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Lectures on Data Management and Data Cleaning for scientists

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Materials for lectures given during my visit to Universidade Federal de Pelotas.

An Introduction to Data Management and Data Cleaning for Scientists

Working with data in a way that is both understandable and reproducible by others is a core competence for research scientists. This four-part lecture series will highlight principals, applications, and free software tools for data management, data processing, and data cleaning in scientific environments. Topics to be discussed include

  • The many faces of information: recognizing data usage and choosing the right structure.
  • Data analyses as a value chain, separating tasks in a clear way.
  • Managing data in organizations and information modeling.
  • Working reproducibly
  • An introduction to systematic data cleaning and data validation for statistics.

The lecture series will be a mix of presentations, quizzes, and some practical assignments. In the later lectures we will do some work with R. No prior knowledge of R is assumed, but attendees who wish to join the assignments should bring a laptop with R preinstalled. Instructions for this will be posted with the lecture materials.


Lectures 2, 3, and 4 will have a hands-on component so make sure you bring a laptop with the necessary software installed (described below).

Lecture Content Materials
1 Structuring data and analyses slides
2 Reproducibility and introduction to R slides 1, slides 2,
3 Data cleaning 1: raw data, data validation slides 1, slides 2, slides 3,
4 Data cleaning 2: fixing errors, missing data slides 1, slides 2, slides 3, slides 4


During some of the lectures we will do some small exercise with R. Here is what you need to install on your laptop to do the exercises.

1. Install R

R is a powerful free and open source language and environment for data analyses and statistics.

Go to and download and install the R version that is suited for your operating system.

2. Install RStudio

RStudio makes it easier to work with R.

Go to, click on Download RStudio, Choose the Free version of RStudio Desktop, and then download and install the RStudio version that is suited for your operating system.

3. Install packages

Copy-paste and execute this code to install all necessary packages for the tutorial (may take a few minutes)

      , "errorlocate"
      , "jsonlite"
      , "lumberjack"
      , "readr"
      , "rspa"
      , "simputation"
      , "stringr"
      , "validate"
      , "XML")
  , dependencies=TRUE)

Some resources

To start learning R, I highly recommend the free online fastR tutorial by Norm Matloff.

I strongly recommend to learn with a group that holds regular meetings. This will give some 'peer pressure' to keep going. It also allows you to discuss and explain to each other items that are difficult at first.

When you learn R it is a good idea to allow yourself to bump into all sorts of applications. One way to do that is to scroll through r-bloggers once a day and read or skim one or two articles collected there. You will get an impression of what people do with R.

  • There are many books with titles like X with R where X can by almost any topic. Once you've worked through the fastR tutorial, you may want to see if there is a book that is interesting for your field of work.
  • The CRAN task views point out packages related to specific views.

After you have familiarized yourself with the basics of R, you may be interested in more advanced ways of doing data manipulation and graphics.

  • If you have large data sets (say, more than one hundred thousand rows) and speed is important for you, I recommend to start learning to work with data.table by Matt Dowle et al..
  • For smaller datasets, I recommend familiarizing yourself with the packages dplyr, tidyr, and ggplot2 for graphics. The R for data science online book by Garret Grolemund and Hadley Wickham is a good place to start with that.

To learn more about reproducible reports with rmarkdown, see the Definitive Guide by Yihui Xie, J. J. Allaire, and Garrett Grolemund.

If you want to learn more about programming in the R language, the free online book the art of R programming by Norm Matloff is a great reference.

Finally, for all things data cleaning, you could consider our book on Statistical data cleaning with applications in R.


Almost all of R is developed by (academic) researchers. Please cite them when you use R or one of its packages. Obtaining citing information is very easy, just type


at the R command-line to get citation information for R. To get the citation for a certain package, just add the name of the package between quotes. For example:



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Lectures on Data Management and Data Cleaning for scientists






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