Man pages for pieterbeck/CanHeMonR
Tools for canopy health monitoring through image analysis
| add_PT_buffer_parishes_borders | Add Outline of the PT PWN Buffer Zone to an Existing Plot |
| ADS100_G2R | Green_over_Red Index simulating ADS100 sensor (ADS100_G2R) |
| ADS100_NDVI | Normalized Difference Vegetation Index simulating ADS100... |
| assign_crowncells_quantile | Assign Polygon Cells Their Quantile Value In A Raster |
| assign_crowncells_quantile_parallel | Assign Polygon Cells Their Quantile Value In A Raster in... |
| BGI1 | Blue Green Index 1 |
| BGI2 | Blue Green Index 2 |
| Blue_index | Blue Index |
| BRI1 | Blue Red Index 1 |
| BRI2 | Blue Red Index 2 |
| calc_neighbours_pix_nrs | Find Neigbour Cells in a Matrix |
| calculate_remoteness_from_binary_raster | Calculate Remoteness Binary raster |
| calculate_TerraBella_indices | Calculate TerraBella spectral indices |
| calibrate_sicktree_model | Calibrate vegetation distribution models |
| calibrate_sicktree_model_multi_tile | Calibrate vegetation distribution models |
| check_im_res | Before Crown Delineation Check Image Resolution Consistency |
| CI | Chlorophyll Index Red Edge |
| classify_maxent_output_based_on_error_stats | Classify maxent output to binary presence absence maps |
| clip_polygons2rasters | Clip Spatialpolygons To The Extent Of A Raster |
| close_crown | Morphological Opening Operation |
| create_overview_of_rasters | Create A Polygon .shp Of Raster File Extents |
| CRI550 | Carotenoid Reflectance Index 550 nm |
| CRI700 | Carotenoid Reflectance Index 700 nm |
| crown_indices_from_bigshape | Crown-level spectral indices for a big shapefile |
| crown_inspector | Inspect Delineated Crowns In Multiple Images |
| CTRI1 | Carter Index 1 |
| CTRI2 | Carter Index 2 |
| CUR | Reflectance Curvature Index |
| datt_CabCx_c | Reflectance Band Ratio |
| datt_NIRCabCx_c | Reflectance Band Ratio Using NIR |
| DMC_G2R | Green_over_Red Index simulating DMC sensor (DMC_G2R) |
| DMC_NDVI | Normalized Difference Vegetation Index simulating DMC sensor... |
| eliminate_split_crown | Clean up Split Polygons |
| ensure_uneven_r_dim | Before Crown Delineation Check Image Dimension Consistency |
| evaluate_crown_growing_efficiency | Evaluate Efficiency Of Crown Delineation By... |
| EVI | Enhanced Vegetation Index |
| extract_mn_sd | Mean And SD From Polygon-on-Brick Overlay |
| fit_simple_polynomial | Fitting Simple Polynomial Models |
| flag_valid_pix | Register Valid Pixels in a Matrix |
| get_band_of_wavelength | Get The Measurements Made In A Chosen Wavelength |
| get_index_or_wavelength_from_brick | Get Spectral Index or Chosen Wavelength From Brick |
| get_TerraBella_scene_date | Get TerraBella Scene Date |
| GM1 | Gitelson & Merzlyak Index 1 |
| GM2 | Gitelson & Merzlyak Index 2 |
| Greenness | Greenness Index |
| grow_crown | Grow a Spectrally Homogenous Object |
| grow_crowns | Outline Tree Crowns In Imagery |
| histnd | Multidimensional Stratification |
| identify_n_neighbours | Find A Polygon's Neighbour Polygons |
| indiv_bands | Get A List Into A df For Easier Manipulation |
| LIC1 | Lichtenthaler Index 1 |
| LIC2 | Lichtenhaler (Blue Over Red) Index 2 |
| LIC3 | Lichtenhaler Index |
| mask_to_PT_buffer_zone | Mask a Raster File to Only Retain Data within the PT PWN... |
| MCARI1 | Modified Chlorophyll Absorption Ratio Index 1 |
| MCARI2 | Modified Chlorophyll Absorption Ratio Index 2 |
| merge_pnt_shp_files_by_attributes | Merge Point Shapefiles By Attributes |
| merge_pols_intersected_by_lines | Merge Polygons Intersected By Lines |
| mod_SR | Modified Simple Ratio |
| MSAVI | Modified Soil-Adjusted Vegetation Index |
| MTVI1 | Modified Triangular Vegetation Index 1 |
| MTVI2 | Modified Triangular Vegetation Index 2 |
| NDVI | Normalized Difference Vegetation Index (NDVI) |
| NPCI | Normalized Pigments Index |
| NPQI | Normalized Phaeophytinization Index |
| OSAVI | Optimised Soil-Adjusted Vegetation Index |
| pairsplot | A Customized Pairs Plot |
| point_at_highest_value_in_polygon | Place Point At Maximum Location |
| polygons_to_seeds | Convert Polygons To Seeds |
| PRI512 | Photochemical Reflectance Index 512 |
| PRI515 | Photochemical Reflectance Index 515 |
| PRI570 | Photochemical Reflectance Index 570 |
| PRI600 | Photochemical Reflectance Index 600 |
| PRI670 | Photochemical Reflectance Index 670 |
| PRI670_570 | Photochemical Reflectance Index 670 570 |
| PRI_CI | Carotenoid/chlorophyll Ratio Index |
| PRIn | Normalized Photochemical Reflectance Index |
| proximity_indices | Make a distance-to-center matrix |
| PSNDc | Pigment Specific Normalized Difference |
| PSRI | Plant Senescing Reflectance Index |
| PSSRa | Pigment Specific Simple Ratio Chlorophyll a |
| PSSRb | Pigment Specific Simple Ratio Chlorophyll b |
| PSSRc | Pigment Specific Simple Ratio Carotenoids |
| RARS | Ratio Analysis Of Reflectance Spectra |
| RDVI | Renormalized Difference Vegetation Index |
| Redness | Redness Index |
| remove_all_NA | Check An Object For NAs |
| remove_holes | Close Holes in Polygons |
| remove_small_pols | Remove Small Polygons |
| rF_predictions_to_polygons | Run An Existing rF In Predictive Mode |
| RNIR_CRI550 | Carotenoid Reflectance Index 550 nm with NIR |
| RNIR_CRI700 | Carotenoid Reflectance Index 700 nm with NIR |
| run_sicktree_model | Run a distribution model using a raster brick as predictors |
| run_sicktree_model_multitile | Run a saved MaxEnt model in predictive mode on a tile of... |
| samp_df | Avoid Data Frames With Too Many Rows |
| sample_false_positives | Sample false positives from a set of binary images |
| sample_for_sicktree_model_multi_tile | Sample training data for image classification from multiple... |
| samplestratified | Take A Stratified Sample Of A Data Set |
| samplestratified_shp | Take A Stratified Sample Of A .SHP With Spectral Indices As... |
| shadow_based_seed_filter | Filter Seeds That Lack Shadows |
| shift_polygons_to_points | Shift Polygons To Points |
| shp_copy | Copy shapefiles between directories |
| sick_tree_errors | Sick tree error calculator |
| SIPI | Structure-Insensitive Pigment Index |
| spectral_indices_for_crowns | Calculate Spectral Indices For Individual Tree Crowns |
| SR | Simple Ratio |
| SRPI | Simple Ratio Pigment Index |
| subtract_control_median | Subtract Band And Polygon Specific Median From Digital... |
| TCARI | Transformed Chlorophyll Absorption in Reflectance Index |
| TCARI_over_OSAVI | Transformed Chlorophyll Absorption in Reflectance Index Over... |
| test_fun | Test function for grid |
| tile_raster_extent | Tile A Raster's Extent |
| tps2d_seeds | Spatially Warp SpatialPoints Using A Set Of Reference Point... |
| train_rF_classifier_on_polygons | Calibrates A Supervised Classification Of Multiband Imagery... |
| TVI | Triangular Vegetation Index |
| VOG1 | Vogelmann Index 1 |
| VOG2 | Vogelmann Index 2 |
| VOG3 | Vogelmann Index 3 |
| watershed_tree_detection | Watershed-Based Tree Detection |
