I'm trying to extract data from tables inside some pdf reports.
I've seen some examples using either pdftools and similar packages I was successful in getting the text, however, I just want to extract the tables.
Is there a way to use R to recognize and extract only tables?
Awsome question, I wondered about the same thing recently, thanks!
I did it, with tabulizer ‘0.2.2’ as @hrbrmstr also suggests. If you are using R > 3.5.x, I'm providing following solution. Install the three packages in specific order:
# install.packages("rJava")
# library(rJava) # load and attach 'rJava' now
# install.packages("devtools")
# devtools::install_github("ropensci/tabulizer", args="--no-multiarch")
Update: After just testing the approach again, it looks like it's enough to just do install.packages("tabulizer") now. rJava will be installed automatically as a dependency.
Now you are ready to extract tables from your PDF reports.
library(tabulizer)
## load report
l <- "https://sedl.org/afterschool/toolkits/science/pdf/ast_sci_data_tables_sample.pdf"
m <- extract_tables(l, encoding="UTF-8")[[2]] ## comes as a character matrix
## Note: peep into `?extract_tables` for further specs (page, location etc.)!
## use first row as column names
dat <- setnames(type.convert(as.data.frame(m[-1, ]), as.is=TRUE), m[1, ])
## example-specific date conversion
dat$Date <- as.POSIXlt(dat$Date, format="%m/%d/%y")
dat <- within(dat, Date$year <- ifelse(Date$year > 120, Date$year - 100, Date$year))
dat ## voilà
# Speed (mph) Driver Car Engine Date
# 1 407.447 Craig Breedlove Spirit of America GE J47 1963-08-05
# 2 413.199 Tom Green Wingfoot Express WE J46 1964-10-02
# 3 434.220 Art Arfons Green Monster GE J79 1964-10-05
# 4 468.719 Craig Breedlove Spirit of America GE J79 1964-10-13
# 5 526.277 Craig Breedlove Spirit of America GE J79 1965-10-15
# 6 536.712 Art Arfons Green Monster GE J79 1965-10-27
# 7 555.127 Craig Breedlove Spirit of America, Sonic 1 GE J79 1965-11-02
# 8 576.553 Art Arfons Green Monster GE J79 1965-11-07
# 9 600.601 Craig Breedlove Spirit of America, Sonic 1 GE J79 1965-11-15
# 10 622.407 Gary Gabelich Blue Flame Rocket 1970-10-23
# 11 633.468 Richard Noble Thrust 2 RR RG 146 1983-10-04
# 12 763.035 Andy Green Thrust SSC RR Spey 1997-10-15
Hope it works for you.
Limitations: Of course, the table in this example is quite simple and maybe you have to mess around with gsub and this kind of stuff.
I would love to know the answer to this as well. But from my experience, you need to use regular expressions to get the data in a format that you want. You can see the following as an example:
library(pdftools)
dat <- pdftools::pdf_text("https://s3-eu-central-1.amazonaws.com/de-hrzg-khl/kh-ffe/public/artikel-pdfs/Free_PDF/BF_LISTE_20016.pdf")
dat <- paste0(dat, collapse = " ")
pattern <- "Berufsfeuerwehr\\s+Straße(.)*02366.39258"
extract <- regmatches(dat, regexpr(pattern, dat))
extract <- gsub('\n', " ", extract)
strsplit(extract, "\\s{2,}")
From here the data can then be looped to create the table as desired. But as you can see in the link, the PDF is not only a table.
