Read Tabular Data from Diverse Sources and Easily Make Them Tidy
file_name which is a path of a file that contains table(s).
read_cells() in the R-console to see whether support is
present for the file type. If support is present, just run
- Just start with a small file, as heuristic-algorithm are not well-optimized (yet).
- If the target table has numerical values as data and text as their attribute (identifier of the data elements), straight forward method is sufficient in the majority of situations. Otherwise, you may need to utilize other functions.
A Word of Warning :
Many functions in this package are heuristic-algorithm based. Thus,
outcomes may be unexpected. I recommend you to try
read_cells on the
target file. If the outcome is what you are expecting, it is fine. If
not try again with
read_cells(file_name, at_level = "compose"). If
after that also the output is not as expected then other functions are
required to be used. At that time start again with
read_cells(file_name, at_level = "make_cells") and proceed to further
The package provides utilities to read, cells from complex tabular data and heuristic detection based ‘structural assignment’ of those cells to a columnar or tidy format.
Read functionality has the ability to read (in a unified manner) structured, partially structured or unstructured tabular data (usually spreadsheets for public data dissemination and aimed for common human understanding) from various types of documents. The tabular information is read as cells. The ‘structure assignment’ functionality has both supervised and unsupervised way of assigning cells data to columnar/tidy format. Multiple disconnected blocks of tables in a single sheet are also handled appropriately.
These tools are suitable for unattended conversation of (maybe a pile of) messy tables (like government data) into a consumable format(usable for further analysis and data wrangling).
Install the CRAN version:
To install the development version from GitHub you’ll need
package in R (comes with
devtools). Assuming you have
can install this package in R with the following command:
# devtools::install_github is actually remotes::install_github remotes::install_github("r-rudra/tidycells")
To start with
tidycells, I invite you to see
vignette("tidycells-intro") or check out
tidycells-website (to see
vignette you need to install the package with vignette. That can be done
in above command (
remotes::install_github) by specifying
build_vignettes = TRUE. Note that, it might be time consuming. CRAN
version comes with prebuilt-vignette).
Let’s take a quick look at an example data as given in
system.file("extdata", "marks.xlsx", package = "tidycells", mustWork = TRUE)
The data looks like (in excel)
tidycells functions in this data
Read at once
# you should have tidyxl installed system.file("extdata", "marks.xlsx", package = "tidycells", mustWork = TRUE) %>% read_cells()
|Score||Male||School A||Student Name||Utsyo Roy||Sheet1||95|
|Score||Male||School A||Student Name||Nakshatra Gayen||Sheet1||99|
|Score||Female||School A||Student Name||Titas Gupta||Sheet1||89|
|Score||Female||School A||Student Name||Ujjaini Gayen||Sheet1||100|
|Score||Male||School B||Student||Indranil Gayen||Sheet1||70|
|Score||Male||School B||Student||S Gayen||Sheet1||75|
|Score||Female||School B||Student||Sarmistha Senapati||Sheet1||81|
|Score||Female||School B||Student||Shtuti Roy||Sheet1||90|
|Score||Male||School C||Name||I Roy||Sheet1||50|
|Score||Male||School C||Name||S Ghosh||Sheet1||59|
|Score||Female||School C||Name||S Senapati||Sheet1||61|
|Score||Female||School C||Name||U Gupta||Sheet1||38|
read_cells is a set of ordered operations connected
together. The flowchart of
Let’s understand step by step procedures followed by
# if you have tidyxl installed d <- system.file("extdata", "marks.xlsx", package = "tidycells", mustWork = TRUE) %>% read_cells(at_level = "make_cells") %>% .[]
# or you may do d <- system.file("extdata", "marks_cells.rds", package = "tidycells", mustWork = TRUE) %>% readRDS()
d <- numeric_values_classifier(d) da <- analyze_cells(d)
After this you need to run
compose_cells (with argument
print_attribute_overview = TRUE)
dc <- compose_cells(da, print_attribute_overview = TRUE)
If you want a well-aligned columns then you may like to do
# bit tricky and tedious unless you do print_attribute_overview = TRUE in above line dcfine <- dc %>% dplyr::mutate(name = dplyr::case_when( data_block == 1 ~ major_row_left_2_1, data_block == 2 ~ major_col_bottom_1_1, data_block == 3 ~ major_row_left_1_1 ), sex = dplyr::case_when( data_block == 1 ~ major_row_left_1_1, data_block == 2 ~ major_col_bottom_2_1, data_block == 3 ~ minor_row_right_1_1 ), school = dplyr::case_when( data_block == 1 ~ minor_col_top_1_1, data_block == 2 ~ minor_corner_topLeft_1_1, data_block == 3 ~ minor_col_top_1_1 )) %>% dplyr::select(school,sex, name, value)
head(dcfine) looks like
|School A||Male||Utsyo Roy||95|
|School A||Male||Nakshatra Gayen||99|
|School A||Female||Titas Gupta||89|
|School A||Female||Ujjaini Gayen||100|
|School B||Male||Indranil Gayen||70|
|School B||Male||S Gayen||75|
This is still not good right! You had to manually pick some weird column-names and spent some time and energy (when it was evident from data which columns should be aligned with whom).
collate_columns functions does exactly this for you. So instead of
manually picking column-names after compose cells you can simply run
# collate_columns(dc) should be same with # direct read_cells() result except table_tag column collate_columns(dc) %>% head()
|Score||Male||School A||Student Name||Utsyo Roy||95|
|Score||Male||School A||Student Name||Nakshatra Gayen||99|
|Score||Female||School A||Student Name||Titas Gupta||89|
|Score||Female||School A||Student Name||Ujjaini Gayen||100|
|Score||Male||School B||Student||Indranil Gayen||70|
|Score||Male||School B||Student||S Gayen||75|
Looks like staged example! Yes, you are right this is not always
perfect (same is true for
analyze_cells also). However, if the data is
somehow helpful in demystifying underlying columns structure (like this
one), then this will be useful.
read_cells (all functionalities combined),
collate_columns are here to ease your pain in data
wrangling and reading from various sources. It may not be full-proof
solution to all types of tabular data. It is always recommended to
perform these tasks manually whenever expected results are not coming.
Plots and Interactive Modules
The package provides
ggplot based plots and
shiny based interactive
visualisations for understanding how the heuristic is functioning and
also provides object (like
The shiny package is required for interactive modules. Most of the features are self-explanatory and guided.
Check out interactive documentation of any of these functions listed below. All of these functions are available as RStudio Addins.
Here are screenshots of each interactive widgets.
- Plot tune (part of all modules)
visual_crop()for data crop and deletion of sections
visual_va_classify()for interactive VA classification
visual_data_block_inspection()this shows how the heuristic has performed the analysis after
visual_orientation_modification()for modification to heuristic based results
visual_traceback()this is for observing how the original data is composed to form the final output. (
compose_cellsis called internally)
For each of these modules, there is a dynamic plot option available from plotly. If you have that package, the corresponding tab will be activated. Since all of these modules are entirely optional the dependency is kept at tidycells ‘suggests’ level only.
Reference and Related Projects
- tidyxl: Read Untidy Excel Files: Imports non-tabular from Excel files into R. Exposes cell content, position and formatting in a tidy structure for further manipulation. Tokenizes Excel formulas. Supports ‘.xlsx’ and ‘.xlsm’ via the embedded ‘RapidXML’ C++ library http://rapidxml.sourceforge.net. Does not support ‘.xlsb’ or ‘.xls’.
- unpivotr: Unpivot Complex and Irregular Data Layouts Tools for converting data from complex or irregular layouts to a columnar structure. For example, tables with multilevel column or row headers, or spreadsheets. Header and data cells are selected by their contents and position, as well as formatting and comments where available, and are associated with one other by their proximity in given directions. Functions for data frames and HTML tables are provided. Major parts of the package right now fully depend on unpivotr. The tidycells package would have never existed without this wonderful package from Duncan Garmonsway.
- The rsheets project: It hosts several R packages (few of them are in CRAN already) which are in the early stages of importing spreadsheets from Excel and Google Sheets into R. Specifically, have a look at these projects which seems closely related to these projects : jailbreaker, rexcel (README of this project has a wonderful reference for excel integration with R).
- readabs: Download and
Tidy Time Series Data from the Australian Bureau of Statistics The
readabspackage helps you easily download, import, and tidy time series data from the Australian Bureau of Statistics from within R. This saves you time manually downloading and tediously tidying time series data and allows you to spend more time on your analysis.
- ezpickr: Easy Data Import Using GUI File Picker and Seamless Communication Between an Excel and R Gives ability for choosing any rectangular data file using interactive GUI dialog box, and seamlessly manipulating tidy data between an ‘Excel’ window and R session.
- The tidyABS package: The
tidyABSpackage converts ABS excel tables to tidy data frames. It uses rules-of-thumb to determine the structure of excel tables, however it sometimes requires pointers from the user. This package is in early development.
- The hypoparsr package: This package takes a different approach to CSV parsing by creating different parsing hypotheses for a given file and ranking them based on data quality features.
This package incomplete without following packages (apart from the
unpivotr which is the core package on which tidycells depends
largely, as mentioned above). Each of these packages are in suggests
tidycells. (The read_cells basically, performs unification
on several functions from various packages to give you support for
different file types. These are listed below.)
- readr: for csv (in melted format)
- readxl: for reading xls (if xlsx is present by default xlsx will be used for xls)
- xlsx: for reading xls (also it has capabilities to read xlsx)
- tidyxl: really fast library for reading xlsx
- docxtractr : for docx and doc (it has a system level dependency now)
- tabulizer : for pdf
- XML : for html/xml type files
- stringdist :
for enhanced string matching in