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README.Rmd
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README.Rmd
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---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "##"
)
```
# tabulapdf: Extract tables from PDF documents <img src="man/figures/logo.svg" align="right" height="139" alt="" />
[](https://github.com/ropensci/tabulapdf/actions/workflows/R-CMD-check.yaml)
[](https://github.com/ropensci/software-review/issues/42)
[](https://buymeacoffee.com/pacha)
**tabulapdf** provides R bindings to the [Tabula java library](https://github.com/tabulapdf/tabula-java/), 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](https://cran.r-project.org/package=rJava), which
implies a system requirement for Java. This can be frustrating, especially on
Windows. The preferred Windows workflow is to use
[Chocolatey](https://chocolatey.org/) to obtain, configure, and update Java.
You need do this before installing rJava or attempting to use tabulapdf. More on
[this](#installing-java-on-windows-with-chocolatey) and
[troubleshooting](#troubleshooting) below.
tabulapdf is not available on CRAN, but it can be installed from rOpenSci's
R-Universe:
```r
install.packages("tabulapdf", repos = c("https://ropensci.r-universe.dev", "https://cloud.r-project.org"))
```
To install the latest development version:
```r
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:
```r
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:
```r
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](https://github.com/ropensci/tabulapdf/issues).
* Get citation information for `tabulapdf` in R doing `citation(package = 'tabulapdf')`
* License: Apache
[](https://ropensci.org)