Re: [R] scatterplot to boxplot translation?
You need to create some grouping for your cut points (0-100, etc). See ?cut Then, you can use boxplot and formula (y ~ NEWVARIABLE from cut) boxplot(y ~ cut(x)) There may be other ways to do this, but the above should work. TF -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Vining, Kelly Sent: Friday, December 09, 2011 1:11 PM To: Vining, Kelly; r-help@r-project.org Subject: Re: [R] scatterplot to boxplot translation? My apologies if anyone is seeing this twice...looks like my previous message didn't come through... Dear UseRs, I have a feeling this is a relatively simple question, but I'm having a hard time getting my head around it. I have a simple x-y scatterplot with many points, as shown below(attached). I'd like to make a boxplot of this by interval, such that there is one box representing the points in the 0-100 interval, one for the 101-200 interval, and so on. How do I structure my R data frame to be able to generate such a boxplot? From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Vining, Kelly Sent: Friday, December 09, 2011 11:01 AM To: r-help@r-project.org Subject: [R] scatterplot to boxplot translation? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] annotate histogram
See rug() and use col=2 to get red. So, as an example ... x - rchisq(100, df=2) hist(x) abline(v=median(x), lty=2) rug(x, col=2) TF -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Wendy Sent: Tuesday, November 01, 2011 10:22 AM To: r-help@r-project.org Subject: [R] annotate histogram Hi all, I want to make a histogram like the one show http://nar.oxfordjournals.org/content/39/suppl_1/D1011/F1.expansion.html here , but I did not figure out how to add the red marks at the bottom of the bars. Could anybody help? Thank you very much -- View this message in context: http://r.789695.n4.nabble.com/annotate-histogram-tp3963960p3963960.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] misclassification matrix
I think what you are looking for is ?table and/or ?prop.table So, let's say you have two matrices: ACTUAL and CLASS, you can ... table(ACTUAL, CLASS) Or, diag(1-prop.table(table(ACTUAL, CLASS), 1)) to get row percentages and take the diagonal. So, using your example: # table() as above would render the following matrix mat - matrix(c(100, 25, 10, 250, 100, 5, 50, 25, 40), 3) and prop.table() renders: prop.table(mat, 1) [,1] [,2] [,3] [1,] 0.250 0.625 0.125 [2,] 0.167 0.667 0.167 [3,] 0.1818182 0.0909091 0.7272727 In the above, the diagonal is the % correctly classified. diag(1-prop.table(mat, 1)) [1] 0.750 0.333 0.2727273 TF -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Gregory Ryslik Sent: Wednesday, October 06, 2010 10:19 AM To: R Help Subject: [R] misclassification matrix HI Everyone, I am working with the following situation. I have n observations and j possible outcomes and each one of the n observations is assigned a class from 1 to j. Furthermore, this process is done m times (for some large m 1000). What I want to do is create a misclassification matrix which tells me for each one of the possible classes, how many observations were classified correctly, and then how many were incorrectly at each level. Here is an example of what I mean 0 12 Misclassification 0 100 250 50 .75 1 25 100 25 .33 2 10 5 40 .2727273 For each one of the 1 to j elements, I can use a nested for loop to count how many were classified as 0, are in 1, etc and then construct such matrix. Thus for each element I have j comparisons and then I have j total rows leading to an O(j^2) running time. Any way I can avoid such a for loop and perhaps make it run a bit quicker? If not, any ideas then at least how to avoid the double for loop and make the code more aesthetically pleasing? As always, thank you for your help! Kind regards, Greg __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] does package QuantPsych function lm.beta can handle resultsof a regression with weights?
The original function was created for a simple example. It never was
written to address weighted regression. A quick fix will work for you
situation.
### The original is:
lm.beta -
function (MOD)
{
b - summary(MOD)$coef[-1, 1]
sx - sd(MOD$model[-1])
sy - sd(MOD$model[1])
beta - b * sx/sy
return(beta)
}
A newer modification:
lm.betaW -
function (MOD)
{
b - summary(MOD)$coef[-1, 1]
sx - sd(MOD$model[-1][1])
sy - sd(MOD$model[1])
beta - b * sx/sy
return(beta)
}
The above should do the trick.
TF
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Dimitri Liakhovitski
Sent: Thursday, July 22, 2010 12:35 PM
To: r-help@r-project.org
Subject: [R] does package QuantPsych function lm.beta can handle
resultsof a regression with weights?
Hello, and sorry for not providing an example.
I run a regular linear regression (using lm) and use weights with it
(weights = ...).
I use QuantPsych package, its function lm.beta to extract standardized
regression weights from my lm regression object.
When I don't use weights, everything is fine.
But when I do use weights, I get an error that refers to lm.beta code:
In b * sx : longer object length is not a multiple of shorter object
length
This happens because there is an extra column in the object:
regr$model that lm.beta is using to get at the betas.
Is there some other package that just gives me the standardized
regression weights - even if I used weights for regression?
Thank you!
--
Dimitri Liakhovitski
Ninah Consulting
www.ninah.com
__
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http://www.R-project.org/posting-guide.html
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Re: [R] The output of script is hidden in console
There are probably numerous ways, but one is to add print() to the functions that you wish to display in the console. For example, in your source file, Instead of summary(x) try print(summary(x)) This should do the trick. Tom Fletcher -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of vtvdung Sent: Tuesday, January 05, 2010 9:42 AM To: r-help@r-project.org Subject: [R] The output of script is hidden in console Hi everyone, I execute a script with source(filename) The script has effect but i don't see the output on console screen.Why? I'm a newbie. Thanks :handshake: -- View this message in context: http://n4.nabble.com/The-output-of-script-is-hidden-in-console-tp999095p 999095.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] Creating Dummy Variables in R
Is your variable Clarity a categorical with 4 levels? Thus, the need for k-1 (3) dummies? Your error may be the result of creating k instead of k-1 dummies, but can't be sure from the example. In R, you don't have to (unless you really want to) explicitly create separate variables. You can use the internal contrast functions. See ?contr.treatment Which is dummy coding by default. You can specify which group is the reference group. Alternatively, if you prefer effects coding, you can see ?contr.sum There are others as well. Tom Fletcher -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of whitaker m. (mw1006) Sent: Wednesday, December 16, 2009 8:59 AM To: r-help@r-project.org Subject: [R] Creating Dummy Variables in R Hi, I am trying to create a set of dummy variables to use within a multiple linear regression and am unable to find the codes within the manuals. For example i have: Price Weight Clarity IF VVS1VVS2 5008 1 0 0 1000 5.2 0 0 1 8643 01 0 3402.6 0 0 1 90 0.5 1 0 0 4502.3 0 1 0 Where price is dependent upon weight (single value in each observation) and clarity (split into three levels, IF, VVS1, VVS2). I am having trouble telling the program that clarity is a set of 3 dummy variables and keep getting error messages, what is the correct way? Any helps is greatly appreciated. Matthew __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to calculate the area under the curve
See package ROCR. Then see ?performance; in the details, it describes a measure of auc. Tom Fletcher -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of olivier.abz Sent: Thursday, October 22, 2009 9:23 AM To: r-help@r-project.org Subject: [R] How to calculate the area under the curve Hi all, I would like to calculate the area under the ROC curve for my predictive model. I have managed to plot points giving me the ROC curve. However, I do not know how to get the value of the area under. Does anybody know of a function that would give the result I want using an array of specificity and an array of sensitivity as input? Thanks, Olivier -- View this message in context: http://www.nabble.com/How-to-calculate-the-area-under-the-curve-tp260105 01p26010501.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] ltm package error for grm (IRT)
Ben, This is because you do not have all the possible response options represented for each item. For example, in your data below, item 2 has no '1's. I don't know if there is a workaround for this (other than deleting an item or faking a response), or if this is a function of IRT itself? Tom Fletcher -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of ben kelcey Sent: Wednesday, October 14, 2009 4:32 PM To: r-help@r-project.org Subject: [R] ltm package error for grm (IRT) Using the grm function (graded response IRT model) in the ltm package I receive the following error: Error: subscript out of bounds for several scales I'd like to examine. Here's a small example that if run a few times will likley produce the error at least once ch-array(round(runif(50,1,5)),c(10,5)) grm(ch,start.val=random) ## or grm(ch,constrained=F,IRT.param=T,start.val=random) I have cannot figure out where I have gone wrong and was unable to find mention of similar errors in the archives. Any help would be much appreciated. A subset of my actual data that produces the same error is pasted below Thank you, ben t2_sr1 t2_sr2 t2_sr3 t2_sr4 t2_sr5 1 5 1 5 5 1 4 1 4 4 4 2 4 2 1 4 5 4 1 4 1 5 5 1 5 1 4 1 5 5 3 2 4 2 4 5 3 5 1 1 4 2 4 4 2 1 4 1 4 5 2 4 4 4 2 1 4 2 3 4 2 2 4 3 2 2 4 2 3 3 4 3 2 3 3 2 5 2 5 5 1 4 1 4 4 3 3 2 3 4 2 4 2 3 4 3 3 3 2 2 sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] car_1.2-16 epicalc_2.9.2.7 survival_2.35-4 foreign_0.8-37 faraway_1.0.4 [6] ltm_0.9-1 polycor_0.7-7 sfsmisc_1.0-8 mvtnorm_0.9-7 msm_0.9.3 [11] MASS_7.2-48 loaded via a namespace (and not attached): [1] tools_2.9.2 [[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] trouble printing from graphics device in R 2.7.2
Is there a setting change (or other minor fix) that can be done without an install of either the patched or development versions to address the printing issue described below. It is my understanding that these versions are 'source code' and not compiled for 'easy' installation. Thanks Tom -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jenny Drnevich Sent: Tuesday, September 16, 2008 8:47 AM To: Prof Brian Ripley Cc: r-help@r-project.org Subject: Re: [R] trouble printing from graphics device in R 2.7.2 Thank you! It works now. It's good to know that it was a bug and not something stupid that I was doing. Cheers, Jenny At 01:32 PM 9/12/2008, Prof Brian Ripley wrote: I've tracked this down to the clipping bug fix reported in the CHANGES file. There is another bug fix in R-devel that does not affect printing, so your first option is to use one of the R-devel snapshots on CRAN. I'll move the R-devel fix to R-patched shortly, so tonight's R-patched snapshot should also work. On Wed, 10 Sep 2008, Jenny Drnevich wrote: Hi, I've been using R for many years and have always tried to keep my R version up to date, and when I switched from 2.7.1 to 2.7.2 I'm suddenly having trouble printing from the graphics device. I have Windows XP, and installed both versions of R from the binaries. If I start 2.7.2 and simply do: plot(1:10) the default R Graphics Device window opens as usual. However, when I use the menu in that window to File - Print, the graph that is printed is cut off below ~2 on the y-axis and ~10 on the x-axis if I don't resize the Graphics window; resizing the window bigger does result in more of the graph printed, but it's still cut off on the y-axis. Everything prints fine in R 2.7.1 (sessionInfo()s below), and all other versions of R I've had on this exact same computer for the last 3 years printing to the same printer, which is why I think it's something with R 2.7.2. I even tried un-installing and re-installing 2.7.2, but the problem persisted. Using the menu to save the graphic in various formats seems to work fine - the entire graph is visible in the .png, .pdf, etc. files. I didn't see anything in the changes or the archives about this... so what's going on and how do I fix it so I can continue to use 2.7.2? Thanks, Jenny sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base sessionInfo() R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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, [EMAIL PROTECTED] 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
