Dear R experts, how are you?
I have a data bank in long format as below:
species month year plot density
sp1 1 2001 1 39
sp2 1 2001 1 6
sp3 1 2001 1 17
sp2 1 2001 2 35
sp3 1 2001 2 15
sp4 1 2001 2 27
sp1 2 2001 1 29
sp3 2 2001 1 49
sp4 2 2001 1 1
sp1 2 2001 2 8
sp4 2 2001 2 20
sp5 2 2001 2 41
... ... ... ... ...
I want to estimate the mean density of species in each month/year. So I
want to take the mean density of the plots for each month/year (there are
more than two plots). I used the function aggregate to make that
aggregate (density~species*month*year, mean, data=df)
species month year density
1 sp1 1 2001 39.0
2 sp2 1 2001 20.5
3 sp3 1 2001 16.0
4 sp4 1 2001 27.0
5 sp1 2 2001 18.5
6 sp3 2 2001 49.0
7 sp4 2 2001 10.5
8 sp5 2 2001 41.0
Not all species were sampled in all plots, and for those unsampled species
the estimated density should be zero for that plot. But the function
aggregate won?t make that. It will just look for densities of sampled
species and if it finds records of that species in two or more plots, then
it will take the average, but if it find only one value it will use that
unique value and the mean density will be biased.
So I think I should first transform this data to wide format, including all
combinations of species, month, year and plots, include zero where is NA?s,
retransform back to long format and continue with the analysis. But I don?t
know how to make it.
Thank you very much for any help and all the best for 2015!!
--
Diego PJ
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