pandoc's markdown "table" in rmarkdown-2.0 cheat sheet doesn't work with tex markdown

pbm · January 17, 2020, 5:23pm

I have an error in rmarkdown using Pandoc's Markdown "tables" as shown in rmarkdown-2.0 cheat sheet with pdf markdown which doesn't appear html or word markdown. What am I doing wrong? How do I fix it.

my session information is:

sessionInfo()

R version 3.6.2 (2019-12-12)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:

[1] LC_COLLATE=English_United States.1252

[2] LC_CTYPE=English_United States.1252

[3] LC_MONETARY=English_United States.1252

[4] LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:

[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):

[1] compiler_3.6.2 magrittr_1.5 tools_3.6.2 htmltools_0.4.0

[5] yaml_2.2.0 Rcpp_1.0.3 stringi_1.4.5 rmarkdown_2.0

[9] knitr_1.27 stringr_1.4.0 xfun_0.12 digest_0.6.23

[13] rlang_0.4.2 evaluate_0.14

The following code works fine with html, and word markdown:

title: "An All Possible Models Procedure"
author: "Peter B. Mandeville"
date: "`r format(Sys.time(),'%I:%M %p %d %B %Y')`"
output:
pdf_document :
latex_engine : pdflatex #xelatex
html_document:
df_print: paged
toc: yes
toc_float: true
number_sections: true
word_document:
toc: yes

knitr::opts_chunk$set(echo = TRUE)

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)

Including Plots

You can also embed plots, for example:

plot(pressure)

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Abbreviations

This is a test

Abbreviation	Meaning
AIC	Akaike's Information Criterion
B
BIC	Bayesian Information Criterion
Cp	Mallows C_p
CV	Cross-Validation
D	Discrimination index — likelihood ratio χ2 divided by the sample size
Dxy	Dxy:Somers’ rank correlation between predicted probability that Y = 1 vs. the binary Y values. This equals 2(C − 0.5) where C is the “ROC Area or concordance probability
EDA	Exploratory Data Analysis

However, it produces an error in pdf markdown

This is the error message:

output file: test-error2.knit.md

! Missing number, treated as zero.

\protect
l.156 ...nter}\rule{0.5\linewidth}{\linethickness}
\end{center}

Error: LaTeX failed to compile test-error2.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See test-error2.log for more info.
Execution halted

What am I doing wrong? How do I fix it?

Thank you very much.

pbm

technocrat · January 17, 2020, 6:43pm

Here's what I found

---
title: "table"
output:
  pdf_document:
    latex_engine : pdflatex
--- 

"```"{r, echo=FALSE}
knitr::opts_chunk$set(echo = TRUE)
.# kable_table <- knitr::kable(mtcars[1:5,]) # undefined control seq
xtable_table <- xtable::xtable(mtcars[1:5,])
"```"

"`r xtable_table`"

pbm · January 18, 2020, 4:59pm

Thank you technocrat, but the problem persists. I include the same reprex reformatted.

---
title: "test"
author: "pbm"
date: "`r format(Sys.time(),'%I:%M %p %d %B %Y')`"
output: 
  pdf_document :
    latex_engine : pdflatex
  word_document:
    toc: yes
  html_document:
    df_print: paged
    toc: yes
    toc_float: true
    number_sections: true
---

```{r setup,include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

Required Packages

  library(tinytex)
  library(knitr)
  library(kableExtra)
  library(xtable)

Dataframe

Abbreviation <- c("AIC","B","BIC","Cp","CV","D","Dxy","EDA") 
Meaning <- c(
  "Akaike's Information Criterion",
  "",
  "Bayesian Information Criterion",
  "Mallows $C_p$",
  "Cross-Validation",
  "Discrimination index — likelihood ratio χ2 divided by the sample size", 
  "Dxy:Somers’ rank correlation between predicted probability that Y = 1 vs. the binary Y values. This equals $2(C − 0.5)$ where C is the “ROC Area or concordance probability",
  "Exploratory Data Analysis"
)
df <- data.frame(Abbreviation,Meaning)
dim(df)
class(df)
df


## kable

```{r}
kable(df)

Runs with "Run Current Chunk" and "Knit to HTML" but not with "Knit to PDF".

xtable

xtable(df)