One of the reasons that R has so much functionality is that people have incorporated a lot of academic code written in C, C++, Fortran and Java into various packages. Libraries written in these languages are often both robust and fast. If you are using R to support people in a particular field, you may be called upon to incorporate some outside code into your R environment. Unfortunately, much of the documentation on how to do this is written at a very high level. In this post we will distil some of the available information on calling C code from R into three “Hello World” examples.Continue reading
Ten UNIX commands every data manager should know
Working with data from varied sources can be frustrating — some data will be in CSV format; some in XML; some available as HTML pages; other data as relational databases or MS Excel spreadsheets.
This post will cover the UNIX tools that every data manager needs to be familiar with in order to work with varied data sources.Continue reading
Data Structures – Tabular vs. Relational
With enough effort it is possible to fit a square peg into a round hole. But we have all learned — sometimes more than once — that it is much easier if peg and hole have the same shape.Continue reading
Logging and error handling in operational systems
Operational systems, by definition, need to work without human input. Systems are considered “operational” after they have ben thoroughly tested and shown to work properly with a variety of input.
However, no software is perfect and no real-world system operates with 100% availability or 100% consistent input. Things occasionally go wrong – perhaps intermittently. In a situation with occasional failures it is vitally important to have good logging and error handling. The MazamaCoreUtils R package helps with these tasks.Continue reading
Despite what they say, size does matter.
Successful data management is all about finding the proper tools and formats for dealing with your data. There is no one-size-fits-all solution. The very first question you should be asking yourself is: “How much data are we talking about?”Continue reading
Best Best Practices Ever!
Every once in a while I read something that is so insightful, so clearly written and so well documented that it enters my own personal pantheon of “Best Ever” documents. I recently added a new, simply divine article titled Best Practices for Scientific Computing and hope that everyone reading this post also takes the time to read that article. I’m including the outline here only to encourage you to read the article in it’s entirety. It is extremely well written.Continue reading
When k-means clustering fails
Letting the computer automatically find groupings in data is incredibly powerful and is at the heart of “data mining” and “machine learning”. One of the most widely used methods for clustering data is k-means clustering. Unfortunately, k-means clustering can fail spectacularly as in the example below.Continue reading
Optimizing Data Access – Know your Hardware
The Library of Congress has a lot of information — hundreds of millions of pages of books and manuscripts. But no one has ever suggested that we store all of that information in a single, billion-page book. Instead, individual books are stored on shelves in stacks in rooms according to an organized system. Managing large datasets is just the same: data should exist in manageable sized files stored in hierarchically organized directories. Unfortunately, many people working with large datasets try to do just the opposite. This post describes how converting thirty 200Gb files into three million 200Kb files reduced data access times from several hours to under a second.Continue reading
Data Management Questionnaire
Sometimes merely filling out a questionnaire can cause you to think about problems in a new way. When asked to answer a question that has never occurred to you before, you may find yourself reevaluating some of your core assumptions — assumptions you may not have known you had. That is the power of asking questions. Our data management questionnaire poses questions in 12 categories that will help you figure out what you need, what you want, and perhaps give you a hint of how to get there.Continue reading
Standard Country Names
What’s in a name? That which we call a rose
By any other name would smell as sweet.
Ahhh love. Juliet speaks lovely poetry but we learn, as the story unfolds, that names and the identification they impart are in fact extremely important. This is no less true in data management where country names are anything but standardized.Continue reading