TL;DR 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.
Motivation I have had a lot of calculations lately that involve some sort of normalization or scaling a group of related values, each group by a different factor.
Lets setup an example where we will have 1e5 values in 10 groups, each group of values being normalized by their own value.
TL;DR 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 factor and round them. The constant depends on how much accuracy you need.
IRanges?? IRanges is a bioconductor package for interval algebra of integer ranges. It is used extensively in the GenomicRanges package for finding overlaps between various genomic features. For genomic features, integers make sense, because one cannot have fractional base locations.
TL;DR 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.
If you are in another country, donate to your local Alzheimer’s charity and email me with the subject walk so I count it towards my total.
Links:
My donation page (Charity report on Alzheimer’s Association)
Facebook Fundraising Page (if you want to share it!
TL;DR 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 knitrProgressBar (cran github).
Why Yet Another Progress Bar?? I didn’t set out to create another progress bar package. But I really liked dplyrs style of progress bar, and how they worked under the hood (thanks to the examples from Bob Rudis).
As I used them, I noticed that no progress was displayed if you did rmarkdown::render() or knitr::knit().
TL;DR 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 their code.
Motivation I recently created the knitrProgressBar package. It is a really simple package, that takes the dplyr progress bars and makes it possible for them to write progress to a supplied file connection. The dplyr package itself is licensed under MIT, so I felt fine taking the code directly from dplyr itself.
TL;DR 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 before using them in your script.
Setup Lets set up a new docopt string, that includes both string and numeric arguments.
" Usage: test_numeric.R [--string=<string_value>] [--numeric=<numeric_value>] test_numeric.R (-h | --help) test_numeric.R Description: Testing how values are passed using docopt. Options: --string=<string_value> A string value [default: Hi!
TL;DR Use a short bash script to do deployment from your own computer directly to your *.github.io domain.
Why? So Yihui recommends using Netlify, or even Travis-CI in the Blogdown book. I wasn’t willing to setup a custom domain yet, and some of my posts involve a lot of personally created packages, etc, that I don’t want to debug installation on Travis. So, I wanted a simple script I could call on my laptop that would copy the /public directory to the repo for my github.
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 time and the Posted on date, you may notice that some posts show disagreement between them. This is because I decided to move all of my old blog posts from blogspot to here, and keep the original posted dates.
Manual Linking? 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 figure manually, either because you want to generate something manually and convert it (say for going from SVG of lots of points to hi-res PNG), or because it is a figure from something else (like this figure from wikipedia).
Where to?
TL;DR 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 something almost all women have faced), I realized that my younger self was #partoftheproblem. I think many other men are part of the problem, even though they might not think so. I didn’t think I was part of the problem either. I hope that other men might read this and critically evaluate if they are #partoftheproblem.
Robert is a senior research associate in bioinformatics at the Moseley Bioinformatics and Systems Biology Lab, which is part of the Markey Cancer Center at the University of Kentucky. I work with our collaborators to analyse a variety of -omics data, including transcriptomics and metabolomics using both previously established and newly developed methods.
I have 12 years experience analysing -omics level data, and 7 as an R programmer and developer. I authored the
categoryCompare Bioconductor package
for comparing -omics data using annotations.