Tag Archives: Hadley Wickham

A speed test comparison of plyr, data.table, and dplyr

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Guest post by Jake Russ

For a recent project I needed to make a simple sum calculation on a rather large data frame (0.8 GB, 4+ million rows, and ~80,000 groups). As an avid user of Hadley Wickham’s packages, my first thought was to use plyr. However, the job took plyr roughly 13 hours to complete.

plyr is extremely efficient and user friendly for most problems, so it was clear to me that I was using it for something it wasn’t meant to do, but I didn’t know of any alternative screwdrivers to use.

I asked for some help on the manipulator Google group , and their feedback led me to data.table and dplyr, a new, and still in progress, package project by Hadley.

What follows is a speed comparison of these three packages incorporating all the feedback from the manipulator folks. They found it informative, so Tal asked me to write it up as a reproducible example.

Continue reading A speed test comparison of plyr, data.table, and dplyr

Do more with dates and times in R with lubridate 1.1.0

This is a guest post by Garrett Grolemund (mentored by Hadley Wickham)

Lubridate is an R package that makes it easier to work with dates and times. The newest release of lubridate (v 1.1.0) comes with even more tools and some significant changes over past versions. Below is a concise tour of some of the things lubridate can do for you. At the end of this post, I list some of the differences between lubridate (v 0.2.4) and lubridate (v 1.1.0). If you are an old hand at lubridate, please read this section to avoid surprises!

Lubridate was created by Garrett Grolemund and Hadley Wickham.

Parsing dates and times

Getting R to agree that your data contains the dates and times you think it does can be a bit tricky. Lubridate simplifies that. Identify the order in which the year, month, and day appears in your dates. Now arrange “y”, “m”, and “d” in the same order. This is the name of the function in lubridate that will parse your dates. For example,

library(lubridate)
ymd("20110604"); mdy("06-04-2011"); dmy("04/06/2011")
## "2011-06-04 UTC"
## "2011-06-04 UTC"
## "2011-06-04 UTC"

Parsing functions automatically handle a wide variety of formats and separators, which simplifies the parsing process.

If your date includes time information, add h, m, and/or s to the name of the function. ymd_hms() is probably the most common date time format. To read the dates in with a certain time zone, supply the official name of that time zone in the tz argument.

arrive < - ymd_hms("2011-06-04 12:00:00", tz = "Pacific/Auckland")
## "2011-06-04 12:00:00 NZST"
leave <- ymd_hms("2011-08-10 14:00:00", tz = "Pacific/Auckland")
## "2011-08-10 14:00:00 NZST"

Setting and Extracting information

Extract information from date times with the functions second(), minute(), hour(), day(), wday(), yday(), week(), month(), year(), and tz(). You can also use each of these to set (i.e, change) the given information. Notice that this will alter the date time. wday() and month() have an optional label argument, which replaces their numeric output with the name of the weekday or month.

second(arrive)
## 0
second(arrive) < - 25
arrive
## "2011-06-04 12:00:25 NZST"
second(arrive) <- 0
wday(arrive)
## 7
wday(arrive, label = TRUE)
## Sat

Time Zones

There are two very useful things to do with dates and time zones. First, display the same moment in a different time zone. Second, create a new moment by combining a given clock time with a new time zone. These are accomplished by with_tz() and force_tz().

For example, I spent last summer researching in Auckland, New Zealand. I arranged to meet with my advisor, Hadley, over skype at 9:00 in the morning Auckland time. What time was that for Hadley who was back in Houston, TX?

meeting < - ymd_hms("2011-07-01 09:00:00", tz = "Pacific/Auckland")
## "2011-07-01 09:00:00 NZST"
with_tz(meeting, "America/Chicago")
## "2011-06-30 16:00:00 CDT"

So the meetings occurred at 4:00 Hadley’s time (and the day before no less). Of course, this was the same actual moment of time as 9:00 in New Zealand. It just appears to be a different day due to the curvature of the Earth.

What if Hadley made a mistake and signed on at 9:00 his time? What time would it then be my time?

mistake < - force_tz(meeting, "America/Chicago")
## "2011-07-01 09:00:00 CDT"
with_tz(mistake, "Pacific/Auckland")
## "2011-07-02 02:00:00 NZST"

His call would arrive at 2:00 am my time! Luckily he never did that.

Continue reading Do more with dates and times in R with lubridate 1.1.0

Engineering Data Analysis (with R and ggplot2) – a Google Tech Talk given by Hadley Wickham

It appears that just days ago, Google Tech Talk released a new, one hour long, video of a presentation (from June 6, 2011) made by one of R’s community more influential contributors, Hadley Wickham.

This seems to be one of the better talks to send a programmer friend who is interested in getting into R.

Talk abstract

Data analysis, the process of converting data into knowledge, insight and understanding, is a critical part of statistics, but there’s surprisingly little research on it. In this talk I’ll introduce some of my recent work, including a model of data analysis. I’m a passionate advocate of programming that data analysis should be carried out using a programming language, and I’ll justify this by discussing some of the requirement of good data analysis (reproducibility, automation and communication). With these in mind, I’ll introduce you to a powerful set of tools for better understanding data: the statistical programming language R, and the ggplot2 domain specific language (DSL) for visualisation.

The video

More resources

Article about plyr published in JSS, and the citation was added to the new plyr (version 1.5)

The plyr package (by Hadley Wickham) is one of the few R packages for which I can claim to have used for all of my statistical projects. So whenever a new version of plyr comes out I tend to be excited about it (as was when version 1.2 came out with support for parallel processing)

So it is no surprise that the new release of plyr 1.5 got me curious. While going through the news file with the new features and bug fixes, I noticed how (quietly) Hadley has also released (6 days ago) another version of plyr prior to 1.5 which was numbered 1.4.1. That version included only one more function, but a very important one – a new citation reference for when using the plyr package. Here is how to use it:

install.packages("plyr") # so to upgrade to the latest release
citation("plyr")

The output gives both a simple text version as well as a BibTeX entry for LaTeX users. Here it is (notice the download link for yourself to read):

To cite plyr in publications use:
Hadley Wickham (2011). The Split-Apply-Combine Strategy for Data
Analysis. Journal of Statistical Software, 40(1), 1-29. URL
http://www.jstatsoft.org/v40/i01/.

I hope to see more R contributers and users will make use of the ?citation() function in the future.

Call for proposals for writing a book about R (via Chapman & Hall/CRC)

Rob Calver wrote an interesting invitation on the R mailing list today, inviting potential authors to submit their vision of the next great book about R. The announcement originated from the Chapman & Hall/CRC publishing houses, backed up by an impressive team of R celebrities, chosen as the editors of this new R books series, including:

Bellow is the complete announcement:
Continue reading Call for proposals for writing a book about R (via Chapman & Hall/CRC)

Rose plot using Deducers ggplot2 plot builder

The (excellent!) LearnR blog had a post today about making a rose plot in
ggplot2.

Following today’s announcement, by Ian Fellows, regarding the release of the new version of Deducer (0.4) offering a strong support for ggplot2 using a GUI plot builder, Ian also sent an e-mail where he shows how to create a rose plot using the new ggplot2 GUI included in the latest version of Deducer. After the template is made, the plot can be generated with 4 clicks of the mouse.

Here is a video tutorial (Ian published) to show how this can be used:

The generated template file is available at:
http://neolab.stat.ucla.edu/cranstats/rose.ggtmpl

I am excited about the work Ian is doing, and hope to see more people publish use cases with Deducer.

ggplot2 plot builder is now on CRAN! (through Deducer 0.4 GUI for R)

Ian fellows, a hard working contributer to the R community (and a cool guy), has announced today the release of Deducer (0.4) to CRAN (scheduled to update in the next day or so).
This major update also includes the release of a new plug-in package (DeducerExtras), containing additional dialogs and functionality.

Following is the e-mail he sent out with all the details and demo videos.

Continue reading ggplot2 plot builder is now on CRAN! (through Deducer 0.4 GUI for R)

New versions for ggplot2 (0.8.8) and plyr (1.0) were released today

As prolific as the CRAN website is of packages, there are several packages to R that succeeds in standing out for their wide spread use (and quality), Hadley Wickhams ggplot2 and plyr are two such packages.
plyr image
And today (through twitter) Hadley has updates the rest of us with the news:

just released new versions of plyr and ggplot2. source versions available on cran, compiled will follow soon #rstats

Going to the CRAN website shows that plyr has gone through the most major update, with the last update (before the current one) taking place on 2009-06-23. And now, over a year later, we are presented with plyr version 1, which includes New functions, New features some Bug fixes and a much anticipated Speed improvements.
ggplot2, has made a tiny leap from version 0.8.7 to 0.8.8, and was previously last updated on 2010-03-03.

Me, and I am sure many R users are very thankful for the amazing work that Hadley Wickham is doing (both on his code, and with helping other useRs on the help lists). So Hadley, thank you!

Here is the complete change-log list for both packages:
Continue reading New versions for ggplot2 (0.8.8) and plyr (1.0) were released today