Man pages for jbferet/biodivMapR
biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images
| apply_continuum_removal | prepares data to run multithreaded continuum removal |
| apply_kmeans | Applies Kmeans clustering to PCA image and writes spectral... |
| biodivMapR-package | biodivMapR: biodivMapR: an R package for a- and ß-diversity... |
| build_image_from_list | rebuilds full image from list of subsets |
| center_reduce | center and reduce data matrix based on known mean and SD |
| change_resolution_HDR | change resolution in a HDR file |
| check_data | Checks if the data to be processed has the format type... |
| check_update_mask_format | check if the format of the mask is as expected: integer,... |
| compute_ALPHA_FromPlot | compute alpha diversity from spectral species computed for a... |
| compute_alpha_metrics | Computes alpha diversity metrics based on spectral species |
| compute_BCdiss | compute the bray curtis dissimilarity matrix corresponding to... |
| compute_BETA_FromPlots | compute beta diversity from spectral species computed for a... |
| compute_beta_metrics | computes beta diversity metrics |
| compute_FD | compute functional diversity metrics for an array, given a... |
| compute_Functional_metrics | Map functional diversity metrics based on spectral species |
| compute_NN_from_ordination | compute the nearest neighbors among kernels used in NMDS |
| compute_spectral_species | this function reads PCA file and defines the spectral species... |
| compute_spectral_species_FieldPlots | compute spectral species for a subset of pixels provided in a... |
| compute_SSD | compute spectral species distribution from original spectral... |
| continuumRemoval | Computes continuum removal for matrix shaped data: more... |
| convert_PCA_to_SSD | Convert PCA into SSD based on previous clustering |
| create_hdr | create a hdr file for a raster |
| create_mask_from_threshold | create a mask based on NDVI, Green reflectance and NIR... |
| define_output_directory | define output directory and create it if necessary |
| define_output_subdir | define output directory and subdirectory and create it if... |
| define_pixels_per_iter | defines the number of pixels per iteration based on a... |
| diversity_from_plots | gets alpha diversity indicators from plot |
| ENVI_type2bytes | get information corresponding to data type defined in ENVI |
| exclude_spectral_domains | define Water Vapor bands based on spectral smapling of... |
| extract.big_raster | Extract bands of sparse pixels in image data cube |
| extract_pixels | extracts sample points from binary image file |
| extract_pixels_coordinates | Extracts pixels coordinates from raster intersecting a... |
| extract_samples_from_image | extracts pixels from image based on their coordinates |
| filter_PCA | perform filtering based on extreme values PCA identified... |
| filter_prior_CR | Filter data prior to continuum removal: - values are expected... |
| get_alpha_metrics | Computes alpha diversity metrics from distribution |
| getBCdiss | Computes BC dissimilarity for a given matrix |
| get_byte_order | does the system work with little endians or big endians? |
| getFD | get functional diversity metrics from dataframe This function... |
| Get_FunctionalMetrics_From_Traits | Prepare for the computation of the functional diversity... |
| get_gdal_info | Get GDAL info as a nested list |
| get_HDR_name | get hdr name from image file name, assuming it is BIL format |
| get_image_bands | gets rank of spectral bands in an image |
| get_random_subset_from_image | extract random subset of pixels from an image |
| get_Shannon | computes shannon index from a distribution (faster than... |
| get_Simpson | computes Simpson index from a distribution (faster than... |
| get_SSpath | defines path for the spectral species raster file. Depends on... |
| get_sunlit_pixels | Gets sunlit pixels from SpectralSpecies_Distribution_Sunlit |
| ind2sub | convert image coordinates from index to X-Y |
| ind2sub2 | convert image coordinates from index to X-Y image coordinates... |
| init_kmeans | computes k-means from nb_partitions subsets taken from... |
| IQR_outliers | This function computes interquartile range (IQR) criterion,... |
| kmeans_progressr | applies results of ordination to full image based on nearest... |
| list_shp | Get list of shapefiles in a directory |
| map_alpha_div | maps alpha diversity indicators based on prior selection of... |
| map_beta_div | maps beta diversity indicator based on spectral species... |
| map_functional_div | maps functional diversity indicators based on prior selection... |
| map_spectral_species | maps spectral species based on PCA file computed previously |
| mean_filter | applies mean filter to an image |
| minmax | this function performs rescaling and either defines min and... |
| mnf | Function to perform MNF |
| noise | this function |
| ordination_to_NN | #' computes NMDS # #' @param MatBCdist BC dissimilarity... |
| ordination_to_NN_list | computes nearest neighbors of a SSD subset with samples used... |
| pca | Function to perform PCA on a matrix |
| perform_PCA | Performs PCA for all images and create PCA file with either... |
| perform_radiometric_filtering | Performs radiometric filtering based on three criteria: NDVI,... |
| prepare_HDR_SSD | prepares Spectral species distribution (SSD) file and header |
| prepare_HDR_Sunlit | prepare for writing sunlit proportion file |
| print_error_message | prints an error message if problems occur |
| raster2BIL | converts a raster into BIL format as expected by biodivMapR... |
| read_BIL_image_subset | reads subset of an ENVI BIL image |
| read_bin_subset | reads a subset from a binary image |
| read_ENVI_header | Reads ENVI hdr file |
| read_image_bands | read specific image bands from image |
| read_image_subset | reads subset of lines from an image |
| repmat | R equivalent of repmat (matlab) |
| revert_resolution_HDR | revert resolution in a HDR file |
| rm_invariant_bands | remove constant bands |
| RowToLinear | get max index for each row and convert into linear index |
| select_PCA_components | Check if principal components are properly selected as... |
| spectral_band_unit | Check spectral band units and convert from nanometer to... |
| split_image | defines the number of pieces resulting from image split |
| split_line | ENVI functions |
| split_pixel_samples | splits a set of pixels to be sampled in an image based on... |
| sub2ind | convert image coordinates from X-Y to index |
| update_shademask | updates an existing mask |
| WeightedCoordsNN | Compute the weighted coordinates of a spatial unit based on... |
| where_to_read | defines which byte should be read for each part of an image... |
| where_to_read_kernel | defines which byte should be read for each part of an image... |
| where_to_write_kernel | defines which byte should be written for each part of an... |
| Write_Big_Image | write an image which size is > 2**31-1 |
| write_ENVI_header | writes ENVI hdr file |
| Write_Image_NativeRes | write an image resulting from "window processing" at native... |
| write_PCA_raster | writes an ENVI image corresponding to PCA |
| write_raster | Writes a matrix or an array into a ENVI BIL raster |
| write_StarsStack | This function writes a stars object into a raster file |
| ZipFile | Zips an image file |
