excelDataGuide simplifies reading data from spreadsheet data reporting templates (DRT’s) into R.
A data reporting template is an Excel file for standardized reporting and processing of experimental data. Such templates reduce the time spent on data analysis and encourage or force users to provide data in a structured manner so that errors and misinterpretations are minimized. The excelDataGuide package avoids the problem of having to write and maintain code to read data from complicated spreadsheet DRT’s. Furthermore, it provides an infrastructure to check the validity of data, to read data in the correct data types and to wrangle data when appropriate or desired. It thereby facilitates enables the Interoperability, the I of the FAIR principles for DRT’s.
The package provides a simple interface to read data from Excel files and convert them into R objects. We assume that data is organized in three types of data structures: key-value pairs, tabular data and microplateplate-formatted data. The locations of these data structures in the Excel template are provided by a data guide, which is a YAML file, a human- as well as machine-readable structured file format.
You can install the development version of excelDataGuide from GitHub with:
# install.packages("pak")
pak::pak("SystemsBioinformatics/excelDataGuide")The basic usage of the package only requires one command with two file paths: the path to the Excel data file and the path to the data guide file. Here is an example:
library(excelDataGuide)
datafile <- system.file("extdata", "example_data.xlsx", package = "excelDataGuide")
guidefile <- system.file("extdata", "example_guide.yml", package = "excelDataGuide")
data <- read_data(datafile, guidefile)The output of the read_data() function is a list object containing the
data in a structured manner. The structure is determined for a large
part by the design of the data guide.
Provide guide and template structures for data types without upper size limit, like time series with no pre-determined length.