Package ‘photobiologyFlecks’ it is at a very early stage of development. This package is incomplete, subject to changes and possibly useful.
The package attempts to facilitate the analysis of time series of irregulary varying irradiance data. It will support of fragmented time series were data acquisition takes place at high frequency during bursts separated by gaps with no data. As my own data consist in some cases in multivariate time series with several millions of observations grouped in bursts of tenths of thousands, I aim at efficient code. As a personal challenge, I aim to see if this is possible using pure R code with well know packages.
This package will be released as part of a suite of R packages for photobiological calculations described at the r4photobiology.
Examples
No examples yet, as the data files that this package is designed to work with are too large to include as data in the package. A toy data set will be needed.
Installation
Installation of the most recent stable version from CRAN:
# NOT IN CRAN
# install.packages("photobiology")Installation of the current unstable version from R-Universe CRAN-like repository:
install.packages('photobiologyFlecks',
repos = c('https://aphalo.r-universe.dev',
'https://cloud.r-project.org'))The two approaches above, automatically install dependencies.
Installation of the current unstable version from GitHub:
# install.packages("devtools")
devtools::install_github("aphalo/photobiologyFlecks")Installation from GitHub sources does not automatically install dependencies. Once package ‘photobiologyFlecks’ is installed, installation of the remaining or missing packages from CRAN should be done manually.
Documentation
HTML documentation is available at (https://docs.r4photobiology.info/photobiologyFlecks/), including an User Guide.
References
Durand M, Matule B, Burgess AJ, Robson TM. 2021. Sunfleck properties from time series of fluctuating light. Agricultural and Forest Meteorology 308-309, 108554. DOI: https://doi.org/10.1016/j.agrformet.2021.108554
Contributing
Pull requests, bug reports, and feature requests are welcome at (https://github.com/aphalo/photobiologyFlecks).
Citation
If you use this package to produce scientific or commercial publications, please cite according to:
citation("photobiologyFlecks")
#> To cite package 'photobiologyFlecks' in publications use:
#>
#> Aphalo P, Durand M (2026). _photobiologyFlecks: Analysis of sun- and
#> shade flecks_. R package version 0.0.0.9000,
#> <https://docs.r4photobiology.info/photobiologyFlecks/>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {photobiologyFlecks: Analysis of sun- and shade flecks},
#> author = {Pedro J. Aphalo and Maxime Durand},
#> year = {2026},
#> note = {R package version 0.0.0.9000},
#> url = {https://docs.r4photobiology.info/photobiologyFlecks/},
#> }