The standard zooplankton, phytoplankton, and microbial plankton time series analyses and graphical visualizations used by COPEPODITE were initially developed in-support-of and in-collaboration-with multiple SCOR and ICES plankton time series working groups.
At this time, a comprehensive "methods" document does not exist, but it is in the works.
Until this is available, we will redirect you to the reports and publications that use, contain, and describe these techniques. The most recent of those reports is below:
A simple analysis for a complex data type.
The COPEPOD / COPEPODITE / WG125 / WGZE / WG137 / WGPME "standard time series analysis and visualization" methods are designed to allow for easy comparison of plankton (and other hydrographic variables) of different types, methods, and sampling frequencies (e.g., "biomass sampled three times per year" vs. "copepod abundance sampled weekly").
This is accomplished by looking at relative changes in the data values within a single time-series, relative to the long term average of those data, expressed as a unit-less ratio (or "anomaly").
A full summary of this method is summarized in O'Brien et al. 2013 and O'Brien et al. 2012, available via links above and below.
Paerl, H.W., K. Yin, T.D. O'Brien, SCOR Working Group 137: "Global Patterns of Phytoplankton Dynamics in Coastal Ecosystems": An introduction to the special issue of Estuarine, Coastal and Shelf Science, Estuarine, Coastal and Shelf Science, Volume 162, 5 September 2015, Pages 1-3, ISSN 0272-7714, https://dx.doi.org/10.1016/j.ecss.2015.07.011
O'Brien, T.D., Wiebe, P.H., and Falkenhaug, T. (Eds). 2013. ICES Zooplankton Status Report 2010/2011. ICES Cooperative Research Report No. 318. 208 pp.
Document Link: CRR-318 Zooplankton Status Report: 28 MBytes
Mackas, D.L., P. Pepin, H. Verheye, Interannual variability of marine zooplankton and their environments: Within- and between-region comparisons, Progress in Oceanography, Volumes 97-100, May-July 2012, Pages 1-14, ISSN 0079-6611, https://dx.doi.org/10.1016/j.pocean.2011.11.002">https://dx.doi.org/10.1016/j.pocean.2011.11.002
O'Brien, T.D., Wiebe, P.H., and Hay, S. (Eds). 2010. ICES Zooplankton Status Report 2008/2009. ICES Cooperative Research Report No. 307. 152 pp.
Document Link: CRR-307 Zooplankton Status Report: 6.5 MBytes
O'Brien, T.D., Lopez-Urrutia, A., Wiebe, P.H., and Hay, S. (Eds). 2008. ICES Zooplankton Status Report 2006/2007. ICES Cooperative Research Report No. 292. 168 pp.
Document Link: CRR-292 Zooplankton Status Report: 10.7 MBytes
Mackas, D. L., Thomson, R. E., and Galbraith, M. 2001. Changes in the zooplankton community of the British Columbia continental margin, 1985–1999, and their covariation with oceanographic conditions. Canadian Journal of Fisheries and Aquatic Sciences, 58: 685–702