通过 render_function() 渲染多个参数化的 Rmarkdown 文件失败 [英] Rendering multiple parametrized Rmarkdown files by render_function() fails
问题描述
我编写了一份参数化报告，该报告将为大约 120 个中心以两种不同的语言创建单独的报告.到目前为止，报告是由编织按钮创建的(效果很好).
I wrote a parametrized report that will create individual reporting for ~120 centers in two different languages. The reports are created by the knit-button so far (which works perfectly fine).
灵感来自@djnavarro 的推文(https://twitter.com/djnavarro/status/1101623527787429a>) 我尝试编写一个函数来在一个命令中呈现多个参数化报告，但是，该函数失败并显示错误，如下面的最小表示:
Inspired by @djnavarro's tweet (https://twitter.com/djnavarro/status/1101623527872970754) I tried writing a function to render multiple parametrized reports in one command, however, the function fails with Error as shown in the minimal reprex below:
名为 summary_cyl.Rmd 的 .Rmd 文件
The .Rmd-file called summary_cyl.Rmd
---
output: pdf_document
params:
cyl: 4
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
```
## R Markdown - report for cyl == `r params$cyl`
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
mtcars %>%
filter(cyl == params$cyl) %>%
count
```
带有标题、函数和调用的 .R 文件:
The .R-file with the tibble, the function and the call:
library(tidyverse)
# setting up the tibble with all the param values
param_infos <- tibble(cyl = c(4, 6, 8))
根据 https://bookdown.org/yihui/rmarkdown/params-knit.html#knit-with-custom-parameters:
render_report <- function(file = "summary_cyl.Rmd", cyl) {
rmarkdown::render(file, params = list(
cyl = cyl
), envir = new.env(),
output_file = paste0("summary-", cyl, "-", ".pdf")
)
}
单独调用该函数可以正常工作，它会在所需文件夹中为我创建一个具有所需结果的 PDF:
Calling the function alone works fine, it creates me a PDF with the desired results in the desired folder:
render_report(cyl = 6)
尝试使用@djnavarro 的方法失败:
Trying to use @djnavarro's approach fails:
param_infos %>%
transpose() %>%
walk(render_report)
错误信息是:path.expand(path) 错误:'path' 参数无效
我不知道在哪里找到错误:我以前从未使用过 purrr::walk() 并且我不完全确定 render_function()> 在后台执行..Rmd 文件和 .R 文件都位于同一文件夹中.有没有人知道可能是什么问题?
I don't know where to locate the error: I never used purrr::walk() before and I'm not completely sure about what the render_function() does in the background. Both - the .Rmd-file and the .R file - are located in the same folder. Does anyone have an idea what might be the problem?
我的 session.info:
my session.info:
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.0 readr_1.3.1
[6] tidyr_0.8.2 tibble_2.0.99.9000 ggplot2_3.1.0 tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0.1 cellranger_1.1.0 pillar_1.3.1.9000 compiler_3.5.2 plyr_1.8.4
[6] tools_3.5.2 digest_0.6.18 packrat_0.5.0 lubridate_1.7.4 jsonlite_1.6
[11] evaluate_0.13 nlme_3.1-137 gtable_0.2.0 lattice_0.20-38 pkgconfig_2.0.2
[16] rlang_0.3.1 cli_1.0.1 rstudioapi_0.9.0 yaml_2.2.0 haven_2.1.0
[21] xfun_0.5 withr_2.1.2 xml2_1.2.0 httr_1.4.0 knitr_1.21
[26] hms_0.4.2 generics_0.0.2 grid_3.5.2 tidyselect_0.2.5 glue_1.3.0.9000
[31] R6_2.4.0 fansi_0.4.0 readxl_1.3.0 rmarkdown_1.11 modelr_0.1.4
[36] magrittr_1.5 backports_1.1.3 scales_1.0.0 htmltools_0.3.6 rvest_0.3.2
[41] assertthat_0.2.0 colorspace_1.4-0 tinytex_0.10 utf8_1.1.4 stringi_1.3.1
[46] lazyeval_0.2.1 munsell_0.5.0 broom_0.5.1 crayon_1.3.4
带有两个参数的新测试:
new testing with two params:
---
output: pdf_document
params:
cyl: 4
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
```
## R Markdown - report for cyl == `r params$cyl`
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
mtcars %>%
filter(cyl == params$cyl) %>%
count
```
列表:
library(tidyverse)
# setting up the tibble with all the param values
param_infos <- tibble(cyl = c(4, 6, 8), vs = c(0, 0, 1))
函数:
render_report <- function(file = "summary_cyl.Rmd", cyl, vs) {
rmarkdown::render(file, params = list(
cyl = cyl,
vs = vs
), envir = new.env(),
output_file = paste0("summary-", cyl, vs, "-", ".pdf")
)
}
电话(有效):
render_report(cyl = 4, vs = 1)
什么不起作用但甚至没有给出错误:
what does not work but not even give an error:
param_infos %>%
transpose() %>%
walk(render_report, "summary_cyl.Rmd")
我也尝试过 purrr::walk2() 但没有任何反应 - 我什至没有收到错误消息.
I also tried purrr::walk2() but nothing happens - I dont even get an error.
推荐答案
walk 默认情况下将输入值作为函数的第一个未指定参数传递，因此在您的情况下，它会导致调用:
walk by default passes the input value as the first not specified argument of a function, so in your case it results in call like:
render_report(file = 4)
要避免这种情况，请在 walk 中指定 file 参数:
To avoid this specify file argument inside walk:
param_infos %>%
transpose() %>%
walk(render_report, file = "summary_cyl.Rmd")
注意，现在 file 是 walk 的参数，它将通过 walk 传递给 render_report.
Note, that now file is argument of walk and it will be passed to render_report by walk.
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