Hi,

I was working with your functions trying to find why Fns value from DOC function differ from matlab. In my case, matlab gives a fns = 0.90494, while a summary of fns from DOC function
Fns Data
Min. :0.0004263 Real:200
1st Qu.:0.0622336
Median :0.0901535
Mean :0.0933056
3rd Qu.:0.1154092
Max. :0.7046036

I think that the mistake is in the DOC.boot function at ## Detect negative slope section. If I change point <- which(slope>0) to point <- which.max(slope>0) it almost mimic the matlab, because I obtain a fns = 0.9407. This change tries to do the same that the find(LocalSlope>0,1,'last')), which, if I am not wrong, should pick the last value (or max in R notation).
I run R with a set.seed(100), and run doc<-DOC(otus,R=200), and then:
xs <- seq(0,1,by=0.001)

Lowess

LOW <- loess(rJSD~Overlap,data=doc$DO,span=0.2,degree=1,family="symmetric",iterations=4,surface="interpolate")
LOW.P <- data.frame(predict(LOW,xs))

## Detect negative slope
# Smooth prediction
ma <- function(x,n=5){filter(x,rep(1/n,n), sides=2)}
low.ma <- ma(LOW.P[,1])
slope <- diff(low.ma)/diff(xs)
point <- which.max(slope>0) ### modified version
neg.slope <- xs[point[length(point)]]
    # Fns
Fns <- sum(doc$DO$Overlap>neg.slope,na.rm=T)/length(doc$DO$Overlap)

otus.txt

Hi,

I am working with your function to do analysis like those proposed in Nature paper. In some cases Matlab needs to much time and I found that in R it can be done faster.
My problem is that I want a different figure than default plot. I run the function with
DOC_out<-DOC(otus,R=100,cores=24) and get the default plot with plot(DOC_out), which is attached. In that plot the median Fns is over 0.95, but if I run median(DOC_out$FNS[,1]) I get 0.8722449. I used a set.seed(100) in my R session.
I think that it is my fault but I cannot see what I am doing wrong, because as you state in this web page the vertical line is the median Fns value from bootstraps.
Another question is: default settings (not R or the number of cores) are the "correct" to "mimic" the original function? And how I should get the P values of original matlab code?

Thank you very much,

Manuel

otus.zip

This error occured when I set cores > 1, because lme4 package could not loaded automatically in tasks. So I modified DOC.boot.R file in line53, as following:

llboot <- foreach(i = 1:R,.options.snow = opts, .packages = "lme4", .export = "mov.avg") %dopar% {

In which I added the .packages parameter, and It works.
Here's my R session info:
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] compiler_4.2.0