Man pages for Mamie/PILAF
PILAF: Phylodynamics InfLuenzA Forecast
| AsBackwardTime | Convert Ordered Time as Time to Last Time Point |
| AsForwardTime | Convert Time to Last Timepoint as Normal Time |
| BNPR_forecast | Forecast using Bayesian Nonparametric phylodynamics |
| BNPR_to_df | Convert BNPR object summary statistics to data frame |
| compare | Generic function for comparison |
| compare.Forecast | Compare performance of two models by AE and W |
| computeAEW | Compute absolute error and width between forecast and truth. |
| compute_peak_week | Compute peakk week and peak ILI for each season |
| ComputePropCnst | Compute Proportionality Constant |
| compute_truncation_time | Compute the date of the Monday of the week for truncation |
| create_data_avail_table | Create data availability table |
| create_grid | Create grid of time and week |
| create_season_task_list | Create a list of tasks to run for each season |
| evaluate | Generic function for evaluation |
| evaluate.Forecast | Evaluate the Forecast |
| find_peak_week | Find the peak week amd peak ILI from samples |
| find_season_range | Find the starting and ending time of a season |
| forecast | Constructor to Forecast object |
| forecast.PILAF | Forecast a PILAF Object. |
| forecast.PILAF.count | Forecast using Only Count |
| forecast.PILAF.joint | Forecast using Count and Coalescent events |
| forecast_starting | Forecast starting at given time |
| generate_task_list | Generate task list |
| get_summary_stats | Get summary statistics from samples |
| is.Forecast | Check if an Object is Forecast |
| is.PILAF | Check if an Object is PILAF |
| LOSO_forecast | Leave one season out evaluation |
| MASE | Mean absolute scaled error |
| mean_coverage | Mean coverage |
| PILAF | Constructor to PILAF object |
| plot.Forecast | Plot the Forecast Results |
| plot_MCC_Ne | Plot MCC tree and skygrid effective population size |
| plot.PILAF | Plot PILAF trajectory |
| plot_trajectory | Plot a Ne trajectory |
| plot_traj_heatmap | plot real CDC time series data |
| PoissonTimeSampling | Poisson Process Simulation |
| SimulateCoalCounts | Simulate Coalescent Counts |
| SimulateILISampCoalCounts | Simulate ILI, Sampling, and Coalescent counts |
| SimulateILISampCoalCountsN | Simulate ILI, Sampling, and Coalescent counts N Times |
| SMAPE | Symmetric mean absolute percentage error |
| summary.Forecast | Summarize the Forecast |
| summarySE | Compute SE for given variable. |
| truncate_BNPR_PS | Fit BNPR_PS with truncated data |
| truncate_data | Truncates a phylogentic tree |
| visualize_flu_season | Visualize the time series for each Flu Season |
