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"
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