Man pages for Blakemassey/baear
Functions for Bald Eagle Data Manipulation and Model Fitting
| AddCruiseBehavior | Adds cruise behavior |
| AddFlightBehavior | Adds flight behavior |
| AddHomeConEdgeDistanceBAEA | Adds home and conspecific edge distances to 'baea' dataframe |
| AddHomeRangeKernelsBAEA | Creates and exports homerange kernels |
| AddNestBehavior | Adds nest behavior to baea dataframe |
| AddNestConDist | Adds nest and conspecific distances |
| AddNormDens | Adds Normal Distribution Density |
| AddPerchBehavior | Add perch behavior |
| AddRoostBehavior | Adds roost behavior to dataframe |
| AddSeason | Adds 'season' to dataframe |
| AddTimeStepProportion | Adds time step proportions |
| AnalyzePairLocations | Analyses overlap of homeranges in paired nest locations |
| BehaviorSubModelBAEA | Submodel for behavioral transisitions in BAEA IBM |
| Bin1DimByGroup | Bin one dimension vector by group |
| Bin2Dim | Bin two-dimension vectors |
| CalculateMode | Calculate mode |
| Capitalize | Capitalize string |
| ConvertNestIdToNum | Converts nest alphanumeric id to nest numeric id |
| ConvertNestNumToId | Converts nest numeric id to nest alphanumeric id |
| ConvertStepDataCoordinates | Convert step data coordinates to WGS84 |
| CreateColorsByAny | Creates colors based on any factor in the dataframe |
| CreateConNestDistRasters | Creates conspecific and nest distance raster for each baea in... |
| CreateFlightPathSegments | Create a dataframe of flight path segments |
| CreateHomeRangeKernelsBAEA | Create homerange kernels for the BAEA nests |
| CreateHomeRangeKernelsInterpolate | Create homerange kernels based on interpolating empiricial... |
| CreateHomeRangeKernelsPareto | Create home range kernels using a Pareto distribution |
| CreateHomeRangeKernelsParetoGamma | Create home range kernels based on Pareto and Gamma functions |
| CreateListIndex | Create list index |
| CreateNewPars | Create new parameters list |
| CreateTimeStepsBAEA | CreateTimeStepsBAEA |
| CreateTimeStepsInStepIntervalBAEA | CreateTimeStepsinStepIntervalBAEA |
| CutProportion | Convert data into factors |
| CutProportionMid | Convert data into midpointS |
| DensAsymGenVonMises | Density of asymetric generalized von Mises |
| DensGenVonMises | Density of asymetric generalized von Mises |
| ExtractFlightSpeed | Extracts flight data |
| ExtractMovements | Extract movement data |
| ExtractParsBySex | Extract parameters by sex |
| ExtractParsMatrix | Extract parameters matrix |
| ExtractRoostData | Extracts roost data |
| ExtractRoostPars | Extracts roost parameters |
| ExtractTransitionProbabilities | Extract 'momentuHMM' transition matrix probabilities |
| FilterByNestCriteria | Filter Locations by Nest Behavior Criteria |
| FilterByRoostCriteria | Filter Locations by Roost Criteria |
| FilterLocations | Filter locations by individual and dates |
| FitArrival | Fits arrival parameter |
| FitBehavior | Fits behavior parameter |
| FitDeparture | Fits departure parameters |
| FitGammaParsToData | Fits Gamma parameter |
| FitGenVonMisesDensityToArray | Fit generalized Von Mises density to array |
| FitGenVonMisesParsToData | Fit generalized von Mises parameter to data |
| FitNormalDensityToArray | Fits a Normal density to an array |
| FitNormalParsToData | Fits normal parameters to data |
| FitParetoDensityToArray | Fit Pareto density to array |
| FitParetoParsToData | Fits Pareto parameters to data |
| FitRoost | Fits roost parameters |
| FitStepLength | Fit step length data |
| FitWrappedCauchyDensityToArray | Fit wrapped Cauchy density to array |
| FitWrappedCauchyParsToData | Fits a wrapped Cauchy distribution |
| FitWrappedNormalDensityToArray | Fit wrapped Normal density to array |
| FitWrappedNormalParsToData | Fit wrapped Normal parameters to data |
| GetDateTime | Get datetime info |
| IfElseTimedateCompare | Compares two times and returns greater or lesser value |
| IfElseTimedateNA | Finds time value that is not NA |
| LastDailySubModelBAEA | LastDailySubModelBAEA |
| LogisticByInflection | Logistic by inflection |
| NLLBeta | Negative Log-likelihood of a Beta distribution |
| NLLGamma | Negative Log-likelihood of a Gamma |
| NLLGenVonMises | Negative log-likelihood of general von Mises |
| NLLPareto | Pareto negative Log-Likelihood function |
| NLLWeibull | Negative log-likelihood of the Weibull function |
| NonlinearRangeRescale | NonlinearRangeRescale |
| PlotBehaviorProportionBar | Plots daily behavior proportions as bars |
| PlotBehaviorProportionLine | Plots daily behavior proportions as lines |
| PlotBetaCDF | Plot Beta cumulative distribution function |
| PlotBetaPDF | Plot Beta probability density function |
| PlotCauchyPDF | Plot Cauchy probability density function |
| PlotColorPalette | Plots selected color palettes |
| PlotColorPie | Plots colors in pie chart |
| PlotGammaPDF | Plots Gamma probability distribution function |
| PlotHistAndGenVonMises | Plot histogram of data and generalized von Mises distribution |
| PlotHistAndNormal | Plots histogram and Normal distribution |
| PlotHistAndPareto | Plots a histogram of the data and a Pareto distribution |
| PlotHistAndWrappedCauchy | Plots a histogram with a wrapped Cauchy distribution |
| PlotHistAndWrappedNormal | Plot histogram and wrapped Normal distribution |
| PlotHistogramByVar | Plot histogram by grouping variable |
| PlotLogisticInflectionPDF | Plot logistic probability density function |
| PlotLogisticPDF | Plot Logistic probability distribution function |
| PlotParetoPDF | Plot Pareto probability density function |
| PlotParsBeta | Plot Beta probability density functions |
| PlotProbabilityRaster | Plot 3D raster of selected cells given a probability raster... |
| PlotRoostECDF | Plot roost behavior ECDF |
| PlotRoostHistogram | Plots roost behavior probability distribution |
| PlotStepLengths | Plot step lengths histogram |
| PlotTwoLogisticCDF | Plot two logistic probability density functions... |
| PlotTwoLogisticInflectionPDF | Plot two logistic probability density function |
| PlotWeibullCDF | Plot Weibull cumulative distribution function |
| PlotWeibullPDF | Plot Weibull cumulative distribution function |
| RemoveExcept | Removes all objects in global environment except selected... |
| ReplaceFilesText | Replace text in files |
| SaveGGPlot | Save last printed ggplot |
| SavePlot | Saves last plot |
| SimplifySimSpatialBAEA | Simplify the sim object so that the sim's object size is... |
| SummarizeFitdist | Summarizes a 'fitdist' object |
| SummarizeSE | Summarize data and standard error |
| ThemeBlack | Black theme for ggplot |
| TicMsg | Message for tic of tictoc |
| TocMsg | Message for toc of tictoc |
| UpdateAgentStatesBAEA | Update agent_state object in BAEA IBM |
| UpdateAgentStepDataBAEA | Update the step_data object in a BAEA IBM |
| UpdateSpatialBAEA | UpdateSpatialBAEA |
