[R] recode: how to avoid nested ifelse

this if the example became any more complicated. I'm unable to remember a less error prone method :). But I expect you might. Here's my working example code ## Paul Johnson pauljohn at ku.edu ## 2013-06-07 ## We need to create an ordinal factor from these indicators ## completed elementary school es - c(0

Re: [R] recode: how to avoid nested ifelse

(factor(x, levels = c(000, 100, 110, 111), labels = c(none, es,hs, cg))) none es hs cg 4112 Cheers, Josh *Drawn from comments by Judea Pearl one lively session. On Fri, Jun 7, 2013 at 6:13 PM, Paul Johnson pauljoh...@gmail.com wrote: In our

[R] Windows R_LIBS_USER confusion under R-3.0.1

I would appreciate ideas about MS Windows install issues. I'm at our stats summer camp and have been looking at a lot of Windows R installs and there are some wrinkles about R_LIBS_USER. On a clean Win7 or Win8 system, with R-3.0.1, we see the user library for packages defaulting to

Re: [R] 2SLS / TSLS / SEM non-linear

Please consider using the R package systemfit. It has existed for about 10 years, I've used it many times happily :) I've not used gmm package, I'm not criticizing it. But I have good results from systemfit. It has good documentation. This package contains functions for fitting simultaneous

[R] [R-pkgs] update: rockchalk 1.8.0

This will appear on CRAN mirrors soon. It's my update for Spring, 2013. I keep track of R problems that arise in the regression course and try to facilitate them. There are functions for describing data, presenting regression plots and tables, some regression diagnostics. Most of the usages are

Re: [R] complexity of operations in R

On Thu, Jul 19, 2012 at 11:11 AM, Bert Gunter gunter.ber...@gene.com wrote: Hadley et. al: Indeed. And using a loop is a poor way to do it anyway. v - as.list(rep(FALSE,dotot)) is way faster. -- Bert Its not entirely clear to me what we are supposed to conclude about this. I can

[R] device mismatch, coordinates trouble with X11 and pdf devices

packages: [1] stats graphics grDevices utils datasets methods base ## Paul Johnson paulj...@ku.edu ## 2012-08-10 ## ## I've got trouble with a mis-match between screen and pdf devices. ## Please run this and tell me if the point z's marker is on the ## intersection of the 2 circles for you

[R] shade overlapping portions of circles (or other shapes)

I'm making some illustrations and it would be convenient to automatically shade the overlapping portions of circles. These illustrations are for Social Choice theory, a field in political science and economics. I've wrestled together some examples so you can see what I mean, but have not

[R] premature evaluation of symbols. Is that the way to describe this problem?

words here. I've built a toy example that will illustrate the problem, you tell me the words for it. ## Paul Johnson 2014-04-10 dat - data.frame(x = rnorm(50),y = rnorm(50)) m1 - lm(y ~ x, dat) myRegFit - function(model, nd) predict(model, nd) mySpecialFeature - function(model, ci){ pargs

Re: [R] very basic HLM question

2011/2/5 Sebastián Daza sebastian.d...@gmail.com: Hi everyone, I need to get a between-component variance (e.g. random effects Anova), but using lmer I don't get the same results (variance component) than using random effects Anova. I am using a database of students, clustered on schools

Re: [R] different results in MASS's mca and SAS's corresp

On Sat, Feb 5, 2011 at 9:19 AM, David Winsemius dwinsem...@comcast.net wrote: On Feb 4, 2011, at 7:06 PM, Gong-Yi Liao wrote: Dear list:  I have tried MASS's mca function and SAS's PROC corresp on the  farms data (included in MASS, also used as mca's example), the  results are different:

Re: [R] boostrap an nls regression

Hello! On Thu, Feb 3, 2011 at 6:27 AM, m234 mhairialexan...@gmail.com wrote: II functional response for 2 data sets: nls(eaten~(a*suppl)/(1+a*h*suppl) where eaten is the number of prey eaten by a predator and suppl is the number of prey initially supplied to the same predator. I have

[R] example to demonstrate benefits of poly in regression?

Here's my little discussion example for a quadratic regression: http://pj.freefaculty.org/R/WorkingExamples/regression-quadratic-1.R Students press me to know the benefits of poly() over the more obvious regression formulas. I think I understand the theory on why poly() should be more

Re: [R] example to demonstrate benefits of poly in regression?

On Mon, Apr 1, 2013 at 12:42 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Apr 1, 2013 at 1:20 PM, Paul Johnson pauljoh...@gmail.com wrote: Here's my little discussion example for a quadratic regression: http://pj.freefaculty.org/R/WorkingExamples/regression-quadratic-1.R

Re: [R] DUD (Does not Use Derivatives) for nonlinear regression in R?

On Apr 1, 2013 1:10 AM, qi A send2...@gmail.com wrote: Hi, All SAS has DUD (Does not Use Derivatives)/Secant Method for nonlinear regression, does R offer this option for nonlinear regression? I have read the helpfile for nls() and could not find such option, any suggestion? nelder-mead

Re: [R] Superscript

On Thu, Apr 4, 2013 at 4:39 AM, Shane Carey careys...@gmail.com wrote: Hi William, for (i in one:length(DATA_names)) if ((grepl(_,DATA_names[i]))==TRUE) DATA_names[i]-f(DATA_names[i])) I keep getting an error saying: incompatible types (from symbol to character) in subassignment

Re: [R] Make barplot with error bars, anova out of a table

Hi On Thu, Apr 11, 2013 at 6:43 AM, Simza alex_steckba...@gmx.at wrote: Helo everybody, I'm new to R and have some issues with my data in R. My raw data look like that: ID Day size 1 1 7 1 1 7.2 1 1 7.1 2 1 7.3 2 1 7.4 2 1 7.2 3 1 7 3 1 7.1 3 1 7.5 4 1 7.3 4 1 7.2 4 1 7.6 1 2 7 1 2 7.2 1 2

[R] Needed: Beta Testers and Summer Camp Students

Greetings. I'm teaching linear regression this semester and that means I write more functions for my regression support package rockchalk. I'm at a point now were some fresh eyes would help, so if you are a student in a course on regression, please consider looking over my package overview

Re: [R] pglm package: fitted values and residuals

On Wed, Apr 24, 2013 at 3:11 AM, alfonso.carf...@uniparthenope.it wrote: I'm using the package pglm and I'have estimated a random probit model. I need to save in a vector the fitted values and the residuals of the model but I can not do it. I tried with the command fitted.values using the

Re: [R] pglm package: fitted values and residuals

On Wed, Apr 24, 2013 at 4:37 PM, Achim Zeileis achim.zeil...@uibk.ac.at wrote: On Wed, 24 Apr 2013, Paul Johnson wrote: On Wed, Apr 24, 2013 at 3:11 AM, alfonso.carf...@uniparthenope.it wrote: I'm using the package pglm and I'have estimated a random probit model. I need to save in a vector

[R] Trouble with methods() after loading gdata package.

Greetings to r-help land. I've run into some program crashes and I've traced them back to methods() behavior after the package gdata is loaded. I provide now a minimal re-producible example. This seems bugish to me. How about you? dat - data.frame(x = rnorm(100), y = rnorm(100)) lm1 - lm(y ~ x,

Re: [R] significantly different from one (not zero) using lm

It is easy to construct your own test. I test against null of 0 first so I can be sure I match the right result from summary.lm. ## get the standard error seofb - sqrt(diag(vcov(lm1))) ## calculate t. Replace 0 by your null myt - (coef(lm1) - 0)/seofb mypval - 2*pt(abs(myt), lower.tail = FALSE,

[R] Automatic way to embed fonts into all pdf output?

This is a feature request. Or else a howto request. Can there be some simple, automatic way to make fonts embed into pdf output? Could this be in options() or par()? Why? I recently wanted to create a paper for a conference in a format called AAAI (which I had never heard of before because I

Re: [R] R installation error

Meenu: You have an elementary Linux setup and configuration problem to understand first, before you worry about configuring and compiling your own R. I agree strongly that this is something that all linux users should learn to do, but compiling R itself is like climbing Mt Everest as your first

[R] [R-pkgs] rockchalk_1.5.4 posted

Greetings: rockchalk is a collection of functions to facilitate presentation of regression models. It includes some functions that I have been circulating for quite some time (such as outreg) as well as several others. The main aim is to allow people who do not understand very much R to survive

[R] predictOMatic for regression. Please try and advise me

and let me know how its use could be enhanced, or what other features you might want. I know folks are busy, so to save you the trouble of actually running the code, I also paste in a session demonstrating one run through. Here's the code: ##Paul Johnson ## 2012-04-20 ## Facilitate creation

Re: [R] Solve an ordinary or generalized eigenvalue problem in R?

On Fri, Apr 20, 2012 at 2:18 PM, Jonathan Greenberg j...@illinois.edu wrote: Ok, I figured out a solution and I'd like to get some feedback on this from the R-helpers as to how I could modify the following to be package friendly -- the main thing I'm worried about is how to dynamically set the

[R] what folder to run write_PACKAGES in?

I set up a local repo for testing packages. My packages are not showing up from the repository when viewed by Linux clients. I suspect this is a web administrator/firewall issue, but it could be I created the repo wrongly. I am supposed to run write_PACKAGES separately in each R-version folder.

Re: [R] glmmADMB

On Tue, May 8, 2012 at 5:16 PM, rbuxton moy...@hotmail.com wrote: http://r.789695.n4.nabble.com/file/n4618871/Data_for_list_serve.csv Data_for_list_serve.csv Here is my data, hope this helps. The LESP CHUCKLE , FTSP FLIGHT, and ANMU CHIRRUP are the dependent variables, I want to run one

Re: [R] low R square value from ANCOVA model

On Tue, May 8, 2012 at 3:45 PM, array chip arrayprof...@yahoo.com wrote: Thanks again Peter. What about the argument that because low R square (e.g. R^2=0.2) indicated the model variance was not sufficiently explained by the factors in the model, there might be additional factors that should

Re: [R] glmmADMB

On Tue, May 8, 2012 at 9:06 PM, rbuxton moy...@hotmail.com wrote: Update! I changed the site categories. I noticed that I had coded them as North, South, East, West on different islands, which may have caused confusion in the model. [...] mod - glmmadmb(LESP.CHUCKLE~ 1+(1|ISLAND),

[R] Windows Task Scheduler and R updates. Need basic tips

This is a basic Windows system administrator problem, asked by a Linux guy who is helping out in a Windows lab. I want to keep R packages up to date on MS Windows 7 with a job in the Task Scheduler. I have an R program that I can run (as administrator) that updates the existing packages and then

Re: [R] Names of Greek letters stored as character strings; plotmath.

On Sat, May 19, 2012 at 11:07 AM, William Dunlap wdun...@tibco.com wrote: parse(text=paste(...)) works in simple cases but not in others.  The fortune about it is there because it is tempting to use but if you bury it in a general purpose function it will cause problems when people start using

[R] Build error on RedHat EL 5.5: byte-compiling package 'compiler'

Greetings R-help! In case anybody has worked on an old Redhat system lately, can you remember what is the cause of this problem? I don't think this is a fatal problem, because I can get around it by uninstalling all of the R RPM packages and re-running the build. But if R is installed, the build

Re: [R] R Memory Issues

Dear Emiliano: When they say to read the posting guide, mostly they mean read the posting guide. But I'll tell you the short version. 1. Include a full runable R program that causes the trouble you are concerned about. Include the data or a link to the data, usually the smallest possible

[R] Ask if an object will respond to a function or method

In the rockchalk package, I want to provide functions for regression objects that are "well behaved." If an object responds to the methods that lm or glm objects can handle, like coef(), nobs(), and summary(), I want to be able to handle the same thing. It is more difficult than expected to ask a

[R] xvfb? cron job updates R packages, fails on some requiring X11

In Centos 7 systems, I wrote a script that runs on the cron and I notice some package updates and installs fail like this: Error : .onLoad failed in loadNamespace() for 'iplots', details: call: .jnew("org/rosuda/iplots/Framework") error: java.awt.HeadlessException: No X11 DISPLAY variable

Re: [R] Error installing packages

On Wed, Oct 19, 2016 at 10:31 AM, David Winsemius wrote: > >> On Oct 19, 2016, at 4:54 AM, Kevin E. Thorpe >> wrote: >> >> Hello. >> >> I am posting this on behalf of one of my students who is getting error >> messages when installing some

[R] Interesting quirk with fractions and rounding

Hello, R friends My student unearthed this quirk that might interest you. I wondered if this might be a bug in the R interpreter. If not a bug, it certainly stands as a good example of the dangers of floating point numbers in computing. What do you think? > 100*(23/40) [1] 57.5 > (100*23)/40

Re: [R] Prediction plots

I have done this a lot. Would you mind installing my pkg rockchalk and then run example(plotSlope) and example(plotCurve)? If the output is close to what you want, you can adjust my code. The vignette explains. 1. Create newdata object 2. Run that through predict 3. Make plot None of this is

Re: [R] Interesting quirk with fractions and rounding

ting floats. I wonder now if all uses of > or < with numeric variables are suspect. Oh well. If everybody posts their advice, I will write a summary. Paul Johnson University of Kansas On Apr 21, 2017 12:02 AM, "PIKAL Petr" <petr.pi...@precheza.cz> wrote: > Hi &g

Re: [R] Peformance question

I dont understand your code. But I do have suggestion. Run the functions in the profiler, maybe differences will point at the enemy. Know what I mean? Rprof('check.out') #run code Rprof(NULL) summaryRprof('check.out') Do that for each method. That may be uninformative. I wondered if you tried

Re: [R] Interesting quirk with fractions and rounding

rt is right. I have to read more books. I studied Golub and van Loan and came away with healthy fear of matrix inversion. But when you look at user contributed regression packages, what do you find? Matrix inversion and lots of X'X. Paul Johnson University of Kansask The key (in your example)

[R] workaround for "package building problem Centos 7 & R 3.4.1"

This is for the problem I posted about last Friday. First, the happy part, a workaround: $ cd ~/R/x86_64-redhat-linux-gnu-library/3.4 $ ln -sf /usr/share/R/library/* . After that, all of the packages are found by R CMD check. R CMD check looks in the ~/R/x86_64-redhat-linux-gnu-library/3.4

[R] package building problem Centos 7 & R 3.4.1

Dear everybody: Packages that DO pass the package check on my Ubuntu 17.04 laptop with R 3.4.1 and Mac OSX do not build on Centos 7 with R 3.4.1. I'm pretty sure I have an environment defect, but cannot find it. I find posts from various people about this problem since 2012. But I've checked

Re: [R] package building problem Centos 7 & R 3.4.1

On Aug 12, 2017 11:58 AM, "José Abílio Matos" <jaoma...@gmail.com> wrote: On Friday, 11 August 2017 22.51.12 WEST Paul Johnson wrote: > Dear everybody: > > Packages that DO pass the package check on my Ubuntu 17.04 laptop with > R 3.4.1 and Mac OSX do not build o

Re: [R] Plotting log transformed predicted values from lme

In the rockchalk package, I have a function called newdata that will help with this. Plenty of examples. Probably my predictOmatic function will just work. Motivation is in the vignette. Paul Johnson University of Kansas On Aug 9, 2017 11:23 AM, "Alina Vodonos Zilberg" <alina.vodo

Re: [R] Install package "diagram"

On Wednesday, August 16, 2017, AbouEl-Makarim Aboueissa < abouelmakarim1...@gmail.com> wrote: > Dear All: > > I am trying to install the package "diagram". It is in the list. But when I > selected the package to install it, it says: > > Question: "would you like to use a personal library

[R] function pointers?

We have a project that calls for the creation of a list of many distribution objects. Distributions can be of various types, with various parameters, but we ran into some problems. I started testing on a simple list of rnorm-based objects. I was a little surprised at the RAM storage

Re: [R] [ESS] M-x R gives no choice of starting dir

If Emacs is not asking for starting directory, it is very likely your init file has this somewhere: (setq ess-ask-for-ess-directory nil) On Mon, Sep 11, 2017 at 3:23 PM, Enrico Schumann wrote: > On Mon, 11 Sep 2017, Christian writes: > >> Hi, >> >> I experienced a

[R] looking for formula parser that allows coefficients

Can you point me at any packages that allow users to write a formula with coefficients? I want to write a data simulator that has a matrix X with lots of columns, and then users can generate predictive models by entering a formula that uses some of the variables, allowing interactions, like y ~

Re: [R] Transforming data for nice output table

On Mon, Aug 20, 2018 at 2:17 PM David Doyle wrote: > > Hello everyone, > > I'm trying to generate tables of my data out of R for my report. > > My data is setup in the format as follows and the example can be found at: > http://doylesdartden.com/R/ExampleData.csv > > LocationDate

[R] lm equivalent of Welch-corrected t-test?

Long ago, when R's t.test had var.equal=TRUE by default, I wrote some class notes showing that the result was equivalent to a one predictor regression model. Because t.test does not default to var.equal=TRUE these days, I'm curious to know if there is a way to specify weights in an lm to obtain

Re: [R] Problems to obtain standardized betas in multiply-imputed data

lm.beta, it actually standardizes variables and runs regression. lm.beta resales coefficients instead. Paul Johnson University of Kansas On Wed, Sep 26, 2018, 5:03 AM CHATTON Anne via R-help wrote: > Dear all, > > I am having problems in obtaining standardized betas on a multiply-imput

Re: [R] ANOVA in R

t post hoc comparisons. In car package, Anova function will help. I may teach Anova soon, we'll see if I have better answer then. Paul Johnson University of Kansas On Wed, Oct 10, 2018, 1:14 AM Thanh Tran wrote: > Hi eveyone, > I'm studying about variance (ANOVA) in R and have some questio

Re: [ESS] how to edit openbugs model file?

Thanks, everybody. I'm taking the suggestion Martin offered, since this thing is required to be named *.txt in the current OpenBUGS. Solution Put this at the end of the *.txt file: # Local Variables: # mode: R # End: That works. This question was raised by an interesting problem. This might

[ESS] working directory lost when R session closes

Do you notice this: cd into a folder, say "~/tmp/project/R" and start emacs with a file in there. The working directory correctly shows "~/tmp/project/R". Then launch an R session. When you quit the R session, and start a new R session, the working directory changed, it becomes "~/tmp/project".

Re: [ESS] Ever consider changing indentation on #?

of the markdown-style commentary? > > Here is an R file that has "Rstudio sections" that begin with #. I just tested with their gui and the magic recipe for howto is written below. It is something like Emacs org mode, I suppose. Code folding. This is an example of a file that

[ESS] starting directory not detected correctly anymore

Greetings. I want to have ESS know the working directory from shell pwd, I don't want it to ask me. I have a setting in my init.el that used to work that way: ;; start R in current working directory, don't let R ask user: (setq ess-ask-for-ess-directory nil) Recently, it has stopped working.

Re: [ESS] starting directory not detected correctly anymore

sets the default >> directory to the package directory. It looks like it treats your tmp >> directory >> as a package. @Lionel? >> >> Vitalie >> >>>> On Thu, Nov 30 2017 18:59, Paul Johnson wrote: >> >>> Greetings. >> >>> I

Re: [ESS] [R] M-x R gives no choice of starting dir

If Emacs is not asking for starting directory, it is very likely your init file has this somewhere: (setq ess-ask-for-ess-directory nil) On Mon, Sep 11, 2017 at 3:23 PM, Enrico Schumann wrote: > On Mon, 11 Sep 2017, Christian writes: > >> Hi, >> >> I experienced a

[ESS] polymode indents everything when editing Rmd file?

I wonder if I've got polymode set up correctly. I have Ubuntu 17.10 Emacs 25.2 Ess 17.11, it works well to edit R files. Today I installed polymode from melpa, When I open an Rmd file, I can visually see a difference. The code chunks are likely shaded areas. Also, some keywords within the R

Re: [ESS] polymode indents everything when editing Rmd file?

t a polymode problem. I just don't like markdown-mode so much. If anybody has tips for working with Rmd files, I'm all ears at this point. Best pj > Best, > Ista > > On Tue, Feb 6, 2018 at 11:24 AM, Paul Johnson <pauljoh...@gmail.com> wrote: >> I wonder if I've got polymod

[ESS] re-mapping C-RET in 18.10, avoiding conflict with CUA mode

I'm running Ubuntu-18.10 and the new packaging for elpa-ess provides ESS 18.10. I still like CUA mode rectangles and so I want to remap C-RET to S-RET. 5 years ago Vitalie S told me how to do that. The stanza in init.el was: ;; Change shortcut "run this line" to use Shift-Return ;; Suggested by

Re: [ESS] re-mapping C-RET in 18.10, avoiding conflict with CUA mode

till discussing the change. For now > just replace "ess-mode" with "ess" and it should be fine. The change to > *-visibility-* is needed. > > In the future release both ess-mode and ess will work. > > > Vitalie > > >> On Wed, Oct 24 2018 14

[ESS] Run roxygen examples: how now?

In functions with roxygen examples, until very recently I could run the examples even though they had the roxygen comment "##'" at the beginning. Emacs/ESS would, literally, let me do "next" over and over again to run example code. Today I realize that does not happen anymore, Emacs/ESS is

Re: [ESS] Run roxygen examples: how now?

On Wed, Jan 30, 2019 at 4:37 PM Alex Branham wrote: > > On Wed 30 Jan 2019 at 12:34, Paul Johnson via ESS-help < > ess-help@r-project.org> wrote: > > > In functions with roxygen examples, until very recently I could run the > > examples even thoug

Re: [ESS] Run roxygen examples: how now?

On Mon, Feb 4, 2019 at 9:22 AM Alex Branham wrote: > > > In my init file I have S-RET as the replacement for C-RET, but I've > tested > > this both ways and get same behavior. After removing the init file, > when I > > do C-RET, then the one line I'm on will run, but the focus jumps over the >

[ESS] Roxygen Update is "off by one" in function

confidence interval bound ##' @param arrow.width Arrowhead length must be specified in inches. See ?arrows ##' @param width Thickness of shaded column ##' @param col Color for a bar ##' @param opacity 120 is default, that's partial see through. ##' @return NONE ##' @export ##' @author Paul Johnson

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