similar to: Shy Suggestion?

Dear Mr Moderator, please let me through. I want to reply to my own thread. I once subscribed to this list, but then my subscription was not accepted. Now to the business: The final failure came from missing .install.macbinary() function. I grepped R-patched sourcesand the only instance of .install.macbinary() was the call to the function in R- patched/src/library/utils/R/packages2.R (stupid

rolf at math.unb.ca said: > If I say something like > if(x .gt. 42.d0) stop > then indeed everything stops, i.e. R falls over. I'd ***like*** to be > able to print out an informative error message (which I guess could be > done - In Fortran: subroutine foo(..., ier) integer ier ier=0 ... if (x .gt. 42.d0) then ier=1 return endif

I find it a bit peculiar that a package skeleton created with a utils function package.skeleton() fails subsequent R CMD check. I do understand that the function is intended to produce only a skeleton that should be edited by the package author. I think that it would be justified to say that the skeleton *should* fail the test. However, I have two arguments against intentional failure: * When you

Canberra distance is defined in function `dist' (standard library `mva') as sum(|x_i - y_i| / |x_i + y_i|) Obviously this is undefined for cases where both x_i and y_i are zeros. Since double zeros are common in many data sets, this is a nuisance. In our field (from which the distance is coming), it is customary to remove double zeros: contribution to distance is zero when both x_i

Canberra distance is defined in function `dist' (standard library `mva') as sum(|x_i - y_i| / |x_i + y_i|) Obviously this is undefined for cases where both x_i and y_i are zeros. Since double zeros are common in many data sets, this is a nuisance. In our field (from which the distance is coming), it is customary to remove double zeros: contribution to distance is zero when both x_i

Dear R folks, One of the fantastic new tools in R is `Sweave'. I have tested it so much that I know it works and produces fine documentation, and with (GNU) Emacs/ESS it is nice to work with, too. I started to have a look at including some Swoven (is that a strong verb?) documentation with my R package, but it seems that there is no model to copy among those packages that I have installed in

--==_Exmh_1801894504P Content-Type: text/plain; charset=us-ascii Dear R folks, Initially I had a plotting routine using logarithmic y-axes that failed after repeated calls if I tried to restore the graphical parameters (which I wanted to do because I used `layout' within the routine. I tried to isolate the problem and found out that the following code with logarithmic axis is sufficient for

Thanks for the attention paid to my rpoblem. Please find enclosed the matrix with my dissimilarities. This is the only case in which sammon(), from the MASS package, gives me this kind of problems. Domenico > > > -----Messaggio originale----- > > Da: Jari Oksanen [mailto:jarioksa at sun3.oulu.fi] > > Inviato: mercoled?? 20 aprile 2005 11.53 > > A: Domenico Cozzetto >

Message 2 of today: it works now. After re-installing R.app from the same R-2.1.0.dmg file, and fixInNamespace'ing(*) install.packages(), I managed to update 23 outdated packages from CRAN binaries for MacOS X. What I did was to: 1. change call to .install.macbinaries() into call to install.binaries() in install.packages(). install.binaries() is a function defined utils/R/aqua/GUI.R. 2. I

Dear peRsons, I have a Sweave document which demonstrates the usage of step() function. With current R version 2.5.0 the step() function was changed so that the heading of trace=TRUE output for each model is printed using command message(): if (trace) message("\nStep: AIC=", format(round(bAIC, 2)), "\n",

Dear developers, I just noticed that step() function currently prints the current model using message(), but the resulting model using print(). The relevant commands within the step() body are: if (trace) message("Start: AIC=", format(round(bAIC, 2)), "\n", cut.string(deparse(as.vector(formula(fit)))), "\n") (with example() output:) Start: AIC=190.69

Full_Name: Jari Oksanen Version: 2.0.1, 2.1.0 beta (2005-04-17) OS: Linux Submission from: (NULL) (130.231.102.145) If name ends with "and", such as "Roeland Lastname", citation() will chop "and" as a separate word giving "Roel and Lastname". This is the case in the upcoming release of vegan (1.6-8) just submitted to CRAN. Basically, this seems to happen

The package mvpart is now available. mvpart includes partitioning based on (1) multivariate numeric responses and (2) dissimilarity matrices. The package mvpart is a modification of rpart -- -- authors of original: Terry M Therneau and Beth Atkinson <atkinson at mayo.edu>, and R port of rpart Brian Ripley <ripley at stats.ox.ac.uk>. Includes some modified routines from vegan --

The package mvpart is now available. mvpart includes partitioning based on (1) multivariate numeric responses and (2) dissimilarity matrices. The package mvpart is a modification of rpart -- -- authors of original: Terry M Therneau and Beth Atkinson <atkinson at mayo.edu>, and R port of rpart Brian Ripley <ripley at stats.ox.ac.uk>. Includes some modified routines from vegan --

Full_Name: Jari Oksanen Version: R 2.1.0 OS: MacOS 10.3.9 Submission from: (NULL) (130.231.102.145) For various reasons (which need not be expanded here) I have tried to update my long neglected R in MacOS X using handy command line tool update.packages() using readily available binaries of contributed packages at CRAN. However, this fails with message saying that packages xxxx_*_tar.gz is not

Hi After trying a simple decorana analysis (from the vegan package) on a simple data frame which contains no NA's the following error was returned: > tt_decorana(covN) Error in decorana(covN) : NA/NaN/Inf in foreign function call (arg 1) Have any vegan users come across this error and know what can be done about it? Cheers, J

Dear vegan team, Vegan development happens now completely in github. R-Forge repository is no more in sync with github. I tried to commit all github changes to R-Forge, but a week ago I got a conflict in file and I haven't had time to resolve that conflict. You can follow vegan development and vegan discussion also without signing to github. The system seems to be completely open and does not

Dear all, I didn't find any graphical solution in the package "mva" to plot the canonical scores from a CCA (canonical correlation analysis). Does anybody knows how to plot or has anybody already programmed : - the map of the canonical scores, - the graph of the canonical weights, - the correlation circle i.e. the canonical loadings ? Thank you for help ...

Dear Colleagues, As a novice I was trying to calculate Shannon diversity index using diversity function in vegan package and kept having same error message. Error in sum(..., na.rm = na.rm) : invalid 'mode' of argument My dataset is from microarray and have abundant missing values, so I tried labeling them as NA and 0, but still same error message. Shannon index is negative

Dear all, in package Hmisc `rcorr' computes a matrix of Spearman's `rho' rank correlation coefficients for all possible pairs of columns of a matrix. What if I want a matrix of rank correlation coefficients for pair of columns of two different matrices? I have the same question about distance metrics in package Vegan. The function 'vegdist' computes distance indexes for all