Doc: Improve readme

README.Rmd

@@ -6,7 +6,7 @@ bibliography: paper/bibliography.bib
 
 ![R](https://img.shields.io/badge/r-%23276DC3.svg?style=for-the-badge&logo=r&logoColor=white)
 <a href="https://zenodo.org/badge/latestdoi/268765075"><img src="https://zenodo.org/badge/268765075.svg" alt="DOI"></a>
-[![codecov](https://app.codecov.io/gh/adrientaudiere/MiscMetabar/graph/badge.svg?token=NXFRSIKYC0)](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
+[![codecov](https://codecov.io/gh/adrientaudiere/MiscMetabar/graph/badge.svg?token=NXFRSIKYC0)](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md) 
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![CodeFactor](https://www.codefactor.io/repository/github/adrientaudiere/miscmetabar/badge/master)](https://www.codefactor.io/repository/github/adrientaudiere/miscmetabar/overview/master)
@@ -26,7 +26,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# MiscMetabar <a href="https://adrientaudiere.github.io/MiscMetabar/"><img src="man/figures/logo.png" align="right" height="138" alt="MiscMetabar website" /></a>
+# MiscMetabar <a href="https://adrientaudiere.github.io/MiscMetabar/"><img src="https://adrientaudiere.github.io/MiscMetabar/reference/figures/logo.png" align="right" height="138" alt="MiscMetabar website" /></a>
 
 See the pkgdown documentation site [here](https://adrientaudiere.github.io/MiscMetabar/) and the [package paper](https://doi.org/10.21105/joss.06038) in the Journal Of Open Softwares. 
 
@@ -46,7 +46,7 @@ BiocManager.
 You can install the stable version from [GitHub](https://github.com/)
 with:
 
-```{r, results = 'hide'}
+```{r, results = 'hide', eval=FALSE}
 if (!require("devtools", quietly = TRUE)) {
   install.packages("devtools")
 }
@@ -56,7 +56,7 @@ devtools::install_github("adrientaudiere/MiscMetabar")
 You can install the development version from
 [GitHub](https://github.com/) with:
 
-```{r, results = 'hide'}
+```{r, results = 'hide', eval=FALSE}
 if (!require("devtools", quietly = TRUE)) {
   install.packages("devtools")
 }
@@ -71,7 +71,7 @@ See vignettes in the [MiscMetabar](https://adrientaudiere.github.io/MiscMetabar/
 For an introduction to metabarcoding in R, Please visite the [state of the field](https://adrientaudiere.github.io/MiscMetabar/articles/states_of_fields_in_R.html) vignettes. The [import, export and track](https://adrientaudiere.github.io/MiscMetabar/articles/import_export_track.html) vignette explains how import and export `phyloseq` object. Its also show how to summarize useful information (number of sequences, samples and clusters) accross bioinformatic pipelines. 
 
 If you are interested in ecological metrics, see the vignettes describing [alpha-diversity](https://adrientaudiere.github.io/MiscMetabar/articles/alpha-div.html) and [beta-diversity](https://adrientaudiere.github.io/MiscMetabar/articles/beta-div.html) analysis. 
-The vignette [filter taxa and samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html) describes some data-filtering processes using MiscMetabar and the [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html) tutorial introduces the different way of clustering already-clustered OTU/ASV. The vignette [tengeler]() explore the dataset from Tengeler et al. (2020) using some MiscMetabar functions.
+The vignette [filter taxa and samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html) describes some data-filtering processes using MiscMetabar and the [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html) tutorial introduces the different way of clustering already-clustered OTU/ASV. The vignette [tengeler](https://adrientaudiere.github.io/MiscMetabar/articles/tengeler.html) explore the dataset from Tengeler et al. (2020) using some MiscMetabar functions.
 
 For developers, I also wrote a vignette describing som [rules of codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html). 
 

README.md

@@ -1,7 +1,7 @@
 
 ![R](https://img.shields.io/badge/r-%23276DC3.svg?style=for-the-badge&logo=r&logoColor=white)
 <a href="https://zenodo.org/badge/latestdoi/268765075"><img src="https://zenodo.org/badge/268765075.svg" alt="DOI"></a>
-[![codecov](https://app.codecov.io/gh/adrientaudiere/MiscMetabar/graph/badge.svg?token=NXFRSIKYC0)](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
+[![codecov](https://codecov.io/gh/adrientaudiere/MiscMetabar/graph/badge.svg?token=NXFRSIKYC0)](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
 [![Contributor
 Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md)
 [![License: GPL
@@ -13,7 +13,7 @@ v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 <!-- devtools::build_readme() -->
 
-# MiscMetabar <a href="https://adrientaudiere.github.io/MiscMetabar/"><img src="man/figures/logo.png" align="right" height="138" alt="MiscMetabar website" /></a>
+# MiscMetabar <a href="https://adrientaudiere.github.io/MiscMetabar/"><img src="https://adrientaudiere.github.io/MiscMetabar/reference/figures/logo.png" align="right" height="138" alt="MiscMetabar website" /></a>
 
 See the pkgdown documentation site
 [here](https://adrientaudiere.github.io/MiscMetabar/) and the [package
@@ -91,8 +91,10 @@ samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html)
 describes some data-filtering processes using MiscMetabar and the
 [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html)
 tutorial introduces the different way of clustering already-clustered
-OTU/ASV. The vignette [tengeler]() explore the dataset from Tengeler et
-al. (2020) using some MiscMetabar functions.
+OTU/ASV. The vignette
+[tengeler](https://adrientaudiere.github.io/MiscMetabar/articles/tengeler.html)
+explore the dataset from Tengeler et al. (2020) using some MiscMetabar
+functions.
 
 For developers, I also wrote a vignette describing som [rules of
 codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html).