# Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

## Documentation for package ‘hopach’ version 1.12.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

boot2fuzzy | function to write MapleTree files for viewing bootstrap estimated cluster membership probabilities based on hopach clustering results
boothopach | functions to perform non-parametric bootstrap resampling of hopach clustering results
bootmedoids | functions to perform non-parametric bootstrap resampling of hopach clustering results
bootplot | function to make a barplot of bootstrap estimated cluster membership probabilities
correlationordering | function to compute empirical correlation between distance in a list and distance by a metric
dissmatrix | functions to compute pair wise distances between vectors
dissvector | functions to compute pair wise distances between vectors
distancematrix | functions to compute pair wise distances between vectors
distancevector | functions to compute pair wise distances between vectors
dplot | function to make a pseudo-color image of a distance matrix with the row and column ordering based on HOPACH clustering results.
golub | Gene expression dataset from Golub et al. (1999)
hopach | function to perform HOPACH hierarchical clustering
hopach2tree | function to write MapleTree files for viewing hopach hierarchical clustering results
improveordering | function to compute empirical correlation between distance in a list and distance by a metric
labelstomss | Functions to compute silhouettes and split silhouettes
labelstosil | Functions to compute silhouettes and split silhouettes
makeoutput | function to write a text file with hopach output
makeTree | function to write MapleTree files for viewing hopach hierarchical clustering results
medstosil | Functions to compute silhouettes and split silhouettes
msscheck | Functions to compute silhouettes and split silhouettes
prune | function to prune a HOPACH tree.
silcheck | Functions to compute silhouettes and split silhouettes
vectmatrix | functions to compute pair wise distances between vectors