw-them-on-a-2-dimmentional-plot-tp2330413p2331408.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] Quick q. on lists
Hi All, Anyone know how to quickly query some summary information on the components of a list? For example, I have a list that contains dataframes (originally generated by using split() on one large data frame). I simply want to know the number of rows in the longest dataframe from the list. Example, if my list has 3 data frames, and the first has 2 rows, the second 8 rows, and the third 3 rows, I want to ask something like: max(nrow(myList)) which would ideally return 8. but this is obviously wrong syntax. Currently, I'm looping through each of the data frames in the list, searching for the max rows, but I'm sure there must be a faster way. Thanks, Jonatahn __ 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] (no subject)
Kalaivani Mani manikalaivani at yahoo.co.in writes: To R group Help Desk (We're not the help desk (!!) You can buy support from various companies if you want ...) I am a user of R software. I am facing a problem while using frailtyPenal command in R.2.11.1. When I use these command, R closes completely without any prior alert message. Can I know what would be the reason? My data size is 7050 records with atleast 25 variables. R stopping, if you have not been writing your own low-level (C/FORTRAN) code, constitutes a bug by definition -- but the bug is in the contributed 'frailtypack' package, rather than in base R. Try contacting the maintainer of the package [maintainer(frailtypack)]. You will want to provide them with at least the results of sessionInfo() , which will let them know what operating system you are using (which may well be important in dealing with this sort of bug), as well as the versions of R and frailtypack. good luck Ben Bolker __ 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] ROCR predictions
At the heart of this you have a problem in incomplete conditioning. You are computing things like Prob(X x) when you know X=x. Working with a statistician who is well versed in probability models will undoubtedly help. Frank Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University On Thu, 19 Aug 2010, Assa Yeroslaviz wrote: Hello everybody, yes I'm sorry. I can see it is not so easy to understand. I'l try to explain a bit more. The experiment was used to compare two (protein domain) data bases and find out whether or not the results founded in one are comparable to the second DB. the first column shows the list of the various inputs in the DB, the second lists the various domains for each gene. the p-value column calculates the probability that the found in column four (Expected) to be found by chance. in column five the expected values was listed. The calculation of the TP,TN,FP,FN was made many times, each time with a different p-value (from p=1,...,p=10E-12) as a threshold to calculate the various values of TP,TN, etc. The goal of this calculation was to find the optimal p-value wit ha maximum of TP and a minimum of FP. To do so I thought about making the column of p-values my predictions and the values in the column Is.Expected (TRUE,FALSE) to my labels. This how I calculated my first ROC curve: pValue - read.delim(file = p=1.txt, as.is= TRUE) desc1 - pValue[[p.value]] label1 - pValue[[Is.Expected]] # after changing the values of TRUE = 0, FALSE = 1 pred - prediction(desc1, label1) perf - performance(pred, tpr, fpr) plot(perf, colorsize = TRUE) my question are as follow: 1. Am I right in my way of thinkning, that the p-values here are predictions? I know you said I need to decided it for myself, but I'm not sure. If they are, than I will have the same predictions for each and every calculation of ROCR. Will it make any difference at the prediction? 2. how can i calculate the other p-values thresholds? Do I need to do each separately, or is there a way of combining them? I hope you can still help we with some hints or further advieces. Thanks Assa On Wed, Aug 18, 2010 at 07:55, Claudia Beleites cbelei...@units.it wrote: Dear Assa, you need to call prediction with continuous predictions and a _binary_ true class label. You are the only one who can tell whether the p-values are actually predictions and what the class labels are. For the list readers p is just the name of whatever variable, and you didn't even vaguely say what you try to classify, nor did you offer any explanation of what the columns are. The only information we get from your table is that p-value has small and continuous values. From what I see the p-values could also be fitting errors of the predictions (e.g. expressed as a probability that the similarity to the predicted class is random). Claudia Assa Yeroslaviz wrote: Dear Claudia, thank you for your fast answer. I add again the table of the data as an example. Protein ID Pfam Domain p-value ExpectedIs Expected True Postive False Negative False Positive True Negative NP_11.2 APH 1.15E-05APH TRUE1 0 0 0 NP_11.2 MutS_V 0.0173 APH FALSE 0 0 1 0 NP_62.1 CBS 9.40E-08CBS TRUE1 0 0 0 NP_66.1 APH 3.83E-06APH TRUE1 0 0 0 NP_66.1 CobU0.009 APH FALSE 0 0 1 0 NP_66.1 FeoA0.3975 APH FALSE 0 0 1 0 NP_66.1 Phage_integr_N 0.0219 APH FALSE 0 0 1 0 NP_000161.2 Beta_elim_lyase 6.25E-12Beta_elim_lyase TRUE1 0 0 0 NP_000161.2 Glyco_hydro_6 0.002 Beta_elim_lyase FALSE 0 0 1 0 NP_000161.2 SurE0.0059 Beta_elim_lyase FALSE 0 0 1 0 NP_000161.2 SapB_2 0.0547 Beta_elim_lyase FALSE 0 0 1 0 NP_000161.2 Runt0.1034 Beta_elim_lyase FALSE 0 0 1 0 NP_000204.3 EGF 0.004666118 EGF TRUE1 0 0 0 NP_000229.1 PAS 3.13E-06PAS TRUE1 0 0 0 NP_000229.1 zf-CCCH 0.2067 PAS FALSE 0 1 1 0 NP_000229.1 E_raikovi_mat 0.0206 PAS FALSE 0 0 0 0 NP_000388.2 NAD_binding_1 8.21E-24NAD_binding_1 TRUE1 0 0 0 NP_000388.2 ABM 1.40E-08NAD_binding_1 FALSE 0 0 1 0 NP_000483.3 MMR_HSR11.98E-05MMR_HSR1TRUE1 0 0 0 NP_000483.3 DEAD2.30E-05MMR_HSR1FALSE 0 0 1 0 NP_000483.3 APS_kinase 1.80E-09MMR_HSR1
Re: [R] Quick q. on lists
Jonathan wrote: Hi All, Anyone know how to quickly query some summary information on the components of a list? For example, I have a list that contains dataframes (originally generated by using split() on one large data frame). I simply want to know the number of rows in the longest dataframe from the list. Example, if my list has 3 data frames, and the first has 2 rows, the second 8 rows, and the third 3 rows, I want to ask something like: max(nrow(myList)) which would ideally return 8. max(sapply(myList, nrow)) but this is obviously wrong syntax. Currently, I'm looping through each of the data frames in the list, searching for the max rows, but I'm sure there must be a faster way. Thanks, Jonatahn __ 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] Quick q. on lists
You need sapply max(sapply(myList, nrow)) Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Jonathan Verzonden: donderdag 19 augustus 2010 17:42 Aan: r-help Onderwerp: [R] Quick q. on lists Hi All, Anyone know how to quickly query some summary information on the components of a list? For example, I have a list that contains dataframes (originally generated by using split() on one large data frame). I simply want to know the number of rows in the longest dataframe from the list. Example, if my list has 3 data frames, and the first has 2 rows, the second 8 rows, and the third 3 rows, I want to ask something like: max(nrow(myList)) which would ideally return 8. but this is obviously wrong syntax. Currently, I'm looping through each of the data frames in the list, searching for the max rows, but I'm sure there must be a faster way. Thanks, Jonatahn __ 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. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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] Quick q. on lists
Hi Jonathan, Try this: # list of data frames mylist - list(d1 = matrix(rnorm(100), ncol = 10), d2 = matrix(rnorm(100), ncol = 5), d3 = matrix(rnorm(100), ncol = 20)) # max number of rows max(do.call(c, lapply(mylist, nrow))) # [1] 20 HTH, Jorge On Thu, Aug 19, 2010 at 11:42 AM, Jonathan wrote: Hi All, Anyone know how to quickly query some summary information on the components of a list? For example, I have a list that contains dataframes (originally generated by using split() on one large data frame). I simply want to know the number of rows in the longest dataframe from the list. Example, if my list has 3 data frames, and the first has 2 rows, the second 8 rows, and the third 3 rows, I want to ask something like: max(nrow(myList)) which would ideally return 8. but this is obviously wrong syntax. Currently, I'm looping through each of the data frames in the list, searching for the max rows, but I'm sure there must be a faster way. Thanks, Jonatahn __ 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] functions and multiple levels
Thanks for the replies, it wasn't quite what I wanted but it has given me
some more code for working out averages.
I have managed to construct something that nearly works
level.1 level.2 observation
1 1 0.5
1 1 0.2
1 2 0.6
1 2 0.4
2 3 0.8
2 3 0.7
2 4 0.6
2 4 0.4
# read data (copy above to clipboard)
dat - read.table(clipboard,head=T)
mean.lev- function(a, b, c) {
lev.1-rep(tapply(c, a, mean),each=2)
lev.2-tapply(c, b, mean)
ss.lev-(lev.1-lev.2)^2
ss.lev.n-ss.lev*(length(c)/max(b))
return(as.matrix(ss.lev,ss.lev.n,nrow=max(b)))
}
mean.lev(level.1, level.2, observation)
The only problem is that it won't print both ss.lev and ss.lev.n, does
anyone know to to get it to print both?
I want it in a function as above because I have lots of data sets to apply
it to.
Thanks Chris
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Re: [R] probabilities from predict.svm
Hi Steve-- Thanks for your interest in helping me figure this out. I think the problem has to do with the values of the probabilities returned from the use of the model to predict occurrence in a new dataframe. The svm model I referenced in the original message (svm.model) does a good job classifying species presence and absence in the test data set I used. So I don't think the problem is with building the predictive svm per se. The problem comes when I take that model and use it to calculate probabilities based on the climate predictors--the resulting probabilities range from 0-1, but the probability of presence associated with specific cells just does not make sense. If you take a look at the maps I attached in the original message I think the problem becomes very clear; the maps model the probability of occurrence for the American Crocodile--a species with an entirely tropical distribution. The second map looks exactly like the prediction map for the species should--the warmer colors essentially delineate the geographic range of the species. The first map, with probabilities extracted from the use of svm.model to predict occurrence as a function of climate variables in the same area (the predict.data dataframe) does not make any sense. I don't think the problem is with getting the probabilities in the right place, because the relative position of predicted values and NA's used to define the map make sense--the map looks like a map of southern North America and northern South America, just as it should. So the probabilities are in the right place on the map. The problem is that the probabilities associated with each individual cell are, in a word, wrong. The original model (svm.model) was parameterized with 10,000 pseudoabsences drawn from throughout the entire region, so the range of climate values used to create the original model is the same as that reflected in the data I am using to build the prediction map. I can't think of any reason that the probabilities returned from pred.map-predict(svm.model, predict.data, probability=T)should be so off-base, but it seems like they are. Any thoughts? James -Original Message- From: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com] Sent: Thursday, August 19, 2010 10:24 AM To: Watling,James I Cc: r-h...@lists.r-project.org Subject: Re: [R] probabilities from predict.svm Hi James, I'd like to help you out, but I'm not sure I understand what the problem is. Does the problem lie with building a predictive SVM, or getting the right values (class probabilities) to land in the right place on your map/plot? -steve On Wed, Aug 18, 2010 at 3:09 PM, Watling,James I watli...@ufl.edu wrote: Dear R Community- I am a new user of support vector machines for species distribution modeling and am using package e1071 to run svm() and predict.svm(). Briefly, I want to create an svm model for classification of a factor response (species presence or absence) based on climate predictor variables. I have used a training dataset to train the model, and tested it against a validation data set with good results: AUC is high, and the confusion matrix indicates low commission and omission errors. The code for the best-fit model is: svm.model -svm(as.factor(acutus)~p_feb+p_jan+p_mar+p_sep+t_feb+t_july+t_june+t_mar,cost=1, gamma=1, probability=T) Because ultimately I want to create prediction maps of probabilities of species occurrence under future climate change, I want to use the results of the validated model to predict probability of presence using data describing future conditions. I have created a data frame (predict.data) with new values for the same predictor variables used in the original model; each value corresponds to an observation from a raster grid of the study area. I enabled the probability option when creating the original model, and acquire the probabilities using the predict function: pred.map -predict(svm.model, predict.data, probability=T). However, when I use probs-attr(pred.map, probabilities) to acquire the probabilities for each grid cell, the spatial signature of the probabilities does make sense. I have extracted the column of probabilities for class = 1 (probability of presence), and the resulting map of the study area is spatially accurate (it has the right shape), but the probability values are incorrect, or at least in the wrong place. I am attaching a pdf (SVM prediction maps) of the resulting map using probabilities obtained using the code described above (page 1) and a map of what the prediction map should look like given spatial autocorrelation in climate predictors (page 2, map generated using openmodeller). Note that the openmodeller map was created with the same input data and same svm algorithm (also using code from libsvm) as the model in R, just run using different software. I don't know why the prediction map
Re: [R] ifelse command
It would help us help you if you could give a description of what your ultimate goal is here. Is it to simulate the dice? Then you may want to just use the dice function in the TeachingDemos package (or you can animate the rolling with plot.rgl.die and roll.rgl.die in the same package). Or is it to understand more use of the sample function? Your original post did the correct thing with sample, but then immediately threw away the results without using them. Is it to better understand random number generation? Better understand putting values into categories? Use cut or findInterval (or others). The more you help us understand your goals, the better we can help you. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Philip Wong Sent: Wednesday, August 18, 2010 8:46 PM To: r-help@r-project.org Subject: Re: [R] ifelse command well to be honest, it is a assignment for the Bayesian statistic paper I wish to take later in the academic year. But I'm a slow learner, so I'm going to try out some of the assignments posted in the university forum hoping to get some practice in advance. Could you please elaborate more on the set.seed() function, I understood from the ?set.seed the general idea of set.seed (if I didn't misunderstood it). I could stimulate a six side dice by set.seed(1:6) with n number of runs using runif(), does that meant if I use set.seed() I don't need to use the prob=c(1,1,2,3,2,1)/10) to create my bias dice? -- View this message in context: http://r.789695.n4.nabble.com/ifelse- command-tp2329538p2330591.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] Why does Bootstrap work for one of similar models but not for the other?
In future, when posting data in your message use dput() or textConnection() so that helpeRs can more easily load them. I was not able to replicate your results. Here's what I got: Bootstrap Statistics : originalbiasstd. error t1* 0.99975370 0.0044205644 0.04110232 t2* -0.06091574 -0.0078646847 0.05778133 t3* 0.27506204 0.0006121326 0.05296862 t4* -0.03040424 0.0002096330 0.02826951 sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] datasets splines grid tcltk stats graphics grDevices [8] utils methods base other attached packages: [1] boot_1.2-42 TinnR_1.0.3 R2HTML_1.59-1 Hmisc_3.7-0 [5] survival_2.35-8 svSocket_0.9-48 lattice_0.18-3 MASS_7.3-5 What does getOption(digits) give you just before you run each bootstrap? Bert Gunter Genentech nonclinical Statistics On Thu, Aug 19, 2010 at 12:50 AM, Reiko Akiyama reiko.akiy...@ebc.uu.se wrote: Dear all, Could anyone help me figure out why bootstrap works for one of similar models but not for the other and how I can solve it? I am using R 2.11.1 in Windows and would like to get confidence intervals for my models A and B by bootstrapping. However, bootstrap gives expected output for the model A but not for B, which I found was puzzling because the structure of the models is similar as I describe below. I had another person running the models in another computer and the same thing happens so this does not seem to be computer-specific. I could not find a clue for a solution in the R archive or in the R book (at least to the extent I understood). Here are the properties of the models A and B and what happens when I run bootstrap. modelA: rA~stA1+ stA2+stA3 model B: rB~stB1+stB2+stB3 The variables for the models A and B are in the same dataset called ?data?. The sample size is 32 for both models and the value range and distribution of the variables in the two models are similar. (Variables from both models are at the end of this enquiry.) [bootstrap of the model A] A.fun-function(data,indices)coefficients(lm(rA~stA1+ stA2+stA3,data=data[indices,])) bootA-boot(data,A.fun,1000);bootA ORDINARY NONPARAMETRIC BOOTSTRAP Call: boot(data = data, statistic = A.fun, R = 1000) Bootstrap Statistics : original bias std. error t1* 1.00016501 -0.004350842 0.05309877 t2* 0.02343475 0.008501989 0.07638795 t3* -0.01602954 -0.004980400 0.07806805 t4* 0.03601194 -0.005417404 0.08510128 [bootstrap of the model B] B.fun-function(data,indices)coefficients(lm(rB~stB1+stB2+stB3),data=data[indices,]) bootB-boot(data,B.fun,1000);bootB ORDINARY NONPARAMETRIC BOOTSTRAP Call: boot(data = data, statistic = B.fun, R = 1000) Bootstrap Statistics : original bias std. error t1* 0.99975370 0 0 t2* -0.06091574 0 0 t3* 0.27506203 0 0 t4* -0.03040424 0 0 What am I missing here? I highly appreciate any comments and suggestions. Best Wishes, Reiko Akiyama Uppsala University Sweden [Variables from the model A] rA [1] 0.7100881 1.0406464 1.1100229 0.6182664 0.7345739 1.0577865 0.6856024 [8] 0.5264447 1.5793340 1.1793993 0.6488737 1.0214076 1.3589618 1.0528893 [15] 1.5242409 1.3761019 0.9427032 0.6794809 1.4752693 0.7737512 1.0120797 [22] 0.8692458 1.2079660 1.0610513 0.8570029 0.9794319 1.0957395 0.8243552 [29] 0.4162586 1.4079334 1.0692132 1.1059419 stA1 [1] -0.9126354 -0.8331680 -1.0239203 -0.3721959 -0.5311308 0.7564474 [7] -1.1828933 -1.2146727 -0.8172593 -0.9921410 -0.5152602 -0.9285442 [13] -0.4198840 -0.9444529 -0.4198840 -0.8331680 1.2810163 1.4081718 [19] 1.7102091 2.3460247 1.3806653 1.3127957 1.2333282 1.4240806 [25] -0.1337555 -0.1973142 0.2954372 -0.1337555 -0.4039753 -0.3880665 [31] 0.2795666 -0.2291317 stA2 [1] -0.2292617 -0.4917962 -0.6437899 -1.2241293 -0.3398026 -2.0946384 [7] -1.0721356 -1.2655821 -1.3484877 -1.8873744 -0.7543307 -0.9615948 [13] -0.3674378 0.4483537 0.8761467 -0.8786892 0.5312593 1.1524988 [19] 0.3234425 -0.4088906 0.5102565 1.1945044 1.7748438 0.6827002 [25] 0.6418001 1.1801340 0.4207184 0.8076114 0.9181522 0.6827002 [31] 0.9037819 0.9181522 stA3 [1] 0.86459627 -0.23416149 -2.00372671 0.04161491 0.78881988 -2.50869565 [7] -0.02608696 -0.84161491 -0.95465839 -0.28012422 0.47080745 0.07577640 [13] 0.84223602 0.24472050 2.83975155 0.43043478 -0.75652174 -0.92795031 [19] 0.29192547 -0.78633540 -0.78385093 -0.51242236 0.59627329 0.19068323 [25] 0.02919255 1.17018634 -0.19440994 0.68385093 1.08881988 -0.28385093 [31] -0.71118012 1.06583851 [Variables from the model B] rB [1] 1.5385568 1.5885100 1.3587255 0.8991566 1.4086787
Re: [R] Linear regression equation and coefficient matrix
Here is a quick example: c1 - cor(iris[,-5]) s1 - sqrt(diag(var(iris[,-5]))) betas - diag( s1 ) %*% c1 %*% diag( 1/s1 ) # now compare: coef( lm( Sepal.Length ~ Sepal.Width, data=iris ) )[2] betas[1,2] But if you cannot work that out on your own, then you really should review linear algebra and linear model theory. Also when dealing with us absent minded professor types (I now have adjunct status at 2 universities, can I rationalize being twice as absent minded now?) it is best to include some context in your post (quote some of the previous conversation) to help us remember which of many discussions we have been part of recently you are asking about. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of ashz Sent: Thursday, August 19, 2010 3:02 AM To: r-help@r-project.org Subject: Re: [R] Linear regression equation and coefficient matrix Dear Greg, Thanks for the tip. As I am new in R can you please provide me a script how do to so. It will help my learning process. Thanks, Asher -- View this message in context: http://r.789695.n4.nabble.com/Linear- regression-equation-and-coefficient-matrix-tp2329804p2330867.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] creation package
At 13:57 19/08/2010, anderson nuel wrote: Dear r-help, I don't use namespace. Well, as I said in my original reply, it would be a good idea to do so. How can I make asia available? Without knowing where asia is that is quite a tough call. How do you access it when you test your code before you try to package it? I think my problem in creating the package in this: I have a singleglobal function (RT) in my package, but inside RT I need to call several other function( comb l,earn_comb, nchoo). When I used package.sekeleton, Iput in lists all the functions(comb l,earn_comb, nchoo,RT),but in the 'man' I left only namepackage-package.Rd and RT.Rd. When I did do this, is it true?? Best Regards 2010/8/18, Michael Dewey mailto:i...@aghmed.fsnet.co.uki...@aghmed.fsnet.co.uk: At 10:27 18/08/2010, anderson nuel wrote: Dear r-help, No, I find errors in the file C:/Rp/namepackage.Rcheck/00check.txt : * using log directory 'C:/Rpackage/namepackage.Rcheck' * using R version 2.10.1 (2009-12-14) * using session charset: ISO8859-1 * checking for file 'namepackage/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'namepackage' version '1.0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking for executable files ... OK * checking whether package 'namepackage' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE comb: no visible global function definition for 'copy_bloc' comb: no visible global function definition for 'copy_interl' * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: comb learn_comb nchoo All user-level objects in a package should have documentation entries. See the chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking examples ... ERROR Running examples in 'namepackage-Ex.R' failed. The error most likely occurred in: ### * RT flush(stderr()); flush(stdout()) ### Name: RT ### Title: RT ### Aliases: RT ### ** Examples data(asia) Warning in data(asia) : data set 'asia' not found RT(asia, c(2,2,2), c(1,2,3),c(a,b,c )) Error in nrow(data) : object 'x' not found Calls: RT - array - nrow Execution halted I think my problem in creating the package in this: I have a singleglobal function (RT) in my package, but inside RT I need to call several other function( comb l,earn_comb, nchoo). When I used package.sekeleton, Iput in lists all the functions(comb l,earn_comb, nchoo,RT),but in the 'man' I left only namepackage-package.Rd and RT.Rd. When I did do this, is it true?? Are you using a namespace? If not I think it may help you with the warnings about documentation. The other warning tells you R cannot find asia. You need to make it available. Best Regards, 2010/8/16, Uwe Ligges mailto:lig...@statistik.tu-dortmund.delig...@statistik.tu-dortmund.de: On 16.08.2010 18:52, anderson nuel wrote: Dear r-help, the file C:/Rp/namepackage.Rcheck/00install.out : * install options are ' --no-html' * installing *source* package 'namepackage' ... ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** MD5 sums * DONE (namepackage) So it was successful. Uwe Best Regards, 2010/8/14, Uwe Liggesmailto:lig...@statistik.tu-dortmund.delig...@statistik.tu-dortmund.de: On 14.08.2010 11:21, anderson nuel wrote: Dear r-help, I run R CMD INSTALL : c:\RpR CMD INSTALL namepackage *installing to library'c:/PROGRA~1/R/R-210~1-1/library' *installing *source* 'namepackage'... **R **preparing package for lazy loading **help Avis:./man/namepackage-package.Rd:25:'' inatttendue **installing help indices **building package indices **MD5sums *DONEnamepackage best OK, but strange that checking the package fails now in its installation checks. Can you send us the file C:/Rp/namepackage.Rcheck/00install.out please. Uwe Ligges 2010/8/13, Uwe Liggesmailto:lig...@statistik.tu-dortmund.delig...@statistik.tu-dortmund.de: In my previous maiul I asked you to run R CMD INSTALL at first (rather than R CMD check).
[R] Pass By Value Questions
I understand R is a Pass-By-Value language. I have a few practical questions, however. I'm dealing with a large dataset (~1GB) and so my understanding of the nuances of memory usage in R is becoming important. In an example such as: d - read.csv(file.csv); n - apply(d, 1, sum); must d be copied to another location in memory in order to be used by apply? In general, is copying only done when a variable is updated within a function? Would the following example be any different in terms of memory usage? d - read.csv(file.csv); n - apply(d[,2:10], 1, sum); or can R reference the original d object since no changes to the object are being made? I'm familiar with FF and BigMemory, but are there any packages/tricks which allow for passing such objects by reference without having to code in C? Regards, Jeff Allen __ 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 reports
Your question brings up a bit of a philosophical issue (or possibly economic theory). The idea is the contrast between specialization and generalization. A purely specialized program will only do one thing (but hopefully do that one thing well), the ultimate generalized program will do everything (but usually none of the things very well, have you ever tried eating with one of those pocket knives that has a built in fork and spoon?) most fall somewhere in between on the specialization/generalization continuum. So when someone wants to do something that is not currently done in a program the question is: Do we make the program more general by adding this capability? Or do we delegate that task to another program that already specializes in that?. The answer will be different for different programs/programmers/users/... What you detail below as the benefits of SAS proc report actually includes several tasks. Tasks that statistical programs do well like grouping and summarizing of data should be in the stats program. In the case of R there are multiple ways, but I would suggest you look at the reshape and plyr packages which make a lot of this easy (while still giving more power than SAS proc report). Then there is the display of the data and/or summaries. R does have the basic print capabilities, but if you want more control and extras like headers/footers, titles, etc. then this is better done by delegating those jobs to more specialized programs (LaTeX, HTML, OpenOffice, MSWord, etc.), R has interfaces to many of these to make that delegation easy (and the results end up looking much nicer than SAS proc report). If that is not sufficient for your needs then you can either create your own package that does what you want, contribute to other efforts, or motivate someone else to do this for you. Personally I have not used SAS proc report for quite a while, so I did a quick internet search and found a quick tutorial with examples (of both input and output). The main result was a good reminder of why I don't use SAS proc report any more and why I do use R and the other specialized programs that it interfaces with. Hope this helps (or at least provokes thought), -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Donald Paul Winston Sent: Thursday, August 19, 2010 5:43 AM To: r-help@r-project.org Subject: Re: [R] R reports Oops, I meant 4GL. Part of SAS involves more or less declarative coding where SAS figures out how to process the information and you don't have to. Sweave and html generators in R are not what I'm looking for. I'm looking for a function whose arguments are data, column names, grouping variables, summary stats, titles, footnotes, etc. Sort of like what plot does except the function will generate a report. I suppose you could specify an output format or printer device as plain text, rich text, pdf, or html. -- View this message in context: http://r.789695.n4.nabble.com/R-reports- tp2330733p2331037.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] assign multiple variables at once
R community, Brian generously provided the following code (see below) but I could not get it to run and it produced this error (after a few minutes of run time): Error: evaluation nested too deeply: infinite recursion / options(expressions=)? I am using Tinn-R and on the IO screen I also received the following code: source(.trPaths[5], echo=TRUE, max.deparse.length=150) I am not sure whether the code is errant or whether I did not implement it correctly. Does anyone know what could be the source of these errors? Thank you, Mike Hosack -Original Message- From: Brian Diggs [mailto:dig...@ohsu.edu] Sent: Friday, August 13, 2010 4:11 PM To: Hosack, Michael Cc: r-help@r-project.org Subject: Re: assign multiple variables at once On 8/13/2010 11:08 AM, Hosack, Michael wrote: R Experts, I would like to create a series of variables without having to assign a separate line of code for each new variable. My dataframe (DF) contains two groups of linked variables (ESP1:ESP9) and (ECRL1:ECRL9). Within ESP1:ESP9 are abbreviated species codes (full dataframe contains 26 codes). ECRL1 represents the number of species x in variable ESP1 harvested, and so on through ESP9 and ECRL9. What I want to do is create 26 new variables (one for each unique species code) that contains the number harvested (ECRL) for each corresponding species code listed for each row of the data set. Example (row 14), the new variable YP Harvest would equal 90 (ECRL2) and WP Harvest would equal 0 (ECRL1), all other species code var's would contain NA. I hope I made this clear enough. Thank you, Mike Current method: one line per species EBTCH1.h$YP.H- with(EBTCH1.h,ifelse(ESP1 %in% 'YP',ECRL1,ifelse(ESP2 %in% 'YP',ECRL2, ifelse(ESP3 %in% 'YP',ECRL3,ifelse(ESP4 %in% 'YP',ECRL4,ifelse(ESP5 %in% 'YP',ECRL5, ifelse(ESP6 %in% 'YP',ECRL6,ifelse(ESP7 %in% 'YP',ECRL7,ifelse(ESP8 %in% 'YP',ECRL8, ifelse(ESP9 %in% 'YP',ECRL9,0)) DF- structure(list(MM = c(5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), DD = c(3L, 3L, 3L, 3L, 3L, 3L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L), DTYPE = c(2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1), TOD = c(2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1), SITENUM = c(102, 104, 104, 104, 101, 101, 102, 103, 101, 101, 101, 101, 103, 103, 103 ), CURTIM = c(1450L, 1736L, 1755L, 1804L, 1950L, 2007L, 1150L, 1450L, 2000L, 1003L, 1030L, 1036L, 1300L, 1310L, 1320L), GRPFSH = c(2L, 2L, 2L, 2L, 2L, 3L, 1L, 2L, 3L, 2L, 4L, 1L, 1L, 3L, 1L), EEFF = c(11.5, 19, 5, 20, 0, 0, 5, 8, 0, 0, 0, 0, 3, 12, 6), ESP1 = c(SMB, SMB, SMB, SMB, NA, NA, YP, YP, NA, NA, NA, NA, RG, WP, WP), ESP2 = c(NA, RB, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, SMB, YP, YP), ESP3 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, RB, RBS, NA), ESP4 = c(NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_), ESP5 = c(NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_), ESP6 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), ESP7 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), ESP8 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), ESP9 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), ECRL1 = c(0L, 0L, 0L, 0L, 0L, 0L, 4L, 5L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), ECRL2 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 90L, 30L), ECRL3 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), ECRL4 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), ECRL5 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), ECRL6 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), ECRL7 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), ECRL8 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), ECRL9 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L)), .Names = c(MM, DD, DTYPE, TOD, SITENUM, CURTIM, GRPFSH, EEFF, ESP1, ESP2, ESP3, ESP4, ESP5, ESP6, ESP7, ESP8, ESP9, ECRL1, ECRL2, ECRL3, ECRL4, ECRL5, ECRL6, ECRL7, ECRL8, ECRL9), row.names = c(NA, 15L), class = data.frame) Michael, An easier approach is to reshape this into a long format (one row for each ESP/ECRL combination, carrying the rest of the identifying variables), and then reshape it back to wide format using the ESP value to define the new column: # for convenience, variables that don't vary for each observation idvar - names(DF)[1:8] DFr - reshape(DF, varying=list(c(ESP1,ESP2,ESP3,ESP4,ESP5,ESP6,ESP7,ESP8,ESP9),
[R] plotmath question
Hi all, let me give a simple example: b-20 I would like to print ylab as P20 where P is printed in Italic font. When I do the following: plot(1, ylab=expression(paste(italic(P),b,sep=))) I got y axis label printed as Pb instead of P20. What is the best solution to print platmath symbols with value of the variable at the same time? Thanks John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotmath question
Try this, b = 20 plot(1, ylab= bquote(italic(P) * .(b)) ) HTH, baptiste On 19 August 2010 20:02, array chip arrayprof...@yahoo.com wrote: Hi all, let me give a simple example: b-20 I would like to print ylab as P20 where P is printed in Italic font. When I do the following: plot(1, ylab=expression(paste(italic(P),b,sep=))) I got y axis label printed as Pb instead of P20. What is the best solution to print platmath symbols with value of the variable at the same time? Thanks John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Baptiste Auguié Departamento de Química Física, Universidade de Vigo, Campus Universitario, 36310, Vigo, Spain tel: +34 9868 18617 http://webs.uvigo.es/coloides __ 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] plotmath question
On Aug 19, 2010, at 2:02 PM, array chip wrote: Hi all, let me give a simple example: b-20 I would like to print ylab as P20 where P is printed in Italic font. When I do the following: plot(1, ylab=expression(paste(italic(P),b,sep=))) I got y axis label printed as Pb instead of P20. What is the best solution to print platmath symbols with value of the variable at the same time? ?substitute ?plotmath plot(1, ylab=substitute(list(italic(P)*b), list(b=b) ) ) Or: ?bquote plot(1, ylab=bquote(italic(P)*.(b) ) ) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trimmed Sample
You can look at the code for mean.default and see how it does the trimming, then you can use that to create your own trimmed version to pass to other functions. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Turn Fall Sent: Tuesday, August 17, 2010 5:13 AM To: r-help@r-project.org Subject: [R] Trimmed Sample I know about the trimmed mean function. Is there a function that trims values of an array, vector ect cheers -- View this message in context: http://r.789695.n4.nabble.com/Trimmed- Sample-tp2328139p2328139.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] plotmath question
Thanks, yes it worked! What about if I want to print as P2, A where A is just letter A and 2 is from variable b. John - Original Message From: baptiste auguie baptiste.aug...@googlemail.com To: array chip arrayprof...@yahoo.com Cc: r-h...@stat.math.ethz.ch Sent: Thu, August 19, 2010 11:08:10 AM Subject: Re: [R] plotmath question Try this, b = 20 plot(1, ylab= bquote(italic(P) * .(b)) ) HTH, baptiste On 19 August 2010 20:02, array chip arrayprof...@yahoo.com wrote: Hi all, let me give a simple example: b-20 I would like to print ylab as P20 where P is printed in Italic font. When I do the following: plot(1, ylab=expression(paste(italic(P),b,sep=))) I got y axis label printed as Pb instead of P20. What is the best solution to print platmath symbols with value of the variable at the same time? Thanks John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Baptiste Auguié Departamento de Química Física, Universidade de Vigo, Campus Universitario, 36310, Vigo, Spain tel: +34 9868 18617 http://webs.uvigo.es/coloides __ 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] Pass By Value Questions
On 19/08/2010 12:57 PM, li...@jdadesign.net wrote: I understand R is a Pass-By-Value language. I have a few practical questions, however. I'm dealing with a large dataset (~1GB) and so my understanding of the nuances of memory usage in R is becoming important. In an example such as: d - read.csv(file.csv); n - apply(d, 1, sum); must d be copied to another location in memory in order to be used by apply? In general, is copying only done when a variable is updated within a function? Generally R only copies when the variable is modified, but its rules for detecting this are sometimes overly conservative, so you may get some unnecessary copying. For example, d[1,1] - 3 will probably not make a full copy of d when the internal version of [- is used, but if you have an R-level version, it probably will. I forget whether the dataframe method is internal or R level. In the apply(d, 1, sum) example, it would probably make a copy of each row to pass to sum, but never a copy of the whole dataframe/array. Would the following example be any different in terms of memory usage? d - read.csv(file.csv); n - apply(d[,2:10], 1, sum); or can R reference the original d object since no changes to the object are being made? This would make a new object containing d[,2:10], and would pass that to apply. I'm familiar with FF and BigMemory, but are there any packages/tricks which allow for passing such objects by reference without having to code in C? 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.
Re: [R] Automated plot and linear regression line/data
?pairs
?lattice::splom
?lattice::panel.xyplot
pairs( state.x77, panel=function(x,y){
points(x,y)
abline(lm(y~x), col='red')
})
library(lattice)
splom( ~state.x77, type=c('p','r') )
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of ashz
Sent: Tuesday, August 17, 2010 3:47 AM
To: r-help@r-project.org
Subject: [R] Automated plot and linear regression line/data
Hi,
I have an excel sheet (already imported to R) with multiple columns and
I am
looking for a way in R that will allow me to generate a plot for every
possible pair and its linear regression line/data.
Any tip/idea/script how do to so.
Thanks,
As hz
--
View this message in context: http://r.789695.n4.nabble.com/Automated-
plot-and-linear-regression-line-data-tp2328027p2328027.html
Sent from the R help mailing list archive at Nabble.com.
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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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] plotmath question
On Aug 19, 2010, at 2:24 PM, array chip wrote: Thanks, yes it worked! What about if I want to print as P2, A where A is just letter A and 2 is from variable b. ?plotmath plot(1, ylab= bquote(italic(P) *,*.(b)~A) ) John - Original Message From: baptiste auguie baptiste.aug...@googlemail.com To: array chip arrayprof...@yahoo.com Cc: r-h...@stat.math.ethz.ch Sent: Thu, August 19, 2010 11:08:10 AM Subject: Re: [R] plotmath question Try this, b = 20 plot(1, ylab= bquote(italic(P) * .(b)) ) HTH, baptiste On 19 August 2010 20:02, array chip arrayprof...@yahoo.com wrote: Hi all, let me give a simple example: b-20 I would like to print ylab as P20 where P is printed in Italic font. When I do the following: plot(1, ylab=expression(paste(italic(P),b,sep=))) I got y axis label printed as Pb instead of P20. What is the best solution to print platmath symbols with value of the variable at the same time? Thanks John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Baptiste Auguié Departamento de Química Física, Universidade de Vigo, Campus Universitario, 36310, Vigo, Spain tel: +34 9868 18617 http://webs.uvigo.es/coloides __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotmath question
Thanks David! John - Original Message From: David Winsemius dwinsem...@comcast.net To: array chip arrayprof...@yahoo.com Cc: baptiste auguie baptiste.aug...@googlemail.com; r-h...@stat.math.ethz.ch Sent: Thu, August 19, 2010 11:34:07 AM Subject: Re: [R] plotmath question On Aug 19, 2010, at 2:24 PM, array chip wrote: Thanks, yes it worked! What about if I want to print as P2, A where A is just letter A and 2 is from variable b. ?plotmath plot(1, ylab= bquote(italic(P) *,*.(b)~A) ) John - Original Message From: baptiste auguie baptiste.aug...@googlemail.com To: array chip arrayprof...@yahoo.com Cc: r-h...@stat.math.ethz.ch Sent: Thu, August 19, 2010 11:08:10 AM Subject: Re: [R] plotmath question Try this, b = 20 plot(1, ylab= bquote(italic(P) * .(b)) ) HTH, baptiste On 19 August 2010 20:02, array chip arrayprof...@yahoo.com wrote: Hi all, let me give a simple example: b-20 I would like to print ylab as P20 where P is printed in Italic font. When I do the following: plot(1, ylab=expression(paste(italic(P),b,sep=))) I got y axis label printed as Pb instead of P20. What is the best solution to print platmath symbols with value of the variable at the same time? Thanks John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Baptiste Auguié Departamento de Química Física, Universidade de Vigo, Campus Universitario, 36310, Vigo, Spain tel: +34 9868 18617 http://webs.uvigo.es/coloides __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Pass By Value Questions
On Thu, 2010-08-19 at 14:27 -0400, Duncan Murdoch wrote: On 19/08/2010 12:57 PM, li...@jdadesign.net wrote: I understand R is a Pass-By-Value language. I have a few practical questions, however. I'm dealing with a large dataset (~1GB) and so my understanding of the nuances of memory usage in R is becoming important. In an example such as: d - read.csv(file.csv); n - apply(d, 1, sum); must d be copied to another location in memory in order to be used by apply? In general, is copying only done when a variable is updated within a function? Generally R only copies when the variable is modified, but its rules for detecting this are sometimes overly conservative, so you may get some unnecessary copying. For example, d[1,1] - 3 will probably not make a full copy of d when the internal version of [- is used, but if you have an R-level version, it probably will. I forget whether the dataframe method is internal or R level. In the apply(d, 1, sum) example, it would probably make a copy of each row to pass to sum, but never a copy of the whole dataframe/array. Would the following example be any different in terms of memory usage? d - read.csv(file.csv); n - apply(d[,2:10], 1, sum); or can R reference the original d object since no changes to the object are being made? This would make a new object containing d[,2:10], and would pass that to apply. Since d is a data.frame, subsetting the columns would create a new data.frame, as Duncan says. However, the columns of the new data.frame would internally _reference_ the appropriate columns of d, until either were modified. This does not apply to row subsetting. That is, d[2:10,] would create a new data.frame and copy the relevant data. Nor does it apply to _any_ subsetting of matrices. I'm familiar with FF and BigMemory, but are there any packages/tricks which allow for passing such objects by reference without having to code in C? It's difficult to determine exactly when data is copied internally by R. The tracemem function may be used to track when entire objects are duplicated. However, tracemem would not detect the duplication that occurs, for example, when subsetting the rows of d. Otherwise, we can monitor memory usage with gc(), and experiment with code on a trial and error basis. I have had limited success in avoiding duplication by utilizing R environments. See for example http://biostatmatt.com/archives/663 . However, this may be more trouble that it's worth. -Matt 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. -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ 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] plotmath question
On Aug 19, 2010, at 2:46 PM, array chip wrote: Thanks David! I see that I didn't produce the correct answer, but perhaps I'm being thanked for something that was generalizable in that direction. Better would have ben one of these: plot(1, ylab= bquote(italic(P) *.(b)*,*~A) ) plot(1, ylab= bquote(paste(italic(P),.(b),,) ~ A) ) In the second instance, paste() is a plotmath expression function, rather than the character vector function that lives out in the free- range R. -- David. - Original Message From: David Winsemius dwinsem...@comcast.net On Aug 19, 2010, at 2:24 PM, array chip wrote: Thanks, yes it worked! What about if I want to print as P2, A where A is just letter A and 2 is from variable b. ?plotmath plot(1, ylab= bquote(italic(P) *,*.(b)~A) ) John - Original Message From: baptiste auguie baptiste.aug...@googlemail.com Try this, b = 20 plot(1, ylab= bquote(italic(P) * .(b)) ) HTH, baptiste On 19 August 2010 20:02, array chip arrayprof...@yahoo.com wrote: Hi all, let me give a simple example: b-20 I would like to print ylab as P20 where P is printed in Italic font. When I do the following: plot(1, ylab=expression(paste(italic(P),b,sep=))) I got y axis label printed as Pb instead of P20. What is the best solution to print platmath symbols with value of the variable at the same time? Thanks John David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotmath question
David, yes, I now see how it worked. Thanks again, John - Original Message From: David Winsemius dwinsem...@comcast.net To: array chip arrayprof...@yahoo.com Cc: baptiste auguie baptiste.aug...@googlemail.com; r-h...@stat.math.ethz.ch Sent: Thu, August 19, 2010 12:12:46 PM Subject: Re: [R] plotmath question On Aug 19, 2010, at 2:46 PM, array chip wrote: Thanks David! I see that I didn't produce the correct answer, but perhaps I'm being thanked for something that was generalizable in that direction. Better would have ben one of these: plot(1, ylab= bquote(italic(P) *.(b)*,*~A) ) plot(1, ylab= bquote(paste(italic(P),.(b),,) ~ A) ) In the second instance, paste() is a plotmath expression function, rather than the character vector function that lives out in the free- range R. -- David. - Original Message From: David Winsemius dwinsem...@comcast.net On Aug 19, 2010, at 2:24 PM, array chip wrote: Thanks, yes it worked! What about if I want to print as P2, A where A is just letter A and 2 is from variable b. ?plotmath plot(1, ylab= bquote(italic(P) *,*.(b)~A) ) John - Original Message From: baptiste auguie baptiste.aug...@googlemail.com Try this, b = 20 plot(1, ylab= bquote(italic(P) * .(b)) ) HTH, baptiste On 19 August 2010 20:02, array chip arrayprof...@yahoo.com wrote: Hi all, let me give a simple example: b-20 I would like to print ylab as P20 where P is printed in Italic font. When I do the following: plot(1, ylab=expression(paste(italic(P),b,sep=))) I got y axis label printed as Pb instead of P20. What is the best solution to print platmath symbols with value of the variable at the same time? Thanks John David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] csv vs. data frame
Hi, I am neither a statistician nor a user of R. I am a programmer trying to provide my users (both statisticians and R users) data in a format that works best for them. What is a data frame? Is source data easier to work with in this format or a csv file? Or yet another format? Thanks for your time. Bruce [[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 include trend (drift term) in arima.sim
I have been trying to simulate from a time series with trend but I don't see how to include the trend in the arima.sim() call. The following code illustrates the problem: # Begin demonstration program x - c(0.168766559, 0.186874000, 0.156710548, 0.151809531, 0.144638812, 0.142106888, 0.140961714, 0.134054659, 0.138722419, 0.134037018, 0.122829846, 0.120188714, 0.122060497, 0.137424358, 0.113311269, 0.125051374, 0.103707302, 0.08121, 0.094848588, 0.100941354, 0.096845633, 0.072098064, 0.081167803, 0.068140319, 0.063988361, 0.053722446, 0.051986886, 0.044317196, 0.032021664, 0.023656304, 0.025620223, 0.012297433, -0.003523446, -0.005782116, -0.027448303, -0.034745961, -0.042594172, -0.058662672, -0.072392916, -0.089123923, -0.093551415, -0.105782822, -0.117481560, -0.126549691, -0.141332587, -0.158428491, -0.166864452, -0.167363354, -0.177367386, -0.198326344, -0.218109541, -0.232391155, -0.237220250, -0.244477140, -0.255906978, -0.279480229) #Fit arima(p=1,d=2,q=1) Arima - arima(x, order = c(1,2,1)) Arima$coef #Simulate from the fitted model: set.seed(1) x.sim - arima.sim(list(order = c(1,2,1), ar = Arima$coef[1], ma = Arima$coef[2]), n = 1000, sd = sqrt(Arima$sig)) Arima2 - arima(x.sim, order = c(1,2,1)) Arima2$coef # We recover the ar and ma coefficients but we haven't included the drift # in the simulation so the simulated series is well wide of the mark. The # following plots demonstrate how wide: par(mfrow = c(1,2)) plot(ts(x), main = Data) plot(x.sim, main = Simulated data) # End demonstration program The documentation for arima.sim() isn't terribly clear on this area. Any ideas? -- View this message in context: http://r.789695.n4.nabble.com/How-to-include-trend-drift-term-in-arima-sim-tp2331581p2331581.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] meta-analysis in R
Dear Sir or Madam, I am trying to explore the citation bias by perfroming meta-analysis. I need to plot a forest plot on some other proportions other than the usual effect size OR,RR, RD. I still do not have any idea after searching google and reading relevant books. Can anyone kindly help? Thank you in advance. Best wishes weiwei [[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] Can't read/write to _nonfi
Good afternoon,
Hope you all have a wonderful day. I am glad to be here. Hope you could
help me with the following errors that i have been trying to figure it all
out since last week.
I am using Splus from Insightful, and as i read, R and Splus are very
similar. So hope you could help me.
I have been continously received these error messages after i ran my small
program for couple of times.
Can' access to file _nonfi
Can't create file for assigning last.dump
(C:/WORKSPACE/DUNG/.Data/___bd40
It is frustrating since the program is so small , and as i look into my
project, the _nonfi is there under the data folder. So i don't know what the
compiler is complained about. Since i am new to Splus language, I have no
clue what i need to do.
for (i in 1: 1)
{
x - rnorm (1000);
y - rnorm (1000)
newx - x
newy - y
hist (newx)
hist (newy)
}
If you happen to know what i need to do, please help me.
Thank you so much,
Min
--
View this message in context:
http://r.789695.n4.nabble.com/Can-t-read-write-to-nonfi-tp2331707p2331707.html
Sent from the R help mailing list archive at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Can't read/write to _nonfi
I don't think I understand what the problem is... The code that you
provided works just fine without the for loop statement. as for the
can't access... The example that you provided doesn't address this.
Unless I am totally misunderstanding. R is an interpreted language
not compiled. Please, as to the instructions appended to the end of
each email, provide a minimal self-contained reproducible example.
Stephen
On Thu, Aug 19, 2010 at 1:48 PM, minh dtr...@student.gsu.edu wrote:
Good afternoon,
Hope you all have a wonderful day. I am glad to be here. Hope you could
help me with the following errors that i have been trying to figure it all
out since last week.
I am using Splus from Insightful, and as i read, R and Splus are very
similar. So hope you could help me.
I have been continously received these error messages after i ran my small
program for couple of times.
Can' access to file _nonfi
Can't create file for assigning last.dump
(C:/WORKSPACE/DUNG/.Data/___bd40
It is frustrating since the program is so small , and as i look into my
project, the _nonfi is there under the data folder. So i don't know what the
compiler is complained about. Since i am new to Splus language, I have no
clue what i need to do.
for (i in 1: 1)
{
x - rnorm (1000);
y - rnorm (1000)
newx - x
newy - y
hist (newx)
hist (newy)
}
If you happen to know what i need to do, please help me.
Thank you so much,
Min
--
View this message in context:
http://r.789695.n4.nabble.com/Can-t-read-write-to-nonfi-tp2331707p2331707.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.
--
Stephen Sefick
| Auburn University |
| Department of Biological Sciences |
| 331 Funchess Hall |
| Auburn, Alabama |
| 36849 |
|___|
| sas0...@auburn.edu |
| http://www.auburn.edu/~sas0025 |
|___|
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.
-K. Mullis
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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] csv vs. data frame
Do not post such questions to this list. Read an Introduction to R first, please. -- Bert On Thu, Aug 19, 2010 at 12:55 PM, Bruce Como br...@lmcsoftware.com wrote: Hi, I am neither a statistician nor a user of R. I am a programmer trying to provide my users (both statisticians and R users) data in a format that works best for them. What is a data frame? Is source data easier to work with in this format or a csv file? Or yet another format? Thanks for your time. Bruce [[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. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml __ 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't read/write to _nonfi
Min,
For S+-specific questions the S-news mailing list
would be better.
s-n...@wubios.wustl.edu
Unlike R, S+ stores its data objects in files, one file
per object. The ___nonfi (___nonfiles) file contains
a mapping for object names to file names, for those
objects whose names cannot be unambiguously used as
file names.
The copies of the error messages look garbled to me.
They are definitely missing some characters and I don't
see the Can't access to ... message in the S+ source
code, but perhaps I'm not looking in the right version
Can' access to file _nonfi
Can't create file for assigning last.dump
(C:/WORKSPACE/DUNG/.Data/___bd40
What version of S+ are you using and what are the precise
error messages?
Do you own the C:/WORKSPACE/DUNG directory or is
it someone else's? If it is someone else's and it
is sufficiently protected, you may not be able write
files into it. Can you create any other data objects?
E.g., can you successfully execute the following?
qaz - 1:10
print(qaz)
and
Q.A.Z. - log(qaz)
print(Q.A.Z)
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of minh
Sent: Thursday, August 19, 2010 11:48 AM
To: r-help@r-project.org
Subject: [R] Can't read/write to _nonfi
Good afternoon,
Hope you all have a wonderful day. I am glad to be here.
Hope you could
help me with the following errors that i have been trying to
figure it all
out since last week.
I am using Splus from Insightful, and as i read, R and
Splus are very
similar. So hope you could help me.
I have been continously received these error messages after
i ran my small
program for couple of times.
Can' access to file _nonfi
Can't create file for assigning last.dump
(C:/WORKSPACE/DUNG/.Data/___bd40
It is frustrating since the program is so small , and as i
look into my
project, the _nonfi is there under the data folder. So i
don't know what the
compiler is complained about. Since i am new to Splus
language, I have no
clue what i need to do.
for (i in 1: 1)
{
x - rnorm (1000);
y - rnorm (1000)
newx - x
newy - y
hist (newx)
hist (newy)
}
If you happen to know what i need to do, please help me.
Thank you so much,
Min
--
View this message in context:
http://r.789695.n4.nabble.com/Can-t-read-write-to-nonfi-tp2331
707p2331707.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] csv vs. data frame
Bruce Como wrote: Hi, I am neither a statistician nor a user of R. I am a programmer trying to provide my users (both statisticians and R users) data in a format that works best for them. It sounds like they would be the best ones to ask then. What is a data frame? Is source data easier to work with in this format or a csv file? Or yet another format? A data.frame is a class of a certain type of R object. It is basically a way to store rectangular data, rows for observations, columns for variables. Since R objects exist in memory, you can write out things like data.frames to disk with the ?save function, so others can load them with the ?load function. I think your users will have to tell you what is easiest for them. __ 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] Aggregate Help
Please let me know if this is or is not the right place to ask these types of questions. Warning: I am new to R by two days. I have a simple dataset. I have loaded the dataset successfully using the following code: Filepath=(C:\temp\\pilot\dataset1.txt) Pilot=read.table(filepath, header=TRUE) Dataset1.txt is delimited and looks like this: Dateillness count 2006/01/01 derm17 2006/01/01 derm35 2006/01/02 derm24 2006/01/02 derm80 . . . Total records like this approximately 18,000 I would like to use the aggregate function to sum the count by similar date and illness, so it should look like this after the aggregate 2006/01/01 derm52 2006/01/02 derm104 . . . And, the illness changes to fever with the same pattern. I would like to aggregate the same illnesses by date in the same fashion. A nudge in the right direction would be appreciated. Thanks. Ken Hall Computer Scientist Division of Healthcare Information (DHI) (proposed) Public Health Surveillance Program Office (proposed) Office of Surveillance, Epidemiology, Laboratory Services (OSELS) (proposed) Centers for Disease Control Prevention (CDC) k...@cdc.gov Mobile: 404-993-3311 Office: 404-498-6839 [[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] Gathering different data types for aov etc
Hello List Folks. I¹m trying to do manova using a function which assembles
the response (LHS) and factors (RHS) from different sources. When I do so,
the model routines complain that I'm passing a list for the RHS when I don't
think I am.
Here's a toy example:
r - matrix(rnorm(30), ncol = 3) # toy data
td - list(d = rnorm(10),
f1 = sample(c(A, B), 10, replace = TRUE),
f2 = sample(c(C, D), 10, replace = TRUE))
toyFn -
function(my.list, my.data, fac = NULL) {
response - my.data
fac - data.frame(my.list[fac])
#str(fac) # a data frame!
man - manova(response ~ fac)
print(summary(man))
invisible(man)
}
toyFn(td, r, fac = f1)
toyFn(td, r, fac = c(f1, f2))
Bot attempts just above gives the following error:
Error in model.frame.default(formula = response ~ fac, drop.unused.levels =
TRUE) :
invalid type (list) for variable 'fac'
But fac inside the function is a data frame. What am I missing here?
Also, I want the function to use this formula: response ~ f1:f2 but once I
get past my problem of data type, I don't think what I have so far will do
the interaction, in fact, I suspect it will use only f1 or perhaps f1 + f2,
just a hunch. Any suggestions to make this more elegant and robust? I've
been reading about model frames etc but don't quite see how to do a simple
example such as this.
Thanks, Bryan
*
Bryan Hanson
Professor of Chemistry Biochemistry
DePauw University, Greencastle IN USA
sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] datasets tools grid graphics grDevices utils stats
methods base
other attached packages:
[1] faraway_1.0.4 GGally_0.2 xtable_1.5-6 mvbutils_2.5.1
ggplot2_0.8.8
[6] proto_0.3-8reshape_0.8.3 ChemoSpec_1.45 R.utils_1.4.0
R.oo_1.7.2
[11] R.methodsS3_1.2.0 rgl_0.91 lattice_0.18-5 mvoutlier_1.4
plyr_1.0.3
[16] RColorBrewer_1.0-2 chemometrics_0.8 som_0.3-5
robustbase_0.5-0-1 rpart_3.1-46
[21] pls_2.1-0 pcaPP_1.8-1mvtnorm_0.9-9 nnet_7.3-1
mclust_3.4.4
[26] MASS_7.3-5 lars_0.9-7 e1071_1.5-23 class_7.3-2
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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] Aggregate Help
Ken - Try aggregate(Pilot$Count,list(Date=Pilot$Date,illness=Pilot$illness),sum) If you don't want to keep typing Pilot, use with(Pilot,aggregate(Count,list(Date=Date,illness=illness),sum)) Notice that the aggregated variable will be called x in the output data frame from aggregate. - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Thu, 19 Aug 2010, Hall, Ken (CDC/OSELS/NCPHI) wrote: Please let me know if this is or is not the right place to ask these types of questions. Warning: I am new to R by two days. I have a simple dataset. I have loaded the dataset successfully using the following code: Filepath=(C:\temp\\pilot\dataset1.txt) Pilot=read.table(filepath, header=TRUE) Dataset1.txt is delimited and looks like this: Dateillness count 2006/01/01 derm17 2006/01/01 derm35 2006/01/02 derm24 2006/01/02 derm80 . . . Total records like this approximately 18,000 I would like to use the aggregate function to sum the count by similar date and illness, so it should look like this after the aggregate 2006/01/01 derm52 2006/01/02 derm104 . . . And, the illness changes to fever with the same pattern. I would like to aggregate the same illnesses by date in the same fashion. A nudge in the right direction would be appreciated. Thanks. Ken Hall Computer Scientist Division of Healthcare Information (DHI) (proposed) Public Health Surveillance Program Office (proposed) Office of Surveillance, Epidemiology, Laboratory Services (OSELS) (proposed) Centers for Disease Control Prevention (CDC) k...@cdc.gov Mobile: 404-993-3311 Office: 404-498-6839 [[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.
