Analysing an open cohort stepped-wedge clustered trial with repeated individual binary outcomes

February 3, 2020
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Analysing an open cohort stepped-wedge clustered trial with repeated individual binary outcomes

I am currently wrestling with how to analyze data from a stepped-wedge designed cluster randomized trial. A few factors make this analysis particularly interesting. First, we want to allow for the possibility that between-period site-level correlation will decrease (or decay) over time. Second, there is possibly additional clustering at the patient level since individual outcomes will be measured repeatedly...

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Some lessons from rstudio::conf

February 3, 2020
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Some lessons from rstudio::conf

Today I’m departing a little from the problem/context/solution format of these posts to share some things I learned from last week’s rstudio::conf. When I started in R a few years ago, I never thought I would have any place at a coding conference for computer people. But thanks to some help from my lab and my … Continue reading "Some...

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Grid point occurrence records onto a raster

February 3, 2020
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Grid point occurrence records onto a raster

The ‘gridRecords‘ function, which has just been added to the ‘fuzzySim‘ package (from version 2.6 on), takes a raster stack and a set of spatial coordinates of a species’ presence (and optionally absence) records, and returns a data frame with … Continue reading →

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Conference feelings: from newbie to sponsor

February 2, 2020
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Conference feelings: from newbie to sponsor

In the summer of 2008, nearly 12 years ago, I attended my first R/Bioconductor conference: BioC2008. Just last week I went to my second rstudio::conf(2020) which I greatly enjoyed. After some tweets exchanges today, I started reflecting on my journey and wanted to share my thoughts. Why I like going to conferences I typically enjoy going to conferences, though I also...

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Working with audio in R using av

Working with audio in R using av

The latest version of the rOpenSci av package includes some useful new tools for working with audio data. We have added functions for reading, cutting, converting, transforming, and plotting audio data in any popular audio / video format (mp3, mkv, aac, etc). The functionality can either be used by itself, or to prepare audio data for further analysis in R...

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The palindrome of 02.02.2020

February 2, 2020
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The palindrome of 02.02.2020

As of writing this blog-post, today is February 2nd, 2020. Or as I would say it, 2nd of February, 2020. There is nothing magical about it, it is just a sequence of numbers. On a boring Sunday evening, what could…Read more ›

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R Tip: Check What Repos You are Using

February 2, 2020
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In a lot of our R writing we casually say “install from CRAN using install.packages('PKGNAME')” or “update your packages by using update.packages(ask = FALSE, checkBuilt = TRUE) (and answering ‘no’ to all questions about compiling).” We recently became aware that for some users this isn’t complete advice. The above depends on your R install pointing … Continue reading R...

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rstudio::conf 2020 Slides on Futures

February 1, 2020
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rstudio::conf 2020 Slides on Futures

Design: Dan LaBar

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Primitive Functions List

February 1, 2020
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Ever wondered which R functions are actually passed to internal C code? Well, wonder no more as it turns out there is an unexported named list within the methods package providing instructions for turning builtin and special functions into generic functions. Wrapping this list with names() gives us the list of all R functions which wrap calls to .Primitive(). names(methods:::.BasicFunsList) #...

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Get and Set List Elements with magrittr

February 1, 2020
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Introduction Did you know that the magrittr pipe, %__%, can be used for more than just data.frames and tibbles? In this blog post, we look at how we can create get and set functions for list elements. Getting List Elements First, let’s create a simple list. z1 %. How can we do that? Well we can pipe our list into a . which...

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A guide to encoding categorical features using R

February 1, 2020
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In this article, we will look at various options for encoding categorical features. We will also present R code for each of the encoding techniques. Categorical feature encoding is an important data processing step required for using these features in many statistical modelling and machine learning algorithms. The material in the article is heavily borrowed from the post Smarter Ways...

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Monsters

February 1, 2020
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Monsters

Ooh, see the fire is sweepin’Our very street todayBurns like a red coal carpetMad bull lost its way(Gimme Shelter, The Rolling Stones) After following this easy tutorial, you will be able to create tiled images from a photograph. You may want to use your own portrait or some other as I did. I use geom_tile: … Continue reading Monsters...

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The significance of the region on the salary in Sweden, a comparison between different occupational groups

The significance of the region on the salary in Sweden, a comparison between different occupational groups

In my last post, I found that the region has a significant impact on the salary of engineers. Is the significance of the region unique to engineers or are there similar correlations in other occupational groups? Statistics Sweden use NUTS (Nomenclature des Unités Territoriales Statistiques), which is the EU’s hierarchical regional division, to specify the regions. The F-value from the Anova...

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Comparing Ensembl GTF and cDNA

January 31, 2020
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Comparing Ensembl GTF and cDNA

It seems that most people think Ensembl’s GTF file and cDNA fasta file mean the same transcripts: Watch out! @ensembl's Fasta and GTF annotation files available via https://t.co/2AhCSnL7py do not match (there are transcripts in the GTF not found in the Fasta file. Anyone else expected...

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50+ Free DataSets for DataScience Projects

January 31, 2020
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50+ Free DataSets for DataScience Projects

Hello All, This is just a short note to specify that the list of FREE datasets is updated for 2020. There are 50+ sites and links to the newly released Google Dataset search engine. So, have fun exploring these data repositories to master programming, create stunning visualizations and build your own unique project portfolios. Some The post 50+ Free...

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Lewis Carroll’s proposed rules for tennis tournaments by @ellis2013nz

January 31, 2020
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Lewis Carroll’s proposed rules for tennis tournaments by @ellis2013nz

Last week I wrote about the impact of seeding the draw in a tennis tournament. Seeding is one way to increase the chance of the top players making it to the final rounds of a single elimination tournament, leading to fairer outcomes and to a higher cha...

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rco: Make Your R Code Run Faster Today!

January 31, 2020
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The rco package can optimize R code in a variety of different ways. The package implements common subexpression elimination, constant folding, constant propagation, dead code elimination, among other very relevant code optimization strategies. Currently, the rco could be downloaded as a GitHub package. The rco  package functions as an RStudio Addin, be used through a shiny GUI … Continue reading rco:...

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15+ Resources to Get Started with R

January 31, 2020
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15+ Resources to Get Started with R

R is the second most sought after language in data science behind Python, so gaining mastery of R is a prerequisite to a thriving career in the field. Whether you’re an experienced developer or a newbie considering a career move, here are some excellent resources so you can get started with R. [Related Article: Data-Driven Exploration … Continue reading 15+...

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Beginners guide to Bubble Map with Shiny

January 31, 2020
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Beginners guide to Bubble Map with Shiny

Map Bubble Map bubble is type of map chart where bubble or circle position  indicates geoghraphical location and bubble size is used to show differences in magnitude of quantitative variables like population. We will be using Highcharter package to show earthquake magnitude and depth . Highcharter is a versatile charting library to build interactive charts, … Continue reading Beginners...

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nnetsauce for R

January 30, 2020
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nnetsauce for R

nnetsauce is now available to R users (currently, a development version). As a reminder, for those who are interested, the following page illustrates different use-cases for the nnetsauce, including deep learning application examples. This post from September 18 is about an Adaptive Boosting (boosting) algorithm variant available in the nnetsauce. This other post from September 25 presents a Bootstrap...

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A Shiny App for Tracking Moral Networks

January 30, 2020
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A Shiny App for Tracking Moral Networks

Background This is a post outlining a ShinyApp that I made for visualising inter-participant agreement on quesions relating to Haidt’s Moral Foundations (e.g., Haidt and Joseph 2008). This is part of a line of research on moral judgements, inspired by DAFINET project, where I aim to investigate the role of agreement with others in the robustness of moral judgements. It...

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Comparing Ensembl GTF and cDNA

January 30, 2020
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Comparing Ensembl GTF and cDNA

It seems that most people think Ensembl’s GTF file and cDNA fasta file mean the same transcripts: Watch out! @ensembl's Fasta and GTF annotation files available via https://t.co/2AhCSnL7py do not match (there are transcripts in the GTF not found in the Fasta file. Anyone else expected...

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An efficient way to install and load R packages

January 30, 2020
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What is a R package and how to use it? Inefficient way to install and load R packages More efficient way What is a R package and how to use it? Unlike other programs, only fundamental functionalities come by default with R. You will thus often need to install some “extensions” to perform the analyses you want. These extensions which are are collections...

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another easy Riddler

January 30, 2020
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another easy Riddler

A quick riddle from the Riddler In a two-person game, Abigail and Zian both choose between a and z. Abigail win one point with probability .9 if they choose (a,a) and with probability 1 if they choose (a,z), and two points with probability .4 if they choose (z,z) and with probability .6 if they choose

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Building the R Community in Southern Africa

January 30, 2020
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Building the R Community in Southern Africa

By Heather Turner, Chair of Forwards, the R Foundation taskforce for underrepresented groups in the R Community In this post I will give the background to the Forwards Southern Africa... The post Building the R Community in Southern Africa appeared first on R Consortium.

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Supplement to ‘Nonparametric estimation of the service time distribution in discrete-time queueing networks’

Great news: a scientific article I have co-authored has been accepted for publication and can now be found online here or via the DOI 10.1016/j.spa.2020.01.011. Yes, my list of publications has been amended 1. This article has been through quite a leng...

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Create a Notebook to Explore Country-Level CO2 Emissions With a Few Clicks

Create a Notebook to Explore Country-Level CO2 Emissions With a Few Clicks

Assume that you have some new data that you want to explore. The new CRAN version of the ‘ExPanDaR’ package helps by providing a (customized) R notebook containing all building blocks of an exploratory data analysis with a few clicks. Install the Package and Start ExPanD First, you need to install the package. I recommend installing the Github development version of the package as it...

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Applied Bayesian Statistics Using Stan and R

January 29, 2020
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Applied Bayesian Statistics Using Stan and R

Whether researchers occasionally turn to Bayesian statistical methods out of convenience or whether they firmly subscribe to the Bayesian paradigm for philosophical reasons: The use of Bayesian statistics in the social sciences is becoming increasingly widespread. However, seemingly high entry costs still keep many applied researchers from embracing Bayesian methods. Next to a lack of familiarity with the underlying...

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R Consortium Simplifies Membership Structure to Increase Opportunities for Silver Level Members

January 29, 2020
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Two membership levels now available: Platinum and Silver SAN FRANCISCO, January 29, 2020 – The R Consortium, a Linux Foundation project supporting the R Foundation and R community, today announced... The post R Consortium Simplifies Membership Structure to Increase Opportunities for Silver Level Members appeared first on R Consortium.

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