Extract Tables from PDFs
tabulizer provides R bindings to the Tabula java library, which can be used to computationaly extract tables from PDF documents.
Note: tabulizer is released under the MIT license, as is Tabula itself.
Installation
tabulizer 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 tabulizer. More on this and troubleshooting below.
To install the latest CRAN version:
install.packages("tabulizer")To install the latest development version:
if (!require("remotes")) {
install.packages("remotes")
}
# on 64-bit Windows
remotes::install_github(c("ropensci/tabulizerjars", "ropensci/tabulizer"), INSTALL_opts = "--no-multiarch")
# elsewhere
remotes::install_github(c("ropensci/tabulizerjars", "ropensci/tabulizer"))Code Examples
The main function, extract_tables() provides an R clone of the Tabula
command line application:
library("tabulizer")
f <- system.file("examples", "data.pdf", package = "tabulizer")
out1 <- extract_tables(f)
str(out1)
## List of 4
## $ : chr [1:32, 1:10] "mpg" "21.0" "21.0" "22.8" ...
## $ : chr [1:7, 1:5] "Sepal.Length " "5.1 " "4.9 " "4.7 " ...
## $ : chr [1:7, 1:6] "" "145 " "146 " "147 " ...
## $ : chr [1:15, 1] "supp" "VC" "VC" "VC" ...By default, it returns the most table-like R structure available: a
matrix. It can also write the tables to disk or attempt to coerce them
to data.frames using the output argument. It is also possible to
select tables from only specified pages using the pages
argument.
out2 <- extract_tables(f, pages = 1, guess = FALSE, output = "data.frame")
str(out2)
## List of 1
## $ :'data.frame': 33 obs. of 13 variables:
## ..$ X : chr [1:33] "Mazda RX4 " "Mazda RX4 Wag " "Datsun 710 " "Hornet 4 Drive " ...
## ..$ mpg : num [1:33] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...
## ..$ cyl : num [1:33] 6 6 4 6 8 6 8 4 4 6 ...
## ..$ X.1 : int [1:33] NA NA NA NA NA NA NA NA NA NA ...
## ..$ disp: num [1:33] 160 160 108 258 360 ...
## ..$ hp : num [1:33] 110 110 93 110 175 105 245 62 95 123 ...
## ..$ drat: num [1:33] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...
## ..$ wt : num [1:33] 2.62 2.88 2.32 3.21 3.44 ...
## ..$ qsec: num [1:33] 16.5 17 18.6 19.4 17 ...
## ..$ vs : num [1:33] 0 0 1 1 0 1 0 1 1 1 ...
## ..$ am : num [1:33] 1 1 1 0 0 0 0 0 0 0 ...
## ..$ gear: num [1:33] 4 4 4 3 3 3 3 4 4 4 ...
## ..$ carb: int [1:33] 4 4 1 1 2 1 4 2 2 4 ...It is also possible to manually specify smaller areas within pages to
look for tables using the area and columns arguments to
extract_tables(). This facilitates extraction from smaller portions of
a page, such as when a table is embeded in a larger section of text or
graphics.
Another function, extract_areas() implements this through an
interactive style in which each page of the PDF is loaded as an R
graphic and the user can use their mouse to specify upper-left and
lower-right bounds of an area. Those areas are then extracted
auto-magically (and the return value is the same as for
extract_tables()). Hereβs a shot of it in action:
locate_areas() handles the area identification process without
performing the extraction, which may be useful as a debugger.
extract_text() simply returns text, possibly separately for each
(specified) page:
out3 <- extract_text(f, page = 3)
cat(out3, sep = "\n")
## len supp dose
## 4.2 VC 0.5
## 11.5 VC 0.5
## 7.3 VC 0.5
## 5.8 VC 0.5
## 6.4 VC 0.5
## 10.0 VC 0.5
## 11.2 VC 0.5
## 11.2 VC 0.5
## 5.2 VC 0.5
## 7.0 VC 0.5
## 16.5 VC 1.0
## 16.5 VC 1.0
## 15.2 VC 1.0
## 17.3 VC 1.0
## 22.5 VC 1.0
## 3Note that for large PDF files, it is possible to run up against Java
memory constraints, leading to a java.lang.OutOfMemoryError: Java heap space error message. Memory can be increased using
options(java.parameters = "-Xmx16000m") set to some reasonable amount
of memory.
Some other utility functions are also provided (and made possible by the Java Apache PDFBox library):
extract_text()converts the text of an entire file or specified pages into an R character vector.split_pdf()andmerge_pdfs()split and merge PDF documents, respectively.extract_metadata()extracts PDF metadata as a list.get_n_pages()determines the number of pages in a document.get_page_dims()determines the width and height of each page in pt (the unit used byareaandcolumnsarguments).make_thumbnails()converts specified pages of a PDF file to image files.
Installing Java on Windows with Chocolatey
In command prompt, install Chocolately if you donβt already have it:
@powershell -NoProfile -ExecutionPolicy Bypass -Command "iex ((new-object net.webclient).DownloadString('https://chocolatey.org/install.ps1'))" && SET PATH=%PATH%;%ALLUSERSPROFILE%\chocolatey\bin
Then, install java using Chocolatelyβs choco install command:
choco install jdk7 -y
You may also need to then set the JAVA_HOME environment variable to
the path to your Java installation (e.g., C:\Program Files\Java\jdk1.8.0_92). This can be done:
- within R using
Sys.setenv(JAVA_HOME = "C:/Program Files/Java/jdk1.8.0_92")(note slashes), or - from command prompt using the
setxcommand:setx JAVA_HOME C:\Program Files\Java\jdk1.8.0_92, or - from PowerShell, using the .NET framework:
[Environment]::SetEnvironmentVariable("JAVA_HOME", "C:\Program Files\Java\jdk1.8.0_92", "User"), or - from the Start Menu, via
Control Panel Β» System Β» Advanced Β» Environment Variables(instructions here).
You should now be able to safely open R, and use rJava and tabulizer.
Note, however, that some users report that rather than setting this
variable, they instead need to delete it (e.g., with
Sys.setenv(JAVA_HOME = "")), so if the above instructions fail, that
is the next step in troubleshooting.
Troubleshooting
Some notes for troubleshooting common installation problems:
- On Mac OS, you may need to install a particular version of Java prior to attempting to install tabulizer.
- On a Unix-like, you need to ensure that R has been installed with
Java support. This can often be fixed by running
R CMD javareconfon the command line (possibly withsudo, etc. depending on your system setup). - On 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 βPropertiesβ on the right-click context menu. Alternatively, you can ensure write permission by choosing βRun as administratorβ when launching R (again, from the right-click context menu).
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
tabulizerin R doingcitation(package = 'tabulizer')
