add change in viginettes

DESCRIPTION

@@ -22,3 +22,4 @@ Suggests:
     tidyverse,
     treeio
 VignetteBuilder: knitr
+Year: 2024

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)

docs/index.html

@@ -416,12 +416,17 @@ <h3>Data</h3>
 </div>
 <div id="package-utilization" class="section level3">
 <h3>Package Utilization</h3>
-<p>This package will utilize: 1. Finding and clustering the
-monophylectic groups in the tree 2. Add the parameter of the clusters:
+<p>This part of package, <code>genclus</code> will utilize:</p>
+<ol style="list-style-type: decimal">
+<li><p>Finding and clustering the monophylectic groups in the
+tree</p></li>
+<li><p>Add the parameter of the clusters:
 <code>bootstrap_treshold</code>, <code>data_range</code>, and
-<code>samearea</code> 3. Keep the maximum monophylectic groups in the
-cluster identify</p>
-<p>the <code>bootstrap_treshold</code> is the minimum bootstrap value to
+<code>samearea</code></p></li>
+<li><p>Keep the maximum monophylectic groups in the cluster
+identify</p></li>
+</ol>
+<p>The <code>bootstrap_treshold</code> is the minimum bootstrap value to
 be considered as a cluster. The <code>data_range</code> is the range of
 the days to be considered as a cluster. The <code>samearea</code> is the
 boolean value to consider the same area as a cluster.</p>

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