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taddallas / metacom

R package for the analysis of metacommunity structure
GNU General Public License v3.0
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BoundaryClump fuction: package version #12

Closed DaniloCVieira closed 6 years ago

DaniloCVieira commented 6 years ago

Dear Dallas,

I am working with your package and I find out that "BoundaryClump" produces a different result from the example described in Dallas, 2014. In other words, a community before "Gleasonian - p=0.15" {metacom v1.3}, now is classified as "Clumped" - p= 0.001 {metacom v1.5}

Visually, the results from the earliar version seems to be more corret to me. Could you confirm which of the versions is correct?

I used the "varespec" data {vegan}, with default settings to compare the results. Thank you in advance,

Danilo Vieira

Dallas, T. 2014. Metacom: An R package for the analysis of metacommunity structure. - Ecography (Cop.). 37: 402–405.

{metacom v1.3}

install.packages("metacom", repos="https://cran.r-project.org/src/contrib/Archive/metacom/metacom_1.3.tar.gz") data(varespec) BoundaryClump(varespec) ## Results from (Dallas, 2014) index P df 1 1.238462 0.1513498 41 ---------> non- significant p value- Gleasonian community

{metacom v1.5}

install.packages('metacom') require(metacom) data(varespec) BoundaryClump(varespec) name stat 1 index 1.607692308 2 p 0.001895953 ---------> significant p value - Clumped community 3 df 21.000000000

taddallas commented 6 years ago

Hello Danilo. The issue I think comes from whether BoundaryClump was used to measure range clumping versus community clumping. Version 1.5 looks across species and measures the tendency for species distributions among sites to clump (range clumping). Version 1.3 took a community perspective, but I was told that most of the time researchers actually want to calculate the metric from the range perspective. The results are the same if you transpose the matrix. 

install.packages("metacom", repos="https://cran.r-project.org/src/contrib/Archive/metacom/metacom_1.3.tar.gz")
data(varespec)
BoundaryClump(t(varespec))

install.packages('metacom')
metacom::BoundaryClump(varespec)

Sorry for the confusion.

DaniloCVieira commented 6 years ago

Thank you very much for your help! Kind regards,