ggplot2

R and Google Visualization API: Fish harvests

January 17, 2011 | Scott Chamberlain

I recently gathered fish harvest data from the U.S. National Oceanic and Atmospheric Administarion (NOAA), which I downloaded from Infochimps. The data is fish harvest by weight and value, by species for 21 years, from 1985 to 2005. Here is a link to a google document of the data I used below: ...
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Survival paper (update)

January 13, 2011 | csgillespie

In a recent post, I discussed some  statistical consultancy I was involved with. I was quite proud of the nice ggplot2 graphics I had created. The graphs nicely summarised the main points of the paper: I’ve just had the proofs from the journal, and next to the graphs there ...
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Area plots unmasked

December 15, 2010 | dan

RESULTS OF THE GREAT AREA PLOT QUIZ If you are the type of reader who remembers things from last week, you may remember the great area plot quiz we had running. This week, we are excited to announce that the results are in. The plot above shows answers to the ... [Read more...]

Once again, chart critics and graph gurus welcome

December 10, 2010 | dan

HOW TO DISPLAY A LINE PLOT WITH COUNT INFORMATION? In a previously-mentioned paper Sharad and your DSN editor are writing up, there is the above line plot with points. The area of each point shows the count of observations. It’s done in R with ggplot2 (hooray for Hadley). We ... [Read more...]

New paper: Survival analysis

December 8, 2010 | csgillespie

Each year I try to carry out some statistical consultancy to give me experience in other areas of statistics and also to provide teaching examples. Last Christmas I was approached by a paediatric consultant from the RVI who wanted to carry out prospective survival analysis. The consultant, Bruce  Jaffray, had ... [Read more...]

Analysis of retractions in PubMed

November 30, 2010 | nsaunders

As so often happens these days, a brief post at FriendFeed got me thinking about data analysis. Entitled “So how many retractions are there every year, anyway?”, the post links to this article at Retraction Watch. It discusses ways to estimate the number of retractions and in particular, a recent ... [Read more...]

Findings increasingly novel, scientists say…

October 29, 2010 | nsaunders

…was the tongue-in-cheek title of an image that I posted to Twitpic this week. It shows the usage of the word “novel” in PubMed article titles over time. As someone correctly pointed out at FriendFeed, it needs to be corrected for total publications per year. It was inspired by a ...
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Nightlights: cool data, bad geocoding

October 14, 2010 | Jeffrey Breen

A global source of population density has been on my low-priority wish list for some time, so I was very excited when I found Steve Mosher’s work with the Nighlights data set. “Nightlights” refers to the artificial lights seen from space at night. Astronomers call it “light pollution” which ...
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ClusterProfiles

October 12, 2010 | R on Guangchuang Yu

It is very common to cluster genes based on their expression profiles, and also very common to integrate Gene Ontology to observe the distribution of biological processes, molecular functions and cellular components for a given gene list. But, what if the two in combination? The Gene Ontology distributions across a ... [Read more...]

Plotting Time Series data using ggplot2

September 30, 2010 | Ralph

There are various ways to plot data that is represented by a time series in R. The ggplot2 package has scales that can handle dates reasonably easily. Fast Tube by Casper As an example consider a data set on the number of views of the you tube channel ramstatvid. A ...
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Maps with ggplot2

September 27, 2010 | James

The ggplot2 package offers powerful tools to plot data in R. The plots are designed to comply with the “grammar of graphics” philosophy and can be produced to a publishable level relatively easily. For users wishing to create a good map without too much thought I would recommend this worksheet. ...
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Did what you write drive what I read?

September 16, 2010 | Timothée

GoogleReader allows you to track your activity, by representing the number of news items read and published by day and by hour. I use it quite a lot to stay up to date with the scientific literature (I subscribed to probably over 30 journals) and a bunch of other feeds. Stuff ... [Read more...]

A quick ggplot2 hack (multiple dataframes)

September 9, 2010 | Timothée

I’m starting to get familiar with ggplot2, and I really like it. I just found a very quick way to use several dataframes within the same plot, provided that the dataframes share columns names. One obvious application is the production (…)Read the rest of this entry » [Read more...]

GEO database: curation lagging behind submission?

August 30, 2010 | nsaunders

I was reading an old post that describes GEOmetadb, a downloadable database containing metadata from the GEO database. We had a brief discussion in the comments about the growth in GSE records (user-submitted) versus GDS records (curated datasets) over time. Below, some quick and dirty R code to examine the ... [Read more...]

How Safe is Your Money?

August 24, 2010 | C

The FDIC regularly publishes a Failed Bank List and related statistics.  This post uses data in the original XLS from the FDIC web site which is formatted for human consumption to produce the charts below using R.  Note that 2010 data be...
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