Hello,
Yes, you can use lapply. Maybe something like the following. Note that
the result is a list with one member per species. (Untested).
ddeg.correlog.list <- lapply(9:11, function(p)
correlog(plant[plant[,p]=="1", 2], plant[plant[,p]=="1", 3],
plant[plant[,p]=="1", 4]))
Hope this helps,
Rui Barradas
Em 23-10-2014 16:06, Sarah escreveu:
Hello List,
I have a database which consist of 912 plots. For each plot, I have the
presence/absence information of 260 species of plants and also 5 different
environmental variables (ddeg, mind, srad, slp, topo).
The dataframe looks like this:
Plot_Number X Y ddeg mind srad slp topo
Galium_mollugo Gentiana_nivalis
1 1 557747.6 149726.8 2598 -625 236363 8 176
0 0
2 2 572499.4 145503.5 2178 -176 161970 14 -137
0 0
3 3 579100.4 151800.4 1208 632 267572 33 129
0 0
4 4 581301.7 150300.1 1645 83 246633 15 -70
0 0
5 5 579838.7 124770.9 1102 1637 158300 2 -231
0 0
6 6 577011.1 121328.6 731 2223 180286 41 70
0 0
Now, what I wanted to do is to calculate spatial autocorrelation of each
environmental variable for each species, but only for the plots where the
species is present.
I will use the correlog function of the package ncf (doesn’t really matter).
The correlog function work with an argument X which is the longitude, an
argument Y which is the latitude and an argument Z which is the variable you
want to test for autocorrelation (in my case, the different environmental
variables).
So, for the first species I have the following script:
ddeg.correlog.9<-correlog(plant[plant[,9]=="1", 2], plant[plant[,9]=="1", 3],
plant[plant[,9]=="1", 4])
X = plant[plant[,9]=="1", 2] —> only the X coordinate where my species 9 is
present
Y = plant[plant[,9]=="1", 3] —> only the Y coordinate where my species 9 is
present
Z = plant[plant[,9]=="1", 4] —> only the value of the environmental variable
where my species 9 is present
plant: dataframe
9: column corresponding to the first species
2: column corresponding to the X coordinate
3: column correspondind to the Y coordinate
4: column corresponding to the first environmental variable
So my question is: how do I repeat this script for every species (basically, I
just have to change the number « 9 » into 10, 11 and so on) ?
I try to write a function but I’m new in R and didn’t manage to do it. I was
also considering to use the function « lapply », but I don’t think I can use it
in this case, isn’t it?
Thank you very much for your help !
Sarah
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