Commit 931fc6cf authored by floriandeboissieu's avatar floriandeboissieu

add flow chart to vignette

parent b3f1fe25
......@@ -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)
......
......@@ -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}
......
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