Pages from R for Photobiology

Introduction to Mixed Effects Models

Pedro J. Aphalo — Wed, 22 Jan 2025 22:00:00 GMT

The content of this page is only lightly edited from overhead transparencies I used in teaching a course on longitudinal data between 2001 and 2005 at the University of Jyväskylä, Finland. Nowadays, package ‘lme4’ provides an alternative approach to the fitting of LME. Package ‘nlme’ does however support the fitting of both LMEs and NLMEs, and is used in these pages. Package ‘nlme’ is one of the recommended packages included in the R installation.

R Packages: Timeline of Updates

Pedro J. Aphalo — Fri, 12 Jul 2024 21:00:00 GMT

The sources of the R packages I have published are in public Git repositories at [GitHub}(https://github.com/aphalo). Out of the packages that I have authored and maintain, 15 are currently available through CRAN. The total number of packages submissions to CRAN (mostly updates) as author and maintainer is 239 since 2016-01-29. The most recent of these updates was published in CRAN on 2026-01-18.

Plotting circular data with ‘ggplot2’

Pedro J. Aphalo — Tue, 05 Mar 2024 22:00:00 GMT

To see the source of this document click on “ CODE” to the right of the page title. The page is written using Quarto which is an enhanced version of R Markdown. The diagrams are created with Mermaid, a language inspired by the simplicity of Markdown.

‘ooacquire’: Spectral Irradiance Algorithms

Pedro J. Aphalo — Fri, 12 Jan 2024 22:00:00 GMT

Package ‘ooacquire’ is part of the R for Photobiology suite of R packages and its full documentation is available on-line. It depends on package ‘rOmniDriver’, whose full documentation is also available on-line.

Alternative approaches

Pedro J. Aphalo — Wed, 29 Nov 2023 22:00:00 GMT

In this page some code chunks are “folded” so as to decrease the clutter. Above the R output, text or plots, you will find a small triangle followed by “Code”. Clicking on the triangle “unfolds” the code chunk making visible the R code used to produce the output shown. The code in the chunks can be copied by clicking on the top right corner, where an icon appears when the mouse cursor hovers over the code listing.

Linear Models

Pedro J. Aphalo — Sun, 26 Nov 2023 22:00:00 GMT

Fitting a model to data consists in finding the parameter values that best explain the data or observations. These parameter values are estimates of those in a larger population of possible observations from which we have drawn a sample or subset. For deciding what is best, we need a criterion, and the most frequently used one is minimizing the “residual variance” by the method of ordinary least squares (OLS).

Theoretical probability distributions

Pedro J. Aphalo — Mon, 20 Nov 2023 22:00:00 GMT

Three Apps or dashboards created with R package Shiny. It takes a few moments to activate the Apps in the server as they are stopped after 10 min without user interaction.

Flow of code execution

Pedro J. Aphalo — Fri, 17 Nov 2023 22:00:00 GMT

In a simple script the code statements are run (= executed, = evaluated) one after another as they appear in the file, from top to bottom. A simple script then always runs the same statements carrying out each time the script is run the same computations.

Design of Experiments

Pedro J. Aphalo — Fri, 20 Oct 2023 21:00:00 GMT

When defining the research hypothesis we need to decide on the range of validity or the “population of interest”. Usually there is compromise to be found between the cost or sensitivity of an experiment and its range of validity.

R at its simplest

Pedro J. Aphalo — Mon, 18 Sep 2023 21:00:00 GMT

For the simplest computations there is little difference between a calculator and R (e.g., if one uses the number pad of the computer keyboard). Nowadays, advanced calculators show the entered text in full, like R does. One uses enter in R, instead of the equals key in a calculator.

Research as a process

Pedro J. Aphalo — Fri, 18 Aug 2023 21:00:00 GMT

I have changed the title of this page from its original P-values, R², AIC, BIC: How do they fit into the research process? into Research as a process: Design, realization, data analysis, and communication. The original title reflected that the usefulness and interpretation of estimates of different statistical parameters depends on the design of an experiment and the nature of the researchers’ hypotheses.

Randomization and independent replicates

Pedro J. Aphalo — Mon, 29 May 2023 21:00:00 GMT

In an experiment we study how the manipulations done by the researcher(s) (treatments; käsittelyt) affect the observed response (vaste- eli tulosmuuttuja). Factors (faktorit) are groups of different manipulations of a single variable. Each of the distinct manipulations within a factor is called a level (e.g. five genotypes such as wild type (WT) and four mutants).

Model fitting in R

Pedro J. Aphalo — Mon, 29 May 2023 21:00:00 GMT

EDA with ‘ggplot2’

Pedro J. Aphalo — Tue, 23 May 2023 21:00:00 GMT

‘ggplot2’ Basics

Pedro J. Aphalo — Tue, 02 May 2023 21:00:00 GMT

Markdown Basics (PARTIAL DRAFT)

Pedro J. Aphalo — Tue, 02 May 2023 21:00:00 GMT

‘ooacquire’: Spectral Irradiance Measurement

Pedro J. Aphalo — Wed, 26 Apr 2023 21:00:00 GMT

Spectral fluorescence with ‘ooacquire’

Pedro J. Aphalo — Wed, 26 Apr 2023 21:00:00 GMT

I used an old Ocean Optics USB2000 array spectrometer with an Ocean Optics reflectance probe type QR200-REF-UV-VIS with the measuring fibre attached to the spectrometer, the excitation fibre attached to an Amphenol SMA “bulkhead” (receptacle flange mount 905-117-5000) while the reference branch remained detached. The probe both delivers the excitation and collects the radiation to be measured. For measurements the probe was set normal to the measured surface.

OmniDriver, Java and the whims of companies

Pedro J. Aphalo — Sun, 19 Mar 2023 22:00:00 GMT

[July 2024] OceanOptics has discontinued support for ‘OmniDriver’, and moved the installer to a page that is not easy to find: https://www.oceanoptics.com/software/resources/discontinued-software/. [August 2025] This made me wrongly think that OmniDriver was no longer available. However, based on answers received from Ocean Optics support, discontinuation of OmniDriver means that it will no longer be updated to support new spectrometer models and that the developer kit version is no longer available for purchase. It can be still downloaded and the runtime installed for free as earlier. Consequently, R can still be used to acquire spectra with package ‘ooacquire’ with ‘rOmniDriver’ as its back end, with most Ocean Optics spectrometers.

R Packages

Pedro J. Aphalo — Fri, 03 Mar 2023 22:00:00 GMT