[R] rms::latex.anova broken?

[Kevin E. Thorpe]

I figured I should follow-up to say the function is not broken, rather 
it was me not paying close attention to recent release notes.

Frank Harrell kindly informed me (thanks Frank) that with recent 
versions of Hmisc/rms I should use options(prType="latex") for LaTeX 
output to behave correctly.

Kevin

On 02/07/2017 02:23 PM, Kevin E. Thorpe wrote:
> 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