This website is focused on the use of R for all analyses. For most ordination methods we will use vegan package written by Jari Oksanen et al., with some functions also from ade4 by Stephen Dray & Anne B. Dufour and labdsv by Dave Roberts. You may want to, however, learn also some other software options. For most ordination methods, an excellent and user-friendly solution is CANOCO 5 (Windows only) developed by Cajo ter Braak & Petr Šmilauer, an update of favourite CANOCO for Windows 4.5 (see ad on Fig. 2 and check here if you want to know how does CANOCO 5 compare with vegan from the view of CANOCO authors). Although I prefer to do ordination analyses in R, I sometimes opt for CANOCO 5 because of its convenience, and also because it does great ordination diagrams (R is still staying behind in this aspect). Cluster analysis (and also most of the ordination methods) are available in PC-ORD 6 software of Bruce McCune et al. (see here for comparison of CANOCO 5 to PC-ORD 6); I must admit I do not favour this software for somewhat not an intuitive workflow, but it does offer a rather wide range of multivariate methods (some more elaborated than in CANOCO 5, e.g. NMDS with more options and detail report). For analysis of diversity (e.g. diversity indices or rarefaction) you may consider using EstimateS 9 by Robert R. Colwell. These are just some examples with which I am familiar; you may find a range of other (free or paid) software.
To conclude, the limnophase in oxbow lakes is stable water conditions, whereas the river is a dynamic environment. The disorder caused high biodiversity. The continuous disturbances are natural to rivers and the driving force for the ever-changing co-dominants. Species occurring in the river must continuously adapt to unstable conditions, and the rate of biodiversity is quite high. This rate is a reflection of co-dominance of many species. In the neighboring W-1 and W-2 lakes, the development of phytoplankton was undisturbed in the springtime when algal blooms occurred. From the beginning of June in the W-1 and W-2 lakes, free-floating plants covered the water surface which limited the growth of algal populations The lowest abundance of phytoplankton was recorded in the Ma lake with abundant submerged vegetation. There was no dominance of Cyanobacteria in any of the studied reservoirs.
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