在 tabulizer 包中使用 extract_tables() 函数时出现问题：

Question

我正在尝试从 PDF 中抓取表格，但从我的本地目录而不是 web-browser（因为它没有直接在浏览器中打开）。然而，我将 pdf 下载到我的本地目录并尝试从那里只阅读我的表格！[=20=]

当我运行我的代码：

PATH <-"C:\Users\gabrielburcea\Rprojects\Reports_scraping\data_scraped\icnarc_29052020\icnarc_200529.pdf"  
test <- extract_tables(PATH, output = "data.frame", pages = c(10, 11))

我收到以下在 Internet 上找不到的错误：

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", .jfindClass(class),  : 
java.io.FileNotFoundException: /Library/Frameworks/R.framework/Versions/3.6/Resources/library (Is a directory)

有办法解决这个问题吗？

我正在尝试抓取的 .pdf 已从 this website.
下载到我的计算机该报告标题为 ICNARC COVID-19 report 2020-05-29.pdf，可以使用页面 right-side 的 link 下载。

下面是 traceback() 在我收到错误消息后的输出。

   8: stop(list(message = "java.io.FileNotFoundException: /Library/Frameworks/R.framework/Versions/3.6/Resources/library (Is a directory)", 
           call = .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", 
               .jfindClass(class), .jarray(p, "java/lang/Object", dispatch = FALSE), 
               .jarray(pc, "java/lang/Class", dispatch = FALSE), evalString = FALSE, 
               evalArray = FALSE, use.true.class = TRUE), jobj = new("jobjRef", 
               jobj = <pointer: 0x7fd1ba0972b0>, jclass = "java/io/FileNotFoundException")))
    7: .jcheck(silent = FALSE)
    6: .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", .jfindClass(class), 
           .jarray(p, "java/lang/Object", dispatch = FALSE), .jarray(pc, 
               "java/lang/Class", dispatch = FALSE), evalString = FALSE, 
           evalArray = FALSE, use.true.class = TRUE)
    5: .J(Class@name, ...)
    4: new(J("java.io.FileInputStream"), name <- localfile)
    3: new(J("java.io.FileInputStream"), name <- localfile)
    2: load_doc(file, password = password, copy = copy)
    1: extract_tables(PATH, output = "data.frame", pages = c(10, 11))

和sessionInfo() returns这个：

    R version 3.6.1 (2019-07-05)
    Platform: x86_64-apple-darwin15.6.0 (64-bit)
    Running under: macOS Mojave 10.14.6
    
    Matrix products: default
    BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
    
    locale:
    [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.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_0.8.5     purrr_0.3.3     readr_1.3.1     tidyr_1.0.3     tibble_3.0.1   
     [8] ggplot2_3.3.0   tidyverse_1.3.0 tabulizer_0.2.2
    
    loaded via a namespace (and not attached):
    
         [1] Rcpp_1.0.1          cellranger_1.1.0    pillar_1.4.3        compiler_3.6.1      dbplyr_1.4.2       
         [6] tools_3.6.1         lubridate_1.7.4     jsonlite_1.6        lifecycle_0.2.0     gtable_0.3.0       
        [11] nlme_3.1-140        lattice_0.20-38     pkgconfig_2.0.2     png_0.1-7           rlang_0.4.6        
        [16] reprex_0.3.0        cli_2.0.2           DBI_1.0.0           rstudioapi_0.11     haven_2.2.0        
        [21] rJava_0.9-12        withr_2.1.2         xml2_1.3.2          httr_1.4.1          fs_1.3.1           
        [26] hms_0.5.3           generics_0.0.2      vctrs_0.3.0         grid_3.6.1          tidyselect_1.1.0   
        [31] glue_1.3.1          R6_2.4.0            fansi_0.4.0         readxl_1.3.1        modelr_0.1.8       
        [36] magrittr_1.5        scales_1.0.0        tabulizerjars_1.0.1 backports_1.1.4     ellipsis_0.3.0     
        [41] rvest_0.3.5         assertthat_0.2.1    colorspace_1.4-1    stringi_1.4.6       munsell_0.5.0      
        [46] broom_0.5.6         crayon_1.3.4

在此先感谢您的帮助！

Answer 1

如评论中所述，代码在 windows 上运行良好。

library(tabulizer)
link <- "https://www.icnarc.org/DataServices/Attachments/Download/8419d345-c7a1-ea11-9126-00505601089b"
dfr.list <- extract_tables(link, output="data.frame", pages=10:11)

要从列表中取出每个 table，请使用 list2env，您将 env=ironment 设置为 .GlobalEnv，这是您的工作空间 getwd()。事先你需要给未命名的列表名称。

names(dfr.list) <- paste0("dfr", 1:length(dfr.list))  ## give names
list2env(dfr.list, envir=.GlobalEnv)  ## put to environment

ls()
# [1] "dfr.list"    "dfr1"        "dfr2"        "dfr3"        "link"  
# [2] "tables.list"

.pdf 提取通常并不完美，之后我们必须清理数据。要改善结果，请尝试使用 area=、columns= 和 extract_tables 的选项，阅读帮助页面 ?extract_tables，查阅文档。

在 tabulizer 包中使用 extract_tables() 函数时出现问题：

Trouble using extract_tables() function in tabulizer package:

pdf

macos

r

pdf-scraping

web-scraping