rms::latex.anova broken?

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rms::latex.anova broken?

Kevin E. Thorpe
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: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016

______________________________________________
[hidden email] 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.
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Re: rms::latex.anova broken?

Frank Harrell
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 <[hidden email]>
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 <[hidden email]>
> To: R Help Mailing List <[hidden email]>
>
> 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: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.
Frank Harrell
Department of Biostatistics, Vanderbilt University
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Re: rms::latex.anova broken?

Kevin E. Thorpe
In reply to this post by 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: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016

______________________________________________
[hidden email] 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.