NEWS bomb

[swihart]

Actually, during publication. we got some warnings while converting the .md documents:

** Files: DESCRIPTION NAMESPACE[warning] Could not convert TeX math '(FLIBS) to end of line 14.8.99 print.gnlr: corrected errors in printing fmr, gnlr3, and nlmm output fnenvir.tvcov: corrected error for undefined ex1a (-> ex2a) Pareto, gnlmm, hstudent, kalcount, kalseries, pkpd, read.list, read.surv,  tvctomat: orrected examples 18.7.99 hidden.r, chidden.r: corrected one error message  added printout of degrees of freedom 14.7.99 binnest.f: modified comments to comple with standard Fortran (thanks  to Martin Maechler) ------------------------------------------------------------------------------ version 0.5 ----------------------------------------------------------------------------- 29.6.99 plot.response: remove NAs when calculating default ylim 28.6.99 gnlr.r, gnlr3.r, fm.r, nordr.r, gnlmm.r: check if user gives a nonlinear formula in linear argument and correctly handle it 27.6.99 finterp: corrected error message when non-nmeric vector supplied restovec: corrected printing of total times when negative times present added transform methods for response, tccov, and tvcov objects 4.6.99 gar.r: corrected error in printing shape functions 22.6.99 binnest.f: modified to compile with g77 8.6.99 binnest: binary random effects model with tw levels of nesting 7.6.99 restovec: added an additional check for nest variable in lists 6.6.99 logitord.f: corrected bug in calculation of Hessian (and s.e. 1.6.99 elliptic: added multivariate Student t distribution 11.5.99 finterp.r: functions allowed in W&R formulae carma.r, elliptic.r, kalseries.r, kalcount.r kalsurv.r: allow factor variables finterp: can locate and use indices for individuals and nesting as  factor covariates 10.5.99 tcctomat.r, tvctomat.r: allo factor variables finterp, fnenvir: changed to check for factor variables 6.5.99 elliptic.r: allow variance to be a function of the mean function 4.5.99 gar.: changed normal distribution shape parameter from sd to variance 3.5.99 profile and iprofile: fixed to plot correctly with nesting 1.5.99 tcctomat, tvctomat allow dataframes 28.4.99 tvctomat: time-varying covariates can be factors elliptic.r, gnlr.r, gnlr3.r, fmr.r, gnlmm.r, gar.r: location and shape  functions an have common parameters 26.4.99 restovec: weights allowed for lists finterp, fnenvir: can find the times when envir is a repeated object gar.r: allow shapeto be a function of the location function 23.4.99 gnlr.r, gnlr3.r, fmr.r, nordr.r, nlr.r, elliptic.r, gnlmm.r, gar.r,  kalseries.r, kalcount.r, kalsurv.r, eh.r: do not require  envir if response has class, repeated corrected bugs in restovec and plot.response (Lorenz Gygax) 22.4.99 generalized plot.residuals tvctmat: allow calculation of more than one interaction with  time-constant covariates at a time finterp and fnenvir: allow variables in environment to have samename  as a function 21.4.99 correction of 18.1.99 by Brian Ripley wrong: dist.c put back in gnlm 20.4.99 ksurvb.c: corrected bug when time-varying covariateselliptic.r: added option to ccov and tvcov to give covariate names  when response has class, repeated carma.r: added option to ccov to give covariate names wen response  has class, repeated 19.4.99 changed plot.profile to profile and plot.iprofile to iprofile 18.4.99 elliptic.r: added recursive predicted values wen AR(1) and/or random effect 16.4.99 gnlr.r, gnlr3.r, fmr.r, nordr.r, gnlmm.r, ehr.r: changed order of  parameters when function with linear part 15.9.99 eh: corrected two errors when lambda function with linear part nordr.r: n changed to nrows 13.4.99 carma.r: corrected predicted values when response is transfomed gar.r, kalseries.r: changed handling of transformed responses ------------------------------------------------------------------------------ version 0.4 ----------------------------------------------------------------------------- 12.4.99 added dependency on rmutil to DESCRIPTION 11.4.99 elliptic.f: correctedhandling of dose for PKPD model when  time-varying covariates are present 6.4.99 elliptic.r, gnlmm.r, gar.r, kalseries.r, kalcount.r, kalsurv.r, ehr.r,  nord.r, nlr.r: modified to use fnenvir 5.4.99 gnlr.r, gnlr3.r, fmr.r: modified to use fnenvir 4.4.99 fnenvir: checks functions for covariates and parameters and modifies them to read from data objects 1.4.99 elliptic.r: modified to use model formulae with unknowns finterp.r: added data objects as environment tvctomat tcctomat: can combine two data objects 31.3.99 gar.r: modified to use model formulae with unknowns 30.3.99 rmna: check if a covariate only has one value aftr NA removal fixed examples docs so that they work 29.3.99 kalcount.r, kalsurv.r, ehr.r: modified to use model formulae with unknowns 28.3.99 gnlmm.r, kalseres: modified to use model formulae with unknowns restovec: added coordinates to response class for spatial data 26.3.99 gnlr.r, gnlr3.r, fmr.r, nordr.r, nlr.: modified to use model formulae with unknowns 24.3.99 changed language check to inherits formula in all functions added methods for extracting elements fro data objects finterp.r: transforms model formulae with unknowns into functions 22.3.99 restovec: times no longer required for clustered data  type attributeadded carma.r, elliptic.r, kalseries.r kalcount.r: check to see if times available 15.3.99 rmaov.r: wrote documentation pkpd.r : added two new models and corected one other 13.3.99 restovec: allow ties in times 23.2.99 gar.c: corrected Laplace cdf and allowed negative values 11.2.99 ehr: corrected for ties kalsur.r: prints out "birth process" when applicable instead of  renewal process logitord.r: removed DUP=F from Fortran call 8.2.99 km.r: fixed bug in plot.dist.kmwhen several groups are plotted  (Gareth Ridall) 7.2.99 improved handling of variable names in tcctomat, tvctomat, and  functions calling them rmaov.r: splitplot aov from Ralf Goertz 6.2.99 glmm.r: accepts transformed data if dataframe supplied 5.2.99 km.r: fixed bug for double lines with censored observations (Greth Ridall) ehr.r: modified handling of language 4.2.99 km.r: added print.km to remove attributes restovec: accepts all response data, not just repeated meaurements tvctomat: added calculation of interactions 2.2.99 restovec: added adding several column matrices in lists with censoring kalsurv.r: added delta opton 1.2.99 glmm.r: binary response with binomial handled correctly 30.1.99 plot.iprofile.carma: corrected nind argument restovec, carma, elliptic, kalcount, klseries: added how to handle `times'  for clustered data to docs 28.1.99 bivbinom.r, marghom.r: minor corrections rs.r: improved printout 26.1.99 readrm.r: crrected lty specification in plot.response added option to plot points 24.1.99 gnlr.r, gnlr3.r, fmr.r, gnlmm.r: y can have classes, response or repeated addd DUP=F to all .C and .Fortran calls pbirth.r: binomial data distributions 22.1.99 readrm.r: added ... for graphics options in plot.response and plot.repeate 21.1.99 rmna: added checks that ccov and tvcov have correct class 19.1.99 dist.c: changed static romberg to romberg2 and added static interp carma.r, chidde.r, elliptic.r, gar.r, hidden.r, kalcount.r, kalseries.r, kalsurv.r: allow response to have class, repeated restovec: allow delta to be a dataframe 18.1.99 orrections by Brian Ripley gnlm: removed redundant dist.c enclosed library.dynam in .First.lib potthoff.r: added matrix dimension checks util.r: removed orthfunction potthoff.r: replaced orth by contr.poly 17.1.99 carma.r, chidden.r, elliptic.r, gar.r, hidden.r, kalcount.r, kalseries.r,  kalsurv.r: copy response ector more efficiently restovec: added total time for survival data coxre.r: reorganized for efficiency, eliminating data.frame cprocess.r: times can have clss, response 16.1.99 gnlr.r, gnlr3.r, fmr.r, gnlmm.r: removed -delta/2 in right censoring  calculation dist.r, gnlr3.r, gar.c, hidden.f: changed parametrizaton of Burr to  agree with kalsurv.r elliptic.r: use var(y) to get initial estimate of variance ----------------------------------------------------------------------------- version 0.3 ------------------------------------------------------------------------------ 14.1.99 kalsurv.r: corrected printing of number ofsubjects and observations 2.1.99 cprocess.r: allow event counts with unequal times added mode="double" to is.vector 29.12.98 corrected minor bugs in fmr 28.1.98 corrected abs bug for Laplace in kalman C functions 27.12.98 restovec: corrected binary totals when given as a vector gar: added Levy, Pareto, generalize inverse Gauss, and  power exponential distributions hidden and chidden: added various overdispersed and continuous distributions 22.12.98 hidden and chidden added filter calculation and plots 21.12.98 moved Student t from gnlr to gnlr3 renamed beta as Pareto in kalcount, kalseries, and kalsurv corrected various inor errors in fmr and gnlr3 20.12.98 dist.r, gnlr.r, fmr.r: added gamma count and Pareto distributions 18.12.98 chidden: continuous-time hidden Markov chainmodels 7.12.98 dist.r, gnlr.r, fmr.r: added Levy distribution removed .so from Makefiles and library.dynam 6.12.98 util.r: added spectral decomposition to mep 5.12.98 rmutil: added several p and d functions gnlr3.r: added censored generalized inverse Gaussian and power  exponential distributions 2.12.98 int.r: vetorized Romberg integration 1.12.98 int.r: added option for Romberg integration 30.11.98 updated libraries with Brian Ripley's corrections 25.11.98 hidden: alow values in the transition matrix to be fixed at 0 or 1 24.11.98 hidden: added independence model 23.11.98 inthaz.c: changed header include bessel: removedfunction gnlr3.r: changed to internal bessel function 14.11.98 hidden: added multinomial distribution 12.11.98 hidden.f: corrected Poisson and binomial calcuations 5.11.98 carmasub.f and survkit.f: changes for compatibility with g77 ------------------------------------------------------------------------------ vesion 0.2 ------------------------------------------------------------------------------ 2.11.98 ehr.r: corrected printing coefficients with linear and other arameters 1.11.98 km.r: corrected NaNs in log 29.10.98 carma.r: corrected printout of mean time km.r: corrected ylab for cdf 26.10.98 rmna: handles NAs in tie-constant covariates properly carma.r and elliptic.r: accept ccov of class, tccov cprocess.r: added plots from counts of events 19.10.98 changed to inherits) throughout rationalized printing of gnlr, gnlr3, fmr, gnlmm and moved to rmutil added delta option to carma and elliptic 18.10.98 carma.r and elliptic.r: aded handling of delta when y has class, response 17.10.98 gar.r: added cloglog link 12.10.98 gnlmm.r: corrected handling of delta when y has class, response 1.10.98 replaced tapply() with collapse() in bivbinom, catmiss, glmm, gnlmm, ehr, coxre 10.10.98 ehr.r check for singular covariance matrix  print names of vriables for coefficients when language 8.10.98 kcountb.c: corrected dplogis call gnlmm.r: corrected calls to ddp, dmp, ddb, and dmb coxre.r: removed as.is=T n data.frame corrected printing shape parameters when language used in gnlr, gnlr3, fmr, gnlmm 7.10.98 rs.r: put in check that all covariates are positive glmm.r: set censor to F for binomial data dist.c: changed ddp, dmp, ddb, and dmb to log and introduced weights 6.10.98 kseries.c: corrected error in serial upate kalseries.r: correcting printing error when there is an interaction kalsurv: added serial update inthaz.c: put back ihlogis (disappeared with nmath) renaed wr.r as util.r moved det and %**% from repeated and growth to rmutil/R/util.r 5.10.98 corrected check in carma, elliptic, gar, and kalseries for nonpositie  transformed values 4.10.98 glmm.r: corrected two errors 1.10.98 extended residual plots to all of class recursive kalcount, kalseries, kalsurv: return mea profiles in z', rendering as TeX:
! ctions allowed in W&R formulae carma.r,
!                    ^
! unexpected '&'
! expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", \\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathu", "\\pmb", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phatom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\acute, "\\grave", "\\breve", "\\check", "\\dot", "\\ddot", "\\dddot", "\\ddddot", "\\mathring", "\\vec", "\\overrightarrow", "\\overleftarrow", "\\hat", "\\wideha", "\\widehat", "\\tilde", "\\widetilde", "\\bar", "\\overbrace", "\\overbracket", "\\overline", "\\underbrace", "\\underbracket", "\\underline", "\\underbar, "\\ensuremath", "(", ")", "[", "]", "\\{", "\\}", "\\lbrack", "\\lbrace", "\\rbrack", "\\rbrace", "\\llbracket", "\\rrbracket", "\\langle", "\\rangle", "\\floor", "\\rfloor", "\\lceil", "\\rceil", "|", "\\|", "\\lvert", "\\rvert", "\\vert", "\\lVert", "\\rVert", "\\Vert", "\\ulcorner", "\\urcorner", "\\bigg", "\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+, ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\", "\\operatorname" or end of input
[warning] Could not convert TeX math 'pred as well as a mean function nbkal.r: corrections corrected and updated a lot of docs 30.9.98 moved kalsurv to eventlibrary renamed rmtools as rmutil inthaz.c: corrected error from change to nmath 29.8.98 kalsurv.r: added recursive fitted values kalseries.r: added recursiv fitted values updated plot.residuals for recursive class 27.9.98 corrected docs for plot.profile, plot.iprofile added covind.default plot.iprofile: correcte default settings 24.9.98 gettvc.r: allow an option for ties bessel.r: only calculate one kind of function 20.9.98 gettvc.r: allow NAs in time-varying covarite  corrected for ties between response and covariate tvctomat: allow tvcov to already have class, "tvcov" added as.double in all Fortran and C calls 18.9.98plotrm.r: corrected bug in plot.iprofile due to new covind() 16.9.98 pkpd.r: corrected mu2.0o2c and added mu2.0o2cfp 15.9.98 replaced Bessel, Gauss-Hermite, nd integration routines bessel.r: added docs 14.9.98 moved wr to rmtools and added docs added covind function to rmtools 12.9.98 kalserie.r: added delta optin tcctomat.Rd: corrected alias created new library, rmtools 11.9.98 dist.r: added beta binomial dist.c: simplified calls to overdispersion functions autocor.: corrected pergram kalserie.r: corrected error in printing parameters with torder>0 kserieb.c: corrected error when mu function used 10.9.98 readlist.r: corected binomial totals for lists in restovec fmr.r: removed unnecessary code gar.r: added overdispersed binomial data dist.r: allow dispersion to be a scalar hen mean is a vector  created documentation for p and d functions 9.9.98 nordr.r: corrected weights for adjacent categories model  test for p>1 in proportionl odds gar.r: added checks on times and mu arguments  added binomial data corrected docs for elliptic, gar, kalcount, kalseries, kalsurv, nbkal  for z', rendring as TeX:
! lready have class, "tvcov" added as.doub
!                    ^
! unexpected '"'
! expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", \\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathu", "\\pmb", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phatom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\acute, "\\grave", "\\breve", "\\check", "\\dot", "\\ddot", "\\dddot", "\\ddddot", "\\mathring", "\\vec", "\\overrightarrow", "\\overleftarrow", "\\hat", "\\wideha", "\\widehat", "\\tilde", "\\widetilde", "\\bar", "\\overbrace", "\\overbracket", "\\overline", "\\underbrace", "\\underbracket", "\\underline", "\\underbar, "\\ensuremath", "(", ")", "[", "]", "\\{", "\\}", "\\lbrack", "\\lbrace", "\\rbrack", "\\rbrace", "\\llbracket", "\\rrbracket", "\\langle", "\\rangle", "\\floor", "\\rfloor", "\\lceil", "\\rceil", "|", "\\|", "\\lvert", "\\rvert", "\\vert", "\\lVert", "\\rVert", "\\Vert", "\\ulcorner", "\\urcorner", "\\bigg", "\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+, ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\", "\\operatorname" or end of input
[warning] This document format requires a nonempty <title> element.
! Please specify either 'title' or 'pagetitle' in the metadata.
! Falling back to 'NEWS'
 NEWS.md



Any ideas?
Pls fix and resubmit.

Best,
Uwe Ligges

[swihart]

From what I can tell it did not like the $ and the & and the "" around tvcov. So I'll put all $ in , all & in and change the quotes. And resbumit.