CODEWITHSUNDEEP
rlatexr-markdownknitrhmisc
JWilliman
JWilliman

Reputation: 3883

Using R Hmisc summary/summaryM latex command within Knitr Markdown pdf

I have been trying to get the Hmisc latex.summary and latex.summaryM examples to work within a pdf document created using Knitr in RStudio. But keep getting error messages. The example data is:

options(digits=3)
set.seed(173)
sex <- factor(sample(c("m","f"), 500, rep=TRUE))
country <- factor(sample(c('US', 'Canada'), 500, rep=TRUE))
age <- rnorm(500, 50, 5)
sbp <- rnorm(500, 120, 12)
label(sbp) <- 'Systolic BP'
units(sbp) <- "mmHg"
treatment <- factor(sample(c("Drug","Placebo"), 500, rep=TRUE))
sbp[1] <- NA


# Generate a 3-choice variable; each of 3 variables has 5 possible levels
symp <- c('Headache','Stomach Ache','Hangnail',
          'Muscle Ache','Depressed')
symptom1 <- sample(symp, 500,TRUE)
symptom2 <- sample(symp, 500,TRUE)
symptom3 <- sample(symp, 500,TRUE)
Symptoms <- mChoice(symptom1, symptom2, symptom3, label='Primary Symptoms')

And I want to create a pdf document that contains the tables

tab1 <- summary(sex ~ treatment + Symptoms, fun=table)
tab2 <- summaryM(age + sex + sbp + Symptoms ~ treatment,
          groups='treatment', test=TRUE)

I'm running R version 3.5.2 (2018-12-20), RStudio 1.1.463, Hmisc_4.2-0, and have installed tinytex using tinytex::install_tinytex().

After a few hours trial and error I discovered how, and am posting the code below in case it helps others.

Upvotes: 0

Views: 733

Answers (1)

JWilliman
JWilliman

Reputation: 3883

The following code works for me, note;

Requirement for relsize latex package when Hmisc::units attribute is used to prevent the following failed to compile error.

! Undefined control sequence.
<recently read> \smaller

The mylatex function is taken from https://stackoverflow.com/a/31443576/4241780, and is required for removing unwanted output.

The option file = "" is needed to prevent the error

Error in system(comd, intern = TRUE, wait = TRUE) : 'yap' not found 
Calls: <Anonymous> ... print -> print.latex -> show.latex -> show.dvi -> system

The use of the where = "!htbp" option ensures that the tables remain where they are placed and do not float to the top of the page (by default where = "!tbp") https://tex.stackexchange.com/a/2282. 

---
title: "Untitled"
author: "Author"
date: "15 April 2019"
output: 
  pdf_document: 
     extra_dependencies: ["relsize"]
---

```{r setup, include=FALSE}

library(Hmisc)
library(dplyr)

mylatex <- function (...) {
    o <- capture.output(latex(file = "", where = "!htbp", ...))
    # this will strip /all/ line-only comments; or if you're only
    #  interested in stripping the first such comment you could
    #  adjust accordingly
    o <- grep('^%', o, inv=T, value=T)
    cat(o, sep='\n')
}

```

```{r data}

# As in question above ...

```

Here is the first table

```{r tab1, results = "asis"}

tab1 <- summary(sex ~ treatment + Symptoms, fun=table)

mylatex(tab1)

```

Here is the second table

```{r tab2, results = "asis"}

tab2 <- summaryM(age + sex + sbp + Symptoms ~ treatment, test=TRUE)

mylatex(tab2)

```

Upvotes: 1

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