update diversity_from_plots

update diversity_from_plots

biodivMapR v1.13.0

Change

• allow use of any vector format (including gpkg, shp... ) for validation plots provided in diversity_from_plots
• allow different crs between raster and vector layers

remove dependency to rgdal and rgeos

biodivMapR v1.12.0

Fix

• remove dependency to rgdal and rgeos (issue #18)

biodivMapR v1.11.1

Change

• possibility to enable / disable progressbar in compute_spectral_species_FieldPlots and init_kmeans

biodivMapR v1.11.0

Fix

• fixed computation of FD metrics
• removed import progress and emstreeR

biodivMapR v1.10.6

Fix

• removed reference to multiprocess, multisession used exclusively from future

biodivMapR v1.10.5

Fix

• fixed bug when producing simpson index from map_alpha_div function
• added importFrom corresponding to progressr in continum removal

biodivMapR v1.10.4

Changes

• removed unused functions (VectorInRasterFootprint, get_BB, get_BB_from_fullImagem get_BB_from_Vector, get_polygonCoord_from_Shp, read_ListRasters, VectorInRasterFootprint, gdal_polygonizeR) in order to reduce dependency to rgeos
• these functions can be found in R package preprocS2

Fix

• fixed bug when computing functional diversity metrics from 1 component only

biodivMapR v1.10.3

Changes

• function map_spectral_species checks if format and dimensions of Input_Mask_File are as expected
• function map_spectral_species now supports Input_Mask_File = FALSE. It writes a blank mask to ensure next processes

Functional diversity fix

fixed computation of functional diversity metrics Feve and Fdiv
--> inspired from method used by package FD

v1.10.2

biodivMapR v1.10.2

Fix

• fixed bug when defining SelectedPCs as a vector in map_spectral_species()
• Updated vignettes

biodivMapR v1.10.1

Fix

• Updated alpha and beta diversity mapping when starting from a classification map

v1.10.0

update v1.10.0

Merge branch 'dev'

# Conflicts:
#	R/Lib_MapBetaDiversity.R

v1.9.11

biodivMapR v1.9.11

Addition

• optimized codes for the computation of spectral species, alpha and beta diversity
• addition of progress bars during the different steps of the computation of spectral species, alpha and beta diversity maps
• systematic use multisession instead of multiprocess

no NMDS anymore

This release does not have NMDS as optional ordination method when computing beta diversty.
Only PCoA

v1.9.7

Addition

• progress bar instead of messages
• future: multisession instead of multiprocess
• added tutorials for the PROGYSAT workshop

Fixes

• install package dissUtils directly from github ('cran/dissUtils') as it was removed from official CRAN repo
• discard marginal spectral species based on number of sunlit pixels, instead of total number of pixels considered (window size or plot used for validation)
• harmonize default value for pcelim
• re-integrate package emstreeR (previously removed from CRAN) used to compute functional divergence
• uses future_lapply only if more than one CPU requested, otherwise use standard lapply
• fixed data type of spectral species derived from supervised classification and output directories for alpha and beta diversity
• fixed error occuring when using custom classification map instead of spectral species map

beta: select #dimensions for ordination of dissimilarity

biodivMapR v1.9.0

Changes

• Added dimMDS defining number of dimensions to run PCoA for beta diversity
• exported functions from beta library
• updated documentation

Fixes

• corrected weighted distance from nearest neighbors: assign exact coordinates of a sample when dissimilarity = 0
• temporary: discarded evenness from functional diversity as it uses emstreeR and requires binding to mlpack

Run biodivMapR with spectral indices stack

biodivMapR v1.8.0

Changes

• Added functionality to allow for computation of spectral diversity maps based on spectral index stack or any raster stack
• added function to compute interquartile range (IQR) and identify outliers
• applied IQR instead of center reduction
• exported most of the functions in the Lib_ImageProcess
• Image sample was removed and placed in external repository
• Major update of vignettes for tutorial

Fixes

• used file.path instead of paste