Hello World! Welcome to the new Mouse Imaging Centre Blog. We created this blog as a place to share things we’ve been thinking about lately. This blog will feature a mixture of technical writing about things we do in our lab including imaging, statistics, and biology. The blog will feature contributions from our staff, students, and PIs…

I have seen clinicians confused over statements such as “the chance of a stroke is 0.5%”, interpreting this as 50%. If we say “the chance of a stroke is 0.005” such confusion is less likely. And I don’t need percent signs everywhere. Percent change has even more problems than percent…

In this post, I’ll show you a few tricks which can make your life using Immutable.js and Redux with TypeScript easier. All the practices are inspired by my recent work on the project Rhyme.com…

We’ve been working on our processing engine, Wallaroo for just under two years now. Our goal has been to make it as easy to build fast, scale-independent applications for processing data…

Like many of the topics I’ve written about, this is a vast one that certainly warrants much, much more than a blog entry. MC simulation in particular, since it is so fundamental to the practice of statistics…

The goal of Cloud Foundry Container Runtime is to simplify deploying and maintaining a Kubernetes cluster. It does a lot to alleviate the day-to-day burdens of an operator so they can focus on how to help their team execute. This is a walkthrough of how to install CFCR and deploy Kubernetes with it…

Due to the special nature, no cool things or question included on this podcast. Matt is an Incident Manager (aka Chaos Specialists) for Google, which means his team is on-call to handle suspected security incidents and other major urgent issues…

Cloud AutoML is a suite of products enabling developers with limited ML expertise to build high quality models using transfer learning and Neural Architecture Search techniques…

That infamous…

The Death of Flash SAP XCelsius was the Ford Fiesta of the BI industry. Inexpensive to run, simple to implement. Businesses could get dashboards up and running in days or hours. We’ve helped clients design over 1,000 XCelsius dashboards over time, so we know how practical and adaptable they were…

If your problem is solved, don’t forget to close this issue…

Don’t get me wrong, I love the HashiCorp products. I’ve been a Vagrant user since way back in my BC (Before Cloud) days and have continued a strong run of success backing the use of HashiCorp product…

IN THIS POST I WANT TO SHARE R code for a simple animated line plot using ggplot2. In the past I’ve shared similar code, but over time my workflow has evolved. So I thought it would be good to post an updated bit of code. We’ll use economic data from the St. Louis Federal Reserve Economic Database (FRED)…

With the release of the American Community Survey, there was an opportunity to take a look at the digital divide in 2016. I was inspired to make a tilegram map similar to those create by NPR. I used the tilegramsR package by Bhaskar Karambelkar. First, here are the packages for the…

When processing data, we often categorize a job as either a batch or streaming job. However, this is a bit of a false dichotomy. In this post, I’ll explore how we ordinarily define batch and stream processing, and show how some tasks that we think of as batch jobs can be seen as a subset of stream processing…

Text-mining - the art of answering questions by extracting patterns, data, etc. out of the published literature - is not easy…

In the previous post of this AirPiConsole series (part1, part2) I used Autossh to create a reverse tunnel from the device to a cloud VPS to permit remote access. The VPS I use is cheap but unreliable so the tunnel was down most of the time so I started looking for a better alternative. The solution came from the Packet Pushers podcast episode PQ134 about ZeroTier…

BOSH is a VM orchestrator; a BOSH Director creates, configures, monitors, and deletes VMs. The BOSH Director interoperates with a number of IaaSes (Infrastructure as a Service), one of which is VMware vSphere, a virtualization platform. BOSH traditionally operates exclusively within the IPv4 networking space (i.e…

Table listing options ok! so given this situation how do you go about resolving it? First, It wasn’t an obvious situation for doing method-level profiling. So, we had to rule-out a few things that came to mind first: Network-related differences including Latency, bandwidth and route differences…

Man City’s unbeaten run ended by a Coutinho-less Liverpool in seven goal thriller Match of the DaySubsOn Saturday an oddity occurred. The kind of ‘Dog didn’t bark in the night’ sort…

Estimation of effect size (ES) with confidence intervals (CI) of ES are much easy to understand and carry much more informations with them making them a preferable way to present results in clinical research. Hope you like the post…

This post is to announce a shiny app I’ve written to test regular expressions in an R environment…

For this post I will be quickly diving into global trends in Tuberculosis incidence rates and exploring whether Tuberculosis eradication is on the horizon. Now to get started, the first step is to get the package (for this post we are using the development version from GitHub) and to load the other packages required for this analysis…

Via the command line you can manage the addins with greater…

Hello, the project that I was talking about earlier is finally over…

Queueing theory has some commonly accepted shorthand to describe characteristics of queuing models. Although across books and peer reviewed articles you will see slight variations, this post outlines commonly accepted terms for reference. The rate at which entities arrive to a queueing system to be processed. E.g…

Why can’t I just have all of the data? I have been updating some code that uses data that I don’t have access to. I used one of the data sets from the survival package but it annoyed me that the variable names were not what I wanted them to be and I couldn’t be bothered changing them…

Ever since I moved to France for my postdoc in September 2016, I’ve tried to practice French whenever I can. One easy way to do that is by consuming YouTube channels in French – great things to put on the the background while I make food for my son, or feed my son, or clean up after feeding my son, etc…

These four plots were prepared for publication with final day coverage of the 2018 Canadian figure skating championships. There were a few troubles with the data, as seen in the code notations below…

Hello everyone, Each customer has a score that corresponds to his probability to churn. Let’s see the score of the five first customers of our database. We draw a table where we show the maximum value for each indicator. Now we want to target a percentage of customers in our database. Let’s sort customers by their score…

Thanks to the extensive feedback we have received on our first Python API, we have decided to release some improvements. So in version 0.4.0, we released some breaking changes to the Python API…

In this post I’ll be an showing an example of using a packed barchart to visualize emote usage in a twitch.tv chat…

Well, I hope to delete the pre-included widgets for now since I do not have…

This next part is the hard part. We need to combine and clean the two datasets. To begin we do two joins, because we need the lat and long data for both the source and the destination airports…

The winter olympics are coming! It is an exciting time to celebrate our favorite sports and feel inspired to do better ourselves. It is going to be interesting this year with the doping ban for Russia as well as many unfortunate injuries and retirements…

This year I made a concerted effort to read more books related to my interests in analytics, math, and data science. I had the pleasure of reading most of these books with a group of people at work, and we met on a regular basis to discuss and gab…

I started skiing at the age of 3 at the station in the Alps called the “Sept Laux” next to Grenoble, France. It was natural to me, but until now I never wondered for how long people have done it. Here is a brief history of how it all began…

Malika is the Global Lead for Google Launchpad Studio. Launchpad is the acceleration engine of Google - running a number of accelerator programs focused on supporting the global startup ecosystem…

Meltdown, Spectre and Linux on AWS: Security vs Performance? The recent announcement of the Meltdown and Spectre attacks against bugs in Intel (and other) CPUs has attracted rapid response from many vendors; Amazon Web Services’ (AWS) response shows that they’ve already patched and protected their infrastructure but you still have work to…

LSE IR Gender and Diversity Project Two shinydashboard posts in a row, that’s a first. As I mentioned on Twitter, I’m not really this productive; rather, the apps had been on the proverbial shelf for a while and I’m just releasing them now…

String substitutions Note - the package I wrote was originally inspired by a challenge a coworker tossed out. It also happened to provide a solution to this SO question which was really cool! Substitutions in strings are best handled with regular expressions which are an amazingly powerful and flexible tool…

Serverless is most commonly thought of as pieces of code executed in a stateless container, e.g. AWS Lambda and Functions-as-a-Service…

With the release of the new version of mlrMBO we added some minor fixes and added a practical feature called Human-in-the-loop MBO. It enables you to sequentially visualize the state of the surrogate model, obtain the suggested parameter configuration for the next iteration and update the surrogate model with arbitrary evaluations…

Join us for our first R Ladies NYC event of 2018! Date: Wednesday, January 10, 2018 Time: 6:30pm Instructor: Joyce Robbins Host: Schapiro Center Columbia…

Search syntax Corpus search Search summary KWIC & BOW Summary and shiny This post demonstrates the use of a simple collection of functions from my R-package corpuslingr…

A relatively routine process for me is to combine multiple files into a single data frame by row…

I recently spotted a time series heat map. So I started on a quest to make my own. Luckily, I found some local data to start with: crimes in Somerville, MA. This data set includes selected crimes in Somerville from…

Hello athletes, welcome on my new platform Sciathlon. The goal for this website is to share findings in sports science and technology. I am a biologist so I am interested in everything related with an athlete’s health such as nutrition, genetics, injuries and conditions related to the kind of activity we do…

The parameters describe: The chart illustrates nicely the different compartments (processes) for a policy over time…

At 3 p.m. today, the Oakland Raiders will hold a press conference to introduce Jon Gruden as their next head coach…

Hi everyone! Today I am listing my favorite sports-related youtube channels, in no particular order, make sure to check them out, they deserve it! TheGingerRunner If you are interested in running and want to learn more about trails, races, athletes, training, gear, nutrition, there are amazing ressources out there that will teach and inspire…

Finally, my package “spanish” was ready for submission on CRAN and now it’s published! Not a great piece of work, just a place to gather a bunch of functions that I was unable to find anywhere else because are related to spanish data…

Confession: I love simulations. In simulations you get to define everything about a model and then see how that model behaves over the long run. It’s like getting the luxury of taking many samples instead of only the one real one we have resources for in an actual study…

Using public school data can help school districts see the bigger picture of what is going on. So why don’t we see more districts taking advantage of this information gold…

In the simulation scenario I’ve concocted, the goal is to increase the number of patients that come in for an important test…

Install the latest version of dbplyr with: Six stringr functions are now supported. Regular expression support varies from database to database, but most simple regular expressions should be ok…

I was recently working on a PDF file with 60 odd pages and I had to crop the lower border of the pages…

Es muy difícil dar ayuda si no se sabe cuál es el problema…

The investigators studied the effect of adding Daratumumab with Bortezomib, Melphalan and Prednisolone in patients with freshly detected Myeloma ineligible for Autologous Bone Marrow Transplantation. The primary outcome was Progression free survival (time to progression or death, whichever was early)…

There is a little piece of software on the Internet that I very much liked…

Recently, I was presenting approach to Thrombotic Microangiopathy in hospital. I made the following notes, which I feel will be beneficial for the residents. a. MAHA (Coombs negative, increased LDH, schistocytes) b. Thrombocytopenia c. Organ injury (ischemic) a. Endothelial dysfunction b. Microinfarcts a…

Happy New Year to one and all! As data scientists/analysts/researchers/programmers/anything else on that crazy data science Venn diagram, I’m assuming all of our new years resolutions involve visualising our data with more sophistication and finesse…

Hello everyone, We can shortly define customer churn (most commonly called “churn”) as customers that stop doing business with a company or a service. There are customer churns in different business area. In this post, we will focus on the telecom area. Here, we want to predict which customers will leave their current telecom provider…

In the first three parts of this series, we looked at the changes in income along the The Orange Line, The Red Line, and The Green Line. I went through my approach for creating a New Yorker inspired visualization of income along the Boston T. For the final post, we take a look at the The Blue Line. Below you will see median household income along each of the four lines of the Boston Blue…

In this post, I’d like to share one of the more unique plots from esvis - the binned effect size plot. The overall purpose of the binned effect size plot is to evaluate if the differences between two distributions are consistent across the scale…

I had three inspirations for this package: This post from Matthew Kay, “I don’t want your monolithic ggplot function”. This beautiful “thematic” interactive1 graph made in highchartr by Jushua Kunst:

A near death experience in Kathmandu, Nepal two years ago (don’t ask). What if, I thought, the mountain itself, is a line plot…

It always starts with a DM on Twitter, where someone shares with me their personal data science ambitions, where they currently are in their plans, and then they follow up with a request for me to help them figure out where to go…

It’s January - time to see how we did on car gas mileage last year! We purchased a used 2011 Ford Fiesta in 2016. It replaced a 1991 Honda CRX, which was running like a champ but was starting to look a little, well, limited in its safety features…

The future of CLI and how Network Engineers will interact with devices is a topic being discussed quite often: “I'll give you my CLI when you pry it from my cold, dead fingers” - said no #CCIE ever, they're busy automating their networks with Python to save time for more creative…

org.apache.drill.common.exceptions.UserRemoteException: DATA_READ ERROR: Selected column ‘COLUMNS’ must have name ‘columns’ or must be plain ‘*’ File Path file:_sample-data_some…

In this blog post, I show various ways to create maps using R. You’ll need to install a lot of packages and download two data sets; the unemployment rate in Luxembourg as well as a shapefile…

A few days ago someone asked me whether I could visualize the terror attacks of recent years in Europe. Here is an attempt to do exactly this…

Now in Rstudio, I load in the needed packages: We could also zoom out and get a map from all of Germany If we wanted to save the map on our computer, we could use the following…

Thanks for stopping…

This release contains the following major changes: The most important change of this release is the use of color and other markup for the output in the terminal: Numeric columns have two displays. If there is room, the full number is displayed, making it easy to compare order of magnitude. Digits after the first three are dimmed to emphasise the important components…

In the first two parts of this series, we looked at the changes in income along the The Orange Line and The Red Line. I went through my approach for creating a New Yorker inspired visualization of income along the Boston T. For this post, we take a look at the The Green Line. Below you will see median household income along each of the four lines of the Boston Green…

Check out the first post in this series for an index of all the other posts. In this post, we’re going to look at extending the work we’ve done earlier by adding another flag into the mix. We’ll use that to improve the way the output of the tool looks when it runs…

I’ve been interested in the relationship between ordinal regression and item response theory (IRT) for a few months now. There are several helpful papers on the topic, here are some randomly picked ones 1 2 3 4 5, and a book…

I’d stop early to reduce the number of lines of code from 7 to 6, and save 8 spaces: Actually if the error message is short enough, I’ll remove curly braces: I’d write it as: I tend to make code a little dense (e.g…

I started working with R around about 5 years ago. Parts of the R world have changed substantially over that time, while other parts remain largely the same. One thing that hasn’t changed however, is that there has never been a simple, high-level text to introduce newcomers to the ecosystem…

Getting the data A couple of months ago I discovered a package developed by Public Health England that makes it easier to extract the data behind their fingertips website (https://fingertips.phe.org.uk/)[... ](https://emmavestesson.netlify.com/2018/01/maps/)

I don’t do nor believe in New Year’s…

At least once a year I meet with a graduate student who has many separate datasets that need to be combined into a single file. The data are usually from a series of data loggers (e.g., iButtons or RFID readers) that record data remotely over a specified time period…

Now, I look for faster playback on everything and am kind of suprised when I can’t find it. However, I use one of these for my music and podcasts. iPod Classic If you’re on OSX there are several free plist generators so that you can get it loaded by launchctl…

I wanted to create a dataframe with stringr functions along with their usage and corresponding examples…

At the end of the year it’s quite common to think about the results accomplished and missed on the last twelve months…

Introduction Thomas Lin Pedersen is the author of a lot of packages, including two that deal with graphs (in the sense of networks), tidygraph for storing and handling graphs, and ggraph for drawing them, ggplot-style…

Below is a recent example, in which I could help ranting. However, when I saw the question, it was already put on hold and I could not answer it, even though I happened to know the answer…

Introduction David Selby, on his blog, explains how to get R up and running on your Android phone (and, by way of proof, wrote the blog post concerned on his phone). Unfortunately, however, he was only able to install R 3.1.1, which means that some of the latest tidyverse goodies are not available. Can we do better? It is possible.…

Check out the first post in this series for an index of all the other posts. In the first parts of this series we explored how to create simple command line utilities in R…

Census nuts/bolts New Mexico & the US Some macro-exploration A simple model Some final notes References In this post we investigate Spanish language maintenance within Hispanic communities in the US utilizing data from the US Census…

🐶>💩 I have a dog. He’s cute and crazy. And he has constant diarrhea (shout out to the pet parents and human baby parents out there, you get used to talking about 💩 real quick). It turns out part of the reason was his diet. The vet just shrugged when I asked how to fix it…

Match of the DayPardew BounceAlan Pardew has a rep as someone who gives a team an instant return, extended runs (good and bad) and ultimate disappointment Well stage one hasn’t happened with WBA as they have yet to win a game in six but how true is it of his four other Premier managerships…

I’m a list-person. Totally. I love ticking off boxes, feeling that I’ve achieved a lot every day…

A major change I want to make about my life as a software developer in 2018 is that I will ask for help more frequently. I have a lot of burden that I hope to shift to other people’s shoulders. Of course, I won’t simply use you as pure labor - I hope you could learn something while helping me. I’ll start listing the simpler tasks in the next few weeks…

In an effort to keep the community up to date with the evolution of the tidyverse, we’ll be doing regular roundups cataloging the latest developments…

I love the start of the New Year for so many reasons, but one of my favorites is the never-ending stream of motivational word art that populates a good 98% of every social media feed for 31 whole days, like so: Then commit to showing up for five minutes a day, five days a week, in the corresponding Slack channel…

After one too many Liquid errors and all the Ruby dependency hell, I’m moving away from Jekyll to Hugo. One less excuse to keep me from posting. A handful of things to note about Hugo: Built with Go. Easy to use. It’s fast. So fast. Local site rebuilds in ~100ms. Immediate feedback as you’re writing because fast. Getting started with Hugo is pretty easy…

This time I’ll violate my principle to write only about purely technical topics on my blog. In the next a couple of paragraphs, I’ll talk about open source software development from a personal perspective. Here are some of the ideas that you can find below: Explanation what open source software is…

In this post I’ll be sharing a computer vision model that was trained to detect the character Fox in the game Super Smash Bros Melee for the Nintendo Gamecube…