Files in jameshay218/zikaProj
zikaInfer
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/OLD.R
R/RcppExports.R
R/example_data.R
R/model.R
R/package.R
R/par_setup.R
R/plots.R
R/plots_new.R
R/post_analyses.R
R/posteriors.R
R/simulations.R
R/state_data.R
R/zzz.R
README.md
RawData/Brazil/brazil_microCeph_28022017.csv
RawData/Brazil/brazil_report_zikv_inc_2016.csv
RawData/Brazil/microceph_reports_2016.csv
RawData/Brazil/microceph_reports_2016_confirmed.csv
RawData/Brazil/salvador_inc_scaled.csv
RawData/Brazil/salvador_microcephaly.csv
RawData/Brazil/state_stats.csv
RawData/Brazil/zika_inc_reports.csv
RawData/Brazil/zikv_inc_faria2016.csv
RawData/Colombia/colombia_microceph_monthly_cuevas2016.csv
RawData/Colombia/colombia_reports_microceph_2017.csv
RawData/Colombia/colombia_reports_microceph_2017_confirmed.csv
RawData/Colombia/microcephaly_dat_weekly_Dec_2017.csv
RawData/Colombia/microcephaly_dat_weekly_Sept_2017.csv
RawData/Colombia/weekly_births_calc.R
RawData/Colombia/zikv_inc_Dec_2017.csv
RawData/Colombia/zikv_inc_Dec_2017_confirmed.csv
RawData/Northeast/deOliveira2017/extraction_readme.txt
RawData/Northeast/deOliveira2017/microCeph_deOliveira2017_clean.csv
RawData/Northeast/deOliveira2017/zikv_inc_deOliveira2017_clean.csv
RawData/Northeast/northeast_microceph.csv
RawData/Northeast/northeast_zikv.csv
RawData/data_key.csv
RawData/data_sources.csv
RawData/google_trends_brazil.csv
RawData/locationInfo.csv
RawData/peak_data.csv
RawData/peak_times_bootstrapped.csv
RawData/peak_times_for_plot.csv
RawData/sources_old.csv
appveyor.yml
build_win.R
data/bahiaIncDat.RData
data/bahiaMicroDat.RData
data/bahiaPeakTimes.RData
data/exampleParTab.RData
data/locationInfo.RData
doc/images/circumferences.png
doc/images/model.png
doc/images/model.svg
doc/images/posterior_count.png
doc/images/posterior_dat.png
inst/doc/S1 Text.pdf
inst/doc/TableS2_vignette.csv
inst/doc/bibliography1.bib
inst/doc/data_sources.csv
inst/doc/figures/Fig1.png
inst/doc/figures/Fig2.png
inst/doc/figures/mechanisms.svg
inst/doc/methods.Rmd
inst/doc/methods.html
inst/doc/methods.pdf
inst/doc/methods/PLOS-submission.eps
inst/doc/methods/methods.Rmd
inst/doc/methods/mybibfile.bib
inst/doc/methods/plos.csl
inst/doc/methods_old.html
inst/doc/model_parameters2.csv
inst/doc/package_use.Rmd
inst/doc/package_use.html
inst/doc/plos.csl
inst/doc/vital_statistics.csv
man/average_buckets.Rd
man/b.calc.Rd
man/calc_deviance.Rd
man/calc_post_mean.Rd
man/calc_post_var.Rd
man/calculate_AR.Rd
man/calculate_BIC.Rd
man/calculate_DIC.Rd
man/calculate_gamma_mode.Rd
man/combine_chains.Rd
man/convert_name_to_location.Rd
man/convert_name_to_location_factor.Rd
man/createLocationParTable.Rd
man/createParTable.Rd
man/create_posterior.Rd
man/cumul_true.Rd
man/density.calc.Rd
man/density_plot_func.Rd
man/density_plot_state.Rd
man/exampleParTab.Rd
man/extra_microceph_calculations.Rd
man/find_peak_times.Rd
man/forecast_CRS.Rd
man/forecast_microceph.Rd
man/fromUnitScale.Rd
man/generateAllowableParams.Rd
man/generateStartingParTab.Rd
man/generate_foi.Rd
man/generate_micro_curve.Rd
man/generate_multiple_data.Rd
man/generate_plot_date_labels.Rd
man/generate_probM.Rd
man/generate_probM_aux.Rd
man/generate_probM_forecast.Rd
man/generate_probM_forecast_OLD.Rd
man/generate_riskI.Rd
man/generate_riskS.Rd
man/generate_y0s.Rd
man/getDaysPerMonth.Rd
man/get_best_pars.Rd
man/get_correct_order.Rd
man/get_epidemic_locations.Rd
man/get_index_pars.Rd
man/get_lower_micro_bound.Rd
man/get_max_micro.Rd
man/get_max_micro_day.Rd
man/get_microceph_range.Rd
man/get_upper_micro_bound.Rd
man/incidence_likelihood.Rd
man/incidence_likelihood_norm.Rd
man/isolate_location.Rd
man/likelihood_probM.Rd
man/likelihood_probM_norm.Rd
man/load_mcmc_chains.Rd
man/locationInfo.Rd
man/make_micro_dat.Rd
man/median.quantile.Rd
man/microceph_v1.Rd
man/microceph_v2.Rd
man/microceph_v3.Rd
man/microceph_v4.Rd
man/mvr_proposal.Rd
man/parTabSetup.Rd
man/parTabSetup_aux.Rd
man/plot_MCMC.Rd
man/plot_best_trajectory_multi.Rd
man/plot_best_trajectory_single.Rd
man/plot_micro_bounds.Rd
man/plot_random_microceph_curves.Rd
man/plot_setup_data.Rd
man/posterior_CRS.Rd
man/posterior_complex_buckets.Rd
man/posterior_inc.Rd
man/posterior_known_inc.Rd
man/posterior_known_inc_seir.Rd
man/posterior_simple_buckets.Rd
man/print_version_names.Rd
man/proposalfunction.Rd
man/r0.calc.Rd
man/r0.vector.Rd
man/read_all_data.Rd
man/read_inipars.Rd
man/rm_scale.Rd
man/run_metropolis_MCMC.Rd
man/scaletuning.Rd
man/setupListPars.Rd
man/setupLocationParTable.Rd
man/setupParsLong.Rd
man/setupParsODE.Rd
man/simeq.Rd
man/solveSEIRModel.Rd
man/solveSEIRModel_lsoda.Rd
man/solveSEIRModel_rlsoda.Rd
man/sum_buckets.Rd
man/sum_n_vector.Rd
man/summarise_chain.Rd
man/to.png.Rd
man/to.svg.Rd
man/toUnitScale.Rd
man/zikaInfer.Rd
scripts/Figures/Fig2.R
scripts/Figures/Fig3.R
scripts/Figures/Fig4.R
scripts/Figures/Fig5.R
scripts/Figures/google_searches.R
scripts/data/peak_times.R
scripts/data/plot_all_data_Fig3.R
scripts/data/raw_data_stats_DEPRECATED.R
scripts/head_circumference/heatmap.R
scripts/job_submissions/#submit_all.R#
scripts/job_submissions/CRS_fitting.R
scripts/job_submissions/cluster_setup.R
scripts/job_submissions/inputs/.~lock.parTab_fixed_switch_early.csv#
scripts/job_submissions/inputs/OLD/allowablePars_1.csv
scripts/job_submissions/inputs/OLD/generic_ini.csv
scripts/job_submissions/inputs/OLD/inipars.csv
scripts/job_submissions/inputs/OLD/jobs_1.csv
scripts/job_submissions/inputs/OLD/parTab_CRS.csv
scripts/job_submissions/inputs/OLD/parTab_CRS2.csv
scripts/job_submissions/inputs/OLD/parTab_a.csv
scripts/job_submissions/inputs/OLD/parTab_fixed_switch.csv
scripts/job_submissions/inputs/OLD/parTab_free.csv
scripts/job_submissions/inputs/OLD/parTab_free_switch.csv
scripts/job_submissions/inputs/OLD/parTab_incpropn.csv
scripts/job_submissions/inputs/parTab_abortion.csv
scripts/job_submissions/inputs/parTab_birthreduction.csv
scripts/job_submissions/inputs/parTab_fixed_incPropn2.csv
scripts/job_submissions/inputs/parTab_fixed_switch_early.csv
scripts/job_submissions/inputs/parTab_fixed_switch_late.csv
scripts/job_submissions/inputs/parTab_forecast.csv
scripts/job_submissions/inputs/parTab_incPropn.csv
scripts/job_submissions/inputs/parTab_propn.csv
scripts/job_submissions/model_fitting_script.R
scripts/job_submissions/model_forecasting.R
scripts/job_submissions/parTab_forecast.csv
scripts/job_submissions/runs_18112017/bahia.R
scripts/job_submissions/runs_18112017/bahia_forecasts.R
scripts/job_submissions/runs_18112017/bahia_forecasts_noreportingchange.R
scripts/job_submissions/runs_18112017/colombia.R
scripts/job_submissions/runs_18112017/multi_3.R
scripts/job_submissions/runs_18112017/nejm.R
scripts/job_submissions/runs_18112017/nejm_forecasts.R
scripts/job_submissions/runs_18112017/nejm_forecasts_noreportingchange.R
scripts/job_submissions/runs_18112017/pernambuco.R
scripts/job_submissions/runs_18112017/reports_2.R
scripts/job_submissions/runs_18112017/reports_3.R
scripts/job_submissions/runs_18112017/rio.R
scripts/job_submissions/runs_18112017/rio_forecasts.R
scripts/job_submissions/submit_all.R
scripts/job_submissions/tmp.R
scripts/other_plots/cor_plots.R
scripts/other_plots/density_plots.R
scripts/results/TableS4.R
scripts/results/TableS5.R
scripts/utility/assess_convergence.R
scripts/utility/combine_all_chains.R
scripts/utility/combine_all_chains_forecasting.R
scripts/utility/param_creation.R
src/RcppExports.cpp
src/rcpp_functions.cpp
src/simpleSEIR.c
src/simpleSEIR_rlsoda.c
src/zzz.c
tests/testthat/test-model.R
tests/testthat/test-model.R~
vignettes/TableS2_vignette.csv
vignettes/bibliography1.bib
vignettes/data_sources.csv
vignettes/figures/Fig1.png
vignettes/figures/Fig2.png
vignettes/figures/mechanisms.svg
vignettes/methods.Rmd
vignettes/methods/PLOS-submission.eps
vignettes/methods/methods.Rmd
vignettes/methods/mybibfile.bib
vignettes/methods/plos.csl
vignettes/model_parameters2.csv
vignettes/package_use.Rmd
vignettes/plos.csl
vignettes/sim_incDat.csv
vignettes/sim_microDat.csv
vignettes/test_1_multivariate_chain.csv
vignettes/test_2_multivariate_chain.csv
vignettes/test_univariate_chain.csv
vignettes/vital_statistics.csv
