Messaggi di Rogue Scholar

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Pubblicato in rOpenSci - open tools for open science
Autore Dom Bennett

In this technote I will outline what phylotaR was developed for, how to install it and how to run it with some simple examples. What is phylotaR? In any phylogenetic analysis it is important to identify sequences that share the same orthology – homologous sequences separated by speciation events. This is often performed by simply searching an online sequence repository using sequence labels.

Pubblicato in rOpenSci - open tools for open science
Autore Matthew Strimas-Mackey

eBird is an online tool for recording birdobservations. The eBird database currently contains over 500 millionrecords of bird sightings, spanning every country and nearly every birdspecies, making it an extremely valuable resource for bird research andconservation. These data can be used to map the distribution andabundance of species, and assess how species’ ranges are changing overtime. This dataset is available for download as a text file;

Pubblicato in rOpenSci - open tools for open science
Autori Sean Hughes, Angela Li, Ju Kim, Malisa Smith, Ted Laderas

Motivation A few weeks ago, as part of the rOpenSci Unconference, a group of us (Sean Hughes, Malisa Smith, Angela Li, Ju Kim, and Ted Laderas) decided to work on making the UMAP algorithm accessible within R. UMAP (Uniform Manifold Approximation and Projection) is a dimensionality reduction technique that allows the user to reduce high dimensional data (multiple columns) into a smaller number of columns for visualization purposes (github,

Pubblicato in rOpenSci - open tools for open science
Autore Shaun Wilkinson

Evolutionary biologists are increasingly using R for building,editing and visualizing phylogenetic trees.The reproducible code-based workflow and comprehensive array of toolsavailable in packages such as ape,phangorn andphytools make R an ideal platform forphylogenetic analysis.Yet the many different tree formats are not well integrated,as pointed out in a recentpost.

Pubblicato in rOpenSci - open tools for open science
Autori Amanda Dobbyn, Jim Hester, Laura DeCicco, Christine Stawitz, Isabella Velasquez

Data == knowledge! Much of the data we use, whether it be fromgovernment repositories, social media, GitHub, or e-commerce sites comesfrom public-facing APIs. The quantity of data available is trulystaggering, but munging JSON output into a format that is easilyanalyzable in R is an equally staggering undertaking.

Pubblicato in rOpenSci - open tools for open science

The drake R package is not only a reproducible research solution, but also a serious high-performance computing engine. The package website introduces drake, and this technical note draws from the guides on high-performance computing and timing in the drake manual. You can help! Some of these features are brand new, and others are newly refactored.

Pubblicato in rOpenSci - open tools for open science
Autore Guangchuang Yu

Phylogenetic trees are commonly used to present evolutionary relationships of species. Newick is the de facto format in phylogenetic for representing tree(s). Nexus format incorporates Newick tree text with related information organized into separated units known as blocks. For the R community, we have ape and phylobase packages to import trees from Newick and Nexus formats.

Pubblicato in rOpenSci - open tools for open science

Our onboarding processensures that packages contributed by the community undergo atransparent, constructive, non adversarial and open review process.Before even submitting my first R package to rOpenSci onboarding systemin December 2015, I spent a fair amount of time reading through previousissue threads in order to assess whether onboarding was a friendly placefor me: a newbie, very motivated to learn more but a newbie nonetheless.I soon got

Pubblicato in rOpenSci - open tools for open science
Autore Evan Odell

I’m excited to announce a new package for accessing official statistics from the UK. nomisr is the R client for the Nomis database. Nomis is run by Durham University on behalf of the UK’s Office for National Statistics (ONS), and contains over a thousand datasets, primarily on the UK labour market, census data, benefit spending and general economic activity.

Pubblicato in rOpenSci - open tools for open science
Autori Maëlle Salmon, Noam Ross

Our onboarding process, thatensures that packages contributed by the community undergo atransparent, constructive, non adversarial and open review process,involves a lot of work from many actors: authors, reviewers and editors;but how much work ? Managing the effort involved in the peer-reviewprocess is a major part of ensuring its sustainability and quality.