Fixing the bridge between biologists and statisticians – Statforbiology

Finally migrating to Quarto

An introduction with R

news

A few months ago, my blogdown-based blogs started giving me a few headaches, after more than seven years of remarkably reliable service. After doing some research on the web…

General code to fit ANOVA models with JAGS and ‘rjags’

R

JAGS

Bayesian_stat

R-bloggers

There is a quote I really love from Marc Kéry’s book, “Introduction to WinBUGS for Ecologists” (2010, p. 11):

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

R

Time_to_event_models

Seed_germination

drcte

drcSeedGerm

R-bloggers

Germination and emergence assays are pretty straightforward to set up: you grab a sample of seeds, put them in a container under controlled environmental conditions…

From ‘’for()’’ loops to the ‘’split-apply-combine’’ paradigm for column-wise tasks in R

R

Data management

tidyverse

dplyr

R-bloggers

Today, I want to discuss performing column-wise tasks on relatively large datasets. These tasks are particularly common in agricultural and biological research, where we…

Some everyday data tasks: a few hints with R (for dinosaurs)

R

R-bloggers

Data management

dplyr

tidyr

tidyverse

It is important to know how to reshape a dataframe for data analysis. Personally, I also value being able to perform the most important reshaping tasks (and other common…

Dual scaled y-axis with ggplot()

R

R-bloggers

ggplot

I have often found myself needing to plot a single graph with two y-axes having different scales. For example, this might be useful for representing temperature and rainfall…

Some useful equations for biological processes

nonlinear regression

R-bloggers

Biological phenomena are often studied by examining how a numerical variable, usually called the response (e.g., the weight or height of an organism), is affected by another…

A collection of self-starters for nonlinear regression in R

R

nonlinear regression

R-bloggers

Usually, the first step in every nonlinear regression analysis is to select the function \(f\) that best describes the phenomenon under study. The next step is to fit this…

Migration from Blogdown to Quarto

R

quarto

More than twenty-five years ago, I had the idea that having a website would be a good way to store my teaching and research materials, keep them organised, retrieve them…

How do we combine errors, in biology? The delta method

R

general

R-bloggers

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 \(X\) and \(Z\)…

Field Research methods in Agriculture

An introduction with R

news

Hi everybody, I have exciting news!

How do we combine errors? The linear case

R

linear models

R-bloggers

In our research work, we usually fit models to experimental data. Our aim is to estimate some biologically relevant parameters, together with their standard errors. Very…

Accounting for the experimental design in linear/nonlinear regression analyses

R

Mixed models

nonlinear regression

nlme

R-bloggers

In this post, I am going to talk about an issue that is often overlooked by agronomists and biologists. The point is that field experiments are very often laid down in…

QQ-plots and Box-Whisker plots: where do they come from?

R

descriptive statistics

R-bloggers

This post is ‘only’ for the most curious students…

Self-starting routines for nonlinear regression models

R

nonlinear regression

R-bloggers

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…

My learning path with blogdown

R

This is my first day at work with blogdown. I must admit it is pretty overwhelming at the beginning …

The Variance Puzzle: Why Doesn’t R Divide by ‘n’?

descriptive statistics

R-bloggers

Teaching Experimental Methodology in master’s courses related to agriculture poses some peculiar challenges. One of them is explaining the difference between population…

Is R dangerous? Side effects of free software for biologists

R

R-bloggers

When I started my career in biology (almost forty years ago), only the luckiest of us had access to advanced statistical software. Licences were very expensive, and it was…