mpqDist is an R package for computing a family of phylogenetically-informed distances and making a interactive plots based on them.
The MPQ distances are a family of distance with a continuous tuning parameter which controls the extent to which the distance is influenced by basal vs. terminal phylogenetic structure.
The package allows the user to give a template for a plot which will be filled in with the full spectrum of tuning parameters.
Given a template, the package creates an interactive version of the plot that allows the user to scan through all the members of the family.
The package can be installed using
devtools::install_github("jfukuyama/mpqDist")
[github]
alto is an R package for aligning topics across a collection of LDA models.
It can be used for exploratory analysis (which topics persist across models? which tend to split into sub-topics?) or to aid in the choice of the number of topics in a final model.
The package can be installed using
devtools::install_github("lasy/alto")
‘localBiplots’ is an R package for doing local biplots, which provide a representation of the relationship between MDS embedding space and data space. An example with precomputed local biplot axes and MDS with several different distances is available here. The example uses several phylogenetically-informed distances, and includes a visualization of the relationship between the local biplot axes and the phylogenetic tree.
The package is available on github, and can be installed using
devtools::install_github('jfukuyam/localBiplots')
adaptiveGPCA is an R package for dimensionality reduction when the variables measured are related to each other.
The primary use case so far has been in microbiome data.
In that case, the variables measured are bacterial species and they are related to each other by a phylogenetic tree.
It can also be used to provide a “guided tour” of the data, an example of which can be seen here.
The package is available on CRAN, and can be installed using
install.packages("adaptiveGPCA")
[paper] [github] [quick start] [long vignette]
treeDA is an R package for sparse, tree-based discriminant analysis for microbiome data.
The package is available on CRAN, and can be installed using
install.packages("treeDA")
phyloseqGraphTest is an R package implementing a permutational version of the Friedman-Rafsky test. It is designed to work with a phyloseq object describing a microbiome experiment, and allows for testing based on minimum spanning trees, k-nearest neighbor graphs, or distance threshold graphs with any of the many distances implemented in phyloseq.
The package is available on CRAN and can be installed using
install.packages("phyloseqGraphTest")
