add flow chart to vignette

README.md

@@ -2,7 +2,7 @@
 
 **[https://jbferet.github.io/biodivMapR](https://jbferet.github.io/biodivMapR/index.html)**
 
-![licence](https://img.shields.io/badge/Licence-GPL--3-blue.svg) 
+[![licence](https://img.shields.io/badge/Licence-GPL--3-blue.svg)](https://www.r-project.org/Licenses/GPL-3)
 [![Build Status](https://travis-ci.org/jbferet/biodivMapR.png?branch=master)](https://travis-ci.org/jbferet/biodivMapR)
 [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/jbferet/biodivmapr?branch=master&svg=true)](https://ci.appveyor.com/project/jbferet/biodivmapr)
 

vignettes/biodivMapR.Rmd

@@ -34,9 +34,13 @@ This tutorial aims at describing the processing workflow and giving the associat
     
 * validate results comparing to field plots measurements
 
+Below is the typical flow chart of the computation of diversity maps with __biodivMapR__ :
 
+<img align="bottom" width="100%" height="100%" src="../man/figures/Figure1_FlowChart_biodivMapR_Process_600DPI.png">
 
-# Processing parameters
+
+
+# Define processing parameters
 
 ## Input / Output files
 The input images are expected to be in ENVI HDR format, BIL interleaved. 
@@ -99,7 +103,8 @@ MaxRAM        = 0.5
 nbclusters    = 50
 ```
 
-# Main processing worflow
+# Compute diversity maps
+
 ## Mask non vegetated / shaded / cloudy pixels
 
 ```{r Mask non vegetated / shaded / cloudy pixels}
@@ -203,7 +208,8 @@ Here, processing our example leads to the following $\alpha$ and $\beta$ diversi
 <img align="bottom" width="100%" height="100%" src="../man/figures/03_AlphaBeta.png">
 
 
-# $\alpha$ and $\beta$ diversity indices from vector layer
+# Compute diversity indices from a vector layer
+
 The following code computes $\alpha$ and $\beta$ diversity from field plots and extracts the corresponding diversity indices from previouly computed `SpectralSpecies` raster in order to perform validation.
 
 ```{r alpha and beta diversity indices from vector layer}