R Markdown，循环输出测试结果 [英] R Markdown, output test results in loop

问题描述

我正在寻找在 for 循环中生成并带有标题的测试结果的格式良好的降价输出.例如

df <- data.frame(x = rnorm(1000),y = 范数(1000)，z = 范数(1000))for (v in c("y","z")) {cat("##", v, " (模型 0)\n")总结(lm(x~1，df))cat("##", v, " (模型 1)\n")总结(lm(as.formula(paste0(x~1+"，v))，df))}

而输出应该是

y(模型 0)

调用:lm(公式 = x ~ 1, 数据 = df)残差:最小 1Q 中值 3Q 最大值-3.8663 -0.6969 -0.0465 0.6998 3.1648系数:估计标准误差 t 值 Pr(>|t|)(拦截) -0.05267 0.03293 -1.6 0.11剩余标准误差:999 自由度上的 1.041

y(模型 1)

调用:lm(formula = as.formula(paste0("x~1+", v)), data = df)残差:最小 1Q 中值 3Q 最大值-3.8686 -0.6915 -0.0447 0.6921 3.1504系数:估计标准误差 t 值 Pr(>|t|)(拦截) -0.05374 0.03297 -1.630 0.103y -0.02399 0.03189 -0.752 0.452剩余标准误差:998 自由度上的 1.042多个 R 平方:0.0005668，调整后的 R 平方:-0.0004346F 统计量:1 和 998 DF 上的 0.566，p 值:0.452

z(模型 0)

等等...

有几个结果讨论了部分问题，例如

解决方案类型 2

当我们想要在 rmarkdown 本身中自动输出多个模型摘要时，我们可以在 1. 选择块选项 results='asis' 之间进行选择，这将产生代码输出，但例如# Model 1 标题，或 2. 选择不选择它，这会产生 Model 1 但破坏代码格式.解决方案是使用该选项并将其与我们可以paste()与另一个sapply()循环内的内联代码结合起来sapply() 用于模型.

在主要的sapply中，我们应用了@G.Grothendieck's 古老的

I'm looking for a nicely formated markdown output of test results that are produced within a for loop and structured with headings. For example

df <- data.frame(x = rnorm(1000),
           y = rnorm(1000),
           z = rnorm(1000))

for (v in c("y","z")) {
  cat("##", v, " (model 0)\n")
  summary(lm(x~1, df))

  cat("##", v, " (model 1)\n")
  summary(lm(as.formula(paste0("x~1+",v)), df))
}

whereas the output should be

y (model 0)

Call:
lm(formula = x ~ 1, data = df)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.8663 -0.6969 -0.0465  0.6998  3.1648 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.05267    0.03293    -1.6     0.11

Residual standard error: 1.041 on 999 degrees of freedom

y (model 1)

Call:
lm(formula = as.formula(paste0("x~1+", v)), data = df)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.8686 -0.6915 -0.0447  0.6921  3.1504 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.05374    0.03297  -1.630    0.103
y           -0.02399    0.03189  -0.752    0.452

Residual standard error: 1.042 on 998 degrees of freedom
Multiple R-squared:  0.0005668, Adjusted R-squared:  -0.0004346 
F-statistic: 0.566 on 1 and 998 DF,  p-value: 0.452

z (model 0)

and so on...

There are several results discussing parts of the question like here or here suggesting the asis-tag in combination with the cat-statement. This one includes headers.

Closest to me request seems to be this question from two years ago. However, even though highly appreciated, some of suggestions are deprecated like the asis_output or I can't get them to work in general conditions like the formattable suggestion (e.g. withlm-output). I just wonder -- as two years have past since then -- if there is a modern approach that facilitates what I'm looking for.

解决方案

Solution Type 1

You could do a capture.output(cat(.)) approach with some lapply-looping. Send the output to a file and use rmarkdown::render(.).

This is the R code producing a *.pdf.

capture.output(cat("---
title: 'Test Results'
author: 'Tom & co.'
date: '11 10 2019'
output: pdf_document
---\n\n```{r setup, include=FALSE}\n
knitr::opts_chunk$set(echo = TRUE)\n
mtcars <- data.frame(mtcars)\n```\n"), file="_RMD/Tom.Rmd")  # here of course your own data

lapply(seq(mtcars), function(i) 
  capture.output(cat("# Model", i, "\n\n```{r chunk", i, ", comment='', echo=FALSE}\n\
                   print(summary(lm(mpg ~ ", names(mtcars)[i] ,", mtcars)))\n```\n"),
                 file="_RMD/Tom.Rmd", append=TRUE))

rmarkdown::render("_RMD/Tom.Rmd")

Produces:

Solution Type 2

When we want to automate the output of multiple model summaries in the rmarkdown itself, we could chose between 1. selecting chunk option results='asis' which would produce code output but e.g. # Model 1 headlines, or 2. to choose not to select it, which would produce Model 1 but destroys the code formatting. The solution is to use the option and combine it with inline code that we can paste() together with another sapply()-loop within the sapply() for the models.

In the main sapply we apply @G.Grothendieck's venerable solution to nicely substitute the Call: line of the output using do.call("lm", list(.)). We need to wrap an invisible(.) around it to avoid the unnecessary sapply() output [[1]] [[2]]... of the empty lists produced.

I included a ". " into the cat(), because leading white space like ` this` will be rendered to this in lines 6 and 10 of the summary outputs.

This is the rmarkdown script producing a *pdf that can also be executed ordinary line by line:

---
title: "Test results"
author: "Tom & co."
date: "15 10 2019"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Overview

This is an example of an ordinary code block with output that had to be included.

```{r mtcars, fig.width=3, fig.height=3}
head(mtcars)
```
# Test results in detail

The test results follow fully automated in detail.

```{r mtcars2, echo=FALSE, message=FALSE, results="asis"}
invisible(sapply(tail(seq(mtcars), -2), function(i) {
  fo <- reformulate(names(mtcars)[i], response="mpg")
  s <- summary(do.call("lm", list(fo, quote(mtcars))))
  cat("\n## Model", i - 2, "\n")
  sapply(1:19, function(j) 
    cat(paste0("`", ". ", capture.output(s)[j]), "`  \n"))
  cat("  \n")
  }))
```

***Note:*** This is a concluding remark to show that we still can do other stuff afterwards.

Produces:

(Note: Site 3 omitted)

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