ropensci/tabulapdf

tabulapdf: Extract tables from PDF documents

tabulapdf provides R bindings to the Tabula java library, which can be used to computationaly extract tables from PDF documents.

Note: tabulapdf is released under the MIT license, as is Tabula itself.

Installation

tabulapdf depends on rJava, which implies a system requirement for Java. This can be frustrating, especially on Windows. The preferred Windows workflow is to use Chocolatey to obtain, configure, and update Java. You need do this before installing rJava or attempting to use tabulapdf. More on this and troubleshooting below.

tabulapdf is available on CRAN, and it can also be installed from rOpenSci’s R-Universe:

# either
install.packages("tabulapdf")

# or
install.packages("tabulapdf", repos = c("https://ropensci.r-universe.dev", "https://cloud.r-project.org"))

To install the latest development version:

if (!require(remotes)) install.packages("remotes")

# on 64-bit Windows
remotes::install_github(c("ropensci/tabulapdf"), INSTALL_opts = "--no-multiarch")

# elsewhere
remotes::install_github(c("ropensci/tabulapdf"))

Code Examples

The main function, extract_tables() provides an R clone of the Tabula command line application:

library(tabulapdf)
f <- system.file("examples", "data.pdf", package = "tabulapdf")
out <- extract_tables(f)
out[[1]]

# # A tibble: 32 × 11
#      mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
#    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#  1  21       6  160    110  3.9   2.62  16.5     0     1     4     4
#  2  21       6  160    110  3.9   2.88  17.0     0     1     4     4
#  3  22.8     4  108     93  3.85  2.32  18.6     1     1     4     1
#  4  21.4     6  258    110  3.08  3.21  19.4     1     0     3     1
#  5  18.7     8  360    175  3.15  3.44  17.0     0     0     3     2
#  6  18.1     6  225    105  2.76  3.46  20.2     1     0     3     1
#  7  14.3     8  360    245  3.21  3.57  15.8     0     0     3     4
#  8  24.4     4  147.    62  3.69  3.19  20       1     0     4     2
#  9  22.8     4  141.    95  3.92  3.15  22.9     1     0     4     2
# 10  19.2     6  168.   123  3.92  3.44  18.3     1     0     4     4
# # ℹ 22 more rows
# # ℹ Use `print(n = ...)` to see more rows

The vignette provides more examples and details on how to use the package.

Installing Java on Windows with Chocolatey

In Power Shell prompt, install Chocolately if you don’t already have it.

Run Get-ExecutionPolicy. If it returns Restricted, then run Set-ExecutionPolicy AllSigned or Set-ExecutionPolicy Bypass -Scope Process. Then, install Chocolatey by running the following command:

Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://community.chocolatey.org/install.ps1'))

Install java using the following command:

choco install openjdk11

You should now be able to safely open R, and use rJava and tabulapdf. From PowerShell, you should see something like this after running java -version:

OpenJDK Runtime Environment (build 11.0.22+7-post-Ubuntu-0ubuntu222.04.1)
OpenJDK 64-Bit Server VM (build 11.0.22+7-post-Ubuntu-0ubuntu222.04.1, mixed mode, sharing)

Troubleshooting

Mac OS and Linux

We tested with OpenJDK version 11. The package is configured to ask for that version of Java. If you have a different version of Java installed, you may need to change the JAVA_HOME environment variable to point to the correct version.

You need to ensure that R has been installed with Java support. This can often be fixed by running R CMD javareconf on the command line (possibly with sudo).

Windows

Make sure you have permission to write to and install packages to your R directory before trying to install the package. This can be changed from “Properties” on the right-click context menu. Alternatively, you can ensure write permission by choosing “Run as administrator” when launching R (again, from the right-click context menu).

Debugging

Load the package like this:

devtools::load_all()
libname = "/home/pacha/R/x86_64-pc-linux-gnu-library/4.4"
pkgname = "tabulapdf"
rJava::.jpackage(pkgname, jars = "*", lib.loc = libname)
rJava::J("java.lang.System")$setProperty("java.awt.headless", "true")

Meta

• Please report any issues or bugs.
• Get citation information for tabulapdf in R doing citation(package = 'tabulapdf')
• License: Apache