Commit 931fc6cf authored by floriandeboissieu's avatar floriandeboissieu
Browse files

add flow chart to vignette

parent b3f1fe25
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
**[https://jbferet.github.io/biodivMapR](https://jbferet.github.io/biodivMapR/index.html)** **[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) [![Build Status](https://travis-ci.org/jbferet/biodivMapR.png?branch=master)](https://travis-ci.org/jbferet/biodivMapR)
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...@@ -34,9 +34,13 @@ This tutorial aims at describing the processing workflow and giving the associat ...@@ -34,9 +34,13 @@ This tutorial aims at describing the processing workflow and giving the associat
* validate results comparing to field plots measurements * 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 ## Input / Output files
The input images are expected to be in ENVI HDR format, BIL interleaved. The input images are expected to be in ENVI HDR format, BIL interleaved.
...@@ -99,7 +103,8 @@ MaxRAM = 0.5 ...@@ -99,7 +103,8 @@ MaxRAM = 0.5
nbclusters = 50 nbclusters = 50
``` ```
# Main processing worflow # Compute diversity maps
## Mask non vegetated / shaded / cloudy pixels ## Mask non vegetated / shaded / cloudy pixels
```{r 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 ...@@ -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"> <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. 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} ```{r alpha and beta diversity indices from vector layer}
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