# Articles by R on The broken bridge between biologists and statisticians

### Seed germination: fitting hydro-time models with R

March 22, 2020 |

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 ...

### Seed germination: fitting hydro-time models with R

March 22, 2020 |

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 ...

### Seed germination: fitting hydro-time models with R

March 22, 2020 |

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 ...

### A collection of self-starters for nonlinear regression in R

February 25, 2020 |

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 ...

### A collection of self-starters for nonlinear regression in R

February 25, 2020 |

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 lea...

### Self-starting routines for nonlinear regression models

February 13, 2020 |

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 ...

### Self-starting routines for nonlinear regression models

February 13, 2020 |

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...

### Some everyday data tasks: a few hints with R (revisited)

January 27, 2020 |

One year ago, I published a post titled ‘Some everyday data tasks: a few hints with R’. In that post, I considered four data tasks, that we all need to accomplish daily, i.e. subsetting sorting casting melting In that post, I used the methods I wa... [Read more...]

### Some everyday data tasks: a few hints with R (revisited)

January 27, 2020 |

One year ago, I published a post titled ‘Some everyday data tasks: a few hints with R’. In that post, I considered four data tasks, that we all need to accomplish daily, i.e. subsetting sorting casting melting In that post, I used the methods I was more familiar with. ... [Read more...]

### Nonlinear combinations of model parameters in regression

January 8, 2020 |

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 ...

### Nonlinear combinations of model parameters in regression

January 8, 2020 |

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...

### Fitting ‘complex’ mixed models with ‘nlme’: Example #4

September 12, 2019 |

Testing for interactions in nonlinear regression Factorial experiments are very common in agriculture and they are usually laid down to test for the significance of interactions between experimental factors. For example, genotype assessments may b...

### Fitting ‘complex’ mixed models with ‘nlme’: Example #2

September 12, 2019 |

A repeated split-plot experiment with heteroscedastic errors Let’s imagine a field experiment, where different genotypes of khorasan wheat are to be compared under different nitrogen (N) fertilisation systems. Genotypes require bigger plots, with r... [Read more...]

### Fitting ‘complex’ mixed models with ‘nlme’: Example #2

September 12, 2019 |

A repeated split-plot experiment with heteroscedastic errors Let’s imagine a field experiment, where different genotypes of khorasan wheat are to be compared under different nitrogen (N) fertilisation systems. Genotypes require bigger plots, with respect to fertilisation treatments and, therefore, the most convenient choice would be to lay-out the experiment ... [Read more...]

### Fitting ‘complex’ mixed models with ‘nlme’: Example #4

September 12, 2019 |

Testing for interactions in nonlinear regression Factorial experiments are very common in agriculture and they are usually laid down to test for the significance of interactions between experimental factors. For example, genotype assessments may be performed at two different nitrogen fertilisation levels (e.g. high and low) to understand whether ...

### Fitting ‘complex’ mixed models with ‘nlme’: Example #3

September 12, 2019 |

Accounting for the experimental design in regression analyses In this post, I am not going to talk about real complex models. However, I am going to talk about models that are often overlooked by agronomists and biologists, while they may be necessary in several circumstances, especially with field experiments. The ...

### Fitting ‘complex’ mixed models with ‘nlme’. Example #1

August 19, 2019 |

The environmental variance model Fitting mixed models has become very common in biology and recent developments involve the manipulation of the variance-covariance matrix for random effects and residuals. To the best of my knowledge, within the frame of frequentist methods, the only freeware solution in R should be based on ... [Read more...]

### Fitting ‘complex’ mixed models with ‘nlme’. Example #1

August 19, 2019 |

The environmental variance model Fitting mixed models has become very common in biology and recent developments involve the manipulation of the variance-covariance matrix for random effects and residuals. To the best of my knowledge, within the fra... [Read more...]

### Germination data and time-to-event methods: comparing germination curves

July 19, 2019 |

Very often, seed scientists need to compare the germination behaviour 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. How ...