Changelog • biodivMapR

addition

add boolean ‘buffer_mw’ in set_options_biodivMapR(‘biodivMapR_tiling’) to control application of a buffer on raster resulting from moving window process
add a message and stop process when biodivMapR_tiling cannot find any raster files with pattern related to features in the file name

fix

fix bug occurring in get_samples_from_tiles and get_plots_from_tiles when path for tileSI includes feature names

change

biodivMapR_tiling now uses plot_names instead of plots (a list of vectors)

fix

fixed bug when samples cannot be extracted in get_plots_from_tiles :
- selplot <- terra::spatSample(…)
- last action of sample_from_plots_beta

addition

use c++ codes to compute alpha and beta diversity metrics directly from chunks
added deprecated functions

addition

added internal c++ codes to compute alpha metrics

changes

update functions metadata and description

addition

added internal c++ codes to compute dissimilarity metrics, instead of dissUtils
included computation of bray-curtis dissimilarity,
- bray-curtis dissimilarity
- bray-curtis turnover
- sorensen dissimilarity
- simpson dissimilarity
- jaccard dissimilarity
- jaccard turnover
prepared for possibility to select clustering
added tests for production of diversity maps, spectral species maps and diversity from classification

changes

changed names of function:
- biodivMapR_full to biodivMapR
- biodivMapR_full_classif to biodivMapR_classif
removed dependency to preprocS2 and bigRaster

fix

fixed biodivMapR_sfs
fixed biodivMapR_classif
fixed biodivMapR_opt_clusters

addition

added function spectral_species_full to produce spectral species map from individual raster
create output_dir when running perform_PCA

fix

fixed biodivMapR_opt_clusters to run in parallel

fix

fixed computation of functional diversity metrics when nbCPU = 1

fix

fixed biodivMapR_opt_clusters bypassing parallel computing

change

fully update documentation

change

biodivMapR_full_classif: add possibility to set compute_beta = TRUE or FALSE
remove TODO.md
use regular expression ‘\.’ when searching for strings including ‘.’:
define ‘get_samples_from_tiles’ in independent file

fix

use lapply instead of future_lapply when calling ‘functional_window_list’ in ‘get_raster_diversity_tile’
compute taxonomic and functional diversity metrics in two steps
compute functional diversity metrics one after the other
fix compression of diversity maps
fix bug when setting more than 1 metric in options$alpha_metrics

change

use with(…, local = TRUE) when using future::plan

fix

add nested ‘try’ in mosaic_from_vrt

addition

add spectral_species_full_tiles to produce spectral species from tiles

addition

add biodivMapR_full_sdm and alphabeta_window_sdm to produce diversity metrics from sdm

fix

name weightIQR instead of weightIRQ

change

remove compute_bc_diss and use only dissUtils::diss instead
rename ‘get_ssd_full’ ‘get_normalized_ssd’
added function ‘file_path_sans_ext’ (copied from zonator) to avoid importing ‘tools’
use ‘progressr’ instead of ‘progress’

addition

add biodivMapR_full_classif to produce diversity metrics from classification map

addition

add option beta_metrics: set to FALSE to skip beta computation
add option moving_window for ‘biodivMapR_full’
add option weightIQR for ‘biodivMapR_full_tiles’
add function crop_border_tile to avoid artifacts between tiles
add function mosaic_from_vrt to produce a mosaic from a vrt

fix

fix bug when checking if mask files already exist
fix bug when generating hill index
use try to avoid error when using compression when calling gdal_utils

change

fd_metrics instead of FDmetric
alpha_metrics instead of alphametrics
add options as input parameter for ‘biodivMapR_full_tiles’ and ‘biodivMapR_full’ in order to reduce nb of inputs
add possibility to define the IQR when sampling with ‘biodivMapR_sample’ and filtering
change name for site_name
updated vignettes

fix

fix bug when feature names overlap (e.g. NDVI vs mNDVI705)
update biodivMapR_full_tiles
update biodivMapR_full_classif
add pcelim as input for biodivMapR_sample and biodivMapR_full_tiles

addition

added function biodivMapR_sample and biodivMapR_full_classif

change

added mosaic_output as input variable for biodivMapR_full_tiles
fixed “BIGTIFF=IF_SAFER” when calling sf::gdal_utils to produce mosaics

change

use continuumRemoval from package prospectr instead of internal function

change

add option “BIGTIFF=IF_SAFER” when calling sf::gdal_utils to produce mosaics

fix

create output_dir if does not exist when calling biodivMapR_full

fix

implement fix to adjust global extent when using CRS 4326 (e.g. modis)
modify sample_from_raster to account for global footprint

change

modify ‘sample_from_plots_beta’ to account for no data available
adjusted min_sun from 0.75 to 0.6 in ‘get_plots_from_tiles’ when sampling to produce beta model

addition

added ‘get_si_tiles_from_raster’ to compute spectral index from raster tile
implemented functional diversity metrics into tile processing

change

delete files corresponding to individual tiles after mosaic

fix

use basename when calling grep to avoid conflict with directory name

fix

fixed bug when SI values < 0

addition

add possibility to change nb_iter and set it to 10 iterations as default

change

updated variable names

fix

account for presence of aux.xml files
fix documentation

fix

sample_from_raster adapted to handle distances when crs of input_rast in deg

addition

modified perform_PCA to allow PCA over any type of data

change

updated documentation

change

optimize tile processing with function get_raster_diversity_tile

fix

fix tile mask management when tiles are empty

change

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

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

change

clean code
add suppressWarnings when calling progressr

change

merge v2 from gitlab repository
update vignettes for use of v2

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

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

change

use package fundiversity to compute diversity metrics

Fix

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

Change

more systematic use of ‘seq_len’

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

Fix

fixed SFS function when using SpatVector instead of SpatVectorCollection

Fix

fixed SFS function when using SpatVector instead of SpatVectorCollection

Fix

update fixed problem occurring when performing PCA without mask

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

Change

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

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

Fix

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

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.

Change

possibility to enable / disable progressbar in compute_spectral_species_FieldPlots and init_kmeans

Fix

fixed computation of FD metrics
removed import progress and emstreeR

Fix

removed reference to multiprocess, multisession used exclusively from future

Fix

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

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

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

Fix

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

Fix

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

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

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

Addition

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

Addition

added Hellinger distance as beta diversity metric

Addition

removed NMDS as possible ordination method when computing beta diversity

Addition

progress bar instead of messages
future: multisession instead of multiprocess

Addition

added tutorials for the PROGYSAT workshop

Fixes

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

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

Fixes

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

Fixes

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

Fixes

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

Fixes

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

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

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

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)

Fixes

added importFrom raster brick in function extract.big_raster

Fixes

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

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

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

Changes

Added functional diversity metrics
updated example script
updated vignette

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

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

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

Changes

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

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

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

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)

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

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