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Open Sustainable Technology

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Recent Releases of biodivMapR

biodivMapR - biodivMapR v2

biodivMapR v2 includes an updated workflow, with more simple and straightforward application of the full process to produce diversity maps.

  • biodivMapR_full is an all in one function to produce the diversity maps.
  • minimum intermediate variables saved to reduce the volume of data produced.
  • possibility to train biodivMapR with a rastrer and apply the model on independent sites.
  • different modalities applicable to biodivMapR for optical data processing are described : spectral transformation, spectral indices.
  • improved support for any raster file format, using terra
  • more functionalities included, to be described in next documentation versions

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet 3 months ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 1 year ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 1 year ago

biodivMapR - Functional diversity fix

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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet almost 2 years ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 2 years ago

biodivMapR - v1.10.0

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 2 years ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 2 years ago

biodivMapR - no NMDS anymore

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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 2 years ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 2 years ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 3 years ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet over 3 years ago

biodivMapR - run biodivMapR directly on classification maps

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet about 4 years ago

biodivMapR - biodivMapR is getting functional

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

  • implemented MNF for dimensionality reduction
  • 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
  • Added functional diversity metrics
  • updated example script
  • updated vignette

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet almost 5 years ago

biodivMapR - includes stars and reads any file format as input

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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet almost 5 years ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet almost 5 years ago

biodivMapR - 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

Biosphere - Biodiversity Analysis and Metrics - R
Published by jbferet about 5 years ago