Some everyday data tasks: a few hints with R (revisited)
Published at January 28, 2020 · 12 min read
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.
In that post, I used the methods I was more familiar with. And, as a long-time R user, I have mainly incorporated in my workflow all the functions from the base R implementation.
...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. Therefore, now and then, I have to build some helper functions, to perform some specific tasks; I usually share these functions within the ‘aomisc’ package, that is available on github (see this link).
...Testing for interactions in nonlinear regression
Published at September 13, 2019 · 11 min read
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 the ranking of genotypes depends on nutrient availability. For those of you who are not very much into agriculture, I will only say that such an assessment is relevant, because we need to know whether we can recommend the same genotypes, e.g., both in conventional agriculture (high nitrogen availability) and in organic agriculture (relatively lower nitrogen availability).
...Fitting 'complex' mixed models with 'nlme': Example #2
Published at September 13, 2019 · 9 min read
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 as a split-plot, in a randomised complete block design. Genotypes would be randomly allocated to main plots, while fertilisation systems would be randomly allocated to sub-plots. As usual in agricultural research, the experiment should be repeated in different years, in order to explore the environmental variability of results.
...Fitting 'complex' mixed models with 'nlme'. Example #1
Published at August 20, 2019 · 9 min read
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 the ‘nlme’ package, as the ‘lmer’ package does not easily permit such manipulations. The ‘nlme’ package is fully described in Pinheiro and Bates (2000). Of course, the ‘asreml’ package can be used, but, unfortunately, this is not freeware.
...Germination data and time-to-event methods: comparing germination curves
Published at July 20, 2019 · 11 min read
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 should such a comparison be performed?
Let’s take a practical approach and start from an appropriate example: a few years ago, some collegues studied the germination behaviour for seeds of a plant species (Verbascum arcturus, BTW…), in different conditions. In detail, they considered the factorial combination of two storage periods (LONG and SHORT storage) and two temperature regimes (FIX: constant daily temperature of 20°C; ALT: alternating daily temperature regime, with 25°C during daytime and 15°C during night time, with a 12:12h photoperiod). If you are a seed scientist and are interested in this experiment, you’ll find detail in Catara et al. (2016).
...Survival analysis and germination data: an overlooked connection
Published at July 2, 2019 · 16 min read
Seed germination data describe the time until an event of interest occurs. In this sense, they are very similar to survival data, apart from the fact that we deal with a different (and less sad) event: germination instead of death. But, seed germination data are also similar to failure-time data, phenological data, time-to-remission data… the first point is: germination data are time-to-event data.
You may wonder: what’s the matter with time-to-event data? Do they have anything special? With few exceptions, all time-to-event data are affected by a certain form of uncertainty, which takes the name of ‘censoring’. It relates to the fact that the exact time of event may not be precisely know. I think it is good to give an example.
...Stabilising transformations: how do I present my results?
Published at June 15, 2019 · 5 min read
ANOVA is routinely used in applied biology for data analyses, although, in some instances, the basic assumptions of normality and homoscedasticity of residuals do not hold. In those instances, most biologists would be inclined to adopt some sort of stabilising transformations (logarithm, square root, arcsin square root…), prior to ANOVA. Yes, there might be more advanced and elegant solutions, but stabilising transformations are suggested in most traditional biometry books, they are very straightforward to apply and they do not require any specific statistical software. I do not think that this traditional technique should be underrated.
...Genotype experiments: fitting a stability variance model with R
Published at June 6, 2019 · 8 min read
Yield stability is a fundamental aspect for the selection of crop genotypes. The definition of stability is rather complex (see, for example, Annichiarico, 2002); in simple terms, the yield is stable when it does not change much from one environment to the other. It is an important trait, that helps farmers to maintain a good income in most years.
Agronomists and plant breeders are continuosly concerned with the assessment of genotype stability; this is accomplished by planning genotype experiments, where a number of genotypes is compared on randomised complete block designs, with three to five replicates. These experiments are repeated in several years and/or several locations, in order to measure how the environment influences yield level and the ranking of genotypes.
...How do we combine errors, in biology? The delta method
Published at May 25, 2019 · 7 min read
In a recent post I have shown that we can build linear combinations of model parameters (see here ). For example, if we have two parameter estimates, say Q and W, with standard errors respectively equal to \(\sigma_Q\) and \(\sigma_W\), we can build a linear combination as follows:
\[ Z = AQ + BW + C\]
where A, B and C are three coefficients. The standard error for this combination can be obtained as:
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