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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
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