Monthly Archives: July 2015

ggtree annotate phylogenetic tree with local images

July 31, 2015
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ggtree annotate phylogenetic tree with local images

In ggtree, we provide a function annotation_image for annotating phylogenetic tree with images. To demonstrate the usage, I created a tree view from a random tree as shown below: set.seed(2015-08-01) p <- ggtree(rtree(10)) + xlim(0, 5)+ ylim(0, 11) We need a data.frame that contains information of taxa labels and image paths. Here I created such a data.frame containing image files downloaded from phylopic. > img_info ...

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Via Plumbr, R can haz Flask

July 31, 2015
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Via Plumbr, R can haz Flask

Turning a simple machine learning model in R into an api just became a whole lot easier. Embarrisingly easy actually, thanks to a lovely package called plumber. Install Assuming that you have devtools installed, all you need to do is type the following: library(devtools) install_github("trestletech/plumber") library(plumber) With this installed, let's create a file that creates an endpoint! Example...

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Streamgraphs in R

July 31, 2015
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Streamgraphs in R

It's not easy to visualize a quantity that varies over time and which is composed of more than two subsegments. Take, for example, this stacked bar chart of religious affiliation of the Australian population, by time: While it's easy to see the how the share of Anglicans (at the bottom of the chart) has changed over time, it's much...

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Rendering LaTeX Math Equations in GitHub Markdown

July 31, 2015
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Rendering LaTeX Math Equations in GitHub Markdown

The Problem: GitHub README.md won't render LaTeX I have many times wondered about getting LaTeX math to render in a README file on GitHub. Apparently, many others ( 1, 2, 3 ), have asked the same question. The common answers are: It cannot (and in some cases, shouldn't) be done. GitHub parsing is done by

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New Zealand Data & APIs on GitHub

July 31, 2015
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New Zealand Data & APIs on GitHub

New data listing for New Zealand Wellington’s PrototypeAlex has created a new GitHub repository aiming to list data about New Zealand. My first reaction was “hmm, will this be an improvement?” After all, we already have data.govt.nz which is meant to be the definitive aggregator of government datasets; we have the Figure.NZ (recently rebranded from “Wiki...

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How to Design Quant Trading Strategies Using R?

July 30, 2015
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How to Design Quant Trading Strategies Using R?

This blog covers in brief the concept of strategy back-testing using R. Before dwelling into the trading jargons using R let us spend some time understanding what R is. R is an open source. There are more than 4000 add on packages,18000 plus members of LinkedIn’s group and close to 80 R Meetup groups currently... The post

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Building a user interface for spatstat

July 30, 2015
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Building a user interface for spatstat

Contents Introduction Get and run it! Roadmap Introduction RStudio developed shiny, an R package that, quoting from their website, “makes it super simple for R users like you to turn analyses into interactive web applications that anyone can use”. It leverages the power of R and its vast collection of packages to allow users to efficiently perform...

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Estimating arrival times of people in a shop using R

July 30, 2015
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Estimating arrival times of people in a shop using R

Since the first time I was taught the Poisson and Exponential distributions I have been wondering how to apply them to model a real world scenario such as arrivals of people in a shop. Last week I was in a big shopping center and I thought that was the perfect time to gather some data so I chose a...

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15 Questions All R Users Have About Plots

July 30, 2015
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15 Questions All R Users Have About Plots

R allows you to create different plot types, ranging from the basic graph types like density plots, dot plots, bar charts, line charts, pie charts, boxplots and scatter plots, to the more statistically complex types of graphs such as probability plots, mosaic plots and correlograms. In addition, R is pretty known for its data visualization The post

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MRAN’s Packages Spotlight

July 30, 2015
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MRAN’s Packages Spotlight

by Joseph Rickert New R packages just keep coming. The following plot, constructed with information from the monthly files on Dirk Eddelbuettel's CRANberries site, shows a plot of the number of new packages released to CRAN between January 1, 2013 and July 27, 2015 by month (not quite 31 months). This is amazing growth! The mean rate is about...

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