Fitting a hydro-thermal-time-model to seed germination data

Published at January 10, 2023 ·  11 min read

This is a follow-up post. If you are interested in other posts of this series, please go to: https://www.statforbiology.com/tags/drcte/. All these posts exapand on a paper that we have recently published in the Journal ‘Weed Science’; please follow this link to the paper. Germination assay This dataset was obtained from previously published work (Mesgaran et al., 2017) with Hordeum spontaneum [C. Koch] Thell. The germination assay was conducted using four replicates of 20 seeds tested at six different water potential levels (0, −0....

The coefficient of determination: is it the R-squared or r-squared?

Published at November 26, 2022 ·  9 min read

We often use the coefficient of determination as a swift ‘measure’ of goodness of fit for our regression models. Unfortunately, there is no unique symbol for such a coefficient and both \(R^2\) and \(r^2\) are used in literature, almost interchangeably. Such an interchangeability is also endorsed by the Wikipedia (see at: https://en.wikipedia.org/wiki/Coefficient_of_determination ), where both symbols are reported as the abbreviations for this statistical index. As an editor of several International Journals, I should not agree with such an approach; indeed, the two symbols \(R^2\) and \(r^2\) mean two different things, and they are not necessarily interchangeable, because, depending on the setting, either of the two may be wrong or ambiguous....

Multi-environment split-plot experiments

Published at September 13, 2022 ·  7 min read

Have you made a split-plot field experiment? Have you repeated such an experiment in two (or more) years/locations? Have you run into troubles, because the reviewer told you that your ANOVA model was invalid? If so, please, stop for awhile and read: this post might help you understand what was wrong with your analyses. Motivating example Let’s think of a field experiment, where 6 genotypes of faba bean were compared under two different sowing times (autumn and spring)....

Meta-analysis for a single study. Is it possible?

Published at July 21, 2022 ·  12 min read

We all know that the word meta-analysis encompasses a body of statistical techniques to combine quantitative evidence from several independent studies. However, I have recently discovered that meta-analytic methods can also be used to analyse the results of a single research project. That happened a few months ago, when I was reading a paper from Damesa et al. (2017), where the authors describe some interesting methods of data analyses for multi-environment genotype experiments....

Should I say ''there is no difference'' or ''the difference is not significant''?

Published at June 1, 2022 ·  5 min read

In a recent manuscript we wrote a sentence similar to the following: “On average, the genotype A gave a yield of 12.4 tons per hectare, while the genotype B gave 10.6 tons per hectare and such a difference was not significant (P = 0.20)”. Perhaps I should point out that we were talking about maize yields… One of the reviewers complained that “This is an example of expression having no place in a scientific paper” and that we should write: “… no difference in yield was found between A and B (P = 0....

Analysing seed germination and emergence data with R (a tutorial). Part 9

Published at January 18, 2022 ·  10 min read

This is a follow-up post. If you are interested in other posts of this series, please go to: https://www.statforbiology.com/tags/drcte/. All these posts expand on a manuscript that we have recently published in the Journal ‘Weed Science’; please follow this link to the paper. In order to work throughout this post, you need to install the ‘drcte’ and ‘drcSeedGerm’ packages, by using the code provided in this page. Quantiles from time-to-event models We have previously shown that time-to-event models (e....

Analysing seed germination and emergence data with R (a tutorial). Part 8

Published at January 18, 2022 ·  8 min read

This is a follow-up post. If you are interested in other posts of this series, please go to: https://www.statforbiology.com/tags/drcte/. All these posts expand on a paper that we have recently published in the Journal ‘Weed Science’; please follow this link to the paper. Predictions from a parametric time-to-event model In previous posts we have shown that time-to-event models (e.g., germination or emergence models) can be used to describe the time course of germinations/emergences for a seed lot (this post) or for several seed lots, submitted to different experimental treatments (this post)....

Analysing seed germination and emergence data with R (a tutorial). Part 7

Published at January 18, 2022 ·  4 min read

This is a follow-up post. If you are interested in other posts of this series, please go to: https://www.statforbiology.com/tags/drcte/. All these posts expand on a paper that we have recently published in the Journal ‘Weed Science’; please follow this link to the paper. Exploring the results of a time-to-event fit: model parameters In the previous post we have shown that time-to-event curves (e.g., germination or emergence curves) can be used to describe the time course of germinations/emergences for a seed lot (this post)....

Analysing seed germination and emergence data with R (a tutorial). Part 6

Published at January 18, 2022 ·  13 min read

This is a follow-up post. If you are interested in other posts of this series, please go to: https://www.statforbiology.com/tags/drcte/. All these posts exapand on a paper that we have recently published in the Journal ‘Weed Science’; please follow this link to the paper. Fitting time-to-event models with environmental covariates In the previous post we have shown that time-to-event curves (e.g., germination or emergence curves) can be used to describe the time course of germinations/emergences for a seed lot (this post)....

Analysing seed germination and emergence data with R: a tutorial. Part 5

Published at December 23, 2021 ·  14 min read

This is a follow-up post. If you are interested in other posts of this series, please go to: https://www.statforbiology.com/tags/drcte/. All these posts exapand on a paper that we have recently published in the Journal ‘Weed Science’; please follow this link to the paper. Comparing germination/emergence for several seed lots Very often, seed scientists need to compare the germination behavior of different seed populations, e.g., different plant species, or one single plant species submitted to different temperatures, light conditions, priming treatments and so on....