similar to: data compression in a package

On 12/29/2017 07:34 AM, Dirk Eddelbuettel wrote: > > On 29 December 2017 at 07:23, Therneau, Terry M., Ph.D. wrote: > | The submission guide has the following cryptic (to me) sentence: > | ?? "Reasonable compression should be used for data (not just .rda files) " > | > | The survival pacakge has a fairly large number of data files --- exactly what should I be > |

This is likely yet another instance of round off error, but it caught me by surprise. tmt% R --vanilla (headers skipped, version 3.0.2 on Linux) > load('qtest.rda') > length(temp) [1] 3622 > max(temp) >= quantile(temp, .98) 98% FALSE I can send the file to anyone who would like to understand this more deeply. The top 3% of the vector is a single repeated value. Terry

I found an issue with the data() command this evening when working on the survival package. 1. I have a lot of data sets in the package, almost all used in at least one vignette, help file, or test.? As a space saving measure, I have bundled many of them together, i.e., the file data/cancer.rda contains 19 data sets, many of them small. The resulting file (using xz compression) is quite a bit

When I run R CMD check on the survival package I invariably get a note: ... * checking for file ?survival/DESCRIPTION? ... OK * this is package ?survival? version ?3.2-6? * checking CRAN incoming feasibility ... NOTE Maintainer: ?Terry M Therneau <therneau.terry at mayo.edu>? ... This is sufficient for the auto-check process to return the following failure message: Dear maintainer,

The current coxme code has functions that depend on bdsmatrix and others that depend on Matrix, both those pacakges define S4 methods for diag. When loaded, the message appears: replacing previous import ?diag? when loading ?Matrix? Questions: 1. Do I need to worry about this? If so, what can I do about it? I suppose I could add an importFrom directive, but it will be a pain unless there

Ben, Looking at your notes, it appears that your solution is to write your own terms() function for lme.? It is easy to verify that the "varnames.fixed" attribute is not returned by the ususal terms function. Then I also need to write my own terms function for the survival and coxme pacakges? Because of the need to treat strata() terms in a special way I manipulate the formula/terms in

Hi, May I know how to obtain the confidence interval of the survival curve of weighted Cox regression model? I tried coxph, cph, and coxphw, but they did not work. Any help would be much appreciated. Thanks, Jeanne -- View this message in context: http://r.789695.n4.nabble.com/Confidence-interval-of-Survival-Curve-of-Weighted-Cox-Regression-tp3308085p3308085.html Sent from the R help mailing

Survfit had a bug in some prior releases due to the use of both unique(times) and table(times); I fixed it by rounding to 15 digits per the manual page for as.character. Yes, I should ferret out all the usages instead, but this was fast and it cured the user's problem. The bug is back! A data set from a local colleage triggers it. I can send the rda file to anyone who wishes. The

I have a test directory for the survival suite, and dyn.load has ceased to work in it. Below shows the log: tmt1075% R --vanilla R version 2.12.2 (2011-02-25) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain

Dear List I have experienced that objects generated with one of my packages used a lot of space when saved on disc (object.size did not show this!). some debugging revealed that formula and call objects carried the full environment of subroutines along, including even stuff not needed by the formula or call. here is a sketch of the problem ,---- | test <- function(x){ | x <-

>>>>> Ben Bolker <bbolker at gmail.com> >>>>> on Thu, 8 Mar 2018 09:42:40 -0500 writes: > Meant to respond to this but forgot. > I didn't write a new terms() function -- I added an attribute to the > terms() (a vector of the names > of the constructed model matrix), thus preserving the information at > the point when

hii guys: i get the message from the asterisk: Started music on hold, class 'default', on Local/s at skype-web-callback-dial-263to263-1775,1 [2008-11-11 14:32:41] WARNING[1781]: format_wav.c:156 check_header: Unexpected freqency 11025 [2008-11-11 14:32:41] WARNING[1781]: file.c:322 fn_wrapper: Unable to open format wav [2008-11-11 14:32:41] WARNING[1781]:

I have been using Ubuntu 12.04 for awhile and built samba from source. I have two servers, both on 12.04. Samba bulid 4.1.11. I would like to upgrade the servers to 14.04 and start using the actual pacakges from ubuntu. How do I get from compiled binarys to using the ubuntu pacakge? Thanks for any help. Jason

I understand about using the newer binaries, but what I really want to "save" is the active directory. Sorry I should have been clear. I do not want to have to rejoin/recreate everything. Thanks. Jason On Mon, Jun 29, 2015 at 10:23 AM, Reindl Harald <h.reindl at thelounge.net> wrote: > > Am 29.06.2015 um 15:06 schrieb Jason Waters: > >> I have been using Ubuntu

I am trying to clear up all the "NOTE"s before a CRAN submission, but am a bit confused about this one.?? What is it complaining about -- that it doesn't like my name? ... * checking for file ?deming/DESCRIPTION? ... OK * this is package ?deming? version ?1.4-1? * checking CRAN incoming feasibility ... [7s/18s] NOTE Maintainer: ?Terry Therneau <therneau.terry at mayo.edu>?

Question: I am trying to impliment a function in R that we use quite regularly in Splus, and it fails due to a lack of the "terms.inner" function in R. The substitute is? Part question and part soapbox: Why remove terms.inner from R? It's little used, but rather innocuous. Mostly soapbox: I figured it was no big deal, as I originally discovered the use of terms.inner from

I'd like to get interaction terms in a model to be in another form. Namely, suppose I had variables age and group, the latter a factor with levels A, B, C, with age * group in the model. What I would like are the variables "age:group=A", "age:group=B" and "age:group=C" (and group itself of course). The coefficients of the model will then be the age effect

Dear R team I noticed a bug in the "medpolish" function in the "stats" package. When I run medpolish(x), with "x" the matrix in the attached .rda file, I get this rather cryptic error: "Error in if (converged) break : missing value where TRUE/FALSE needed In addition: Warning message: In sum(abs(z), na.rm = na.rm) : integer overflow - use

I've created some Splus code for a microarray problem that - needed to be in C, to take advantage of some sparse matrix properties - uses a cholesky decompostion as part of the computation For the cholesky, I used the cholesky2 routine, which is a part of the survival library. It does just what I want and I'm familiar with it (after all, I wrote it). In Splus, this all works

Hello, I'm trying to use coxph() function to fit a very simple Cox proportional hazards regression model (only one covariate) but the parameter space is restricted to an open set (0, 1). Can I still obtain a valid estimate by using coxph function in this scenario? If yes, how? Any suggestion would be greatly appreciated. Thanks!!! [[alternative HTML version deleted]]