At thursday (12.01.2017) we had a chance to attend the first tricity R users group (pomerania, poland) meeting. The meetup was unexpectedly very successful!Cognitive aspects of learning the success can be measured in the time attendees spent on ardently comments and questions after each of 2 great presentations. After every 20-25 min long presentation we could observe 30 min long lively discussion!Cognitive aspects of learning it is amazing that questions lasted longer than presentations. Is it thanks to the climate? Is it due to the nature of a pomeranian community?Cognitive aspects of learning perhaps this is due to excellent organization? In this post I present summary of the meeting, I describe presentations and reveal organizers’ identity.Cognitive aspects of learning

The image processing and the computer vision have gained a significant interest in last 2 decades. The image analysis can be used to detect items or people on images and videos.Cognitive aspects of learning it is widely used in the medicine to detect cancer tissues and to improve brain, lungs and heart diseases diagnostic. The computer automation enabled analyzing terabytes of an image data, based on which we improve our life status and get insights for business decisions.Cognitive aspects of learning in this post I present basic operations that can be applied to a simple image, all thanks to imager package by which I am truly impressed. I also present a quick entropy approach to the image binarization, which applied to images on a greyscale transforms them to the binarized black-and-white output.Cognitive aspects of learning

Due to the incrising interest in the internet and due to the its rising number of users, one can notice the surprising growth in the demand for analyzing data and information in the internet that were left by users and for users.Cognitive aspects of learning many companies and institutions base their business decisions on the extensive research of social media portals and internet forums, where users leave reviews on various products and brands.Cognitive aspects of learning not only the same analysis, but also the ability to obtain data from the internet, is a key part of the puzzle…

The often demand in the biostatistical research is to group patients depending on explanatory variables that are continuous.Cognitive aspects of learning in some cases the requirement is to test overall survival of the subjects that suffer on a mutation in specific gene and have high expression (over expression) in other given gene.Cognitive aspects of learning to visualize differences in the kaplan-meier estimates of survival curves between groups, first the discretization of continuous variable is performed.Cognitive aspects of learning problems caused by categorization of continuous variables are known and widely spread ( harrel, 2015), but in this case there appear a simplification requirement for the discretization.Cognitive aspects of learning in this post I present the maxstat(maximally selected rank statistics) statistic to determine the optimal cutpoint for continuous variables, which was provided it in the survminer package by alboukadel kassambara kassambara.Cognitive aspects of learning

Ten days ago erum2016 conference (european R users meeting 2016) has finished. It was a huge event that attracted over 250 attenders, both from academia and business.Cognitive aspects of learning meeting was a great opportunity to listen to amazing keynotes like heather turner, katarzyna stapor, rasmus bååth, jakub glinka, ulrike grömping, przemyslaw biecek, romain francois, marek gagolewski, matthias templ and katarzyna kopczewska.Cognitive aspects of learning big thank you goes to the whole organizing committee and dr maciej beręsewicz (head) especially! There were 10 workshops, 2 packages sessions, 2 data workflow sessions, 3 methodolody sessions, 1 bior session, 2 business sessions, lightnings talks, a poster session and of course a great welcome party.Cognitive aspects of learning I could not miss a chance to present news from the last release (ver 2.0) of ours archivist package.

What is R? I was asked at the end of my presentation on the 10th cracow R users meetup that was held last friday (30.09.2016).Cognitive aspects of learning I felt strange but absolutely confirmed that R is the language of data science and is designed to performed the statistical data analysis. Later I found out that few of listeners came to the meetup to listen more about docker than R, as my topic was rocker - explanation and motivation for docker containers usage in applications development.Cognitive aspects of learning in this post I present the overview of my presentation. If you are not familiar with using dockers in R applications development, then this is a must read for you!Cognitive aspects of learning

Warsaw R and data analytics enthusiast group is an effort that aims at integrating users of the R language in warsaw, poland. Our group has over 970 members at its meetup page.Cognitive aspects of learning in this post I provide a summary of our group, our last 2 meetups before this season ending and I present plans for the future. Check who we are, what are we talking about, what are our future meetings about and how you can become a member or a co-organizer of warsaw R enthusiasts events.Cognitive aspects of learning

As R users we mostly perform analysis, produce reports and create interactive shiny applications. Those are rather one-time performances. Sometimes, however, the R developer enters the world of the real software development, where R applications should be distributed and maintained on many machines.Cognitive aspects of learning then one really appreciates the value of a proper applications monitoring. In this post I present my last package called rzabbix - the R interface to the zabbix API data.Cognitive aspects of learning

The R package development is a complex process of creating (mostly) a useful software, that will (probably) be used by other users. This means the provided tool should be resistant, immune, well tested and properly documented.Cognitive aspects of learning developers from many different languages have invented various approaches to improve software development, creating documentation or package testing.Cognitive aspects of learning R users have adapted few of them and mostly we use travis for continuous integration, roxygen2 for documentation, devtools for testing and knitr / rmarkdown for writing manuals, tutorials, vignettes and package websites.Cognitive aspects of learning this software development kit causes that the R package structure is rather broad, especially since many of us (R developers) puts source code from different languages into the package root to speed up the performance of created tools.Cognitive aspects of learning moreover we built our software libraries that are based on other packages, which complicates the NAMESPACE of the prepared package and forces the understanding of difference between dependent, imported and suggested packages.Cognitive aspects of learning in this whole ecosystem of development equipment and requirements for proper package structure I’ve been asked what every R package must contain?Cognitive aspects of learning you wouldn’t guess how easy was the answer.

Machine and statistical learning wizards are becoming more eager to perform analysis with spark ML library if this is only possible.Cognitive aspects of learning it’s trendy, posh, spicy and gives the feeling of doing state of the art machine learning and being up to date with the newest computational trends.Cognitive aspects of learning it is even more sexy and powerful when computations can be performed on the extraordinarily enormous computation cluster - let’s say 100 machines on YARN hadoop cluster makes you the real data cruncher!Cognitive aspects of learning in this post I present sparklyr package (by rstudio), the connector that will transform you from a regular R user, to the supa! Data scientist that can invoke scala code to perform machine learning algorithms on YARN cluster just from rstudio!Cognitive aspects of learning moreover, I present how I have extended the interface to K-means procedure, so that now it is also possible to compute cost for that model, which might be beneficial in determining the number of clusters in segmentation problems.Cognitive aspects of learning thought about learnig scala? Leave it - user sparklyr!

Few weeks ago I have a great pleasure of attending bioc 2016: where software and biology connect conference at stanford, where I have learned a lot!Cognitive aspects of learning it wouldn’t be possible without the scholarship that I received from bioconductor (organizers), which I deeply appreciate. It was an excellent place for software developers, statisticians and biologists to exchange their experiences and to better explain their work, as the understanding between collaborators in interdisciplinary teams is essential.Cognitive aspects of learning in this post I present my thoughts and feelings about the event and I share the knowledge that I have learned during the event, i.E. About many ways of downloading the cancer genome atlas data.Cognitive aspects of learning

Text mining is a new challenge for machine wandering practitioners. The increased interest in the text mining is caused by an augmentation of internet users and by rapid growth of the internet data which is said that in 80% is a text data.Cognitive aspects of learning extracting information from articles, news, posts and comments have became a desirable skill but what is even more needful are tools for text mining models diagnostics and visualizations.Cognitive aspects of learning such visualizations enable to better understand the insight from a model and provides an easy interface for presenting your research results to greater audience.Cognitive aspects of learning in this post I present the latent dirichlet allocation text mining model for text classification into topics and a great ldavis package for interactive visualizations of topic models.Cognitive aspects of learning all this on R-bloggers posts!

Feature selection is a process of extracting valuable features that have significant influence on dependent variable.Cognitive aspects of learning this is still an active field of research and machine wandering. In this post I compare few feature selection algorithms: traditional GLM with regularization, computationally demanding boruta and entropy based filter from fselectorrcpp (free of java/weka) package.Cognitive aspects of learning check out the comparison on venn diagram carried out on data from the RTCGA factory of R data packages.

Have you ever suffered because of the impossibility of reproducing graphs, tables or analysis’ results in R?Cognitive aspects of learning have you ever bothered yourself for not being able to share R objects (i.E., plots or final analysis models) within your reports, posters or articles?Cognitive aspects of learning or maybe simply you have too many objects you can’t manage to store in a convenient and handy way? Now you can share partial results of analysis, provide hooks to valuable R objects within articles, manage analysis’ results and restore objects’ pedigree with archivist package and its extension archivist.Github, allautomatically through github without closing rstudio.Cognitive aspects of learning if you are tired of archiving results by yourself, then read how you can became an R hero with the archivist.Github package power.

Hadley wickham’s ggplot2 version 2.0 revolution, at the end of 2015, triggered many crashes in dependent R packages, that finally led to deletions of few packages from the comprehensive R archive network.Cognitive aspects of learning it occured that survmisc package was removed from CRAN on 27th of january 2016 and R world remained helpless in the struggle with the elegant visualizations of survival analysis.Cognitive aspects of learning then a new tool - survminer package, created by alboukadel kassambara - appeared on the R survival scene to fill the gap in visualizing the kaplan-meier estimates of survival curves in elegant grammar of graphics like way.Cognitive aspects of learning this blog presents main features of core ggsurvplot() function from survminer package, which creates the most informative, elegant and flexible survival plots that I have seen!Cognitive aspects of learning

Have you ever encountered R packages versioning issues when one application required different dependent packages versions than other? Have you ever got stuck with your project because of wrong pre-installed software versions on machine on which you should run your code?Cognitive aspects of learning or maybe you had heavy adventures with installing R software on a new machine because you couldn’t recall all installation steps like; what have I done 2 years ago that rcurl works on my local machine but I can’t install it now on my virtual machine with windows?Cognitive aspects of learning or maybe installation of your R project on new machine was easy but admin couldn’t manage with this process, as he’s not regular R user? If you ever find it problematic to move your R applications to other machines, then this docker guid post is for you!Cognitive aspects of learning

Yesterday we have been delivered with the new version of R - R 3.3.0 (codename supposedly educational). This enabled bioconductor (yes, not all packages are distributed on CRAN) to release it’s new version 3.3.Cognitive aspects of learning this means that all packages held on bioconductor, that were under rapid and vivid development, have been moved to stable-release versions and now can be easily installed.Cognitive aspects of learning this happens once or twice a year. With that date I have finished work with RTCGA package and released, on bioconductor, the RTCGA factory of R packages.Cognitive aspects of learning read this quick guide to find out more about this R toolkit for biostatistics with the usage of data from the cancer genome atlas study.

Getting users feedback is always a pleasant moment.Cognitive aspects of learning in most cases in world of open source we are creating tools and applications for people and we love to hear that someone thinks our (generally pet) project is useful.Cognitive aspects of learning mostly this moment is nicer than any paycheck. Check this post to find out how to provide easy interface for collecting the user feedback!

Many people keep asking me whether I have tried sparkr, is it worth using, is it sexy or WHAT is it at all.Cognitive aspects of learning I felt that creating frequently asked questions ( FAQ) in the field of WHAT is that spark/sparkr? Would help many R scientists to understand this big data buzz-tool.Cognitive aspects of learning I have gathered information from the documentation and some code from stackoverflow questions in preparation for the list below.