Hi Chelsea,
A brute force method, but I think it does what you want:
# create a sequence of integers to make checking easy
null.cz<-1:68
separate_interdigitated_vectors<-function(x,nv=2,vlen=17) {
xlen<-length(x)
starts<-seq(1,xlen-vlen*nv+1,by=vlen*nv)
cat(xlen,starts,"\n")
for(start in starts) {
if(start ==1) {
x1<-x[start:(start+vlen-1)]
x2<-x[(start+vlen):(start+vlen*2-1)]
} else {
x1<-c(x1,x[start:(start+vlen-1)])
x2<-c(x2,x[(start+vlen):(start+vlen*2-1)])
}
}
return(list(x1=matrix(x1,ncol=vlen,byrow=TRUE),
x2=matrix(x2,ncol=vlen,byrow=TRUE)))
}
separate_interdigitated_vectors(null.cz)
Jim
On Wed, Nov 20, 2019 at 2:43 AM Chelsea Hinton <chelsearhin...@gmail.com> wrote:
>
> Hello,
>
> I am working to evaluate the structure of shrub-pollinator networks using
> modularity analyses. I have generated 100 null model networks to test for
> modularity and extract c and z scores for each (measuring statistical
> significance in real networks). However, the output of the "czvalues" for
> all 100 null models comes out in one mass clump (See below code). The
> highlighted section in the below code is an example of the null c and z
> values. I have 17 plants in my shrub-pollinator network (represented by the
> whole numbers) and so the first 17 values are the c scores followed by the
> next 17 which are z scores and so on.
>
> Is there a way I can easily separate out the c values from the z values? Or
> should I instead generate 100 null networks individually?
>
> R Code for null model generation and c and z output for nulls:
>
> library(bipartite)
>
> network<-read.csv(file.choose(), header = TRUE, row.names = 1)
>
> nw<-sortweb(network)
> weighted<-as.matrix(nw)
>
> nulls <- nullmodel(weighted, N=100, method=3)
> null.res <- unlist(sapply(nulls, metaComputeModules, USE.NAMES = TRUE)) #takes
> a while ...
> null.res
> ## [[1]]
> ## Slot "likelihood":
> ## [1] 0.1309568
> ##
> ##
> ## [[2]]
> ## Slot "likelihood":
> ## [1] 0.1303186
> ##
> ##
> ## [[3]]
> ## Slot "likelihood":
> ## [1] 0.14044
> .............
>
> ## [[100]]
> ## Slot "likelihood":
> ## [1] 0.1332231
>
> null.cz<-unlist(sapply(null.res, czvalues, level = "lower", USE.NAMES = TRUE
> ))
> null.cz
> ## 1 2 3 4 5 6
> ## 0.64147140 0.74959438 0.62019013 0.65895062 0.73724490 0.72664360
> ## 7 8 9 10 11 12
> ## 0.73553719 0.57500000 0.60204082 0.66000000 0.72000000 0.37500000
> ## 13 14 15 16 17 1
> ## 0.37500000 0.77777778 0.27777778 0.44444444 0.00000000 0.70710678
> ## 2 3 4 5 6 7
> ## 0.70710678 1.10729957 1.68025904 -0.70710678 -0.12539247 0.99339927
> ## 8 9 10 11 12 13
> ## 0.62696233 0.72849280 -0.27007306 -0.86094603 -0.83722650 -0.72727630
> ## 14 15 16 17 1 2
> ## -0.86094603 -0.42633438 -0.70710678 -1.02821822 0.65504683 0.62195782
> ## 3 4 5 6 7 8
> ## 0.65606509 0.70226843 0.71777778 0.58500000 0.71500000 0.74048443
> ## 9 10 11 12 13 14
> ## 0.70000000 0.44444444 0.57142857 0.75000000 0.62500000 0.66666667
> ## 15 16 17 1 2 3
> ## 0.44444444 0.44444444 0.00000000 0.70710678 1.04053196 NA
> ## 4 5 6 7 8 9
> ## 0.70710678 -0.08671100 2.15643011 0.40204629 0.40204629 -0.47514562
>
> Thank you for your time,
>
> Chelsea
>
> [[alternative HTML version deleted]]
>
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