77th Tokyo.R Users Meetup Roundup!

April 23, 2019

(This article was first published on R by R(yo), and kindly contributed to R-bloggers)

As the sakura bloomed in Tokyo, another TokyoR User
was held, this time
at SONY City! On April 13th useRs from all over Tokyo (and some even
from further afield) flocked to Osaki, Tokyo for a special session
focused on beginner R users, BeginneRs. We’ve also had several special
“themed” sessions in the past like TokyoR #69: Bayesian
in June last year as well as
the TokyoR #70: Hadley Wickham + Joe Rickert
last July. Although
mainly for BeginneRs, the LTs for this session were applications of
R/case studies and may be of more interest to non-beginners if you want
to skip ahead to that section.

Like my previous round up posts (for TokyoR
JapanR Conference
I will be going over around half of all the talks. Hopefully, my efforts
will help spread the vast knowledge of Japanese R users to the wider R
community. Throughout I will also post helpful blog posts and links from
other sources if you are interested in learning more about the topic of
a certain talk. You can follow Tokyo.R by searching for the
#TokyoR hashtag on Twitter.

BeginneR Session #1

These were the same set of beginner user focused talks that happens at
the start of every TokyoR meetup:

BeginneR Session #2

Since this was a special BeginneR session, the main talks were all
focused on even more introductory stuff on top of the usual beginner’s
session in the previous section.

kilometer00: Using R for Data Analysis

First up, @kilometer00 talked about doing data analysis with R. As a
brief introduction he talked about what exactly IS data analysis, how we
might go about forming a research problem and hypothesis, and how these
steps are important in figuring out what kind of modeling we might
attempt to do on the data at hand. The modeling techniques
@kilometer00 covered were just the basics such as single/multiple
linear regression and PCA.

In the last part of the talk he covered nested data modelling. By using
group_by() and nest() we can create a data frame that has one row
per group (for example, a row for each species group in the iris
data set) with has a new column called data which is itself a data
frame. Now, instead of having to repeat the modelling code over and over
again for each subset of rows (a model for each species in the iris
data set), by using the purrr::map_*() family of functions you can
apply your model to each of the groups that you specified earlier.

Filled with great explanatory graphics, plots, and code the slides are a
good example of teaching the basics of modelling with R.

Some other resources about modelling with R:

aad34210: Become a useR with R Studio

Another TokyoR organizer, @aad34210, talked about using the R Studio
IDE to maximize R’s strengths for programming and data analysis. After a
brief spiel on the early days of using R solely from the console he
talked about R Studio’s capabilities and the various options that can be
customized to suit your R needs. From installing R Studio, configuring
the four main panes, using R Projects, and using Global options,
aad34210 opened up his own R Studio window and pointed out the various
menu options in thorough detail to help beginneRs navigate without
getting overwhelmed. He rounded off the talk by showing the various
Cheat sheets (included one for R Studio itself) that can be obtained
from the Help tab.

Some other resources one might consider to learn R Studio are:

u_ribo: Version Control and Project Management with R

@u_ribo gave a talk about the benefits of creating a reproducible and
enclosed R environment using git and Docker. As an instructor who has
ran many R workshops, @u_ribo has ran into the problem of his learners
all having different OSs, versions of packages, and versions of R itself
causing much headache for all involved. This is also the case when
working in a team environment where analyses need to be shared and
reproducibility of results is essential.

To reduce these problems he gave a live-demo using a variety of R tools
such as the here package, the usethis package, and managing a
project environment with R Studio Projects (.Rproj). To go further in
depth he also talked about using git (made very easy with its seamless
integration with R Studio) and the use of Docker. To run Docker you
need an Docker “image” and a Docker “container”. An image is a file,
called a Dockerfile, that has the information about and configures the
Operating System for the environment. The container is the the actual
running instance of the “image” that is defined by the Docker file.
Going back to the issue of running a workshop, using Docker allows all
of the participants to run R inside a specific container, an enclosed environment
set up by the instructor, so that all the different dependencies and
version differences won’t prevent you from running the code provided in
the workshop.

Other good introductions to Docker and R:

niszet: Reproducible Reports with R Markdown

@niszet talked about reproducible reporting with R Markdown. He was
certainly the right person to give a talk on this topic as he is the
author of the mini-books, “Create a Word document with R Markdown” and
“Create a PowerPoint presentation with R Markdown”. To begin, he talked
about cases where one writes a document, report, or any kind of output
and how it might be a good idea to be able to create it again for
“future me” or anybody else that might want to take a look. Normally,
you would run into problems such as “where did my data go?”, “how did I
pre-process my data?”, “” but you can mitigate these problems by using R
Markdown reports. Whether it’s importing your raw data, the
pre-processing/modelling/viz code, to the actual report and
documentation write-up R Markdown renders the document in a completely
clean environment each time so the results should be the same, every
time! As noted in the beginning, you can create many different kinds of
output such as Word document, PowerPoint presentation, html document,
presentation slides, and more – even business cards (with the pagedown
package)! Following an explanation of what you can do with R Markdown,
@niszet talked about how exactly one would use it to its best
capabilities. In a live-demo he took us through all the different
components of an R Markdown document:

  • YAML header: Where one defines the “how” of the RMD such as the
    title, template, output directory, output type, etc.
  • Code chunk and options: Where all your code (can be languages
    besides R) that you want to be run should be located. Chunk options such as
    whether to evaluate the code within, toggle showing the code, and
    many more are also specified here.
  • Markdown text: Regular text using markdown. Can also include inline
    code using “.
  • Various buttons/shortcut keys: Such as Ctrl + Shift + K to Knit!

Some other intros to R Markdown:


GotaMorishita: Finding a New Place to Live with R

It’s only been 3 (three!) days since @GotaMorishita started learning R
yet here he was giving a LT on finding a new place to live in Tokyo
using R! Tired of living with his parents @GotaMorishita decided to
live by himself and started thinking about ways to use R and machine
learning to search for a place with an optimal price and location. After
web-scraping a housing website and pre-processing the data he came
across a problem: if he split the data into a training and test set for
selecting the best predictive model then he would be throwing away a
considerable amount of possible candidates for housing.

If @GotaMorishita took out 90% of the houses/apartments from the
training data and kept those as candidates for the test data, it woudl’ve meant
that the training data will have a markedly different distribution
compared to the test data set and the model created from the training
set wouldn’t be as accurate. This problem, called co-variate shifting, is when the training data and
test data have different distributions but the conditional distribution
of the output values given the input data is unchanged. Using standard
methods of model selection such as cross-validation or AIC in this
situation leads to biasedness. However, this problem can be mitigated by
weighting the loss function by importance (the ratio of training and
test input densities). You can find a more detailed description in the
research papers below. @GotaMorishita used xgboost to implement his
models, one with importance weighting and another without, and used
group-wise cross-validation to tune the hyperparameters. The results are
shown below, comparing the overall test scores for all Tokyo districts
(left) and just the Sangenjaya district (right), the RMSE was smaller
when Importance Weighting was used.

Some more info on co-variate shifting and importance weighting:

sk_bono36: Creating Marketing Personas with R and rtweet

@sk_bono36 gave a presentation on using R for marketing purposes with
the rtweet package. In marketing there is a concept called a “persona”
which is a blueprint of what a certain type of person in your target
audience for your product/service is like. A basic persona template
can consist of their name, job title, demographic details, values, and
hobbies. You create these ideal customers through careful market
research involving both social media analytics and
interviewing/surveying the customers themselves. @sk_bono36 focused on
creating a persona (with “自転車/Bicycle” as the keyword for this case
study) by using rtweet then running Japanese text analysis with
RMeCab. Visualizing the data with word clouds and network graphs of
bi-grams he was able to find a lot of information on Twitter users who
have “bicycle” on their profile or tweets and extract the common
characteristics of this type of person.

As a result of his analysis @sk_bono36 was able to create a persona of
people who like bicycles:

  • 20~30 Years Old
  • Owns a road bike
  • Friendly disposition
  • Likes Anime/video games
  • Does weight lifting

Some other intros to the rtweet package:

igjit: Create a type-checker package for R

@igjit, who also presented at
Japan.R back in December on
building an R compiler with
gave a talk about another recent project of his which is a package that
acts as a type checking system for R. A problem that he finds in R is
that errors relating to having the wrong data type in the arguments of R
functions are only found when code is executed, not before. Frustrated
by this @igjit created his own package called
typrr that type checks your code! The
underlying checker that typrr runs is
Flycheck which is a syntax
checking extension for Emacs.

For now, the package only checks for the basic data types found in R,
integer, double, logical, and character and it can only check functions
with one argument only. He rounded off the talk by saying that he
created this package just for fun and he advised all the beginneRs in
the audience that people learn from doing rather than just
reading so to truly get better it’s best to go out and experiment!

Other Talks

Food, Drinks, and Conclusion

Following all of the talks, those who were staying for the after-party
were served sushi and drinks! With a loud rendition of “kampai!”
(cheers!) R users from all over Tokyo began to talk about their
successes and struggles with R. A fun tradition at TokyoR is a
Rock-Paper-Scissors tournament with the prize being free data
science books (I still haven’t won any nor even gotten close to the last rounds)!

The prizes for this month was:

  • A couple copies of “Create a Word document with R Markdown”
    mini-book by niszet.
  • 3 copies of the Japanese translation (by Hoxo-m
    ) of “Feature Engineering for Machine
    Learning” by Alice Zheng and Amanda Casari provided by

TokyoR happens almost monthly and it’s a great way to mingle with
Japanese R users as it’s the largest regular meetup here in Japan. Talks
in English are also welcome so if you’re ever in Tokyo come join us!

To leave a comment for the author, please follow the link and comment on their blog: R by R(yo).

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