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. […]
It’s come up now and then in Reviewer’ comments, written in papers, and during conference questions – are you using environmentally relevant concentrations (ERCs)? It is a good question but I think often over-simplistic in that it creates a false-dichotomy i.e. use of only ERCs is a good thing, and any use of non-ERCs is […]
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 […]
Recently the Australian and New Zealand Water Quality Guidelines (ANZECC) have been updated (Warne et al 2018) and one significant change was the preference of ‘No Effect Concentrations (NECs)’ above other statistical estimates of toxicity such as EC10s and NOECs. Here is a condensed list of the hierarchy from the Guidelines. NECs ECx where x […]
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 […]
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 […]
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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 […]
Some animations using gganimate.
This post will describe how to fit binomial GLMMs to a 3 fixed factor x 1 continuous factor design, a common design in wet-lab experiments. This design is my preferred design I used during my Postdoc for multifactor experiments because it accurately predicts the effect size (ECx) while investigating two factors. For example, you may […]