Tutorial for biodivMapR

Jean-Baptiste Féret, Florian de Boissieu

2019-07-26

This tutorial aims at describing the processing workflow and giving the associated code to compute \(\alpha\) and \(\beta\) diversity maps on an extraction of Sentinel-2 image taken over Cameroun forest. The workflow is composed of the following steps:

1 Processing parameters

1.1 Input / Output files

The input images are expected to be in ENVI HDR format, BIL interleaved. To check if the flormat is good use fucntion check_data. If not they should be converted with function raster2BIL.

A mask can also be set to work on a selected part of the input image. The mask is expected to be a raster in the same format as the image (ENVI HDR), with values 0 = masked or 1 = selected. If no mask is to be used set Input.Mask.File = FALSE.

The output directory defined with Output.Dir will contain all the results. For each image processed, a subdirectory will be automatically created after its name.

Input.Image.File  = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'biodivMapR')
check_data(Input.Image.File)

Input.Image.File  = raster2BIL(Raster.Path = Input.Image.File,
                                       Sensor = 'SENTINEL_2A',
                                       Convert.Integer = TRUE,
                                       Output.Directory = '~/test')
Input.Mask.File   = FALSE

Output.Dir        = 'RESULTS'

The image provided with the package is a subset of tile T33NUD acquired by Sentinel-2A satellite over Cameroonese rainforest in January 4th, 2018.