diff --git a/README.md b/README.md index b07ead8..0f0cde2 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ -# Collecting the Cluster Based Tree and Metadata with huebreaker +# Collecting and Identification the Outbreak Cluster -The goal of `huebreaker` is to find the cluster based tree and metadata of the data. The package is based on the paper: +The goal of Collecting and Identification the Outbreak Cluster `caIRA` is to find the cluster based tree and metadata of the data. The package is based on the paper: Ragonnet-Cronin, M., Hodcroft, E., Hué, S. et al. Automated analysis of phylogenetic clusters. BMC Bioinformatics 14, 317 (2013). @@ -20,17 +20,16 @@ devtools::install_github("Dhihram/huebreaker") his package needs the additional package `tidyverse`, `ape`, `treeio`, and `dplyr` ``` r -library(huebreaker) library(tidyverse) library(ape) library(dplyr) -library(ggtree) library(treeio) +library(caIRA) ``` You need the 2 data in this file, the first data is tree files (newick or nexus) and metadata file. The metadata file consists of `label`, `location`, and `date` columns. The `label` column must be same with the label in tree file. -This package will utilize: +This package with `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 @@ -38,6 +37,6 @@ This package 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. ``` r -res <- huebreaker(tree, metat, bootstrap_threshold = 80, date_range = 30, samearea = TRUE) +res <- genclus(tree, metat, bootstrap_threshold = 80, date_range = 30, samearea = TRUE) ``` -For the manual, you can see [here](https://dhihram.github.io/huebreaker/) +For the manual, you can see [here](https://dhihram.github.io/caIRA/)