Hello,
Please cc the list, the odds of getting more and better answers are greater.
And you should tell us from what package do the function plot.correlog
comes. library(what)?
As for your question, assuming you want to save your plots as PNG files,
you could do something like the following.
fun <- function(p){
fname <- paste0("correlog", p)
png(filename = fname)
plot.correlog(...)
dev.off()
}
ddeg.correlog.list <- lapply(9:20, fun)
See the help page for ?png. It lists several other graphics file formats
you can use.
Hope this helps,
Rui Barradas
Em 24-10-2014 08:23, Sarah escreveu:
Thank you very much, it helped a lot!
I just have another question know. I want to make plot for every
species. I just add the function « plot correlog » to the previous
function and I have now the following script:
ddeg.correlog.list <- lapply(9:20, function(p)
*plot.correlog*(correlog(plant[plant[,p]=="1", 2], plant[plant[,p]=="1",
3],
plant[plant[,p]=="1", 4],increment=2500)))
It’s working, but I wanted to know if there is a way to save each plot.
I found that I can use the dev.off function or the ggplot function of
the package ggplot2, but I can’t figure out how to use it within the
lapply function. Do you think there is a way?
Thank you for your help!
Sarah
Le 23 oct. 2014 à 17:49, Rui Barradas <ruipbarra...@sapo.pt
<mailto:ruipbarra...@sapo.pt>> a écrit :
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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