# July 2015

### ggtree annotate phylogenetic tree with local images

July 31, 2015 |

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 ...

### An Introduction to Plotly for Patent Analytics

July 31, 2015 |

In this article we provide a quick introduction to the online graphing service Plotly to create graphics for use in patent analysis. Plotly is an online graphing service that allows you to import excel, text and other files for visualisation. It also has API services for R, Python, MATLAB and ...

### Via Plumbr, R can haz Flask

July 31, 2015 |

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(... [Read more...]

### Streamgraphs in R

July 31, 2015 |

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 ... [Read more...]

### Rendering LaTeX Math Equations in GitHub Markdown

July 31, 2015 |

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 ... [Read more...]

### New Zealand Data & APIs on GitHub

July 31, 2015 |

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 ... [Read more...]

### How to Design Quant Trading Strategies Using R?

July 30, 2015 |

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 ... [Read more...]

### Building a user interface for spatstat

July 30, 2015 |

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 ... [Read more...]

### Estimating arrival times of people in a shop using R

July 30, 2015 |

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 ...

### 15 Questions All R Users Have About Plots

July 30, 2015 |

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 ... [Read more...]

### MRAN’s Packages Spotlight

July 30, 2015 |

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 ... [Read more...]

### The little mixed model that could, but shouldn’t be used to score surgical performance

July 30, 2015 |

The Surgeon Scorecard Two weeks ago, the world of medical journalism was rocked by the public release of ProPublica’s Surgeon Scorecard. In this project ProPublica “calculated death and complication rates for surgeons performing one of eight elective procedures in Medicare, carefully adjusting for differences in patient health, age and ...

### Empirical bias analysis of random effects predictions in linear and logistic mixed model regression

July 30, 2015 |

In the first technical post in this series, I conducted a numerical investigation of the biasedness of random effect predictions in generalized linear mixed models (GLMM), such as the ones used in the Surgeon Scorecard, I decided to undertake two explorations: firstly, the behavior of these estimates as more and ...

### #rstats Make arrays into vectors before running table

July 29, 2015 |

Setup of Problem While working with nifti objects from the oro.nifti, I tried to table the values of the image. The table took a long time to compute. I thought this was due to the added information about a medical image, but I found that the same sluggishness happened ... [Read more...]

### R Oddities: Strings in DataFrames

July 29, 2015 |

Have you ever read a file into R and then encountered strange problems filtering and sorting because the strings were converted to factors?  For instance, you might think the two data frames, df and df2 below are contain the same data__ df-data____ write.csv(df, 'df.csv')__ df2-read__But ... [Read more...]

### R Oddities: Strings in DataFrames

July 29, 2015 |

Have you ever read a file into R and then encountered strange problems filtering and sorting because the strings were converted to factors?  For instance, you might think the two data frames, df and df2 below are contain the same data__ df-data____ write.csv(df, 'df.csv')__ df2-read__But ... [Read more...]

### But I Don’t Want to Be a Statistician!

July 29, 2015 |

"For a long time I have thought I was a statistician.... But as I have watched mathematical statistics evolve, I have had cause to wonder and to doubt.... All in all, I have come to feel that my central interest is in data analysis...."Opening paragraph from John Tukey "The ... [Read more...]

### But I Don’t Want to Be a Statistician!

July 29, 2015 |

"For a long time I have thought I was a statistician.... But as I have watched mathematical statistics evolve, I have had cause to wonder and to doubt.... All in all, I have come to feel that my central interest is in data analysis...."Opening paragrap... [Read more...]

### Mapping the past and the future with Leaflet

July 29, 2015 |

I have been working on mapping things for a while and I must say that I really like the Leaflet package from Rstudio. It makes it very easy and straight forward to make leaflet maps. A while back I stumbled upon an interactive graphic from The Times, that used census ... [Read more...]

### Player Value Gap Assessment

July 29, 2015 |

Looking at fantasy football projections we have a group of experts providing their views on how a player will do during the football season. We have collected projections from several[...] The post Player Value Gap Assessment appeared first on Fantasy Football Analytics. [Read more...]
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