In recent versions of rms on CRAN there was a non-downward compatible change. To get latex output for summary, anova, and print on fit objects you leave off file="" (because we're usually using knitr anyway) and use
options(prType='latex') anova(f) # LaTeX output You can use options(prType='html') to get special html output for RMarkdown html reports and html notebooks. There are small changes in Hmisc, e.g., leave off file="" for latex(describe()). Frank ------------------------------ Frank E Harrell Jr Professor and Chairman School of Medicine Department of *Biostatistics* *Vanderbilt University* On Wed, Feb 8, 2017 at 12:19 PM, Kevin E. Thorpe <kevin.tho...@utoronto.ca> wrote: > Hi Frank. > > I sent this to r-help yesterday but have not received any answers from the > list readers. I thought I'd send to you directly to see if you had any > insight. Since I posted this yesterday I have updated my R installation to > the latest patched version and still get the errors. > > I use latex(anova(...)) quite a bit so a fix or workaround would by most > appreciated. > > All the best, > > Kevin > > > -------- Forwarded Message -------- > Subject: rms::latex.anova broken? > Date: Tue, 7 Feb 2017 14:23:46 -0500 > From: Kevin E. Thorpe <kevin.tho...@utoronto.ca> > To: R Help Mailing List <r-h...@stat.math.ethz.ch> > > I am re-running some logistic regression analyses using lrm from the rms > package but latex(anova(...)) appears to be broken on my system. > > Here is some anova() output followed by the latex() error for two models > since the error changes. My sessionInfo() follows the other output. I have > updated all my packages and re-installed Hmisc and rms plus dependencies. > The only thing I haven't done yet is update R completely. Has anyone else > encountered this and know how to solve it? > > anova(full) >> > Wald Statistics Response: id14 > > Factor Chi-Square d.f. P > birthweight_kilo 0.87 1 0.3517 > ageinmonth 4.12 1 0.0423 > zbmi 6.49 1 0.0108 > maxtbf 15.16 1 0.0001 > cowsmilk 6.54 1 0.0106 > Male 1.96 1 0.1611 > multivitamin 0.76 1 0.3819 > bottleuse 0.13 1 0.7194 > preterm 0.50 1 0.4811 > AGEINTRO_cowsmilk 0.06 1 0.8032 > AGEINTRO_complefood 0.61 1 0.4356 > TOTAL 30.49 11 0.0013 > >> latex(anova(full),file="",table.env=FALSE,booktabs=TRUE) >> > Error in ifelse(sn %nin% c("d.f.", "MS", "Partial SS"), math(sn), sn) : > could not find function "math" > >> anova(full.nl) >> > Wald Statistics Response: id14 > > Factor Chi-Square d.f. P > birthweight_kilo 3.68 2 0.1588 > Nonlinear 2.65 1 0.1037 > ageinmonth 16.25 2 0.0003 > Nonlinear 13.45 1 0.0002 > zbmi 4.07 2 0.1310 > Nonlinear 0.23 1 0.6323 > maxtbf 15.81 2 0.0004 > Nonlinear 2.57 1 0.1092 > cowsmilk 3.34 2 0.1880 > Nonlinear 1.16 1 0.2821 > Male 1.21 1 0.2711 > multivitamin 0.57 1 0.4494 > bottleuse 0.06 1 0.8100 > preterm 0.01 1 0.9418 > AGEINTRO_cowsmilk 3.65 2 0.1612 > Nonlinear 3.28 1 0.0700 > AGEINTRO_complefood 5.40 2 0.0671 > Nonlinear 4.00 1 0.0455 > TOTAL NONLINEAR 25.41 7 0.0006 > TOTAL 52.13 18 <.0001 > >> latex(anova(full.nl),file="",table.env=FALSE,booktabs=TRUE) >> > Error in paste0(specs$lspace, specs$italics(substring(rowl, 2)), sep = "") > : > attempt to apply non-function > > sessionInfo() >> > R version 3.2.3 Patched (2016-01-31 r70055) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Slackware 14.2 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rms_5.1-0 SparseM_1.74 Hmisc_4.0-2 ggplot2_2.2.1 > [5] Formula_1.2-1 survival_2.40-1 lattice_0.20-34 knitr_1.15.1 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.9 RColorBrewer_1.1-2 plyr_1.8.4 > [4] base64enc_0.1-3 tools_3.2.3 rpart_4.1-10 > [7] digest_0.6.12 polspline_1.1.12 tibble_1.2 > [10] gtable_0.2.0 htmlTable_1.9 checkmate_1.8.2 > [13] nlme_3.1-131 Matrix_1.2-8 mvtnorm_1.0-5 > [16] gridExtra_2.2.1 stringr_1.1.0 cluster_2.0.5 > [19] htmlwidgets_0.8 MatrixModels_0.4-1 grid_3.2.3 > [22] nnet_7.3-12 data.table_1.10.4 foreign_0.8-67 > [25] multcomp_1.4-6 TH.data_1.0-8 latticeExtra_0.6-28 > [28] magrittr_1.5 codetools_0.2-15 MASS_7.3-45 > [31] scales_0.4.1 backports_1.0.5 htmltools_0.3.5 > [34] splines_3.2.3 assertthat_0.1 colorspace_1.3-2 > [37] quantreg_5.29 sandwich_2.3-4 stringi_1.1.2 > [40] acepack_1.4.1 lazyeval_0.2.0 munsell_0.4.3 > [43] zoo_1.7-14 > > > -- > Kevin E. Thorpe > Head of Biostatistics, Applied Health Research Centre (AHRC) > Li Ka Shing Knowledge Institute of St. Michael's Hospital > Assistant Professor, Dalla Lana School of Public Health > University of Toronto > email: kevin.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.