excelDataGuide is an R package designed to streamline the process of importing data from spreadsheet data reporting templates (DRTs) into R.
A data reporting template is a standardized spreadsheet file (in either xls or xlsx format) used for reporting and processing experimental data. These templates significantly reduce the time required for data analysis and encourage users to present their data in a structured format, minimizing errors and misinterpretations.
The excelDataGuide package eliminates the need for users to write and maintain complex code for reading data from intricate spreadsheet DRTs. Additionally, it offers a robust framework for validating data, ensuring the correct data types are utilized, and facilitating data wrangling when necessary. This functionality supports Interoperability for DRTs, a key aspect of the FAIR principles.
The package features a user-friendly interface for extracting data from Excel files and converting it into R objects. It accommodates three types of data structures: key-value pairs, tabular data, and microplate-formatted data. The locations of these structures within the Excel template are specified by a data guide, which is a YAML file — a structured format that is both human- and machine-readable.
You can install the development version of excelDataGuide from GitHub with:
# install.packages("pak")
pak::pak("SystemsBioinformatics/excelDataGuide")The basic usage of the package requires only 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 the format of
which is determined for a large part by the design of the data guide.
We want to provide guide and template structures for data types without upper size limit, like time series with no pre-determined length.