diveristy(): dealing with NA's

[baxter-jeremy]

Hi,

I am very new to diversity/ecological statistical analysis (day 1 in fact!). Thank you for a very useful package and the documentation. A quick comment/observation (and given my lack of ecological experience I am not sure if this is a feature): Consider a data frame named thedf with counts of various species (captured as columns) where each row is a particular site, then
diversity(thedf)
will return the Shannon diversity measure, but a particular site on a particular day (i.e. a row of the df) might be lost/missing for some reason, i.e. the original data might be correctly coded as NA for that entire row in the data frame, but diversity() will return
apply( -x*xlog(x,exp(1), margin=1,sum,na.rm=TRUE)
where x <- sweep(thedf, 1, total= apply(df,1,sum), "/")
i.e. 0 (zero)
Should diversity() not return a NA? Or should there not at least be a warning:

theNAindicies <- which(is.na(rowSums(thedf)))
if ( length(theNAindicies) == 0 ) { warning( "rows of missing data" ) }

Thank you.
Jeremy

[jarioksa]

diversity is a pretty simple function that does not check its input, but that is left as user's responsibility. For instance, it does not even check that input are non-negative. Giving zero-diversity for NA abundances does not look too bad. It would not be too complicated to fix both of these features (reject negative input, give NA if observation has any NA), but this can make diversity slower -- and the function can be called millions of times in simulations. Got to see this.

[gavinsimpson]

@jarioksa Both changes sound useful, from a user point of view. If such checks slow this down to the extent that the negatively impact simulations it sounds like we need a diversity.fit() function that does the actual diversity calculations on known good data, and that we make diversity() more of a user function. (All in the sense of lm and lm.fit).

[jarioksa]

microbenchmark showed no consistent difference in moderate data sets (BCI, Oribatid mites). Haven't merged this yet, but it seemed to work both for a single site and multi-site data sets.

[jarioksa]

Solved with commit 014b250. This commit also checks that data are non-negative.