Dienstag, 9. Mai 2017

Dose-response curve in R: the drc package

Thanks to the analysis of an interesting dataset I discovered the drc package for Dose-Response Analysis using R (Ritz et al, PLOS One 2015, https://doi.org/10.1371/journal.pone.0146021).

It comes with a very powerful optimiser for common models such as logistic function (or Hill function). Compared with the native R implementations using the nls function and self start models such as SSfpl, the drc package is far more reliable and robust: both initial parameter estimation and optimisation run without errors due to singularity : at least in the ~3,000 datasets that I tried, on which drc reported no single mistake, whereas nls failed as much as 600 cases despite of manually setting starting parameters with educated guess.

I still have to understand how the package achieves such good performance. However I am already very glad that we have finally a robust and reliable optimiser for curve fitting, which is a common task in computational biology and bioinformatics.

Figure: a 4-parameter logistic fit done and plotted with drc.

P.S. During the try-and-error process, I also accidentally found a website that is quite robust with regard to curve fitting: https://www.mycurvefit.com. Though I will not use it since I need programmatic access to the fitting capacity, the website's fitting function is quite robust in my opinion, at least better than the few examples that failed nls.