Automated rapid light curve analyses in R

The objective of this post is to simplify and automate the process of conducting rapid light curve analysis from a Walz Pulse Amplitude Modulation Fluorometry (PAM) fluorometer using their WinControl generated csv files. The first time I did this I jumped around between Excel and Graphpad and eventually finished my analysis in under a day. […]


Bundle ballasting model in shiny

A few years ago I was lucky enough to collaborate with prominent researcher in fluid mechanics, Roman Stocker. We developed a mathematical mechanistic model to predict if coral egg-sperm bundles released during coral spawning could possibly sink (ballast) after encounters with sediment grains, as a function of depth, suspended sediment concentration and grain size. However […]

Calculating p-value intervals using bootstrapping

In my previous posts, I showed how we can use simulated data to calculate power and sample size analyses, and estimate distributions around the effect size. But we can also use simulated data to estimate error around p-values. Unless you have been living under a rock, you should know p-values have been getting smashed for […]

Comparing EC50s between two or more GLMM models

In this post I am going to describe how to compare EC50s from two or more GLMM curves. To begin, run the code in my recent post Automated three factor dose-response with binomial GLMMs and ECx’s“ In the post above we calculated the 95% CI around the ECx using an approximation by multiplying the standard error […]

Power/ sample size analysis for dose-response binomial GLMMs

A few tools have come available recently that has aided power analysis of more complicated models. Here I am going to recreate Johnson et al 2015 – Power analysis for generalized linear mixed models in ecology and evolution for typical survival dose-response data. You can also find their examples attached to their paper. How it works […]