diff --git a/DESCRIPTION b/DESCRIPTION index be28a5b..c1dab23 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -22,3 +22,4 @@ Suggests: tidyverse, treeio VignetteBuilder: knitr +Year: 2024 diff --git a/docs/index.Rmd b/docs/index.Rmd index 59345de..5c84a21 100644 --- a/docs/index.Rmd +++ b/docs/index.Rmd @@ -81,9 +81,15 @@ gg ### Package Utilization -This package will utilize: 1. Finding and clustering the monophylectic groups in the tree 2. Add the parameter of the clusters: `bootstrap_treshold`, `data_range`, and `samearea` 3. Keep the maximum monophylectic groups in the cluster identify +This part of package, `genclus` will utilize: -the `bootstrap_treshold` is the minimum bootstrap value to be considered as a cluster. The `data_range` is the range of the days to be considered as a cluster. The `samearea` is the boolean value to consider the same area as a cluster. +1. Finding and clustering the monophylectic groups in the tree + +2. Add the parameter of the clusters: `bootstrap_treshold`, `data_range`, and `samearea` + +3. Keep the maximum monophylectic groups in the cluster identify + +The `bootstrap_treshold` is the minimum bootstrap value to be considered as a cluster. The `data_range` is the range of the days to be considered as a cluster. The `samearea` is the boolean value to consider the same area as a cluster. ```{r} res <- genclus(tree, metat, bootstrap_threshold = 80, date_range = 30, samearea = TRUE) diff --git a/docs/index.html b/docs/index.html index 0e4d634..06e6c55 100644 --- a/docs/index.html +++ b/docs/index.html @@ -416,12 +416,17 @@

Data

Package Utilization

-

This package will utilize: 1. Finding and clustering the -monophylectic groups in the tree 2. Add the parameter of the clusters: +

This part of package, genclus will utilize:

+
    +
  1. Finding and clustering the monophylectic groups in the +tree

  2. +
  3. Add the parameter of the clusters: bootstrap_treshold, data_range, and -samearea 3. Keep the maximum monophylectic groups in the -cluster identify

    -

    the bootstrap_treshold is the minimum bootstrap value to +samearea

  4. +
  5. Keep the maximum monophylectic groups in the cluster +identify

  6. +
+

The bootstrap_treshold is the minimum bootstrap value to be considered as a cluster. The data_range is the range of the days to be considered as a cluster. The samearea is the boolean value to consider the same area as a cluster.

diff --git a/vignettes/cluster_generating.Rmd b/vignettes/cluster_generating.Rmd index 9ccb680..ef7c0ce 100644 --- a/vignettes/cluster_generating.Rmd +++ b/vignettes/cluster_generating.Rmd @@ -17,7 +17,7 @@ The goal of caIRA is to find the cluster based tree and metadata of the data. ## Installation -You can install the development version of caIRA from [GitHub](https://github.com/) with: +You can install the development version of `caIRA` from [GitHub](https://github.com/) with: ``` r # install.packages("devtools") @@ -68,7 +68,7 @@ gg ### Package Utilization -This package will utilize: +This part of package `genclus` will utilize: 1. Finding and clustering the monophylectic groups in the tree 2. Add the parameter of the clusters: `bootstrap_treshold`, `data_range`, and `samearea` 3. Keep the maximum monophylectic groups in the cluster identify