Comments (2)
yes indeed,
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the spectral species files are used to compute alpha and beta diversity metrics. However, the arborescence of the results directory produced with biodivMapR can be deduced directly from the name of the input image file and the type of dimensionality reduction applied.
This is why the functions do not require explicit definition of the path for the spectral species map. -
The file 'Selected_Components.txt' is assumed to be produced after PCA file is produced. Then as for previous answer, biodivMapR deduces the path for 'Selected_Components.txt' and directly reads it when performing next steps. It is possible to bypass the use of the 'Selected_Components.txt' file when computing spectral species, if user provides a vector containing selected features from raste to be used as 'SelectedPCs' input variable. This functionality allows user to perform spectral species mapping from any stacked raster file they decide (as long as provided in ENVI BIL format), for example a selection of spectral indices or other variables derived from one or multiple sensors (assuming the data coresponding to the selected bands of a user defined set of variables does not require additional transformation).
input variables management may be updated in a next version, as the different functions require quite a lot of (too many) input variables, and I understand that this may be confusing and unpractical for users.
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Thank you for your quick response, which has resolved my confusion.
For now, I will try to make sure that all the inputs on my end are as clear as possible, since I haven't got myself familiar with how the deduction works especially when dealing with different directory structure.
Regarding the specific input variables, I will consult the "Reference" section on your website.
The issue is currently fixed on my side.
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Related Issues (20)
- Error during installing the package HOT 5
- Error Example_script from master Branch HOT 8
- Install error HOT 3
- Double forward slash in *select_PCA_components()* function HOT 1
- Unable to read .hdr file generated after using raster2BIL function HOT 3
- Error during executing perform_PCA HOT 1
- dissUtils not available for biodivMapR HOT 1
- Processing data with higher resolution HOT 2
- What is the R version to run dissUtils? HOT 1
- Dependencies on rgdal and rgeos HOT 3
- NAs for simpson index HOT 1
- Processing time for large Sentinel-2 images HOT 2
- +/- inf values in OutputPCA_8_PCs raster HOT 6
- the NAN values exist, it doesn't work HOT 7
- Problem with Component selection for dimensionality reduction HOT 5
- line 144-149 HOT 1
- line 133-137 HOT 1
- Error in perform_PCA/ Issue with data formatting HOT 3
- Diversity maps output resolution HOT 2
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