Files in Mamie/PILAF
PILAF: Phylodynamics InfLuenzA Forecast
.Rbuildignore
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
PILAF.Rproj
R/BNPR_forecast.R
R/PILAF.R
R/data_visualizations.R
R/evaluation.R
R/forecast.R
R/simulation.R
R/simulation_evaluation.R
R/visualization.R
README.md
analysis/debug_forecast.R
analysis/plot_MCC.Rmd
analysis/simulation.Rmd
analysis/summarize_forecasts.R
data-raw/.gitattributes
data-raw/.gitignore
data-raw/20190308_H3N2_SkyGrid/20190307_H3N2_MCC.tree
data-raw/20190308_H3N2_SkyGrid/20190307_H3N2_skygrid_reconstruction.tsv
data-raw/20190308_H3N2_SkyGrid/H3N2_skygrid.sh
data-raw/20190308_H3N2_SkyGrid/NewYork_A_H3N2_20190307_filtered_aligned.log
data-raw/20190308_H3N2_SkyGrid/NewYork_A_H3N2_20190307_filtered_aligned.ops
data-raw/20190308_H3N2_SkyGrid/NewYork_A_H3N2_20190307_filtered_aligned.trees
data-raw/20190318_H1N1_SkyGrid/20190318_H1N1_MCC.tree
data-raw/20190318_H1N1_SkyGrid/20190318_H1N1_skygrid.tsv
data-raw/20190318_H1N1_SkyGrid/H1N1_skygrid.sh
data-raw/20190318_H1N1_SkyGrid/NewYork_A_H1N1_20190318_filtered_aligned.log
data-raw/20190318_H1N1_SkyGrid/NewYork_A_H1N1_20190318_filtered_aligned.ops
data-raw/20190318_H1N1_SkyGrid/NewYork_A_H1N1_20190318_filtered_aligned.trees
data-raw/20190318_Victoria_SkyGrid/20190318_Victoria_MCC.tree
data-raw/20190318_Victoria_SkyGrid/20190318_Victoria_skygrid_reconstruction.tsv
data-raw/20190318_Victoria_SkyGrid/NewYork_B_Victoria_20190318_filtered_aligned.log
data-raw/20190318_Victoria_SkyGrid/NewYork_B_Victoria_20190318_filtered_aligned.ops
data-raw/20190318_Victoria_SkyGrid/NewYork_B_Victoria_20190318_filtered_aligned.trees
data-raw/20190318_Victoria_SkyGrid/Victoria_skygrid.sh
data-raw/20190318_Yamagata_SkyGrid/20190318_Yamagata_MCC.tree
data-raw/20190318_Yamagata_SkyGrid/20190318_Yamagata_skygrid_reconstruction.tsv
data-raw/20190318_Yamagata_SkyGrid/NewYork_B_Yamagata_20190318_filtered_aligned.log
data-raw/20190318_Yamagata_SkyGrid/NewYork_B_Yamagata_20190318_filtered_aligned.ops
data-raw/20190318_Yamagata_SkyGrid/NewYork_B_Yamagata_20190318_filtered_aligned.trees
data-raw/20190318_Yamagata_SkyGrid/Yamagata_skygrid.sh
data-raw/align.sh
data-raw/fasta_qc.R
data-raw/ilinet_data.R
data-raw/install_beagle.sh
inst/extdata/H1N1/20180318_NewYork_H1N1.fasta
inst/extdata/H1N1/MCC.tree
inst/extdata/H1N1/NewYork_A_H1N1_20190318_filtered.fasta
inst/extdata/H1N1/NewYork_A_H1N1_20190318_filtered.tsv
inst/extdata/H1N1/NewYork_A_H1N1_20190318_filtered_aligned.fasta
inst/extdata/H1N1/NewYork_A_H1N1_20190318_filtered_aligned.xml
inst/extdata/H1N1/skygrid_reconstruction.tsv
inst/extdata/H3N2/MCC.tree
inst/extdata/H3N2/NewYork_A_H3N2_20190307.fasta
inst/extdata/H3N2/NewYork_A_H3N2_20190307_filtered.tsv
inst/extdata/H3N2/NewYork_A_H3N2_20190307_filtered_aligned.fasta
inst/extdata/H3N2/NewYork_A_H3N2_20190307_filtered_aligned.xml
inst/extdata/H3N2/skygrid_reconstruction.tsv
inst/extdata/Victoria/20190315_NewYork_B_Victoria.fasta
inst/extdata/Victoria/MCC.tree
inst/extdata/Victoria/NewYork_B_Victoria_20190318_filtered.fasta
inst/extdata/Victoria/NewYork_B_Victoria_20190318_filtered.tsv
inst/extdata/Victoria/NewYork_B_Victoria_20190318_filtered_aligned.fasta
inst/extdata/Victoria/NewYork_B_Victoria_20190318_filtered_aligned.xml
inst/extdata/Victoria/skygrid_reconstruction.tsv
inst/extdata/Yamagata/20190315_NewYork_B_Yamagata.fasta
inst/extdata/Yamagata/MCC.tree
inst/extdata/Yamagata/NewYork_B_Yamagata_20190318_filtered.fasta
inst/extdata/Yamagata/NewYork_B_Yamagata_20190318_filtered.tsv
inst/extdata/Yamagata/NewYork_B_Yamagata_20190318_filtered_aligned.fasta
inst/extdata/Yamagata/NewYork_B_Yamagata_20190318_filtered_aligned.xml
inst/extdata/Yamagata/skygrid_reconstruction.tsv
logo.svg
man/AsBackwardTime.Rd
man/AsForwardTime.Rd
man/BNPR_forecast.Rd
man/BNPR_to_df.Rd
man/ComputePropCnst.Rd
man/LOSO_forecast.Rd
man/MASE.Rd
man/PILAF.Rd
man/PoissonTimeSampling.Rd
man/SMAPE.Rd
man/SimulateCoalCounts.Rd
man/SimulateILISampCoalCounts.Rd
man/SimulateILISampCoalCountsN.Rd
man/compare.Forecast.Rd
man/compare.Rd
man/computeAEW.Rd
man/compute_peak_week.Rd
man/compute_truncation_time.Rd
man/create_data_avail_table.Rd
man/create_grid.Rd
man/create_season_task_list.Rd
man/evaluate.Forecast.Rd
man/evaluate.Rd
man/find_peak_week.Rd
man/find_season_range.Rd
man/forecast.PILAF.Rd
man/forecast.PILAF.count.Rd
man/forecast.PILAF.joint.Rd
man/forecast.Rd
man/forecast_starting.Rd
man/generate_task_list.Rd
man/get_summary_stats.Rd
man/is.Forecast.Rd
man/is.PILAF.Rd
man/mean_coverage.Rd
man/plot.Forecast.Rd
man/plot.PILAF.Rd
man/plot_MCC_Ne.Rd
man/plot_traj_heatmap.Rd
man/plot_trajectory.Rd
man/summary.Forecast.Rd
man/summarySE.Rd
man/truncate_BNPR_PS.Rd
man/truncate_data.Rd
man/visualize_flu_season.Rd
tests/testthat/test_infer_coal_samp.R
tests/testthat/test_simulation.R
tests/testthat/test_simulation.rds
tests/testthat/test_truncation.R
vignettes/BNPRforecast.Rmd
vignettes/BNPRforecastJ.Rmd
vignettes/CDC_data.Rmd
