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opticut: Likelihood Based Optimal Partitioning and Indicator Species Analysis

CRAN version CRAN RStudio mirror downloads Linux build status Windows build status Code coverage status License: GPL v2

Likelihood based optimal partitioning for indicator species analysis and more. Finding the best binary partition for each species based on model selection, possibly controlling for modifying/confounding variables as described in Kemencei et al. (2014).

Versions

Install stable version from CRAN:

install.packages("opticut")

Install development version from GitHub:

devtools::install_github("psolymos/opticut")

User visible changes in the package are listed in the NEWS file.

Report a problem

Use the issue tracker to report a problem.

Typical workflow

library(opticut)

## --- community data ---
y <- cbind(
    Sp1 = c(4,6,3,5, 5,6,3,4, 4,1,3,2),
    Sp2 = c(0,0,0,0, 1,0,0,1, 4,2,3,4),
    Sp3 = c(0,0,3,0, 2,3,0,5, 5,6,3,4))

## --- stratification ---
g <-      c(1,1,1,1, 2,2,2,2, 3,3,3,3)

## --- find optimal partitions for each species ---
oc <- opticut(y, strata = g, dist = "poisson")
summary(oc)
#  Multivariate opticut results, comb = rank, dist = poisson
#
#  Call:
#  opticut.default(Y = y, strata = g, dist = "poisson")
#
#  Best supported models with logLR >= 2:
#      split assoc      I  mu0  mu1 logLR      w
#  Sp3   2 3    ++ 0.6471 0.75 3.50 4.793 0.6962
#  Sp2     3   +++ 0.8571 0.25 3.25 9.203 0.9577
#  2 binary splits
#  1 species not shown

## --- visualize the results ---
plot(oc, cut = -Inf)

## --- quantify uncertainty ---
uc <- uncertainty(oc, type = "asymp", B = 999)
summary(uc)
#  Multivariate opticut uncertainty results
#  type = asymp, B = 999, level = 0.95
#
#      split R      I   Lower  Upper
#  Sp1   1 2 1 0.2860 0.02341 0.5668
#  Sp3   2 3 1 0.6218 0.21456 0.8813
#  Sp2     3 1 0.8274 0.51229 0.9680

Dynamic documents with opticut

Here is a minimal Rmarkdown example: Rmd source, knitted PDF.

References

Kemencei, Z., Farkas, R., Pall-Gergely, B., Vilisics, F., Nagy, A., Hornung, E. & Solymos, P. (2014): Microhabitat associations of land snails in forested dolinas: implications for coarse filter conservation. Community Ecology 15:180--186. [link, PDF]