DESCRIPTION

Package: clustuneR
Title: Molecular clustering implementation and predictive optimization
Version: 1.0
Authors@R: 
    c(person("Connor", "Chato", email = "ConnorChato@gmail.com",
              role = c("aut", "cre")),
    person("Art", "Poon", role=c("aut", "ths")))
Description: clustuneR builds clusters from inputted sequence alignments and/or 
    phylogenetic trees, allowing users to choose between multiple cluster-building 
    algorithms implememented in the package and tune clustering parameters to produce 
    informative clusters. The package also takes in meta-data associated with sequences 
    such as a known collection date or subtype/variant classification. Cluster-level 
    characteristics, such as the range of collection dates or the most common 
    subtype/variant within a cluster can also be identified from these. 
    If a subset of sequences are specified as "New", then clustuneR simulates cluster 
    growth by building clusters in two stages: first clusters are built from sequences 
    which are not specified as new, then the new sequences are added to clusters. 
    Predictive models can then be tested on cluster-level attributes and validated 
    with growth outcomes, to measure how informative a cluster set is.
License: `use_gpl3_license()`
Encoding: UTF-8
Imports: 
  ape (>= 5.3), 
  digest (>= 0.6.25),
  igraph (>= 1.3),
  jsonlite (>= 1.7.2),  
  phangorn (>= 0.7-70),
  phytools (>= 1.0-3)
Depends: 
  data.table (>= 1.12.4), 
  R (>= 3.6.3)
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3