Man pages for jbferet/biodivMapR
biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images
| alphabeta_window | compute alpha and beta diversity metrics from pixel data... |
| alphabeta_window_list | apply alphabeta_window to a list of lists |
| apply_continuum_removal | prepares data into list to apply continuum removal |
| apply_kmeans | apply kmeans to information extracted from an image and... |
| biodivMapR_chunk | apply biodivMapR (computes clusters + diversity metrics) to... |
| biodivMapR_full | computes diversity metrics from raster |
| biodivMapR_full_tiles | computes diversity metrics from raster |
| biodivMapR_OptClusters | apply biodivMapR on a test set for different numbers of... |
| biodivMapR-package | biodivMapR: biodivMapR: an R package for a- and ß-diversity... |
| biodivMapR_SFS | performs SFS to identify combination of input variables... |
| center_reduce | center and reduce data matrix based on known mean and SD |
| check_data | Checks if the data to be processed has the format type... |
| clean_NAsInf | cleans dataframe from NAs and Inf values |
| compute_BCdiss | compute bray curtis dissimilarity matrix corresponding to a... |
| compute_mask_IQR | compute mask based on interquartile range criterion applied... |
| compute_mask_IQR_tiles | get samples for alpha and beta diversity mapping |
| compute_NN_from_ordination | compute the nearest neighbors among kernels |
| continuumRemoval | Computes continuum removal for matrix shaped data: more... |
| define_pixels_per_iter | defines the number of pixels per iteration |
| exclude_spectral_domains | define water vapor bands based on spectral sampling of... |
| explore_kmeans | Compute kmeans from random subset of pixels extracted from an... |
| extract_svc_from_rast | extract pixel information from a raster based on... |
| extract_vect_from_rast | extract pixel information from a raster based on vector... |
| filter_prior_CR | Filter data prior to continuum removal: • values are expected... |
| functional_window | compute functional diversity metrics from pixel data... |
| functional_window_list | apply functional_window to a list of lists |
| get_alpha_from_SSD | computes alpha diversity metrics from SSD |
| get_asset_path | This function gets path from an asset in the JSON file |
| get_BCdiss | Computes BC dissimilarity for a given matrix |
| get_BCdiss_from_SSD | Computes BC dissimilarity for a list of spectral species... |
| get_date | gets acquisition date from S2 image |
| get_diversity_from_plots | computes diversity metrics from validation plots |
| get_functional_diversity | get functional diversity metrics from dataframe This function... |
| get_HDR_name | get hdr name from image file name |
| get_Hill | computes hill number from a distribution The Hill numbers... |
| get_image_bands | gets rank of spectral bands in an image |
| get_kmeans | computes k-means from nbIter subsets taken from dataPCA |
| get_plots_from_tiles | get samples for beta diversity mapping |
| get_raster_diversity | Computes diversity metrics from raster data |
| get_raster_diversity_mw | Computes diversity metrics from raster data based on moving... |
| get_raster_diversity_tile | Computes diversity metrics from raster data based on moving... |
| get_raster_extent | gets raster extent |
| get_samples_from_tiles | get samples for alpha diversity mapping |
| get_Shannon | computes shannon index from a distribution (faster than... |
| get_Simpson | computes Simpson index from a distribution |
| get_spectralSpecies | compute spectral species from inputdata |
| get_SSD_full | get spectral species distribution for all clusters |
| get_stats_from_tiles | get samples from tiles produced with preprocS2 function... |
| get_sunlitwindows | eliminate windows with insufficient sunlit pixels |
| get_valid_pixels | get valid pixels from a list of plots produced with preprocS2... |
| get_valid_pixels_from_tiles | get valid pixels from list of tiles |
| get_xy_samples | get xy of pixels to sample from raster |
| init_kmeans | Compute kmeans from random subset of pixels extracted from an... |
| init_kmeans_samples | Compute kmeans from random subset of pixels extracted from an... |
| init_PCoA | initialize PCoA for beta diversity mapping |
| init_PCoA_samples | initialize PCoA for beta diversity mapping based on samples... |
| IQR_outliers | This function computes interquartile range (IQR) criterion,... |
| IQR_SpatRaster | This function computes interquartile range (IQR) for a... |
| kmeans_iter | computes kmeans for an iteration in biodivMapR |
| kmeans_progressr | applies results of ordination to full image based on nearest... |
| maxRows_chunk | redefined chunks based on the max number of rows per chunk |
| mnf | Function to perform MNF |
| mosaic_tiles | compute spectral indices and composite for a given period of... |
| nbRows_chunk | adjusts number of rows from chunks |
| noise | gets noise |
| pca | performs PCA on matrix X |
| pco | computes PCoA using the cmdscale function original source:... |
| perform_PCA | Performs PCA for all images and create PCA file with either... |
| print_error_message | prints an error message if problems occur |
| produce_win_ID | design a matrix with window ID based on an original raster... |
| radiometricfilter_chunk | Performs radiometric filtering based on three criteria: NDVI,... |
| radiometric_filtering | Performs radiometric filtering based on three criteria: NDVI,... |
| randperm | performs random permutation for k samples among the vector... |
| read_ENVI_header | Reads ENVI hdr file |
| repmat | R equivalent of repmat (matlab) |
| rm_invariant_bands | remove constant bands |
| RowToLinear | get max index for each row and convert into linear index |
| run_biodivMapR | apply biodivMapR to an individual set of rasters (one site) |
| run_biodivMapR_plot | apply biodivMapR to a set of plots identified by a field... |
| sample_exact_raster | sample exact number of pixels from a raster |
| sample_from_plots | get samples for alpha and beta diversity mapping |
| sample_from_plots_alpha | get samples for alpha diversity mapping |
| sample_from_plots_beta | get samples for beta diversity mapping |
| sample_from_raster | sample pixels or plots from raster data |
| sample_from_raster_coords | sample set of pixels defined by row and col from raster data |
| sample_plots_from_raster | sample pixels or plots from raster data |
| sample_raster | sample pixels from raster data |
| save_diversity_maps | save diversity maps as raster data |
| save_diversity_maps_mw | save diversity maps as raster data once moving window process... |
| save_diversity_maps_tile | save diversity maps as raster data |
| scatter_alphabeta | produces a figure summarizing alpha and beta diversity on... |
| select_PCA_components | Check if principal components are properly selected as... |
| spectralspecies_per_polygon | get spectral species corresponding to polygons in a... |
| split_chunk | split chunk into subsets to prepare for parallel processing |
| split_line | ENVI functions |
| update_mask_from_tiles | update mask based on IQR for a series of rasters produced... |
| WeightedCoordsNN | Compute the weighted coordinates of a spatial unit based on... |
| wrapperBig_PCA | this function aims at applying PCA on a raster or list of... |
