Deciphering Life: One Bit at a Time

Weird Correlation Patterns

If you use kendall-tau on a lot of features, with low numbers of samples, weird things may happen.
R
correlation
analysis
bioinformatics
Using kendall-tau on a lot of features, with lower numbers of samples to calculate the correlation across, may result in very weird looking histograms of the correlation…
Apr 3, 2024
Robert M Flight

 

Installing OpenBLAS for self-compiled R

How to compile, and make sure a self-compiled R uses OpenBLAS, which may be faster than the installed one.
R
profiling
openblas
When you compile R from scratch on Linux, it doesn’t use the system BLAS libraries, it uses one that is compiled itself. This BLAS library may be rather slow. If you want to…
Nov 1, 2023
Robert M Flight

Fast Kendall-tau Correlation with Rcpp

How we created a fast implementation of Kendall-tau using Rcpp
c++
R
packages
Check out our {ICIKendallTau} R package if you want access to a fast version of Kendall-tau correlation in R (Robert M. Flight and Moseley 2022b) with only a few dependencies.
May 29, 2023
Robert M Flight

 

targets and Safe Functions

How to make sure {targets} recognizes changes to a ‘safe’ function?
R
targets
workflow
purrr
If you are using the {targets} workflow manager for your analyses, and also using {purrr::safely} (or others) to control possible errors, do not do the simplest version of…
May 8, 2023
Robert M Flight

 

Blog Posts as Email Newsletters

With the new blog2newsletter, you can have email subscribers to your blog controlled by R thanks to gmailr, googlesheets4, and tidyRSS.
R
newsletters
Want to be able to have people subscribe to your blog via email? Check out the {blog2newsletter} package on GitHub (Flight, n.d.).
Jan 19, 2023
Robert M Flight

Climate Data to Analyze Days by Low Temperatures

Inspired by XKCD to figure out how to get local temperature data and plot it.
xkcd
climate-data
In the past few years I’ve seen a lot of spiral graphs of temperature anomolies, temperature records knit into scarves, among others. But, hats off to Randall Munroe’s XKCD…
Dec 27, 2022
Robert M Flight

Journal Impact Factor Distributions

Discovering that journal impact factor distributions are log-normal.
impact-factor
Journal impact factor distributions seem to be log-normal. If we decide they should be used, then at the very least, they should be log-transformed before doing any…
Dec 25, 2022
Robert M Flight

 

targets and Child Documents

How to make sure that main documents update when a child document is modified in a targets workflow.
random-code-snippets
quarto
rmarkdown
targets
Make sure the child document is a target of the workflow, and that the child document target is loaded in the main.
Dec 22, 2022
Robert M Flight

 

Customizing the Displayed Date in Quarto Pubs

Making the date field more useful in quarto docs and publications.
quarto
R
random-code-snippets
If you want to change how the date is displayed in your {quarto} documents, this is handy.
Dec 8, 2022
Robert M Flight

Measuring Changes in Height Over Time

I have a citizen science project I want to try, that involves individuals measureing their own height daily over a long period of two months. I think I figured out how to do it.
R
development
citizen-science
height
I have a possibly really weird theory, that I’ve not been able to find any literature on. I think that over the course of a full menstrual cycle, that some women’s height…
Dec 7, 2022
Robert M Flight

 

Using Academicons in Your Quarto Blog

If you have trouble getting the academicons in your quarto blog, this might help you too!
random-code-snippets
quarto
Install the academicons extension in your Quarto project, and then use the “text” option.
Dec 3, 2022
Robert M Flight

 

Creating an Analysis With a targets Workflow

How I work through an -omics analysis using the targets package.
analysis
development
mass-spectrometry
targets
Setting up an analysis workflow using {targets} can be a little confusing without worked examples. This is my attempt to provide such an example.
Sep 27, 2022
Robert M Flight

 

Compiling Against Python.h

How to make sure that cython can find python.h when using a self compiled python.
python
cython
random-code-snippets
Sometimes, the installed version of Python on your linux system isn’t what you need, and you can’t easily install a newer version system-wide. Of course, you can download…
Jun 22, 2022
Robert M Flight

Project Consultation Template

What our labs project consult template looks like.
research
A little while ago, I was tweeting about the joy of collaborating with people who haven’t included you in their experimental design. One of the tweets was this:
Feb 8, 2022
Robert M Flight

 

Heatmap Colormaps!

Examples of good colormaps to use for heatmaps, both divergent and incremental.
colormaps
visualization
heatmap
random-code-snippets
Nine times out of ten, you probably need just one of the {viridis} colormaps for values that are increasing in one direction. For example, correlation values that are all…
Jan 31, 2022
Robert M Flight

Recreating Correlation Values from Another Manuscript

Documenting my journey trying to recreate some correlations calculated in another manuscript.
reproducibility
correlation
I’ve been working on a manuscript for our newish correlation method, information-content-informed Kendall-tau (ICI-Kendalltau, package currently at (Flight and Moseley 2021))…
Jan 15, 2022
Robert M Flight

 

Cairo and XQuartz in Mac GitHub Actions

Including cairo and xquartz in MacOS github actions
random-code-snippets
cairo
xquartz
development
github
R
I’ve been using GitHub actions to check and test some of my R packages on multiple architectures, which is nice because I work primarily on Linux.
Jan 6, 2022
Robert M Flight

 

Dplyr in Packages and Global Variables

How to include dplyr in a package, and avoid warnings around global variables.
random-code-snippets
packages
dplyr
rlang
R
development
I was recently cleaning up a development package so it would actually pass checks so it could be hosted on our labs new r-universe (“The ’Moseleybioinformaticslab’ Universe,”…
Jan 6, 2022
Robert M Flight

 

Pie Charts in RCy3

How to represent nodes as pie charts using Cytoscape and RCy3
random-code-snippets
rcy3
cytoscape
R
I have a package, {categoryCompare2} (Flight 2022) that I’ve been working on for a while, and recently wanted to make available on our labs r-universe (“The…
Jan 6, 2022
Robert M Flight

 

Reusing ggplot2 Colors

When you want to reuse ggplot2 default colors across plots.
random-code-snippets
ggplot2
visualization
If you are using {ggplot2} a lot in your code, and don’t want to bother with a custom color scheme (I mean, there are lots of good options), but you are also using…
Dec 21, 2021
Robert M Flight

 

Migrating Self-Hosted GitLab Projects to GitHub

We wanted to migrate from self-hosted GitLab projects to GitHub repos. Here is some background on how we accomplished that.
version-control
github
gitlab
Six years ago, we didn’t really look into what the free academic version of GitHub teams provided for private repositories, and instead decided that we should have a…
Nov 25, 2021
Robert M Flight

Zooming GGraph Plots

Some code demonstrating how to zoom into portions of a ggraph.
graphing
ggraph
visualization
random-code-snippets
I was recently working with a largish graph that I am using the ggraph package, and I needed to zoom into a sub-region of the graph.
Nov 11, 2021
Robert M Flight

 

R CMD Check and Non-PDF Vignettes

R CMD Check complaining about missing files? Here was my solution.
packages
random-code-snippets
If you’ve written an R package that you want hosted by CRAN (or even if not hosted), then you generally want to run the infamous R CMD check on your package.
Oct 27, 2021
Robert M Flight

My Vacation in Barometric Pressure

What can we see from my phone’s barometric pressure readings?
graphing
maps
visualization
I recently took a proper vacation, that involved driving from Lexington, KY, USA to Digby, NS, Canada and all points in between. I also have an app, Barometer Reborn, on my…
Sep 20, 2021
Robert M Flight

 

Random Forest Classification Using Parsnip

How to make sure you get a classification fit and not a probability fit from a random forest model using the tidymodels framework.
parsnip
tidymodels
machine-learning
random-forest
random-code-snippets
I’ve been working on a “machine learning” project, and in the process I’ve been learning to use the tidymodels framework (“Tidymodels” 2021), which helps save you from…
Aug 30, 2021
Robert M Flight

Coloring Dendrogram Edges with ggraph

Here is how I got edges colored in a dendrogram with ggraph. Use “node.” in front of the node data column you want.
random-code-snippets
visualization
graphing
dendrogram
I wanted to color the dendrogram edges according to their class in ggraph, and I was getting stuck because of something that isn’t explicitly mentioned in the documentation…
Aug 3, 2021
Robert M Flight

 

Keeping Figures in an Rmd – Word Document

How to make your rmarkdown to word conversion also generate a directory of figures.
random-code-snippets
reproducibility
rmarkdown
I’ve been working with a lot of collaborators who expect Word documents lately. I don’t really like it, but it makes it a lot easier for them to edit and work with things…
Jul 22, 2021
Robert M Flight

My Geographic Introduction

Adapting Piping Hot Data’s Geographic Introduction animation for myself.
maps
graphing
visualization
animation
I thought the recent animated map at Piping Hot Data {Pileggi (2021)} was a really neat way to demonstrate where someone has lived and what their various experiences may…
May 2, 2021
Robert M Flight

Proportional Error in Mass Spectrometry

Demonstrating the existence of proportional error in mass spectrometry measurements.
mass-spectrometry
proportional-error
omics
metabolomics
The other day, Kareem Carr asked for a statistics / data science opinion that results in the daggers being drawn on you (Carr, n.d.), and I replied (Flight, n.d.):
Apr 9, 2021
Robert M Flight

Highlighting a Row of A ComplexHeatmap

A simple way to highlight or bring attention to a row or column in a ComplexHeatmap.
random-code-snippets
heatmap
visualization
The ComplexHeatmap Bioconductor package (Gu, Eils, and Schlesner 2016; Gu 2021a, 2021b) has become my goto for visualizing sample-sample correlation heatmaps, which I use a…
Mar 26, 2021
Robert M Flight

Creating a Map of Routes Weighted by Travel

I made a map of my spouse’s travel since we got Google phones for her birthday last fall. Here’s how I did it.
graphing
maps
visualization
Way back in October 2020, I saw a tweet cross my feed by Esteban on making personal map art, and I was struck by their map (Moro 2020). I was also looking for an idea for my…
Mar 21, 2021
Robert M Flight

 

Random Code Snippets

Introducing random-code-snippets.
random-code-snippets
I’ve been organizing a bunch of random code that I find myself re-using time and time again in a Github Repo (Flight, n.d.). But the repo is not very searchable unless you…
Mar 5, 2021
Robert M Flight

 

Packages Don’t Work Well for Analyses in Practice

I was wrong about using packages to structure statistical analyses. Also why I finally switched to {drake}.
R
development
packages
vignettes
programming
analysis
workflow
targets
drake
Edit 2022-12-03: Don’t use {drake}, use {targets} now. Everything else still applies.
Mar 2, 2021
Robert M Flight

 

Things I Learned About distill

The various things I learned about the distill blog setup while converting posts over from my old blogdown site.
distill
blogdown
rmarkdown
So I converted this site to use distill from my previous blogdown site. This involved a bit of a learning curve to get things right. And my blogdown site was pretty old, as…
Feb 28, 2021
Robert M Flight

 

Using group_by Instead of Splits

How to use group_by instead of split’s to summarize things.
R
dplyr
split
group-by
programming
development
It is relatively easy to use dplyr::group_by and summarise to find items that you might want to keep or remove based on a part_of the item or group in question. I used to use …
Feb 25, 2020
Robert M Flight

 

Narrower PDF Kable Tables

This is how you should make narrower kable tables in rmarkdown PDF documents.
R
knitr
kable
learning
rmarkdown
Don’t bother trying to roll your own function to make narrower kable tables in a PDF document, just use kableExtra.
Nov 6, 2019
Robert M Flight

 

Introducing Scientific Programming

How and when should we get people in academia programming? What if we had a unified front across the science labs?
R
reproducibility
programming
academia
We should get science undergraduate students programming by introducing R & Python in all first year science labs, and continuing throughout the undergraduate classes.
Oct 23, 2019
Robert M Flight

 

Comments enabled via utterances

How I got utterances working on blogdown.
blogdown
commenting
utterances
Utterances is a lightweight commenting platform built on GitHub issues. So you have to have a GitHub account, but I expect most people who comment on this blog already have…
Oct 16, 2019
Robert M Flight

 

Comparisons using for loops vs split

for loops often hide much of the actual logic of your code because of all the necessary boilerplate of running a loop. split-ting your data can oftentimes be clearer, and faster.
R
for-loop
split
purrr
development
Sometimes for loops are useful, and sometimes they shouldn’t really be used, because they don’t really help you understand your data, and even if you try, they might still…
Feb 13, 2019
Robert M Flight

Nicer PNG Graphics

Here are some tips for getting nicer graphics in your rmarkdown outputs.
If you are getting crappy looking png images from rmarkdown html or word documents, try using type='cairo' or dev='CairoPNG' in your chunk options.
Dec 6, 2018
Robert M Flight

Don’t do PCA After Statistical Testing!

You might be tempted to do PCA after a statistical test. Read more to discover why this is a bad idea.
pca
bioinformatics
R
t-test
If you do a statistical test before a dimensional reduction method like PCA, the highest source of variance is likely to be whatever you tested statistically.
Sep 14, 2018
Robert M Flight

Finding Modes Using Kernel Density Estimates

Examples of finding the mode of a univeriate distribution in R and Python.
R
python
kernel-density
pdf
probability-density
programming
If you have a unimodal distribution of values, you can use R’s density or Scipy’s gaussian_kde to create density estimates of the data, and then take the maxima of the…
Jul 19, 2018
Robert M Flight

 

Split - Unsplit Anti-Pattern

Getting some speed using dplyr::join than my more intuitive split –> unsplit pattern.
R
development
programming
purrr
dplyr
join
If you notice yourself using split -> unsplit / rbind on two object to match items up, maybe you should be using dplyr::join_ instead. Read below for concrete examples.
Jul 17, 2018
Robert M Flight

Using IRanges for Non-Integer Overlaps

I wanted to make use of IRanges awesome interval logic, but for non-integer data.
R
iranges
development
programming
The IRanges package implements interval algebra, and is very fast for finding overlaps of two ranges. If you have non-integer data, multiply values by a large constant…
Jun 23, 2018
Robert M Flight

Turn Robert’s Beard Purple!

I’m trying to raise money for the Walk for Alzheimer’s, will you sponsor me?
alzheimers
fundraising
If I raise $100 by August 25ths The Walk to End Alzheimer’s, I will have my beard dyed purple in support of Alzheimer’s awareness.
Jun 20, 2018
Robert M Flight

 

knitrProgressBar Package

Ever wanted a progress bar output visible in a knitr document? Now you can!
packages
R
developement
If you like dplyr progress bars, and wished you could use them everywhere, including from within Rmd documents, non-interactive shells, etc, then you should check out knitrPr…
Feb 19, 2018
Robert M Flight

 

Licensing R Packages that Include Others Code

I wanted to include others code in my package, and couldn’t find any good resources.
R
packages
open-science
licensing
If you include others code in your own R package, list them as contributors with comments about what they contributed, and add a license statement in the file that includes…
Feb 14, 2018
Robert M Flight

 

docopt & Numeric Options

Every input is a string in docopt. Every Input!!
R
development
programming
docopt
If you use the docopt package to create command line R executables that take options, there is something to know about numeric command line options: they should have as.double…
Jan 17, 2018
Robert M Flight

Linking to Manually Inserted Images in Blogdown / Hugo

This is my method to include something manually in a blogdown post.
hugo
R
blogdown
Using blogdown for generating websites and blog-posts from Rmarkdown files with lots of inserted code and figures seems pretty awesome, but sometimes you want to include a…
Dec 27, 2017
Robert M Flight

 

Differences in Posted Date vs sessionInfo()

If you see differences in the sessionInfo output and the date the post was published, this is why.
development
blogdown
If you are a newcomer to my weblog, you may notice that some posts that are R tutorials generally include the output of Sys.time() at the end. If you look closeley at that…
Dec 27, 2017
Robert M Flight

 

Custom Deployment Script

I don’t want to use Netlify for hosting, so I came up with this simple script to deploy my blog.
R
blogdown
development
random-code-snippets
Use a short bash script to do deployment from your own computer directly to your *.github.io domain.
Dec 27, 2017
Robert M Flight

 

I was Part of the Problem

Why do so many men think it’s OK to lavish unwanted attention on women who don’t want it?
metoo
academia
With the recent charges of sexual harassment against some high-profile individuals, and so many women coming forward with #metoo (and the understanding that this is really…
Oct 18, 2017
Robert M Flight

 

Criticizing a Publication, and Lying About It

Critics of our last publication claimed we didn’t make our data available, which is an outright lie.
publications
peer-review
zinc
academia
Other researchers directly criticized a recent publication of ours in a “research article”. Although they raised valid points, they outright lied about the availability of…
Mar 29, 2017
Robert M Flight

Authentication of Key Resources for Data Analysis

NIH is asking for authentication of key resources. How does this apply to data analyses?
reproducibility
open-science
analysis
NIH recently introduced a reproducibility initiative, extending to including the “Authentication of Key Resources” page in grant applications from Jan 25, 2016. Seems to be…
Mar 23, 2016
Robert M Flight

Random Forest vs PLS on Random Data

Comparing random-forest and partial-least-squares discriminant-analysis on random data to show the problems inherent in PLS-DA.
random-forest
machine-learning
partial-least-squares
statistics
analysis
Partial least squares (PLS) discriminant-analysis (DA) can ridiculously over fit even on completely random data. The quality of the PLS-DA model can be assessed using…
Dec 12, 2015
Robert M Flight

Novel Zinc Coordination Geometries

A bit of an explainer on our labs recent publication on finding and classifying zinc coordination geometries in protein structures.
zinc
structural-biochemistry
open-science
reproducibility
visualization
publications
Currently available methods to discover metal geometries make too many assumptions. We were able to discover novel zinc coordination geometries using a less-biased method…
Jun 17, 2015
Robert M Flight

Mouse / Human Transcriptomics and Batch Effects

A recent paper dug into some data from another paper, casting doubts on the first, all thanks to the data being available.
open-science
transcriptomics
batch-effects
publications
peer-review
This 2014 PNAS paper by S. Lin et al (Lin et al., PNAS, 2014) that compares transcription of tissues between species has a flawed experimental design, where species is…
Jun 1, 2015
Robert M Flight

 

First Open Post-Publication Peer Review, with Credit!

A story about my first open peer-review.
open-science
peer-review
publications
Reviewed Jason McDermott’s MDRPred paper on F1000Research!, where my review is posted along side the paper, with a DOI, completely in the open with my name attached. Was a…
Mar 25, 2015
Robert M Flight

 

Being a PhD Student and Post-Doc with Migraines

What it’s like having migraines as a PhD student and PostDoc.
phdisabled
migraines
academia
A blog post on the Weecology group blog by Elita Baldridge on being a PhD student with fibromyalgia, and how they are working through that, caused me to pause and reflect on…
Dec 31, 2014
Robert M Flight

 

Travis-CI to GitHub Pages

How I automatically have some stuff get pushed to GitHub pages from a Travis CI job.
R
reproducibility
travis-ci
github
publishing
I don’t remember how I got on this, but I believe I had a recent twitter exchange with some persons (or saw it fly by) about pushing R package vignettes to the web after…
Nov 5, 2014
Robert M Flight

 

My Career Goals

I don’t want to be a lab PI, but I want to stay in academia.
post-doc
career
academia
I don’t want to be a PI because I enjoy spending time with my family, and don’t think I can handle the stress of juggling multiple grants, people, and deadlines. I want to…
Aug 8, 2014
Robert M Flight

 

Analyses as Packages

Why I think packages make good ways to structure an analysis.
R
development
packages
vignettes
programming
analysis
Edit 2022-12-02: I don’t recommend this approach anymore.
Jul 28, 2014
Robert M Flight

 

Packages vs ProjectTemplate

Why I think packages are better than the projectTemplate package.
R
packages
analysis
development
Imposing a different structure than R packages for distributing R code is a bad idea, especially now that R package tools have gotten to the point where managing a package…
Jul 28, 2014
Robert M Flight

 

Creating an Analysis as a Package and Vignette

A walkthrough creating an analysis project as a package.
R
development
packages
vignettes
analysis
programming
Edit 2022-12-02: I don’t recommend this approach anymore.
Jul 28, 2014
Robert M Flight

 

R Job Notifications Using Twitter

R
twitter
development
programming
There has been some interesting activity about getting R to send a notification somehow when a long running job is completed. The most notable entries I have seen in this…
Jun 30, 2014
Robert M Flight

 

Researcher Discoverability

Why do we need corporate products to enhance “researcher discoverability”?
github
open-science
academia
research
University of Kentucky (UK) recently partnered with the discovery portal KNODE, for helping others to discover potential collaborators at UK. KNODE looks like a large…
Jun 19, 2014
Robert M Flight

 

Bioinformatics Presentations that Lack Results (or Biological Relevance)

Why do people have bionformatics presentations lacking relevance or results?
bioinformatics
academia
research
In bioinformatics research we need to show validated results (if doing classification or discovery of new things), or show biological relevance. If you do neither of those…
Jun 5, 2014
Robert M Flight

 

categoryCompare Paper Finally Out!

My first first author publication since starting my PostDoc is finally out, about my meta-annotation-enrichment software package categoyrCompare.
R
bioconductor
meta-analysis
publications
git
github
open-science
visualization
annotation-enrichment
I can finally say that the publication on my Bioconductor package categoryCompare is finally published in the Bioinformatics and Computational Biology section of Frontiers…
Apr 8, 2014
Robert M Flight

 

Self-Written Function Help

Do you want to be able to read function documentation for your own functions? Make your own package.
R
packages
documentation
development
devtools
roxygen2
docstrings
I have noted at least one instance (and there are probably others) about how Python’s docStrings are so great, and wouldn’t it be nice to have a similar system in R.…
Feb 20, 2014
Robert M Flight

 

Installing MatLab vs Installing R

Personal frustrations around installing MatLab led to this particular rant.
MatLab
R
I retweeted this a few days ago:
Feb 10, 2014
Robert M Flight

 

Package Version Increment Pre- and Post-Commit Hooks

Two git commit hooks for incrementing the package version as part of commits.
R
git
packages
development
programming
random-code-snippets
If you just want the hook scripts, check this gist. If you want to know some of the motivation behind writing them, and about the internals, then read on.
Feb 7, 2014
Robert M Flight

 

Motivated Learning

Two personal stories on times I was very motivated to learn, as part of my Software-Carpentry instructor training.
learning
software-carpentry
git
calculus
As part of the instructor training of Software-Carpentry, we were asked to write a blog post about two things:
Jan 28, 2014
Robert M Flight

 

PubmedCommons API

Pubmed commons is a new commenting system for pubmed articles.
open-science
pubmed
The announcements are out, Pubmed is introducing a commenting system pubmedcommons, theoretically providing a single location for true post-publication peer review. This is…
Oct 22, 2013
Robert M Flight

 

Open vs Closed Analysis Languages

Talking about R & Python vs MatLab as examples of open and closed data analysis languages.
open-science
R
python
MatLab
programming
development
I think data scientists should choose to learn open languages such as R and python because they are open in the sense that anyone can obtain them, use them and modify them…
Oct 21, 2013
Robert M Flight

Pre-Calculating Large Tables of Values

Demonstrating a way to generate a large amount of numbers that otherwise might take a long time to calculate.
R
pre-calculations
programming
development
c++
I’m currently working on a project where we want to know, based on a euclidian distance measure, what is the probability that the value is a match to the another value. i.e. …
Oct 17, 2013
Robert M Flight

 

Portable, Personal Packages

My take on creating simple little packages for your own commonly used functions.
R
packages
development
ProgrammingR had an interesting post recently about keeping a set of R functions that are used often as a gist on Github, and sourceing that file at the beginning of R analys…
Sep 23, 2013
Robert M Flight

 

K-12 Wants Scientists!!

I recently attended a talk about PhD scientists in grade school teaching.
post-doc
academia
science
teaching
It seems that the PostDoc committee here at UK has an interest in providing some information on alternative careers for PostDocs outside of academia. We all know that there…
Sep 19, 2013
Robert M Flight

 

R, RStudio, and Release and Dev Bioconductor

Working with the development version of Bioconductor on linux can be a pain. This is one way to do it.
R
bioconductor
rstudio
programming
packages
development
Update 2021-02-18: Now I would just use the r-docker image and the RStudio interface. I actually just did this recently to test updates to my package.
Sep 17, 2013
Robert M Flight

 

Reproducible Methods

A short missive on reproducibility, especially within computational work.
open-science
reproducibility
bioinformatics
Science is built on the whole idea of being able to reproduce results, i.e. if I publish something, it should be possible for someone else to reproduce it, using the…
Aug 16, 2013
Robert M Flight

 

R Interface for Teaching

What is the best interface for teaching a language like R?
R
teaching
notebooks
Kaitlin Thaney asked on Twitter last week about using Ramnath Vaidyanathan’s new interactive R notebook 1 2 for teaching.
Jul 11, 2013
Robert M Flight

Tim Hortons Density

How far away are most Canadians from a Tim Hortons?
R
mapping
tim-hortons
Inspired by this post, I wanted to examine the locations and density of Tim Hortons restaurants in Canada. Using Stats Canada data, each census tract is queried on…
Jun 5, 2013
Robert M Flight

 

Storing Package Data in Custom Environments

How do you keep track of stuff for your own package without cluttering the users global space or setting a bunch of options?
R
packages
If you do R package development, sometimes you want to be able to store variables specific to your package, without cluttering up the users workspace. One way to do this is…
May 30, 2013
Robert M Flight

 

Writing Up Scientific Results and Literate Programming

My thoughts on using literate programming to investigate and report scientific results
literate-programming
academia
notebooks
reproducibility
As an academic researcher, my primary purpose is to find some new insight, and subsequently communicate this insight to the general public. The process of doing this is…
May 10, 2013
Robert M Flight

Writing Papers Using R Markdown

How I used RMarkdown to write a manuscript
R
open-science
reproducibility
literate-programming
rmarkdown
I have been watching the activity in RStudio and knitr for a while, and have even been using Rmd (R markdown) files in my own work as a way to easily provide commentary on…
Oct 9, 2012
Robert M Flight

 

Journal Club 2012-08-15

A summary of the paper Google Goes Cancer as was discussed in our journal club.
journal-club
I just came back from our Bioinformatic group (a rather loose association of various researchers at UofL interested in and doing bioinformatics) journal club, where we…
Aug 15, 2012
Robert M Flight

 

Creating Custom CDFs for Affymetrix Chips in Bioconductor

Examples of messing with Affymetrix CDF data in Bioconductor.
R
bioconductor
bioinformatics
cdf
affymetrix
microarray
random-code-snippets
For those who don’t know, CDF files are chip definition format files that define which probes on an Affymetrix microarray chip belong together, and are necessary to use any…
Jul 13, 2012
Robert M Flight
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