Groan – my first R package

August 20, 2013
By

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

Being one of two R experts at my current job I figured I should be familiar with package development. Frankly, I’ve been procrastinating on this topic since I started using R in 2007 – I was doing just fine with source() and the section of the R manual on package development fell into the category of TL;DR.

What finally drove me to learn the esoteric details of R packaging were the following two events at work:

  1. A coworker sent out an email announcing a new R analysis script which included a few algorithms I wrote and passed on. It was accompanied by documentation in a README.txt file and employed console menus and user dialogs to ease use. Otherwise, details of what the code was doing were left to code comments.

  2. I read an email train between coworkers after being out of the office and disconnected for a day asking about the correct set of parameters to use in a function I wrote. Fortunately, they figured it out thanks to my excessive commenting habits.

Lesson learned: I no longer write R code just for myself and using code comments as documentation just wasn’t cutting it anymore. I needed an efficient way to:

  • distribute code
  • provide documentation that uses the in-built help system

Unlike Matlab or Python, R does not have an effective way to provide simple documentation for code – functions, objects, etc. There is this post on StackOverflow, but I expect that such functionality should be built into the environment, not hacked on.

Long winded introduction over, I finally dove in. Thankfully, my entry wasn’t too rough. A couple months ago I read a couple posts submitted to R-bloggers regarding “easy” package development using roxygen2, devtools, and RStudio (my R IDE of choice).

My problem to solve: get parameters from biological growth curves
My package: groan

Package: groan
Type: Package
Title: Utilities for biological GROwth curve ANalysis
Version: 1.0
Date: 2013-05-14
Author: W. Lee Pang
Description: groan is a set of tools to assist in the analysis of biological
growth curves
. It provides functions to smooth input data and extract key
parameters such
as specific growth rate (mu), carrying capacity (A), and lag
time
(tau).

Working with microorganisms, a common task is determining a culture’s specific growth rate – e.g. how many times the population will double in an hour. While not a hard task, it can be tedious if numerous cultures are involved, or if the underlying data is noisy.

groan is essentially the R package I wish I had as a grad student and postdoc, but was too occupied otherwise to write.

Yes, the name groan is a pun:

  • “grown” : as in yay the cells grew
  • “groan” : as in ugh, I have to process yet another growth curve

Humor aside, it reduces a CSV of multiple growth curve data points into a table of growth parameters and a summary plot in under 10 lines of code.

From this …

Via …

Y = read.csv('path/to/your/data.csv', stringsAsFactors=F)
Y
= groan.init(Y)
Y
.s = groan.smooth(Y, adaptive=T, method='loess')

U
= groan.mu(Y.s)
U
.s = groan.smooth(U, adaptive=T, method='loess')
U
.f = groan.fit(U.s, method='pulse')

stats
= data.frame(mumax = max(U.f),
t
.lag = groan.tlag(U.f),
gen
= groan.generations(U.f))

plot
(Y) # plot thumbnail grid of raw growth curves

To …

For more information, examples, or to test out the code yourself head to the groan repository on Github.

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