similar to: Experimental Rd parser in trunk.

Hola! I have the following in a .Rd file: \eqn{\mbox{coef} = c(\mbox{coef}[1],\ldots, \mbox{coef}[n]) } {coef = c(coef[1], coef[2], \dots, coef[n])} However, both arguments come out in the latex file! Whats happening? Kjetil Halvorsen

It seems that many package authors do not proofread the help installed with their packages. The Rd converter is not a parser, and it will silently produce incorrect results on incorrect input (and some correct input). Here are a few hints about some common errors: 1) When you run R CMD check you get a PDF manual at <pkg>.Rcheck/<pkg>-manual.pdf. Read through it looking for

I should'nt have sent the last mail so fast. Same problem with \eqn{u_j = a_j + b x + c x^2, \quad j=1, \ldots, r-1} {u[j] = a[j] + b*x + c*x^2 j = 1,\dots,r-1} I thought the problem in the first case could have to do with the use use of \mbox{} (with the braces) within the arguments of \eqn, but here there are none braces in the arguments of \eqn{}{}. Another case giving the

Hi, I am doing a small experiment to test if I can use MathJax ( official site: http://www.mathjax.org ) in R's html help pages (i.e. options(help_type='html')) and it seems working with some minor modifications. The screenshot (rendered by Firefox 4.0 beta and with STIX fonts) of the help page in html format with MathJax enabled is at the following url:

Full_Name: Ross Boylan Version: 2.2.0 OS: Linux Submission from: (NULL) (65.175.48.58) \eqn{{\bf\beta}_j}{b(j)} in my .Rd file produces this error -------------------------------------------- ! Missing $ inserted. <inserted text> $ l.7 \eqn{{\bf\beta}_j}{\bf\beta}_ jnormal-bracket5bracket-normal{b(j)} -- ! Missing $ inserted. <inserted

Dear list, I got an automatic email complaining than some of my packages didn't pass 'R CMD check' for R-2.10.0 alpha anymore. Both of them make use of the "cases" LaTeX environment. Inspecting the log outputs I got: LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Misplaced alignment tab

We have been working on handling Rd (R help) files with R rather than Perl scripts. As part of that work, Duncan has written a parser which has revealed many problems in package help files, and we have added its checks to 'R CMD check' in the R-devel version of R. You can see the results for CRAN packages as part of the daily check at

? Fri, 21 Jul 2023 15:14:09 +0200 Antoine Fabri <antoine.fabri at gmail.com> ?????: > On a closer look it seems like roxygen2 introduces those, when using > markdown backtick quoting, if the quoted content is not syntactic. For > instance: > > #' `c(c(1)` > #' `c(c(1))` > > Will convert the first line to `\verb{c(c(1)}` and the second to >

Do I understand correctly that we don't want Rd files to be valid latex ? This seems odd to me. I see that `tools::parse_Rd()` doesn't like `\verb!foo!` so maybe roxygen2 is actually doing the right thing (as opposed to just trying to) ? `parse_Rd() ` is probably what I need indeed, for some reason I hadn't found it, so that should fix my own issue here thanks a lot. Le ven. 21 juil.

It seems that MASS suggest to judge on the basis of sum(residuals(mode,type="pearson"))/df.residual(mode). My question: Is there any rule of thumb of the cutpoiont value? The paper "On the Use of Corrections for Overdispersion" suggests overdispersion exists if the deviance is at least twice the number of degrees of freedom. Are there any further hints? Thanks. -- Ronggui

I'm currently working on writing up some documentation for some of my code, but am having the darndest time coding in equations. For example, the equation in the following: \details{ Calculated the R Squared for observed endogenous variables in a structural equation model, as well as several other useful summary statistics about the error in thoe variables. R Squared values are

I better report this before I forget again (I think it may also be a problem with \item) : >Paul Gilbert wrote: >> > \section{Model Parameters}{ >> >> I seem to recall having a bit of trouble with this quietly omitting things when the >> last "{" had a space before it or was on a new line. I'm not sure if that >>is still a problem (or if indeed

--=-hiYzUeWcRJ/+kx41aPIZ Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit Hi, on March 10 I filed a wishlist bug report asking for the inclusion of some changes to factanal() and the associated print method. The changes were originally proposed by John Fox in 2005; they make print.factanal() display factor correlations if factanal() is called with rotation =

Hi all, I am using R, Version 1.9.1 alpha (2004-05-25), ISBN 3-900051-00-3 on SunOS fluke 5.9 Generic_117171-02 sun4u sparc SUNW,Sun-Fire-480R Version: sparc-sun-solaris2.9 arch = sparc os = solaris2.9 system = sparc, solaris2.9 status = alpha major = 1 minor = 9.1 year = 2004 month = 05 day = 25 language = R Search Path: .GlobalEnv, package:methods, package:stats, package:graphics,

Is there a weighted median function out there similar to weighted.mean() but for medians? If not, I'll try implement or port it myself. The need for a weighted median came from the following optimization problem: x* = arg_x min (a|x| + sum_{k=1}^n |x - b_k|) where a : is a *positive* real scalar x : is a real scalar n : is an integer b_k: are negative and positive scalars

Hi, I have a function knit_expand() and its source/Rd are below: https://github.com/yihui/knitr/blob/master/R/template.R#L43-L44 https://github.com/yihui/knitr/blob/master/man/knit_expand.Rd When I run R CMD check on the package I get this warning (with both R 2.15.2 and R-devel): * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object

Bug or feature? I get the following error from parse_Rd() when a user Rd macro (including system ones) is invoked with empty argument {}, eg \mymacro{}: Error in tools::parse_Rd(fn) : Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL' A full example is further below with the system macro \CRANpkg{}. In this example it doesn't make sense to use empty argument but

While on the topic of Rd macro arguments, it seems that if a multiline argument is supplied, the lines after the first are silently ignored: f <- tempfile() mac6 <- "\\newcommand{\\mac6}{mac6: #1}" cat(mac6, "\\mac6{2*3 2+2 sin(pi) }\n", file = f) rd <- tools::parse_Rd(f) > rd mac6: 2*3 --- Georgi Boshnakov -----Original Message----- From: Tomas Kalibera

I have constructed the function mml2 (below) based on the likelihood function described in the minimal latex I have pasted below for anyone who wants to look at it. This function finds parameter estimates for a basic Rasch (IRT) model. Using the function without the gradient, using either nlminb or optim returns the correct parameter estimates and, in the case of optim, the correct standard

With help by Kurt and Martin I have written a short proposal for a new R doc source format that should be easier to parse using, e.g., perl. There should be especially a clearer distinction between text and keywords. Here we go, please make comments, corrections, etc. Best, Fritz ********************************************************** Conversion: ----------- A perl module providing