在 Knitr Markdown pdf 中使用 R Hmisc summary/summaryM 乳胶命令

Question

我一直在尝试让 Hmisc latex.summary 和 latex.summaryM 示例在使用 RStudio 中的 Knitr 创建的 pdf 文档中工作。但不断收到错误消息。示例数据为：

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')

我想创建一个包含表格的 pdf 文档

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

我正在运行 R 版本 3.5.2 (2018-12-20)、RStudio 1.1.463、Hmisc_4.2-0，并使用 tinytex::install_tinytex() 安装了 tinytex。

经过几个小时的反复试验，我发现了方法，并在下面发布代码以防它对其他人有所帮助。

Answer 1

以下代码适用于我，注意；

使用Hmisc::units 属性时relsize 乳胶包的要求，以防止出现以下failed to compile 错误。

! Undefined control sequence.
<recently read> \smaller

mylatex 函数取自 https://stackoverflow.com/a/31443576/4241780，是删除不需要的输出所必需的。

需要file = ""选项来防止错误

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

使用where = "!htbp" 选项可确保表格保持在它们所在的位置，并且不会浮动到页面顶部（默认为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)

```