Man pages for nevilamos/FAMEFMR
Functions For DELWP FAME Fire Analysis
| add_xystring | Adds concatenated String of X and Y coordinates of centroids... |
| alginCustomRaster | Align raster extent with template grid |
| autoJFMP | Create Automatic JFMP burn allocation |
| calcBBTFI_2 | Calculate area BBTFI and BBTFI rasters |
| calcDeltaAbund | Summary of changes in relative abundance |
| calc_DraftSpList | Calculate a draft species list for defined polygon |
| calc_G | Calculate Geometric means of columns |
| calc_SpeciesRA | Species' relative abundance calculation and summary |
| calc_TFI_2 | Main Tolerable fire interval (TFI) status calculation |
| calcU_All_Combs | Calculate all combinations of input raster values |
| cellsToHectares | Calculates multiplier to convert from raster cell count to... |
| CIM | Calculate mean and 95% credible interval |
| const_vector | Construct a n-length vector (c(k, ..., k)) |
| ConvertExpert | Convert from old to new expert opinions |
| cropToOutput | Creates an output list containing vectors of input rasters,... |
| DataGen | Generate Growth Stage Optimisation Scores |
| eval_cs | Inequality contraints replacement |
| eval_cs_jac | Jacobian (partial derivative matrix) for the inequalities |
| FAMEFMR-package | FAMEFMR: Functions For DELWP FAME Fire Analysis |
| fhCheck | Basic Checks of input Fire History |
| fhProcess | Wrapper for main fhProcessing |
| fhProcess1 | FIRE History Processing for FAME stage1 |
| fhProcess2 | Second stage of Fire history processing for FAME |
| fireTypeLowToHigh | FireType Low to high |
| generate_random_fire_history | Generate Random Fire History Polygons |
| geoMean | Calculate Geometric mean |
| geomean.fun | Calculate 'geomean' |
| geomean.grad | Calculate geomean objective gradient |
| geomean.obj | Calculate reformulated geomean objective |
| get_Spp_No | Extract VBA (Victorian Biodiversity Atlas) species ID numbers... |
| gso | Growth Stage Optimisation (GSO) |
| inputRasters | Set correct input general rasters |
| jfmp1 | JFMP Stage 1 calculations |
| jfmpBBTFISumm | Summarise areas never BBTFI by scenario. |
| jfmpRASumm | Summary of relative abundance changes comparing JFMP results |
| jfmpSummary | Title Summary of JFMP areas burned and not burned |
| joinDraftJFMP | join draft JFMP inputs |
| Join_Names | Joins one or more lookup tables to table containing ID values... |
| LBY_f | Calculate last burned year matrix (LBY) |
| mainFHProcess | Main Fire History Fire Sequence analysis function |
| makeAbundDataLong | Makes Long format Fauna abundance table |
| make_Draft_GSO_inputs | Calculate the species in each EFG in given area for GSO... |
| makeGS_LU | Make long format Growth Stage Lookup matrix |
| makeGS_Summary | Summarise area by growth stage. |
| make_JFMPNoBurnTab | Summary of changes in relative abundance |
| make_Spp_LU_list | Generate list of species abundance lookup arrays |
| notAllIn | Checks whether all values in one vector are in another vector |
| OptRunCI | Run Credible Intervals on GSO calcs (main GSO function) |
| packageForDashboard | packageForDashboard takes a saved analysis file from FAME and... |
| pipe | Pipe operator |
| prepFH | PrepareFire History |
| readSpatRasterList | Read qs file containing list with SpatRaster objects (... |
| removeEmptyDirs | remove empty directories from path |
| Rule0 | Rule 0: Use mean expert opinion only |
| Rule1 | Rule1: Unweighted mean survey data, otherwise mean expert... |
| Rule1a | Rule1a: Max survey data where available, otherwise max expert... |
| Rule1b | Rule1b: Median survey data where available, otherwise mean... |
| Rule1c | Rule1c: Upper quartile survey data where available, otherwise... |
| Rule2 | Rule2: Weighted average of survey and expert data. |
| Rule2a | Rule2a: Weighted average of max survey and expert data. |
| Rule2b | Rule2b: Weighted average of median survey and expert data. |
| Rule2c | Rule2c: Weighted average of upper quartile survey and expert... |
| Rule3 | Rule3: Mean of survey data only |
| Rule3a | Rule3a: Max of survey data only |
| Rule3b | Rule3b: Median of survey data only |
| Rule3c | Rule3c: Upper quartile of survey data only |
| saveFHsettings | Save Settings for fhProcess() |
| saveJFMPsettings | Save JFMP settings |
| savePUsettings | Save Settings for PU file |
| saveSettingsTable | Save settings to csv file |
| saveSpatRasterList | Save List containing SpatRaster objects ( package terra) |
| saveSPsettings | Save Settings for species calcuations |
| Scenarios | Joins GSO scenarios to input data |
| selectFileServer | Module Server function for file selection |
| selectFileUI | Module UI function for file selection |
| SppRes | Collate species results |
| unlistPivot_wider | Fix Pivot_wider list of lists columns |
| uploadFileServer | uploadFile Server part of uploadFle shiny module |
| uploadFileUI | uploadFile UI part of uploadFle shiny module |
