W-JAX 2018 talk: Deep Learning – a Primer

August 28, 2018
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W-JAX 2018 talk: Deep Learning – a Primer

On November 7th, I’ll be in Munich for the W-JAX conference where I’ll be giving the talk that my colleague Uwe Friedrichsen and I gave at the JAX conference this April again: Deep Learning - a Primer. Let me know if any of you here are going to be...

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Videos from NYC R Conference

August 28, 2018
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The videos from the NYC R conference have been published, and there are so many great talks there to explore. I highly recommend checking them out: you'll find a wealth of interesting R applications, informative deep dives on using R (and a few other applications as well), and some very entertaining deliveries. In this post, I wanted to highlight...

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Bioinformatics series: Mitochondrial Control Region – Part I – Using (GNU Bash + R) to handle large Genbank files in R

August 28, 2018
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Bioinformatics series: Mitochondrial Control Region – Part I –  Using (GNU Bash + R) to handle large Genbank files in R

Hi everyone! In this series we are going to work with a gene called the Mitochondrial Control Region. This series will be about getting some insights into it from sequence analysis. We are going through the entire process, from getting data to reach some conclusions and more importantly raise some questions. All of the bash

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Proteomics Data Analysis (2/3): Data Filtering and Missing Value Imputation

August 28, 2018
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Proteomics Data Analysis (2/3): Data Filtering and Missing Value Imputation

Welcome to Part Two of the three-part tutorial series on proteomics data analysis. The ultimate goal of this exercise is to identify proteins whose abundance is different bewteen the drug-resistant cells and the control. In other words, we are looking for a list of differentially regulated proteins that may shed light on how cells escape Related Post Clean Your Data...

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Visualization of Tumor Response – Spider Plots

August 28, 2018
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Visualization of Tumor Response – Spider Plots

A collection of some commonly used and some newly developed methods for the visualization of outcomes in oncology studies include Kaplan-Meier curves, forest plots, funnel plots, violin plots, waterfall plots, spider plots, swimmer plot, heatmaps, circos plots, transit map diagrams and network analysis diagrams (reviewed here). Previous articles in this blog presented an introduction to … Continue reading Visualization...

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How to self-publish a book: Customizing Bookdown

August 27, 2018
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How to self-publish a book: Customizing Bookdown

Centered around Bookdown, we will review some non-standard customizations in order to self-publish a book.

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What’s this bird? Classify old natural history drawings with R

What’s this bird? Classify old natural history drawings with R

In this new post, we’re taking a break from modern birding data in our birder’s series… let’s explore gorgeous drawings from a natural history collection! Armed with rOpenSci’s packages binding powerful C++ libraries and open taxonomy data, how much information can we automatically extract from images? Maybe not much, but we’ll at least have explored image manipulation, optical character recognition (OCR), language detection, taxonomic name resolution...

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Moving beyond pattern-based analysis: Additional applications of GeoPAT 2

Moving beyond pattern-based analysis: Additional applications of GeoPAT 2

This is the sixth and the last blog post in the series introducing GeoPAT 2 - a software for pattern-based spatial and temporal analysis. In the previous one we presented the pattern-based spatial segmentation - a method for creating regions of homogenous patterns. Here, we will mention other pattern-based methods and show some examples of how you can use pieces of...

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The power of stepped-wedge designs

August 27, 2018
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The power of stepped-wedge designs

Just before heading out on vacation last month, I put up a post that purported to compare stepped-wedge study designs with more traditional cluster randomized trials. Either because I rushed or was just lazy, I didn’t exactly do what I set out to do. I did confirm that a multi-site randomized clinical trial can be more efficient than a...

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Insey Winsey Spider Game Monte-Carlo Simulation

August 27, 2018
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Insey Winsey Spider Game Monte-Carlo Simulation

Time is such a precious commodity especially with a family.  So when your daughter asks to play a board game… you think ‘how long will this take’.  With most board games, one is able to roughly estimate how long the game will take… the Shopping Game, well that can be expected to take 10 minutes with … Continue reading Insey...

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Simplifying World Tile Grid Creation with geom_wtg()

August 27, 2018
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Simplifying World Tile Grid Creation with geom_wtg()

Nowadays (I’ve seen that word used so much in journal articles lately that I could not resist using it) I’m using world tile grids more frequently as the need arises to convey the state of exposure of various services at a global (country) scale. Given that necessity fosters invention it seemed that having a ggplot2... Continue reading →

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Data Science and Insurance (Transcript)

August 27, 2018
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Data Science and Insurance (Transcript)

Here is a link to the podcast. Introducing JD Long Hugo: Hi there JD and welcome to DataFramed. JD: Hey, Hugo. Hugo: ...

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Statistics Sunday: Visualizing Regression

August 27, 2018
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Statistics Sunday: Visualizing Regression

Statistics Sunday: Visualizing Regression I had some much needed downtime this weekend, after an exhausting week, along with some self-care - Saturday I had a one-hour deep tissue massage, which left me a little bruised but much more relaxed, and Sunday I spent a few hours in the salon chair having my color touched up, which left me...

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Happy Birthday R

August 27, 2018
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Happy Birthday R

Happy birthday R! We’re celebrating your 25th anniversary this month. In 1993, when your developers Ross Ihaka and Robert Gentleman – whose two first names probably gave rise to the…

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Specalize in Geo-Spatial Visualizations With Leaflet – Part 1: Exercises

August 27, 2018
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Specalize in Geo-Spatial Visualizations With Leaflet – Part 1: Exercises

Leaflet is a JavaScript library for interactive maps. It is widely used across many platforms, and fortunately it is also implemented as a very user-friendly R package! With leaflet, you can create amazing maps within minutes that are customized exactly to your needs and embed them within your Shiny apps, markdowns, or just view them Related exercise sets: Spatial Data...

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Zero-Inflated Poisson and Negative Binomial Models with GLMMadaptive

August 27, 2018
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Clustered/Grouped Count DataOften cluster/grouped count data exhibit extra zeros and over-dispersion. To account for these features, Poisson and negative binomial mixed effects models with an extra zero-inflation part are used. These models entail a logistic regression model for the extra zeros, and a Poisson or negative binomial model for the remaining zeros and the positive counts. In both models,...

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July 2018: Top 40 New Packages

August 26, 2018
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July 2018: Top 40 New Packages

July was a big month for submitting new packages to CRAN; by my count, 251 unique and truly new packages were accepted. In addition to quantity, I was pleased to see quality and variety. For instance, tropicalSparse, a package for exploring some abstract mathematics, and eChem, a package for teaching analytical chemistry, exemplify R’s expansion into new fields. Below are...

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HypeRIMU

August 26, 2018
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During the last days I updated my R-package HypeRIMU. The latest update of the corresponding Android App HyperIMU allows to submit now JSON data via TCP connection. So I implemented a new function “execute_JSON()”. This function can rece...

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MPT trees published in BRM

August 26, 2018
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MPT trees published in BRM

Multinomial processing trees are recursively partitioned to capture heterogeneity in latent cognitive processing steps. Accompanied by the R function mpttree in the psychotree package, combining partykit::mob and psychotools::mpt. ...

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Adjacent-Categories and Continuation-Ratio Logit Models for Ordinal Outcomes

August 26, 2018
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In the previous post (https://statcompute.wordpress.com/2018/01/28/modeling-lgd-with-proportional-odds-model), I’ve shown how to estimate a standard Cumulative Logit model with the ordinal::clm function and its use case in credit risk models. To better a better illustration of the underlying logic, an example is also provided below, showing how to estimate a Cumulative Logit model by specifying the log likelihood

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Exploring London Crime with R heat maps

August 25, 2018
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Exploring London Crime with R heat maps

Recently, I had a real pleasure to work with various types of data pulled from public APIs, one of them being data.police.uk API. Oh, those hours of pure intellectual exploration it’s given me! I have a soft spot for crime data and I explored it using heat maps in the past. Apart from checking and visualising stats for the...

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MeDaScIn 2018

August 25, 2018
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The annual Melbourne Data Science Initiative (or MeDaScIn, pronounced medicine) is on again next month (24-27 September) with lots of tutorials, and the annual datathon. This year there will be a “Forecasting with R” workshop (25 September) led my two of my Monash colleagues – George Athanasopoulos and Elena Sanina. Another great tutorial will be led by Steph Kovalchik (from Tennis...

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Simulating NXN dimensional Gaussian clusters in R

August 25, 2018
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Simulating NXN dimensional Gaussian clusters in R

Gaussian clusters are found in a range of fields and simulating them is important as often we will want to test a given class discovery tools performance under conditions where the ground truth is known (e.g. K=6). However, a flexible Gaussian cluster simulator for simulating Gaussian clusters with defined variance, spacing, and size does not

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What, No Parentheses?

August 25, 2018
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I’m about to show you an R trick. Various readers may find it cool, useful and interesting, or stupid, useless and an evil deed undermining the sanctity of R’s functional programming nature (“All bow”). But I hope many of you will find the material here rather intriguing if not useful. All this involves a trick … Continue reading What,...

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littler 0.3.4: More updated examples

August 24, 2018
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littler 0.3.4: More updated examples

The fifth release of littler as a CRAN package is now available, following in the now more than ten-year history as a package started by Jeff in 2006, and joined by me a few weeks later. littler is the first command-line interface for R and predates Rscript. And it is (in my very biased eyes) better as it allows for...

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First post in new r-tastic

August 24, 2018
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OK, it had to happen and here it is: I moved my old r-tastic blog to blogdown and I’m not going to look back :) There are numerous resources that will: highlight the advantages of using blogdown with Hugo over other static site generators, such as J...

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About

August 24, 2018
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About r-tastic Data without insights are just meaningless series of numbers or characters. I love diving deep into new datasets, discovering new patterns and exceptions. Getting familiar with data and saying “I know something about you now”, at the end. And that’s exactly what I’m going to do here. This blog is essentially for me to showcase - and remind myself...

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O’Reilly animals in trouble? Conservation status of book covers

August 24, 2018
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What can a kaka, a kakapo, an European rabbit and a grey heron have in common? Well, they might co-habit in the bookshelf of an R user, since they’re all animals on the covers of popular R books: “R Packages”, “R for Data Science”, “Text mining with R” and “Efficient R programming”, respectively. Their publisher, O’Reilly, has now based its brand on covers featuring beautiful gravures of...

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NASA Datanauts!

August 24, 2018
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NASA Datanauts!

An overview of my experience in the NASA Datanaut kickoff session

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