Publications by R on The broken bridge between biologists and statisticians
Split-plot designs: the transition to mixed models for a dinosaur
Those who long ago took courses in ‘analysis of variance’ or ‘experimental design’ … would have learned methods … based on observed and expected mean squares and methods of testing based on ‘error strata’ (if you weren’t forced to learn this, consider yourself lucky). (Douglas Bates, 2006). In a previous post, I already mention...
15015 sym R (5179 sym/11 pcs)
Split-plot designs: the transition to mixed models for a dinosaur
Those who long ago took courses in ‘analysis of variance’ or ‘experimental design’ … would have learned methods … based on observed and expected mean squares and methods of testing based on ‘error strata’ (if you weren’t forced to learn this, consider yourself lucky). (Douglas Bates, 2006). In a previous post, I already mention...
14951 sym R (4902 sym/11 pcs)
lmDiallel: a new R package to fit diallel models. The Gardner-Eberhart models
Another post for this series about diallel mating experiments. So far, we have published a paper in Plant Breeding (Onofri et al., 2020), where we presented lmDiallel, a new R package to fit diallel models. We followed up this paper with a series of four blog posts, giving more detail about the package (see here), about the Hayman’s models type...
8888 sym R (12228 sym/9 pcs)
lmDiallel: a new R package to fit diallel models. The Gardner-Eberhart models
Another post for this series about diallel mating experiments. So far, we have published a paper in Plant Breeding (Onofri et al., 2020), where we presented lmDiallel, a new R package to fit diallel models. We followed up this paper with a series of four blog posts, giving more detail about the package (see here), about the Hayman’s models type...
8888 sym R (12228 sym/9 pcs)
lmDiallel: a new R package to fit diallel models. Multienvironment diallel experiments
In recent times, a few colleagues at my Department and I have devoted some research effort to data management for diallel mating experiments, which we have summarised in a paper (Onofri et al., 2020) and a series of five blog posts (see here). A final topic that remains to be covered relates to the frequent possibility that these diallel experime...
4553 sym R (6313 sym/6 pcs)
The R-squared and nonlinear regression: a difficult marriage?
Making sure that a fitted model gives a good description of the observed data is a fundamental step of every nonlinear regression analysis. To this aim we can (and should) use several techniques, either graphical or based on formal hypothesis testing methods. However, in the end, I must admit that I often feel the need of displaying a simple inde...
4940 sym R (285 sym/1 pcs)
Other useful functions for nonlinear regression: threshold models and all that
In a recent post I presented several equations and just as many self-starting functions for nonlinear regression analyses in R. Today, I would like to build upon that post and present some further equations, relating to the so-called threshold models. But, … what are threshold models? In some instances, we need to describe relationships where t...
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Why are derivatives important in biology? A case-study with nonlinear regression
In general, undergraduate students in biology/ecology courses tend to consider the derivatives as a very abstract entity, with no real usefulness in the everyday life. In my work as a teacher, I have often tried to fight against such an attitude, by providing convincing examples on how we can use the derivatives to get a better understanding abou...
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Analysing seed germination and emergence data with R (a tutorial). Part 1
Introduction to the tutorial Germination/emergence assays are relatively easy to perform, by following standardised procedures, as described, e.g., by the International Seed Testing Association (see here ). In short, we take a sample of seeds and we put them in an appropriate container. We put the container in the right environmental conditions (...
4233 sym R (85 sym/1 pcs)
Analysing seed germination and emergence data with R (a tutorial). Part 2
Survival analysis and germination/emergence data: an overlooked connection Seed germination and emergence data describe the time until the event of interest occurs and, therefore, they can be put together in the wide group of time-to-event data. You may wonder: what’s the matter with time-to-event data? Do they have anything special that needs ...
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