Reproducible research in data science involves making research findings, including
data analysis and code, publicly accessible so others can verify and build upon
them. This ensures transparency and allows for scrutiny of the process and results,
promoting trust in scientific claims.
Key aspects of reproducible research in data science:
Transparency:
Sharing data, code, and analysis methods allows others to understand how results
were obtained.
Verification:
Others can attempt to reproduce the analysis using the provided materials to
confirm the original findings.
Building upon existing work:
A reproducible research workflow allows researchers to easily use and extend the
work of others, accelerating scientific progress.
Trust in science:
Reproducibility underpins trust in science by enabling others to verify the results
and identify potential errors or biases.
Increased accuracy:
Reproducible research increases the likelihood that the research is correct and
reliable, as it allows for more rigorous scrutiny.
Tools and techniques for reproducible research:
Version control:
Using tools like Git to track changes to code and data throughout the project,
allowing for easy rollback to previous versions.
Dynamic document generation:
Using tools like R Markdown to combine code, data, and plain language
explanations into a single document that can be easily executed and updated.
Containerization:
Using Docker to package the environment, including software and dependencies,
so that the code can be run consistently across different systems.
Data management and sharing:
Using tools and platforms to store and share data securely and efficiently, while
adhering to ethical and legal guidelines.
Workflow management:
Using tools and platforms to manage the different steps in the analysis pipeline,
from data collection to model training and evaluation.
Why is reproducible research important in data science?
Complex data analyses:
Data science often involves complex data analyses and models, making
reproducibility essential for verifying the results and identifying potential errors.
Sharing and collaboration:
Data science research is often collaborative, and reproducibility facilitates the
sharing and reuse of data, code, and analysis methods.
Building trust:
Reproducibility builds trust in data science research by allowing others to verify
the results and identify potential biases.
Improving scientific progress:
Reproducibility accelerates scientific progress by allowing researchers to build
upon the work of others and to quickly identify and correct errors.
Tools behind reporting modern data analyses in reproducible research.
Reproducible research in data science relies on a combination of tools and
practices, including programming languages (like R or Python), version control
systems (like Git), and platforms for collaborative coding and sharing (like
GitHub). Tools like Jupyter notebooks and R Markdown allow for combining
code, data, and results in a dynamic format, while platforms like BinderHub
facilitate sharing of entire computing environments.
Here's a more detailed breakdown:
Programming Languages:
R and Python: These are the dominant languages in data science and offer
extensive packages for statistical analysis, data manipulation, and machine
learning.
Version Control:
Git:
A distributed version control system that allows tracking changes to code over
time and collaborating with others.
GitHub:
Platforms that host Git repositories, providing a centralized location for storing
and sharing code.
Collaborative Coding and Sharing:
Jupyter Notebooks:
Interactive computing environments that allow combining code, text, and
visualizations in a single document.
R Markdown:
A tool for creating reproducible reports and documents that combine R code, text,
and visualizations.
To write a documemt using R Markdown.
R Markdown is a file format for making dynamic and static documents with R.
You can create an R Markdown file to save, organize and document your analysis
using code chunks and comments. It is important to create an R Markdown file to
have good communication between your team about analysis, you can create an R
Markdown file to summarize your visuals to stakeholders. R Markdown documents
are written in Markdown. Markdown is a syntax for formatting plain text files. It is
also used to create rich format text in your document.
Why use an R Markdown document?
Documenting your work makes it easy to share your analysis with anyone, R
Markdown lets you create a record of your analysis, conclusions, and decisions in a
document. It binds together your code and your report so you can share every step
of your analysis. R Markdown documents will help stakeholders and team
members understand what you did in your analysis to reach your conclusions. We
also have an interactive option called R Notebook that lets the user run their code
and show the graphs and charts that visualize the code. R Markdown lets you
convert files into other formats like HTML, PDF, Word documents, slide
presentations, and dashboards also.
Creating an R Markdown document
As we know R Markdown is a great tool for documenting your analysis, it is very
easy to create and run R Markdown.
To create R Markdown Open R Studios in the menu bar, and click File -> New File
-> R Markdown...
A window will open like this after clicking R Markdown...
In the dialog box that opens, add the name of the document in the title box. A name
is something that uniquely identifies your document and a name will help you
easily recognize what your analysis is about. For example, we use the penguin
dataset in this article so, I named my R Markdown "Penguins_Plots".
In the author, box enters the author's name.
Next, we can choose our output format. For now, leave the file in the default
output format which is HTML.
In the presentation, we can create a slide show of the R Markdown file.
In Shiny, we can create a shiny document and a Shiny presentation.
In From Template, we can use predefined te
Code Chunk
The next part with gray background in R Markdown is the code chunk. We can run
code chunks at any time.
code chunk
RStudio automatically adds to the notebook with this formatted default code
chunk. Code chunk starts with delimiter ` ` ` {r} and ends with ` ` `
R Markdown can run in two ways:
Run rmarkdown::render("<file_path>"")
Click the knit HTML at the top of the document
The knit drop-down menu includes three main options: HTML, PDF, and Word
document. You can use knit to convert your file to any of these types.
Knitr
A knitR function takes an input file, extracts the R code from it and returns an
output file. It is a dynamic report generalization package. Knitr integrates R code
in various documents like the HTML files, Markdown, Latex etc. An example of
kable() is taken, which uses the knitr package in R. This recipe demonstrates an
example on knitr package.
Step 1 - Install necessary library
install.packages('knitr')
library("knitr")
Step 2 - kable() in R
kable() is a function of knitr package, used for generating tables in R.
data = dimnames(iris3) # using the iris dataset head(data)
Step 3 - Converting into html format
html_file = kable(data,format="html") html_file # converting into html format
Step 4 - Converting into table format
tab = kable(head(data), format = "simple", row.names = TRUE) # converting to
simple table format tab
