[R] rms::latex.anova broken?

Wed Feb 8 19:57:17 CET 2017

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.thorpe at 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.thorpe at utoronto.ca>
> To: R Help Mailing List <r-help at 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.thorpe at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>

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