Files in soniamitchell/SpARKjags

R/DIC.R R/DICtable.R R/SpARKjags-package.R R/Test_SPARK_data.R R/animal_data.R R/animal_lookup.R R/badgroup_posterior.R R/bin_ages.R R/check_fit.R R/clinical.R R/data.R R/defineClinical.R R/delete_results.R R/filter_pathogen.R R/geom_split_violin.R R/get_animal.R R/get_human.R R/get_labels.R R/get_model.R R/get_parameters.R R/get_params.R R/get_vars.R R/human_data.R R/import_data.R R/jags_data.R R/list_models.R R/monitored_variables.R R/onlyCarbapenem.R R/plot_antibiotics.R R/plot_autocorr.R R/plot_caterpillar.R R/plot_correlation.R R/plot_density.R R/plot_density2.R R/plot_jags.R R/removeCarbapenem.R R/run_SpARKjags_model.R R/run_custom_model.R R/run_model.R R/summarise_samples.R R/testPSRF.R R/testSSEF.R R/true_resistance.R R/zzz.R README.md data-raw/process_data.R man/DIC.Rd man/DICtable.Rd man/GeomSplitViolin.Rd man/SpARKcarbapenem-package.Rd man/add_bad_column_hosp.Rd man/add_resistance.Rd man/animal_data.Rd man/animal_lookup.Rd man/badgroup_posterior.Rd man/bin_ages.Rd man/check_fit.Rd man/defineClinical.Rd man/delete_results.Rd man/filter_pathogen.Rd man/get_animal.Rd man/get_human.Rd man/get_labels.Rd man/get_model.Rd man/get_parameters.Rd man/get_params.Rd man/get_params2.Rd man/get_test_data.Rd man/get_vars.Rd man/get_vars2.Rd man/human_data.Rd man/import_data.Rd man/jags_data.Rd man/list_models.Rd man/monitored_variables.Rd man/onlyCarbapenem.Rd man/plot_antibiotics.Rd man/plot_autocorr.Rd man/plot_caterpillar.Rd man/plot_correlation.Rd man/plot_density.Rd man/plot_density2.Rd man/plot_jags.Rd man/removeCarbapenem.Rd man/run_SpARKjags_model.Rd man/run_custom_model.Rd man/summarise_samples.Rd man/testPSRF.Rd man/testSSEF.Rd man/true_resistance.Rd man/wards.Rd models/full_models/a.R models/full_models/asm.R models/full_models/asmag.R models/full_models/asmag2.R models/full_models/asmage.R models/full_models/asmagesq.R models/full_models/asmagg.R models/full_models/asmaggh.R models/full_models/asmaggh_wt_w.R models/full_models/asmagghwtw.R models/full_models/asmaggw.R models/full_models/asmaggw_CarbRes.R models/full_models/asmaggw_CarbSus.R models/full_models/asmaggwc.R models/full_models/asmaggwc_st.R models/full_models/asmaggwcst.R models/full_models/asmaggwhc_st.R models/full_models/asmaggwt.R models/full_models/asmaggwt_w.R models/full_models/asmg.R models/full_models/ass.R models/full_models/null.R models/goodbad_models/(a_c)sm.R models/goodbad_models/(a_c)ss(ag2)_g.R models/goodbad_models/(a_c)ss(ag2)g.R models/goodbad_models/(a_c)ss(ag2)h.R models/goodbad_models/(a_c)ss(ag2)h_wt_w.R models/goodbad_models/(a_c)ss(ag2)w.R models/goodbad_models/(a_c)ss(ag2)wt.R models/goodbad_models/(a_c)ss(ag2)wt_w.R models/goodbad_models/(a_c)ss.R models/goodbad_models/(a_c)ssag.R models/goodbad_models/(a_c)ssag2.R models/goodbad_models/(a_c)ssage.R models/goodbad_models/(a_c)ssagesq.R models/goodbad_models/(a_c)ssg.R models/goodbad_models/a.R models/goodbad_models/a_c.R models/goodbad_models/a_cattle.R models/goodbad_models/a_chicken.R models/goodbad_models/a_companion.R models/goodbad_models/a_companion_subsets.R models/goodbad_models/a_cssagwst.R models/goodbad_models/a_livestock.R models/goodbad_models/a_livestock_subsets.R models/goodbad_models/a_minus.R models/goodbad_models/a_naive.R models/goodbad_models/a_pig.R models/goodbad_models/a_plus.R models/goodbad_models/a_subsets.R models/goodbad_models/a_types.R models/goodbad_models/a_wild.R models/goodbad_models/a_wild_subsets.R models/goodbad_models/ac1.R models/goodbad_models/ac2.R models/goodbad_models/asm.R models/goodbad_models/ass.R models/goodbad_models/assag.R models/goodbad_models/assag2.R models/goodbad_models/assage.R models/goodbad_models/assagesq.R models/goodbad_models/assagg.R models/goodbad_models/assagh.R models/goodbad_models/assagh_wt_w.R models/goodbad_models/assaghwtw.R models/goodbad_models/assagw.R models/goodbad_models/assagwc.R models/goodbad_models/assagwc_st.R models/goodbad_models/assagwcst.R models/goodbad_models/assagwt.R models/goodbad_models/assagwt_w.R models/goodbad_models/assg.R models/goodbad_models/test_a_c.R models/goodbad_models/test_ac1.R models/goodbad_models/test_ac2.R models/goodbad_models/test_ac3.R models/goodbad_models/test_ac4.R models/individual_models/ag.R models/individual_models/ag2.R models/individual_models/age.R models/individual_models/agesq.R models/individual_models/agesq_c.R models/individual_models/agesq_g.R models/individual_models/agesq_wt.R models/individual_models/agesqg.R models/individual_models/b+c.R models/individual_models/bacteria.R models/individual_models/c-wt_w.R models/individual_models/c.R models/individual_models/c_st.R models/individual_models/c_stwt_w.R models/individual_models/c_w.R models/individual_models/c_wt.R models/individual_models/c_wt_st.R models/individual_models/c_wt_st_w.R models/individual_models/c_wt_w.R models/individual_models/cst.R models/individual_models/cwt.R models/individual_models/cwt_w.R models/individual_models/cwt_w[2].R models/individual_models/cwtg_w.R models/individual_models/cwtst_w.R models/individual_models/cwtst_wagesq.R models/individual_models/cwtstw.R models/individual_models/cwtstwagesq.R models/individual_models/cwtw.R models/individual_models/cwtwb.R models/individual_models/g.R models/individual_models/gen1.R models/individual_models/gen2.R models/individual_models/gen3.R models/individual_models/h.R models/individual_models/h_st.R models/individual_models/h_w.R models/individual_models/h_wt.R models/individual_models/null.R models/individual_models/st.R models/individual_models/w_c.R models/individual_models/w_st.R models/individual_models/ward.R models/individual_models/wc.R models/individual_models/wt.R models/individual_models/wt_w.R models/modelling/a.R models/modelling/modelling.R models/scripts/1_model_diagnostics.R models/scripts/1_not_carbapenem.R models/scripts/1_regression_models.R models/scripts/1_resistance_summary.R models/scripts/2_virulence.R models/scripts/3_individual_models.R models/scripts/4_full_models.R models/scripts/5_goodbad.R models/scripts/6_goodbad.R models/scripts/gender.R models/scripts/goodbad_a.R models/scripts/x_ESBL_genes.R tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/test_get_model.R tests/testthat/test_jags_data.R