447 search results for "knitr"

Getting ecology and evolution journal titles from R

August 31, 2012
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So I want to mine some #altmetrics data for some research I'm thinking about doing. The steps would be: Get journal titles for ecology and evolution journals. Get DOI's for all papers in all the above journal titles. Get altmetrics data on each DO...

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Making matrices with zeros and ones

August 30, 2012
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So I was trying to figure out a fast way to make matrices with randomly allocated 0 or 1 in each cell of the matrix. I reached out on Twitter, and got many responses (thanks tweeps!). Here is the solution I came up with. See if you can tell why it...

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Plotting model fits

August 29, 2012
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Plotting model fits

We all know that it is important to plot your data and explore the data visually to make sure you understand it. The same is true for your model fits. First, you want to make sure that the model is fitting...

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Generate simple HTML slides using deck.js and markdown

August 29, 2012
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RStudio and knitr are an excellent conbination for generating dynamic reports. But in this blog, I will show you how to generate HTML-style presentaion using R only. OK, I confess that we still need something else: deck.js and markdown and R.utils. ...

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Setting Up the Development Version of R

August 28, 2012
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My coworkers at Fred Hutchinson regularly use the development version of R (i.e., R-devel) and have urged me to do the same. This post details how I have set up the development version of R on our Linux server, which I use remotely because it is much faster than my Mac. First, I downloaded the R-devel source into ~/local/, which...

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Custom CSS for HTML generated using RStudio

August 26, 2012
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Custom CSS for HTML generated using RStudio

People have been telling me for a while that the latest version of RStudio, the IDE for R, is a great way to generate reports. I finally got around to trying it out and for once, the hype is justified. Start with this excellent tutorial from Jeremy Anglim. Briefly: the process is not so different

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Open Research Data Processes: KMi Crunch – Hosted RStudio Analytics Environment

August 23, 2012
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Open Research Data Processes: KMi Crunch – Hosted RStudio Analytics Environment

One of the possible barriers to widespread adoption of open notebook science is knowing where to start. Video reports of lab experiments hosted on Youtube can be easily embedded in a hosted WordPress blog; a MediaWiki wiki can be used to provide one page per experiment, with change tracking/history on each page and a shadow

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ggplot2 maps with insets

August 22, 2012
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ggplot2 maps with insets

Here's a quick demo of creating a map with an inset within it using ggplot. The inset is achieved using the gridExtra package. Install libraries, set directory, read file setwd("/Users/ScottMac/Dropbox/CANPOLIN_networks_ms/data") # change ...

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Mid-August flotsam

August 20, 2012
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Mid-August flotsam

Reached mid-semester point, with quite a few new lectures to prepare. Nothing extremely complicated but, as always, the tricky part is finding a way to make it meaningful and memorable. Sometimes, and this is one of those times, I sound … Continue reading →

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read raster data in parallel

August 18, 2012
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read raster data in parallel

Use library(parallel) to read raster data in parallel fashion Use library(parallel) to read raster data in parallel fashion Recently, I have been doing some analysis for a project I am involved in. In particular, I was...

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