Archive 2020

Fitting complex mixed models with nlme. Example #5

Published at June 5, 2020 ·  14 min read

A Joint Regression model Let’s talk about a very old, but, nonetheless, useful technique. It is widely known that the yield of a genotype in different environments depends on environmental covariates, such as the amount of rainfall in some critical periods of time. Apart from rain, also temperature, wind, solar radiation, air humidity and soil characteristics may concur to characterise a certain environment as good or bad and, ultimately, to determine yield potential....


AMMI analyses for GE interactions

Published at May 12, 2020 ·  19 min read

The CoViD-19 situation in Italy is little by little improving and I feel a bit more optimistic. It’s time for a new post! I will go back to a subject that is rather important for most agronomists, i.e. the selection of crop varieties. All farmers are perfectly aware that crop performances are affected both by the genotype and by the environment. These two effects are not purely additive and they often show a significant interaction....


Seed germination: fitting hydro-time models with R

Published at March 23, 2020 ·  17 min read

I am locked at home, due to the COVID-19 emergency in Italy. Luckily I am healthy, but there is not much to do, inside. I thought it might be nice to spend some time to talk about seed germination models and the connections with survival analysis. We all know that seeds need water to germinate. Indeed, the absorption of water activates the hydrolytic enzymes, which break down food resources stored in seeds and provide energy for germination....


A collection of self-starters for nonlinear regression in R

Published at February 26, 2020 ·  29 min read

Usually, the first step of every nonlinear regression analysis is to select the function \(f\), which best describes the phenomenon under study. The next step is to fit this function to the observed data, possibly by using some sort of nonlinear least squares algorithms. These algorithms are iterative, in the sense that they start from some initial values of model parameters and repeat a sequence of operations, which continuously improve the initial guesses, until the least squares solution is approximately reached....


Self-starting routines for nonlinear regression models

Published at February 14, 2020 ·  8 min read

In R, the drc package represents one of the main solutions for nonlinear regression and dose-response analyses (Ritz et al., 2015). It comes with a lot of nonlinear models, which are useful to describe several biological processes, from plant growth to bioassays, from herbicide degradation to seed germination. These models are provided with self-starting functions, which free the user from the hassle of providing initial guesses for model parameters. Indeed, getting these guesses may be a tricky task, both for students and for practitioners....


Nonlinear combinations of model parameters in regression

Published at January 9, 2020 ·  11 min read

Nonlinear regression plays an important role in my research and teaching activities. While I often use the ‘drm()’ function in the ‘drc’ package for my research work, I tend to prefer the ‘nls()’ function for teaching purposes, mainly because, in my opinion, the transition from linear models to nonlinear models is smoother, for beginners. One problem with ‘nls()’ is that, in contrast to ‘drm()’, it is not specifically tailored to the needs of biologists or students in biology....