Files in cmhoove14/DDNTD
Density Dependence in Neglected Tropical Diseases
.Rbuildignore
.gitignore
Analysis/.gitignore
Analysis/Analytic_Work.Rmd
Analysis/Analytic_Work.md
Analysis/Fitting_W_and_kappa_to_data_implications_for_mating_prob.Rmd
Analysis/Fitting_W_and_kappa_to_data_implications_for_mating_prob.html
Analysis/Fitting_W_and_kappa_to_data_implications_for_mating_prob.md
Analysis/Garch_Mod.Rmd
Analysis/Garch_Mod.md
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Analysis/Garch_Mod_files/figure-latex/get_opt-1.pdf
Analysis/Garch_Mod_files/figure-latex/int_r0-1.pdf
Analysis/Garch_Mod_files/figure-latex/mod_prep-1.pdf
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Analysis/Garch_Mod_files/figure-markdown_github/opt_test_viz-1.png
Analysis/Garch_Mod_opt.Rmd
Analysis/Garch_Mod_opt.md
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Analysis/Garch_Mod_opt_files/figure-markdown_github/opt_no_dd_plot-1.png
Analysis/Garch_Mod_opt_files/figure-markdown_github/test_decision_dd-1.png
Analysis/IB_model.Rmd
Analysis/Manuscripts_notes/Annotated_bib_schisto_density_dependence.Rmd
Analysis/Manuscripts_notes/Annotated_bib_schisto_density_dependence.docx
Analysis/Manuscripts_notes/Critical_transitions_schisto.Rmd
Analysis/Manuscripts_notes/Critical_transitions_schisto.html
Analysis/Manuscripts_notes/Critical_transitions_schisto.md
Analysis/Manuscripts_notes/Critical_transitions_schisto.pdf
Analysis/Manuscripts_notes/Manuscript/Schisto_reff_manuscript.Rmd
Analysis/Manuscripts_notes/Manuscript/Schisto_reff_manuscript.docx
Analysis/Manuscripts_notes/Manuscript/Schisto_reff_manuscript_age_strat.Rmd
Analysis/Manuscripts_notes/Manuscript/Schisto_reff_manuscript_cache/docx/__packages
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Analysis/Manuscripts_notes/Manuscript/references.bib
Analysis/Manuscripts_notes/Manuscript/~$histo_reff_manuscript.docx
Analysis/Manuscripts_notes/NDD_Influences/potential_ndd_explanations_for_rapid_rebound.Rmd
Analysis/Manuscripts_notes/Questions_hypotheses.Rmd
Analysis/Manuscripts_notes/crit_trans.bib
Analysis/Manuscripts_notes/estimating_Allee_effects.Rmd
Analysis/Manuscripts_notes/ideas_refs.bib
Analysis/Manuscripts_notes/plos.csl
Analysis/Manuscripts_notes/references.bib
Analysis/Manuscripts_notes/schisto_prosp.bib
Analysis/Manuscripts_notes/schisto_prospectus.Rmd
Analysis/Manuscripts_notes/schisto_prospectus.docx
Analysis/Manuscripts_notes/~$notated_bib_schisto_density_dependence.docx
Analysis/Model_Sims.Rmd
Analysis/Model_Sims.md
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Analysis/Model_Sims_files/figure-markdown_github/Reff_curves-1.png
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Analysis/Model_animations.Rmd
Analysis/Model_animations.md
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Analysis/Parameter_estimates_from_observed_inputs_assuming_equilibirum_conditions.Rmd
Analysis/Parameter_estimates_from_observed_inputs_assuming_equilibirum_conditions.md
Analysis/Parameter_estimates_from_observed_inputs_assuming_equilibirum_conditions_files/figure-markdown_github/Lambda_from_Ip-1.png
Analysis/Parameter_estimates_from_observed_inputs_assuming_equilibirum_conditions_files/figure-markdown_github/beta_from_omega_Ip-1.png
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Analysis/Reff_W_bp_plots.Rmd
Analysis/Reff_W_bp_plots.html
Analysis/Reff_W_bp_plots.md
Analysis/Reff_age_strat.Rmd
Analysis/Reff_derivation.Rmd
Analysis/Reff_derivation.md
Analysis/Reff_derivation2.Rmd
Analysis/Reff_derivation2.html
Analysis/Reff_derivation2.md
Analysis/Reff_investigate_files/figure-markdown_github/unnamed-chunk-1-1.png
Analysis/Reff_scratch.Rmd
Analysis/Schisto_stoch_sims.Rmd
Analysis/Schisto_stoch_sims.md
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Analysis/Schisto_stoch_sims_files/figure-markdown_github/stoch_sims_plot_example-1.png
Analysis/Schisto_stoch_sims_files/figure-markdown_github/test_stoch-1.png
Analysis/Schisto_stoch_sims_files/figure-markdown_github/test_stoch-2.png
Analysis/Schisto_stoch_sims_files/figure-markdown_github/unnamed-chunk-1-1.png
Analysis/Senegal_somms_observed_to_modeled.Rmd
Analysis/Senegal_somms_observed_to_modeled.md
Analysis/Senegal_somms_observed_to_modeled_files/figure-markdown_github/alpha_ests-1.png
Analysis/Senegal_somms_observed_to_modeled_files/figure-markdown_github/alpha_ests-2.png
Analysis/Senegal_somms_observed_to_modeled_files/figure-markdown_github/lambda_plot-1.png
Analysis/Senegal_somms_observed_to_modeled_files/figure-markdown_github/worm_burden_plot-1.png
Analysis/age_structured_schisto_model.Rmd
Analysis/age_structured_schisto_model.md
Analysis/age_structured_schisto_model_files/figure-markdown_github/Reff_V12_CWT-1.png
Analysis/age_structured_schisto_model_files/figure-markdown_github/Reff_plot-1.png
Analysis/age_structured_schisto_model_files/figure-markdown_github/V12_Reff_plot-1.png
Analysis/age_structured_schisto_model_files/figure-markdown_github/V12_SAC_MDA-1.png
Analysis/age_structured_schisto_model_files/figure-markdown_github/V12_sim_com_MDA-1.png
Analysis/age_structured_schisto_model_files/figure-markdown_github/sim2-1.png
Analysis/age_structured_schisto_model_files/figure-markdown_github/sim_com-1.png
Analysis/age_structured_schisto_model_files/figure-markdown_github/sim_mda_sac-1.png
Analysis/structural_decisions_refs.bib
DDNTD.Rproj
DESCRIPTION
LICENSE
NAMESPACE
Other/.gitignore
Other/NIMBioS_2019.pptx
Other/NIMBioS_2019v2.pptx
Other/plots_figs/Senegal_comm_worm_burden_dist.png
R/garchitorena_models.R
R/general_helper_functions.R
R/schisto_age_structured_models.R
R/schisto_dynamic_models.R
R/schisto_helper_functions.R
R/schisto_reproduction_numbers.R
R/schisto_stratified_reproduction_numbers.R
README.md
data-raw/model_parameters.R
data-raw/schisto_infection_data.R
data-raw/schistosoma_spp_infection_data.csv
data/age_strat_pars.rda
data/base_pars.rda
data/garch_pars.rda
data/schisto_dat.rda
data/senegal_comms_village_level_summaries.rds
data/senegal_community_haematobium_summaries.rds
man/I_P_get_W_eq.Rd
man/I_get_E.Rd
man/I_get_Lambda.Rd
man/Lambda_Wij.Rd
man/Lambda_Wij_linear.Rd
man/Lambda_get_N_eq.Rd
man/R0_egg_kap_gamma_m.Rd
man/R_eff_W_I.Rd
man/Reff_W.Rd
man/Reff_W_kap.Rd
man/Reff_Wij.Rd
man/Reff_Wij_I_P.Rd
man/W_Ip_eq_solns.Rd
man/W_bp_I_P.Rd
man/W_bp_N_solver.Rd
man/W_bp_R_0.Rd
man/W_ij_get_N_S_E_I.Rd
man/age_strat_fit_mod.Rd
man/age_strat_get_pars.Rd
man/augment_age_strat_parameters.Rd
man/beta_from_eggs.Rd
man/cheever_eggs_to_females.Rd
man/convert_burden_egg_to_worm.Rd
man/cvrg_from_W_bp.Rd
man/cvrg_from_pars.Rd
man/dWdt_W.Rd
man/egg_to_worm_fx.Rd
man/eggs_kap_get_W.Rd
man/eq_W_get_alpha.Rd
man/eq_Ws_get_Omega_Lambda0.Rd
man/eqbm_snails_fit_mod.Rd
man/est_prev_W_k.Rd
man/exp_seq.Rd
man/fit_pars_from_eq_vals.Rd
man/gam_Wxi.Rd
man/garch_discrete_mod.Rd
man/garch_discrete_mod_dd.Rd
man/garch_mod.Rd
man/garch_mod_dd.Rd
man/garch_r0.Rd
man/gen_force_fx.Rd
man/get_Ip_W_bp.Rd
man/get_R0.Rd
man/get_breakpoint_W_N.Rd
man/infection_inputs_get_pars.Rd
man/k_w_fx.Rd
man/latexImg.Rd
man/load_csv_from_googledrive.Rd
man/nil_1.Rd
man/phi_Wk.Rd
man/prev_W_get_k.Rd
man/prev_get_W.Rd
man/prev_intensity_to_clump.Rd
man/prev_kap_get_W.Rd
man/rho_Wk.Rd
man/schisto_age_strat_mod.Rd
man/schisto_base_mod.Rd
man/schisto_mod.Rd
man/schisto_stoch_mod.Rd
man/sim_discrete_mod.Rd
man/sim_garch_mod.Rd
man/sim_int_choice.Rd
man/sim_opt_choice.Rd
man/sim_schisto_mod.Rd
man/sim_schisto_stoch_mod.Rd
man/sim_w_inputs.Rd
man/w_start_get_r0.Rd
man/wbp_fx.Rd
notebook.md
