Function find_optimal [optimus v0.2.0]

keywords

partitioning

title

Find an optimal classification among competing clustering solutions

description

find_optimal takes a clustering solution, or a set of related clustering solutions, fits models based on the underlying multivariate data, and calculates the sum-of-AIC value for the solution/s. The smallest sum-of-AIC value is the optimal solution.

Function gamma_div [hilldiv v1.5.1]

keywords

partitioning

title

Gamma diversity

description

Compute gamma diversity of a system from a matrix (OTU table) containing multiple samples. If a tree is provided, the computed gamma diversity accounts for the phylogenetic relations across OTUs.

Function is.nested [hilldiv v1.5.1]

keywords

partitioning

title

Check if hierachy is nested

description

Multi-level diversity partitioning requires the groups at different hierarchical levels to be nested. i.e. two samples that belong to a common parent group cannot have different grandparent groups. The best example of nested hierarchy is taxonomy: e.g. two species that belong to the same genus cannot belong to different families. This function checks whether the groups specified in a hierarchy table have a nested structure.

Function alpha_div [hilldiv v1.5.1]

keywords

partitioning

title

Alpha diversity

description

Compute alpha diversity of a system comprised of multiple samples from a count (OTU/ASV) table. If a tree object is provided, the computed alpha diversity accounts for the phylogenetic relations across OTUs/ASVs.

Function lrp [longRPart2 v0.2.3]

keywords

partitioning

title

Longitudinal Recursive Partitioning

description

Longitudinal Recursive Partitioning

Function lrp2Plot [longRPart2 v0.2.3]

keywords

partitioning

title

Longitudinal Recursive Partitioning Plotting Function

description

Longitudinal Recursive Partitioning Plotting Function

Function pair_dis_plot [hilldiv v1.5.1]

keywords

partitioning

title

Pairwise dissimilarity plot

description

Visualisation of pairwise dissimilarities

Function pair_dis [hilldiv v1.5.1]

keywords

partitioning

title

Pairwise dissimilarity

description

Computation of pairwise dissimilarities based on Hill numbers diversity partitioning

Function beta_dis [hilldiv v1.5.1]

keywords

partitioning

title

Beta dissimilarity

description

Compute dissimilarity or similarity values based on beta diversities (neutral or phylogenetic) and sample size.

Function rpart.plot [rpart.plot v3.0.9]

keywords

partitioning

title

Plot an rpart model. A simplified interface to the prp function.

description

Plot an rpart model, automatically tailoring the plot for the model's response type. For an overview, please see the package vignette Plotting rpart trees with the rpart.plot package. This function is a simplified front-end to prp, with only the most useful arguments of that function, and with different defaults for some of the arguments. The different defaults mean that this function automatically creates a colored plot suitable for the type of model (whereas prp by default creates a minimal plot). See the prp help page for a table showing the different defaults.