Re: [Bioc-devel] ERROR from SVN: URL access forbidden for unknown reason

On 05/04/2017 12:25 PM, Lluís Revilla wrote: Hi, I am trying to push some changes from my machine to the svn repository of Bioconductor. Since the start of the package I've been using git, so I have prior history before submitting to Bioconductor. And I made some other commits after the

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

Hi John, Thanks for the comment... but that appears to mean that SPSS has a big problem. I have always been told that to include an interaction term in a regression, the only way is to do the multiplication by hand. But then it seems to be impossible to stop SPSS from re-standardizing the

Re: [R-pkg-devel] Package building - compiling multiple dll files from within src directory

On 05/05/2017 2:09 PM, Mark wrote: Hi Uwe, Thank you, I have a series of cc files that use similar function names, so to avoid overriding functions, I thought to compile and load each of the cc files separately. In more detail, I have a series of models for the use in deSolve, they all have

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

Well, one correction -- the 'standardized coefficients' that SPSS shows are based on standardizing all variables separately (so x1, x2, and x1*x2 are all standardized). So with respect to that, the criticism certainly stands. -Original Message- From: Viechtbauer Wolfgang (SP) Sent:

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

Totally agree that standardizing the interaction term is nonsense. But in all fairness, SPSS doesn't do that. In fact, the 'REGRESSION' command in SPSS doesn't compute any interaction terms -- one has to first compute them 'by hand' and then add them to the model like any other variable. So

Re: [Rd] A few suggestions and perspectives from a PhD student

Regarding the anonymous-function-in-a-pipeline point one can already do this which does use brackets but even so it involves fewer characters than the example shown. Here { . * 2 } is basically a lambda whose argument is dot. Would this be sufficient? library(magrittr) 1.5 %>% { . * 2 }

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

Dear Nick, On 2017-05-05, 9:40 AM, "R-devel on behalf of Nick Brown" wrote: >>I conjecture that something in the vicinity of >> res <- lm(DEPRESSION ~ scale(ZMEAN_PA) + scale(ZDIVERSITY_PA) + >>scale(ZMEAN_PA * ZDIVERSITY_PA),

Re: [R-pkg-devel] Package building - compiling multiple dll files from within src directory

Hi Uwe, Thank you, I have a series of cc files that use similar function names, so to avoid overriding functions, I thought to compile and load each of the cc files separately. In more detail, I have a series of models for the use in deSolve, they all have the same initmod and derivs internal

Re: [Rd] A few suggestions and perspectives from a PhD student

On Fri, May 5, 2017 at 1:00 PM, Antonin Klima wrote: > Dear Sir or Madam, > > I am in 2nd year of my PhD in bioinformatics, after taking my Master’s in > computer science, and have been using R heavily during my PhD. As such, I > have put together a list of certain

[Rd] A few suggestions and perspectives from a PhD student

Dear Sir or Madam, I am in 2nd year of my PhD in bioinformatics, after taking my Master’s in computer science, and have been using R heavily during my PhD. As such, I have put together a list of certain features in R that, in my opinion, would be beneficial to add, or could be improved. The

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

>I conjecture that something in the vicinity of > res <- lm(DEPRESSION ~ scale(ZMEAN_PA) + scale(ZDIVERSITY_PA) + > scale(ZMEAN_PA * ZDIVERSITY_PA), data=dat) >summary(res) > would reproduce the SPSS Beta values. Yes, that works. Thanks! - Original Message - From: "peter dalgaard"

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

Thanks, I was getting to try this, but got side tracked by actual work... Your analysis reproduces the SPSS unscaled estimates. It still remains to figure out how Nick got > coefficients(lm(ZDEPRESSION ~ ZMEAN_PA * ZDIVERSITY_PA, data=s1)) (Intercept) ZMEAN_PA

Re: [Rd] complex tests failure

Thanks for the report, handled in configure in 72661 (R-devel). I'll also port to R-patched. Best Tomas On 05/04/2017 03:49 PM, Tomas Kalibera wrote: > > There is no way to control this at runtime. > We will probably have to add a configure test. > > Best, > Tomas > > On 05/04/2017 03:23 PM,

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

I had no problems running regression models in SPSS and R that yielded the same results for these data. The difference you are observing is from fitting different models. In R, you fitted: res <- lm(DEPRESSION ~ ZMEAN_PA * ZDIVERSITY_PA, data=dat) summary(res) The interaction term is the

[Rd] Possible bug in how POSIXct is printed

Greetings R-devel group. When dealing with Inf dates, as.POSIXct seems to return Inf, but is printed as NA: > x1 <- as.POSIXct(Inf, origin = '1970-01-01') > print(x1) [1] NA > is.na(x1) [1] FALSE > is.infinite(x1) [1] TRUE > POSIXlt at least evaluates and prints the result consistently: > x1

Re: [Bioc-devel] Error in BUILD report (anamiR)

Thank you for your efforts. Since the windows ERROR is out of your control we will undeprecate your package. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [R-pkg-devel] Latex got me

On 05/05/2017 5:47 AM, Jim Lemon wrote: Hi, In adding a contributed function to the plotrix package, I keep getting a latex error: * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! File ended while

[R-pkg-devel] Latex got me

Hi, In adding a contributed function to the plotrix package, I keep getting a latex error: * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! File ended while scanning use of \HeaderA.

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

Hi, Here is (I hope) all the relevant output from R. > mean(s1$ZDEPRESSION, na.rm=T) [1] -1.041546e-16 > mean(s1$ZDIVERSITY_PA, > na.rm=T) [1] -9.660583e-16 > mean(s1$ZMEAN_PA, na.rm=T) [1] -5.430282e-15 > > lm.ridge(ZDEPRESSION ~ ZMEAN_PA * ZDIVERSITY_PA, data=s1)$coef ZMEAN_PA >

Re: [R-pkg-devel] Package building - compiling multiple dll files from within src directory

Why do you want to build separate dll files if you want to load all of them anyway? That way you add some overhead, at least. From Writing R Extensions: "A few packages use the src directory for purposes other than making a shared object (e.g. to create executables). Such packages should

Re: [Rd] lm() gives different results to lm.ridge() and SPSS

I asked you before, but in case you missed it: Are you looking at the right place in SPSS output? The UNstandardized coefficients should be comparable to R, i.e. the "B" column, not "Beta". -pd > On 5 May 2017, at 01:58 , Nick Brown wrote: > > Hi Simon, > > Yes, if I