Hi all, how does one correctly set up the input dataframes for an mrpp analysis in VEGAN, assuming a clone sequence library is your sample data? The following example uses the dune meadow vegetation data set to clarify the issue.
EXAMPLE: *Input data*: (a) clone library sequences that have been clustered into OTUs, (b) ecological data associated with the clone sequences (but not necessarily with the OTUs!) *Data matrix preparation*: To produce the observations/sites dataframe (e.g. dune), I assign (1) clones as observations, and (2) OTUs as sites. (Note: Since OTUs can be associated with multiple clone sequences, but each clone sequence can only be associated with one OTU, a dataframe set up with clones as sites and OTUs as observations is not useable.) To produce the environmental variables/sites dataframe (e.g. dune.env), I assign (1) the ecological data as environmental variables, and (2) the OTUs as sites. *Problem*: Given that some OTUs consist of clone sequences with different levels of the ecological variables (e.g. "BF" for some clones and "SF" for others), I either need to produce a combined variable level ("BFandSF"), or I split the OTU into clones homogeneous for the respective ecological variable. Hence, the observations/sites dataframe has now one more site. *My thoughts*: The first solution generates ecological variable levels that I am not interested in. The latter solution (done in various recent publications) might not be statistically sound, as the within-group sites are artificially increased. *My question*: Is the latter approach indeed problematic (e.g. maybe causing a type I error?), and are there strategies to circumvent the problem? Many thanks, Michael -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Setting-up-dataframes-for-MRPP-given-clone-library-data-tp7335129p7335129.html Sent from the r-sig-ecology mailing list archive at Nabble.com. _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology