knitr 模板 - 动态块问题 [英] knitr templating - Dynamic chunks issue

问题描述

以下代码是针对我遇到的问题的非常简化的 MRE.我试图避免使用 R 模板包，例如 brew，而只使用 knit_expand() 来实现我的目标.问题有两个方面:

The following code is a very simplified MRE for an issue I'm experiencing. I'm trying to avoid R template packages, such as brew, and only use knit_expand() to achieve my goals. The issue is twofold:

1. 不会解析生成的块(这在我的实际代码中不会发生，但会发生在 MRE 中)
2. 代替 LaTeX \includegraphics，knitr(或 rmarkdown，或 pandoc)生成用于插入的 RMarkdown 语法数字 (![]).

1. generated chunks don't get parsed (this is not happening in my real code, but happens in MRE)
2. instead of LaTeX \includegraphics, knitr (or rmarkdown, or pandoc) generates RMarkdown syntax for inserting figures (![]).

关于前者，我有一种感觉，这可能与我对 get() 或其参数的错误使用有关.您的建议将不胜感激.MRE 如下('.Rmd' 文件):

In regard to the former, I have a feeling that it might be related to my incorrect use of get() or its argument. Your advice would be very much appreciated. The MRE follows ('.Rmd' document):

---
title: "MRE: a dynamic chunk issue"
author: "Aleksandr Blekh"
output:
  pdf_document:
    fig_caption: yes
    keep_tex: yes
    highlight: NULL
---

```{r, echo=FALSE, include=FALSE}
library(knitr)

opts_knit$set(progress = F, verbose = F)
opts_chunk$set(comment=NA, warning=FALSE, message=FALSE, echo=FALSE, tidy=FALSE)
```

```{r Preparation, results='hide'}

g1 <- plot(cars)
g2 <- plot(iris$Sepal.Length)

myPlots <- list(g1, g2)

bcRefStr <- list("objType" = "fig",
                 "objs" = c("g1", "g2"),
                 "str" = "Plots \\ref{fig:g1} and \\ref{fig:g2}")
```

```{r DynamicChunk, include=FALSE}
chunkName <- "{{name}}"
chunkHeader <- paste0("```{r ", chunkName, ", ")
chunkOptions <- "include=TRUE, results='asis', fig.height=4, fig.width=4, fig.cap='{{name}}'"
chunkHeaderFull <- paste0(chunkHeader, chunkOptions, "}")
chunkBody <- "print(get('{{name}}'))"

latexFigEnvBegin <- "cat('\\\\begin{figure}')"
latexFigEnvEnd <- "cat('\\\\end{figure}')"
latexFigCenter <- "cat('\\\\centering')"

latexObjLabel <- paste0("cat('\\\\caption{\\\\ ", "{{name}}\\\\label{", bcRefStr$objType, ":{{name}}", "}}')")

chunkText <- c(chunkHeaderFull,
               latexFigEnvBegin, latexFigCenter,
               chunkBody,
               latexObjLabel, latexFigEnvEnd,
               "```", "\n")

figReportParts <- lapply(bcRefStr$objs, function (x) knit_expand(text = chunkText, name = x))
```

`r knit(text = unlist(figReportParts))`

推荐答案

最后，我找到了导致问题的原因.第一部分很简单.由于建议的简化，我已从 ggplot2 切换到标准的 R 图形函数.问题在于 plot() 似乎没有返回值/对象，所以这就是为什么在输出中看到的是 NULL，而不是图中.

Finally, I've figured out what was causing the issue. The first part was easy. Due to suggested simplification, I've switched from ggplot2 to standard R graphics functions. The problem is that it appears that plot() doesn't return a value/object, so that's why NULLs has been seen in the output, instead of plots.

第二部分有点棘手，但对相关问题的回答(https://stackoverflow.com/a/24087398/2872891) 阐明了情况.根据这些信息，我能够相应地修改我的 MRE，结果文档显示正确的内容(同样适用于生成的 LaTeX 源，它似乎已准备好进行交叉引用).

The second part was a bit more tricky, but an answer to a related question (https://stackoverflow.com/a/24087398/2872891) clarified the situation. Based on that information, I was able modify my MRE correspondingly and the resulting document appears with correct content (same applies to the generated LaTeX source, which seems to be ready for cross-referencing).

我正在考虑将此代码转换为更通用的函数，以便在我的项目中重用，如果时间允许的话[应该不会花很长时间](@Yihui，这对 knitr 有用吗?项目?).感谢所有花时间分析、帮助或只是阅读这个问题的人.我认为 knitr 的文档应该更清楚地说明与从 RMarkdown 源生成 PDF 文档相关的问题.我针对 MRE 的解决方案如下.

I'm thinking about converting this code into a more generic function for reuse across my project, if time will permit [shouldn't take long] (@Yihui, could this be useful for knitr project?). Thanks to everyone who took time to analyze, help or just read this question. I think that knitr's documentation should be more clear on issues, related to producing PDF documents from RMarkdown source. My solution for the MRE follows.

---
title: "MRE: a dynamic chunk issue"
author: "Aleksandr Blekh"
output:
  pdf_document:
    fig_caption: yes
    keep_tex: yes
    highlight: NULL
---

```{r, echo=FALSE, include=FALSE}
library(knitr)
library(ggplot2)

opts_knit$set(progress = F, verbose = F)
opts_chunk$set(comment=NA, warning=FALSE, message=FALSE, echo=FALSE, tidy=FALSE)
```

```{r Preparation, results='hide'}
library(ggplot2)

g1 <- qplot(mpg, wt, data=mtcars)
g2 <- qplot(mpg, hp, data=mtcars)

myPlots <- list(g1, g2)

bcRefStr <- list("objType" = "fig",
                 "objs" = c("g1", "g2"),
                 "str" = "Plots \\ref{fig:g1} and \\ref{fig:g2}")
```

```{r DynamicChunk, include=FALSE}

latexObjLabel <- paste0("{{name}}\\\\label{", bcRefStr$objType, ":{{name}}", "}")

chunkName <- "{{name}}"
chunkHeader <- paste0("```{r ", chunkName, ", ")
chunkOptions <- paste0("include=TRUE, results='asis', fig.height=4, fig.width=4, fig.cap='", latexObjLabel, "'")
chunkHeaderFull <- paste0(chunkHeader, chunkOptions, "}")
chunkBody <- "print(get('{{name}}'))"

chunkText <- c(chunkHeaderFull,
               chunkBody,
               "```", "\n")

figReportParts <- lapply(bcRefStr$objs, function (x) knit_expand(text = chunkText, name = x))
```

`r knit(text = unlist(figReportParts))`

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