opticut-package | R Documentation |
Likelihood based optimal partitioning and indicator species analysis. Finding the best binary partition for each species based on model selection, with the possibility to take into account modifying/confounding variables as described in Kemencei et al. (2014) <doi:10.1556/ComEc.15.2014.2.6>. The package implements binary and multi-level response models, various measures of uncertainty, Lorenz-curve based thresholding, with native support for parallel computations.
The DESCRIPTION file:
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The main user interface are the opticut
and multicut
functions
to find the optimal binary or multi-level response models.
Make sure to evaluate uncertainty
.
optilevels
finds the optimal number of factor levels.
Peter Solymos [cre, aut], Ermias T. Azeria [ctb]
Maintainer: Peter Solymos <solymos@ualberta.ca>
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. <doi:10.1556/ComEc.15.2014.2.6>
## 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(formula = y ~ 1, strata = g, dist = "poisson") summary(oc) ## visualize the results plot(oc, cut = -Inf) ## quantify uncertainty uc <- uncertainty(oc, type = "asymp", B = 999) summary(uc) ## go beyond binary partitions mc <- multicut(formula = y ~ 1, strata = g, dist = "poisson") summary(mc) ol <- optilevels(y[,"Sp2"], as.factor(g)) ol[c("delta", "coef", "rank", "levels")]
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