NEWS.md

In jbferet/biodivMapR: biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images

biodivMapR2 v2.3.3

addition

• modified perform_PCA to allow PCA over any type of data

change

• updated documentation

biodivMapR2 v2.3.2

change

• optimize tile processing with function get_raster_diversity_tile

biodivMapR2 v2.3.1

fix

• fix tile mask management when tiles are empty

change

• change management of parallel processing for steps where it is not optimal

biodivMapR2 v2.3.0

change

• added functions to process large rasters divided into tiles using get_s2_tiling function from preprocS2 package
• added functions to apply biodivMapR using moving window

biodivMapR2 v2.2.1

change

• clean code
• add suppressWarnings when calling progressr

biodivMapR2 v2.2.0

change

• merge v2 from gitlab repository
• update vignettes for use of v2

biodivMapR2 v2.1.4

fix

• in 'get_diversity_from_plots' :
• initialize Attributes with nrow = nbPlots_init
• initialize functional diversity metrics in Attributes with NA
• correct get_diversity_from_plots : assign to beta diversity values instead of mean Hill
• correct extract_vect_from_rast : update AttributeTable and discard vectors with no data

addition

• create functions init_kmeans_samples and init_PCoA_samples to process samples previously extracted independently from an input raster
• possibility to provide name for output files in addition to directory

change

• possibility to define updated mask file name as input for radiometric_filtering

biodivMapR2 v2.1.3

fix

• correct get_diversity_from_plots: output for FDis corrected to FDis instead of FDiv
• correct spectralspecies_per_polygon : AttributeTable not set to NULL

addition

• computes all functional diversity when running get_diversity_from_plots

biodivMapR2 v2.1.2

change

• use package fundiversity to compute diversity metrics

biodivMapR v2.1.1

Fix

• Fixed testthat
• fixed maps for functional diversity metrics (center reduction of trait space)

Change

• more systematic use of 'seq_len'

biodivMapR v2.1.0

Addition

• added Hill numbers
• added functional diversity

fix

• initialize input_mask to NULL in biodivMapR_Full
• handle chunk with pixels valid but no window valid

biodivMapR v2.0.0

Fix

• fixed SFS function when using SpatVector instead of SpatVectorCollection

biodivMapR v1.14.3

Fix

• fixed SFS function when using SpatVector instead of SpatVectorCollection

biodivMapR v1.14.2

Fix

• update fixed problem occurring when performing PCA without mask

biodivMapR v1.14.1

Fix

• fixed problem occurring when performing PCA without mask
• fixed issue related to plan(multisession), suggested by @rnedelec on github, following documented issue in https://github.com/ropensci/drake/issues/255#issuecomment-365799680

Addition

• option added to display progress bar. Set to FALSE as default

biodivMapR v1.14.0

Change

• added input variables Kmeans_info_path and Kmeans_info in map_spectral_species to allow production from previously computed clusters

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

biodivMapR v1.12.1

Fix

• update example_script and vignettes to fulfill removal to rgdal dependency in the package

biodivMapR v1.12.0

Fix

• issue #18: remove the dependency to rgdal and rgeos using terra and gdalUtilities instead

Change

• remove extract_pixels_coordinates.From.OGR, a unique extract_pixels_coordinates now works for both character or rast/vect inputs

Addition

• add get_gdal_info to get raster gdal info as a nested list.

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

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

biodivMapR v1.10.0

Fix

• now uses red band instead of red edge band for the computation of NDVI --> changes thresholding

changes

• simplified inputs for functions such as map_spectral_species(), init_kmeans(), map_beta_div()
• updated vignettes

biodivMapR v1.9.11

changes

• 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
• addition of functions Compute_ALPHA_SSD_per_window_list, Compute_ALPHA_SSD_per_window, Compute_ALPHA_per_window, prepare_HDR_SSD, prepare_HDR_Sunlit, RW_bytes_all, RW_bytes
• use multisession instead of multiprocess where it was forgotten

biodivMapR v1.9.10

Addition

• use of list for computation of beta diversity
• addition of functions getBCdiss and Normalize_SSD

biodivMapR v1.9.9

Addition

• added Hellinger distance as beta diversity metric

biodivMapR v1.9.8

Addition

• removed NMDS as possible ordination method when computing beta diversity

biodivMapR v1.9.7

Addition

• progress bar instead of messages
• future: multisession instead of multiprocess

biodivMapR v1.9.6.1

Addition

• added tutorials for the PROGYSAT workshop

biodivMapR v1.9.6

Fixes

• install package dissUtils directly from github ('cran/dissUtils') as it was removed from official CRAN repo

biodivMapR v1.9.5

Fixes

• discard marginal spectral species based on number of sunlit pixels, instead of total number of pixels considered (window size or plot used for validation)

Changes

• harmonize default value for pcelim

biodivMapR v1.9.4

Fixes

• re-integrate package emstreeR (previously removed from CRAN) used to compute functional divergence

biodivMapR v1.9.3

Fixes

• uses future_lapply only if more than one CPU requested, otherwise use standard lapply

biodivMapR v1.9.2

Fixes

• fixed data type of spectral species derived from supervised classification and output directories for alpha and beta diversity

biodivMapR v1.9.1

Fixes

• fixed error occuring when using custom classification map instead of spectral species map

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

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

biodivMapR v1.7.0

Changes

• capacity to produce diversity maps based on classification raster

Fixes

• warning eliminated when testing Selected_Features in Lib_MapFunctionalDiversity.R
• Corrected data extraction function using nbands in extract.big_raster and get_random_subset_from_image
• updated extract.big_raster and get_random_subset_from_image in order to account for 2D rasters which cannot be read with brick
• added driver definition when using read_stars (extract.big_raster)
• corrected vignettes (TypePCA used before defined in previous version)

biodivMapR v1.6.2

Fixes

• added importFrom raster brick in function extract.big_raster

biodivMapR v1.6.1

Fixes

• Fixed bug when calling file.edit from linux terminal. initial parameter editor='internal' is not cross platforms. removed it.

biodivMapR v1.6.0

Changes

• Added option to directly compute alpha and beta diversity maps from classification maps, even if it does not correspond to SpectralSpecies file produced from biodivMapR

Fixes

• Fixed bug occuring when calling function diversity_from_plots if no functional duversity map was produced before

biodivMapR v1.5.1

Fixes

• Fixed bug occuring when writing image if initial raster is not a multiple of the window size. no bug occur but the raster files have wrong information
• fixed problem when performing estimation of biodiversity for plots outside of the raster: now the value is NA

biodivMapR v1.5.0

Changes

• Added functional diversity metrics
• updated example script
• updated vignette

biodivMapR v1.4.0

Changes

• implemented MNF
• discarded HDR as input variable from get_random_subset_from_image
• updated example file
• added contribution of F de Boissieu
• changed email address to teledetection.fr
• updated diversity_from_plots
• updated example script

biodivMapR v1.3.1

Fixes

• fixed identification and elimination of pixel samples with NA
• fixed bug occuring when input raster is BSQ interleave, and BSQ reported in PC file and following files

Changes

• finalized preparation for MNF
• improved information in the header files

biodivMapR v1.3.0

Changes

• integrated stars package in order to read any file format, including TIFF format
• developed a generic function to write rasters
• prepared for MNF
• changed default red band for the computation of NDVI: closest band to 690 nm is now selected instead of closest band to 700 nm

biodivMapR v1.2.1

Changes

• added option to convert the mask file into proper format with raster2BIL

biodivMapR v1.2.0

Fixes

• fixed bug raised when processing data over large number of pixels (image products >2^31 bits)
• fixed bug by adding elimination of bands disturbed by water vapor even when ContinuumRemoval set to FALSE

Changes

• Changed name of default directory when saving image after calling raster2BIL
• added documentation for raster data conversion using raster2BIL

biodivMapR v1.1.0

Fixes

• fixed bug in Lib_MapSpectralSpecies: remove constant bands from Subset$DataSubset if needed
• fix bug when continuum removal applied on pixels with constant values which were not filtered in previous stages

Changes

• Updated continuum removal
• Named Continuum_Removal instead of CR
• corrected documetation for perform_radiometric_filtering
• Added an error report when spectral information is not conform with expectations (due to too high noise level for example, usually leading to NaN or Inf values after PCA)
• Changed name for some variables in internal functions for consistency
• will add documentation on how to analyze error reports

biodivMapR v1.0.2

Fixes

Changes

• moved examples to repository root: example files are not installed with package anymore.
• removed Plots reprojection from diversity_from_plots: now, Plots and Raster must be in the same projection. Changed example Plots projection accordingly.
• removed get_projection (useless)

biodivMapR v1.0.1 (Release date: 2019-09-27)

• Added NEWS.md
• Updated README.md: transfered from gitlab.irstea to github
• changed return() into return(invisible())
• updated vignettes & tutorial with latest outputs and figures from code

biodivMapR v1.0.0 (Release date: 2019-09-26)

First release in GitHub Submission accepted to Methods in Ecology and Evolution

jbferet/biodivMapR documentation built on April 12, 2025, 1:32 p.m.