RMarkdown 代码块在预览中有效，但在 "build" with bookdown 时无效

Question

我这里有以下 COVID 19 的 Rmarkdown 代码：

library(tidyverse)
# Importiere Johns Hopkins Github data
confirmedraw <- read.csv( "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv")
deathsraw <- read.csv( "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv")
recoveredraw <- read.csv( "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv")
confirmed <- confirmedraw %>% 
  gather(key="date", value="confirmed", -c(Country.Region, Province.State, Lat, Long)) %>%    group_by(Country.Region, date) %>% 
  summarize(confirmed=sum(confirmed))
deaths <- deathsraw %>% 
  gather(key="date", value="deaths", -c(Country.Region, Province.State, Lat, Long)) %>% 
  group_by(Country.Region, date) %>% 
  summarize(deaths=sum(deaths))
recovered <- recoveredraw %>% 
  gather(key="date", value="recovered", -c(Country.Region, Province.State, Lat, Long)) %>% 
  group_by(Country.Region, date) %>% 
  summarize(recovered=sum(recovered))
summary(confirmed)

country <- full_join(confirmed, deaths) %>% 
  full_join(recovered)

这运行在 RStudio 预览和 R 控制台本身中都很好。

但是，如果我尝试使用 bookdown 构建我的书，最后一行中的 full_join() 将失败。我收到错误：

Error: `by` must be supplied when `x` and `y` have no common variables.
ℹ use by = character()` to perform a cross-join.
Backtrace:
     █
  1. ├─rmarkdown::render_site(output_format = "bookdown::gitbook", encoding = "UTF-8")
  2. │ └─generator$render(...)
  3. │   ├─xfun::in_dir(...)
  4. │   └─bookdown:::render_book_script(output_format, envir, quiet)
  5. │     └─bookdown::render_book(...)
  6. │       └─bookdown:::render_cur_session(...)
  7. │         └─rmarkdown::render(main, output_format, ..., clean = clean, envir = envir)
  8. │           └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  9. │             └─knitr:::process_file(text, output)
 10. │               ├─base::withCallingHandlers(...)
 11. │               ├─knitr:::process_group(group)
 12. │               └─knitr:::process_group.block(group)
 13. │                 └─knitr:::call_block(x)
 14. │                   └─knitr:::block_exec(params)
 15. │                     ├─knitr:::in_dir(...)
 16. │                     └─knitr:::evaluate(...)
 17. │                       └─evaluate::evaluate(...)
 18. │                         └─evaluate:::evaluate_call(...)
 19. │                           ├─evaluate:::timing_fn(...)
 20. │                           ├─base:::handle(...)
 21. │                           ├─base::withCallingHandlers(...)
 22. │                           ├─base::withVisible(eval(expr, envir, enclos))
 23. │                           └─base::eval(expr, envir, enclos)
 24. │                             └─base::eval(expr, envir, enclos)
 25. ├─dplyr::full_join(confirmed, deaths) %>% dplyr::full_join(., recovered)
 26. ├─dplyr::full_join(., recovered)
 27. ├─dplyr::full_join(confirmed, deaths)
 28. └─dplyr:::full_join.data.frame(confirmed, deaths)
 29.   └─dplyr:::join_mutate(...)
 30.     └─dplyr:::join_cols(...)
 31.       └─dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)

如何使用 bookdown 将我的代码更改为运行？

Answer 1

我在进行故障排除时确实遇到了类似的错误。

这是由运行每个 command/chunk 单独解决的，直到它完成，我确实遇到间歇性执行问题，有时我会出错，有时运行成功，我只是重新运行直到完成。

为了更好地帮助我理解，您的 YAML 是什么样的？你究竟是如何构建这本书的？是 gitbook 吗？

我找到解决方案的方法是对簿记有一点了解。我有 2 个文件，index.Rmd 和 01-covid19.Rmd，index.Rmd 是空的，只有书的 YAML。在 01-covid19.Rmd 我粘贴了你的代码

index.Rmd

--- 
title: ""
author: ""
date: "`r Sys.Date()`"
output: bookdown::gitbook
site: bookdown::bookdown_site
description: ""
---

# Introduction {-}

01-covid19.Rmd

# Covid19

```{r}
library(tidyverse)
# Importiere Johns Hopkins Github data
confirmedraw <- read.csv( "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_cov    id19_confirmed_global.csv")
deathsraw <- read.csv( "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid1    9_deaths_global.csv")
recoveredraw <- read.csv( "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_cov    id19_recovered_global.csv")
confirmed <- confirmedraw %>% 
  gather(key="date", value="confirmed", -c(Country.Region, Province.State, Lat, Long)) %>%    group_by(Country.Region, date) %>% 
  summarize(confirmed=sum(confirmed))
deaths <- deathsraw %>% 
  gather(key="date", value="deaths", -c(Country.Region, Province.State, Lat, Long)) %>% 
  group_by(Country.Region, date) %>% 
  summarize(deaths=sum(deaths))
recovered <- recoveredraw %>% 
  gather(key="date", value="recovered", -c(Country.Region, Province.State, Lat, Long)) %>% 
  group_by(Country.Region, date) %>% 
  summarize(recovered=sum(recovered))
summary(confirmed)

country <- full_join(confirmed, deaths) %>% 
  full_join(recovered)

country
```

最终呈现为 Rmarkdown Bookdown 输出，R 代码位于 01 位置。这两个文件必须与其他 Bookdown 依赖项位于同一目录中，还请尝试创建一个新的 R 项目。告诉我，谢谢。

RMarkdown 代码块在预览中有效，但在 "build" with bookdown 时无效

RMarkdown code chunk works in preview but not when "build" with bookdown

r-markdown

bookdown