phytotools-package: Phytoplankton Production Tools

Description Author(s) References


Fits PE and RLC data to one of a four published PE models. Simulates incident irradiance as a function of time and space. Calculates phytoplankton production by transposing modeled PE or RLC data to a water column with a user-defined theoretical in-situ irradiance field.


Greg M. Silsbe Sairah Y. Malkin

Maintainer: Greg Silsbe <>


Eilers, P.H.C. and Peeters, J.C.H. 1988 A model for the relationship between light intensity and the rate of photosynthesis in phytoplankton. Ecological Modeling. 42, 199–215.

Fee, E.J. 1990. Computer programs for calculating in-situ phytoplankton photosynthesis. Canadian technical report for fisheries and aquatic sciences. No. 1740.

Hofierka, J., and Suri, M. 2002 The solar radiation model for Open source GIS: Implementation and applications. Proceedings of the source GIS-GRASS users conference 2002.

Jassby, A.D.and Platt, T. 1976 Mathematical formulation of the relationship between photosynthesis and light for phytoplankton. Limnology and Oceanography. 21, 540–547.

Kirk, J.T.O., 2011 Light and photosynthesis in aquatic environments. Cambridge Press.

Platt, T., Gallegos, C.L. and Harrison, W.G. 1980 Photoinhibition and photosynthesis in natural assemblages of marine phytoplankton. Journal of Marine Research. 38, 687–701.

Silsbe, G.M., and Kromkamp, J.C. 2012 Modeling the irradiance dependency of the quantum efficiency of photosynthesis. Limnology and Oceanography: Methods. 10, 642–652.

Soetaert, K. and Petzoldt, T. 2010 Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME. Journal of Statistical Software. 33, 1?28.

Webb, W.L., Newton, M., and Starr, D. 1974 Carbon dioxide exchange of Alnus rubra: A mathematical model. Oecologia. 17, 281–291.

phytotools documentation built on May 29, 2017, 11:30 a.m.