Files in jameshay218/antibodyKinetics

antibodyKinetics

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

Makefile

NAMESPACE

R/RcppExports.R R/analyses.R R/exampleExposureTab.R R/exampleParTab.R R/exposure_times.R R/ferret_titres.R R/helper.R R/inference.R R/mcmc.R R/model.R R/model_creation.R R/package.R R/plots.R R/posteriors.R R/runParamViewer.R README.md

data/exampleExposureTab.RData

data/exampleParTab.RData

data/exposure_times.RData

data/ferret_titres.RData

data/real_data_simple.csv

data/sim_all/competitive/10_CNTN6MN_data.csv

data/sim_all/competitive/10_CNTN6MN_parTab.csv

data/sim_all/competitive/10_CNTN6MN_plot.png

data/sim_all/competitive/11_CNAN3MN_data.csv

data/sim_all/competitive/11_CNAN3MN_parTab.csv

data/sim_all/competitive/11_CNAN3MN_plot.png

data/sim_all/competitive/12_CNTN3MN_data.csv

data/sim_all/competitive/12_CNTN3MN_parTab.csv

data/sim_all/competitive/12_CNTN3MN_plot.png

data/sim_all/competitive/13_CNAN6BN_data.csv

data/sim_all/competitive/13_CNAN6BN_parTab.csv

data/sim_all/competitive/13_CNAN6BN_plot.png

data/sim_all/competitive/14_CNTN6BN_data.csv

data/sim_all/competitive/14_CNTN6BN_parTab.csv

data/sim_all/competitive/14_CNTN6BN_plot.png

data/sim_all/competitive/15_CNAN3BN_data.csv

data/sim_all/competitive/15_CNAN3BN_parTab.csv

data/sim_all/competitive/15_CNAN3BN_plot.png

data/sim_all/competitive/16_CNTN3BN_data.csv

data/sim_all/competitive/16_CNTN3BN_parTab.csv

data/sim_all/competitive/16_CNTN3BN_plot.png

data/sim_all/competitive/17_CNAY6MY_data.csv

data/sim_all/competitive/17_CNAY6MY_parTab.csv

data/sim_all/competitive/17_CNAY6MY_plot.png

data/sim_all/competitive/18_CNTY6MY_data.csv

data/sim_all/competitive/18_CNTY6MY_parTab.csv

data/sim_all/competitive/18_CNTY6MY_plot.png

data/sim_all/competitive/19_CNAY3MY_data.csv

data/sim_all/competitive/19_CNAY3MY_parTab.csv

data/sim_all/competitive/19_CNAY3MY_plot.png

data/sim_all/competitive/1_CNAN6MY_data.csv

data/sim_all/competitive/1_CNAN6MY_parTab.csv

data/sim_all/competitive/1_CNAN6MY_plot.png

data/sim_all/competitive/20_CNTY3MY_data.csv

data/sim_all/competitive/20_CNTY3MY_parTab.csv

data/sim_all/competitive/20_CNTY3MY_plot.png

data/sim_all/competitive/21_CNAY6BY_data.csv

data/sim_all/competitive/21_CNAY6BY_parTab.csv

data/sim_all/competitive/21_CNAY6BY_plot.png

data/sim_all/competitive/22_CNTY6BY_data.csv

data/sim_all/competitive/22_CNTY6BY_parTab.csv

data/sim_all/competitive/22_CNTY6BY_plot.png

data/sim_all/competitive/23_CNAY3BY_data.csv

data/sim_all/competitive/23_CNAY3BY_parTab.csv

data/sim_all/competitive/23_CNAY3BY_plot.png

data/sim_all/competitive/24_CNTY3BY_data.csv

data/sim_all/competitive/24_CNTY3BY_parTab.csv

data/sim_all/competitive/24_CNTY3BY_plot.png

data/sim_all/competitive/25_CNAY6MN_data.csv

data/sim_all/competitive/25_CNAY6MN_parTab.csv

data/sim_all/competitive/25_CNAY6MN_plot.png

data/sim_all/competitive/26_CNTY6MN_data.csv

data/sim_all/competitive/26_CNTY6MN_parTab.csv

data/sim_all/competitive/26_CNTY6MN_plot.png

data/sim_all/competitive/27_CNAY3MN_data.csv

data/sim_all/competitive/27_CNAY3MN_parTab.csv

data/sim_all/competitive/27_CNAY3MN_plot.png

data/sim_all/competitive/28_CNTY3MN_data.csv

data/sim_all/competitive/28_CNTY3MN_parTab.csv

data/sim_all/competitive/28_CNTY3MN_plot.png

data/sim_all/competitive/29_CNAY6BN_data.csv

data/sim_all/competitive/29_CNAY6BN_parTab.csv

data/sim_all/competitive/29_CNAY6BN_plot.png

data/sim_all/competitive/2_CNTN6MY_data.csv

data/sim_all/competitive/2_CNTN6MY_parTab.csv

data/sim_all/competitive/2_CNTN6MY_plot.png

data/sim_all/competitive/30_CNTY6BN_data.csv

data/sim_all/competitive/30_CNTY6BN_parTab.csv

data/sim_all/competitive/30_CNTY6BN_plot.png

data/sim_all/competitive/31_CNAY3BN_data.csv

data/sim_all/competitive/31_CNAY3BN_parTab.csv

data/sim_all/competitive/31_CNAY3BN_plot.png

data/sim_all/competitive/32_CNTY3BN_data.csv

data/sim_all/competitive/32_CNTY3BN_parTab.csv

data/sim_all/competitive/32_CNTY3BN_plot.png

data/sim_all/competitive/33_CYAN6MY_data.csv

data/sim_all/competitive/33_CYAN6MY_parTab.csv

data/sim_all/competitive/33_CYAN6MY_plot.png

data/sim_all/competitive/34_CYTN6MY_data.csv

data/sim_all/competitive/34_CYTN6MY_parTab.csv

data/sim_all/competitive/34_CYTN6MY_plot.png

data/sim_all/competitive/35_CYAN3MY_data.csv

data/sim_all/competitive/35_CYAN3MY_parTab.csv

data/sim_all/competitive/35_CYAN3MY_plot.png

data/sim_all/competitive/36_CYTN3MY_data.csv

data/sim_all/competitive/36_CYTN3MY_parTab.csv

data/sim_all/competitive/36_CYTN3MY_plot.png

data/sim_all/competitive/37_CYAN6BY_data.csv

data/sim_all/competitive/37_CYAN6BY_parTab.csv

data/sim_all/competitive/37_CYAN6BY_plot.png

data/sim_all/competitive/38_CYTN6BY_data.csv

data/sim_all/competitive/38_CYTN6BY_parTab.csv

data/sim_all/competitive/38_CYTN6BY_plot.png

data/sim_all/competitive/39_CYAN3BY_data.csv

data/sim_all/competitive/39_CYAN3BY_parTab.csv

data/sim_all/competitive/39_CYAN3BY_plot.png

data/sim_all/competitive/3_CNAN3MY_data.csv

data/sim_all/competitive/3_CNAN3MY_parTab.csv

data/sim_all/competitive/3_CNAN3MY_plot.png

data/sim_all/competitive/40_CYTN3BY_data.csv

data/sim_all/competitive/40_CYTN3BY_parTab.csv

data/sim_all/competitive/40_CYTN3BY_plot.png

data/sim_all/competitive/41_CYAN6MN_data.csv

data/sim_all/competitive/41_CYAN6MN_parTab.csv

data/sim_all/competitive/41_CYAN6MN_plot.png

data/sim_all/competitive/42_CYTN6MN_data.csv

data/sim_all/competitive/42_CYTN6MN_parTab.csv

data/sim_all/competitive/42_CYTN6MN_plot.png

data/sim_all/competitive/43_CYAN3MN_data.csv

data/sim_all/competitive/43_CYAN3MN_parTab.csv

data/sim_all/competitive/43_CYAN3MN_plot.png

data/sim_all/competitive/44_CYTN3MN_data.csv

data/sim_all/competitive/44_CYTN3MN_parTab.csv

data/sim_all/competitive/44_CYTN3MN_plot.png

data/sim_all/competitive/45_CYAN6BN_data.csv

data/sim_all/competitive/45_CYAN6BN_parTab.csv

data/sim_all/competitive/45_CYAN6BN_plot.png

data/sim_all/competitive/46_CYTN6BN_data.csv

data/sim_all/competitive/46_CYTN6BN_parTab.csv

data/sim_all/competitive/46_CYTN6BN_plot.png

data/sim_all/competitive/47_CYAN3BN_data.csv

data/sim_all/competitive/47_CYAN3BN_parTab.csv

data/sim_all/competitive/47_CYAN3BN_plot.png

data/sim_all/competitive/48_CYTN3BN_data.csv

data/sim_all/competitive/48_CYTN3BN_parTab.csv

data/sim_all/competitive/48_CYTN3BN_plot.png

data/sim_all/competitive/49_CYAY6MY_data.csv

data/sim_all/competitive/49_CYAY6MY_parTab.csv

data/sim_all/competitive/49_CYAY6MY_plot.png

data/sim_all/competitive/4_CNTN3MY_data.csv

data/sim_all/competitive/4_CNTN3MY_parTab.csv

data/sim_all/competitive/4_CNTN3MY_plot.png

data/sim_all/competitive/50_CYTY6MY_data.csv

data/sim_all/competitive/50_CYTY6MY_parTab.csv

data/sim_all/competitive/50_CYTY6MY_plot.png

data/sim_all/competitive/51_CYAY3MY_data.csv

data/sim_all/competitive/51_CYAY3MY_parTab.csv

data/sim_all/competitive/51_CYAY3MY_plot.png

data/sim_all/competitive/52_CYTY3MY_data.csv

data/sim_all/competitive/52_CYTY3MY_parTab.csv

data/sim_all/competitive/52_CYTY3MY_plot.png

data/sim_all/competitive/53_CYAY6BY_data.csv

data/sim_all/competitive/53_CYAY6BY_parTab.csv

data/sim_all/competitive/53_CYAY6BY_plot.png

data/sim_all/competitive/54_CYTY6BY_data.csv

data/sim_all/competitive/54_CYTY6BY_parTab.csv

data/sim_all/competitive/54_CYTY6BY_plot.png

data/sim_all/competitive/55_CYAY3BY_data.csv

data/sim_all/competitive/55_CYAY3BY_parTab.csv

data/sim_all/competitive/55_CYAY3BY_plot.png

data/sim_all/competitive/56_CYTY3BY_data.csv

data/sim_all/competitive/56_CYTY3BY_parTab.csv

data/sim_all/competitive/56_CYTY3BY_plot.png

data/sim_all/competitive/57_CYAY6MN_data.csv

data/sim_all/competitive/57_CYAY6MN_parTab.csv

data/sim_all/competitive/57_CYAY6MN_plot.png

data/sim_all/competitive/58_CYTY6MN_data.csv

data/sim_all/competitive/58_CYTY6MN_parTab.csv

data/sim_all/competitive/58_CYTY6MN_plot.png

data/sim_all/competitive/59_CYAY3MN_data.csv

data/sim_all/competitive/59_CYAY3MN_parTab.csv

data/sim_all/competitive/59_CYAY3MN_plot.png

data/sim_all/competitive/5_CNAN6BY_data.csv

data/sim_all/competitive/5_CNAN6BY_parTab.csv

data/sim_all/competitive/5_CNAN6BY_plot.png

data/sim_all/competitive/60_CYTY3MN_data.csv

data/sim_all/competitive/60_CYTY3MN_parTab.csv

data/sim_all/competitive/60_CYTY3MN_plot.png

data/sim_all/competitive/61_CYAY6BN_data.csv

data/sim_all/competitive/61_CYAY6BN_parTab.csv

data/sim_all/competitive/61_CYAY6BN_plot.png

data/sim_all/competitive/62_CYTY6BN_data.csv

data/sim_all/competitive/62_CYTY6BN_parTab.csv

data/sim_all/competitive/62_CYTY6BN_plot.png

data/sim_all/competitive/63_CYAY3BN_data.csv

data/sim_all/competitive/63_CYAY3BN_parTab.csv

data/sim_all/competitive/63_CYAY3BN_plot.png

data/sim_all/competitive/64_CYTY3BN_data.csv

data/sim_all/competitive/64_CYTY3BN_parTab.csv

data/sim_all/competitive/64_CYTY3BN_plot.png

data/sim_all/competitive/6_CNTN6BY_data.csv

data/sim_all/competitive/6_CNTN6BY_parTab.csv

data/sim_all/competitive/6_CNTN6BY_plot.png

data/sim_all/competitive/7_CNAN3BY_data.csv

data/sim_all/competitive/7_CNAN3BY_parTab.csv

data/sim_all/competitive/7_CNAN3BY_plot.png

data/sim_all/competitive/8_CNTN3BY_data.csv

data/sim_all/competitive/8_CNTN3BY_parTab.csv

data/sim_all/competitive/8_CNTN3BY_plot.png

data/sim_all/competitive/9_CNAN6MN_data.csv

data/sim_all/competitive/9_CNAN6MN_parTab.csv

data/sim_all/competitive/9_CNAN6MN_plot.png

data/sim_best_model/CNAY6BN/3days_CNAY6BN_data.csv

data/sim_best_model/CNAY6BN/3days_CNAY6BN_parTab.csv

data/sim_best_model/CNAY6BN/3days_CNAY6BN_plot.png

data/sim_best_model/CNAY6BN/protocol_CNAY6BN_data.csv

data/sim_best_model/CNAY6BN/protocol_CNAY6BN_parTab.csv

data/sim_best_model/CNAY6BN/protocol_CNAY6BN_plot.png

data/sim_best_model/CNAY6BN/weekly_CNAY6BN_data.csv

data/sim_best_model/CNAY6BN/weekly_CNAY6BN_parTab.csv

data/sim_best_model/CNAY6BN/weekly_CNAY6BN_plot.png

data/sim_best_model/CNAY6BY/3days_CNAY6BY_data.csv

data/sim_best_model/CNAY6BY/3days_CNAY6BY_parTab.csv

data/sim_best_model/CNAY6BY/3days_CNAY6BY_plot.png

data/sim_best_model/CNAY6BY/protocol_CNAY6BY_data.csv

data/sim_best_model/CNAY6BY/protocol_CNAY6BY_parTab.csv

data/sim_best_model/CNAY6BY/protocol_CNAY6BY_plot.png

data/sim_best_model/CNAY6BY/weekly_CNAY6BY_data.csv

data/sim_best_model/CNAY6BY/weekly_CNAY6BY_parTab.csv

data/sim_best_model/CNAY6BY/weekly_CNAY6BY_plot.png

data/sim_best_model/CNAY6MY/3days_CNAY6MY_data.csv

data/sim_best_model/CNAY6MY/3days_CNAY6MY_parTab.csv

data/sim_best_model/CNAY6MY/3days_CNAY6MY_plot.png

data/sim_best_model/CNAY6MY/protocol_CNAY6MY_data.csv

data/sim_best_model/CNAY6MY/protocol_CNAY6MY_parTab.csv

data/sim_best_model/CNAY6MY/protocol_CNAY6MY_plot.png

data/sim_best_model/CNAY6MY/weekly_CNAY6MY_data.csv

data/sim_best_model/CNAY6MY/weekly_CNAY6MY_parTab.csv

data/sim_best_model/CNAY6MY/weekly_CNAY6MY_plot.png

data/sim_best_model/CNTY6BN/3days_CNTY6BN_data.csv

data/sim_best_model/CNTY6BN/3days_CNTY6BN_parTab.csv

data/sim_best_model/CNTY6BN/3days_CNTY6BN_plot.png

data/sim_best_model/CNTY6BN/protocol_CNTY6BN_data.csv

data/sim_best_model/CNTY6BN/protocol_CNTY6BN_parTab.csv

data/sim_best_model/CNTY6BN/protocol_CNTY6BN_plot.png

data/sim_best_model/CNTY6BN/weekly_CNTY6BN_data.csv

data/sim_best_model/CNTY6BN/weekly_CNTY6BN_parTab.csv

data/sim_best_model/CNTY6BN/weekly_CNTY6BN_plot.png

data/sim_best_model/CNTY6BY/3days_CNTY6BY_data.csv

data/sim_best_model/CNTY6BY/3days_CNTY6BY_parTab.csv

data/sim_best_model/CNTY6BY/3days_CNTY6BY_plot.png

data/sim_best_model/CNTY6BY/protocol_CNTY6BY_data.csv

data/sim_best_model/CNTY6BY/protocol_CNTY6BY_parTab.csv

data/sim_best_model/CNTY6BY/protocol_CNTY6BY_plot.png

data/sim_best_model/CNTY6BY/weekly_CNTY6BY_data.csv

data/sim_best_model/CNTY6BY/weekly_CNTY6BY_parTab.csv

data/sim_best_model/CNTY6BY/weekly_CNTY6BY_plot.png

data/sim_best_model/CNTY6MY/3days_CNTY6MY_data.csv

data/sim_best_model/CNTY6MY/3days_CNTY6MY_parTab.csv

data/sim_best_model/CNTY6MY/3days_CNTY6MY_plot.png

data/sim_best_model/CNTY6MY/protocol_CNTY6MY_data.csv

data/sim_best_model/CNTY6MY/protocol_CNTY6MY_parTab.csv

data/sim_best_model/CNTY6MY/protocol_CNTY6MY_plot.png

data/sim_best_model/CNTY6MY/weekly_CNTY6MY_data.csv

data/sim_best_model/CNTY6MY/weekly_CNTY6MY_parTab.csv

data/sim_best_model/CNTY6MY/weekly_CNTY6MY_plot.png

data/sim_best_model/CYAY6BN/3days_CYAY6BN_data.csv

data/sim_best_model/CYAY6BN/3days_CYAY6BN_parTab.csv

data/sim_best_model/CYAY6BN/3days_CYAY6BN_plot.png

data/sim_best_model/CYAY6BN/protocol_CYAY6BN_data.csv

data/sim_best_model/CYAY6BN/protocol_CYAY6BN_parTab.csv

data/sim_best_model/CYAY6BN/protocol_CYAY6BN_plot.png

data/sim_best_model/CYAY6BN/weekly_CYAY6BN_data.csv

data/sim_best_model/CYAY6BN/weekly_CYAY6BN_parTab.csv

data/sim_best_model/CYAY6BN/weekly_CYAY6BN_plot.png

data/sim_best_model/CYAY6BY/3days_CYAY6BY_data.csv

data/sim_best_model/CYAY6BY/3days_CYAY6BY_parTab.csv

data/sim_best_model/CYAY6BY/3days_CYAY6BY_plot.png

data/sim_best_model/CYAY6BY/protocol_CYAY6BY_data.csv

data/sim_best_model/CYAY6BY/protocol_CYAY6BY_parTab.csv

data/sim_best_model/CYAY6BY/protocol_CYAY6BY_plot.png

data/sim_best_model/CYAY6BY/weekly_CYAY6BY_data.csv

data/sim_best_model/CYAY6BY/weekly_CYAY6BY_parTab.csv

data/sim_best_model/CYAY6BY/weekly_CYAY6BY_plot.png

data/sim_best_model/CYAY6MN/3days_CYAY6MN_data.csv

data/sim_best_model/CYAY6MN/3days_CYAY6MN_parTab.csv

data/sim_best_model/CYAY6MN/3days_CYAY6MN_plot.png

data/sim_best_model/CYAY6MN/protocol_CYAY6MN_data.csv

data/sim_best_model/CYAY6MN/protocol_CYAY6MN_parTab.csv

data/sim_best_model/CYAY6MN/protocol_CYAY6MN_plot.png

data/sim_best_model/CYAY6MN/weekly_CYAY6MN_data.csv

data/sim_best_model/CYAY6MN/weekly_CYAY6MN_parTab.csv

data/sim_best_model/CYAY6MN/weekly_CYAY6MN_plot.png

data/sim_best_model/CYAY6MY/3days_CYAY6MY_data.csv

data/sim_best_model/CYAY6MY/3days_CYAY6MY_parTab.csv

data/sim_best_model/CYAY6MY/3days_CYAY6MY_plot.png

data/sim_best_model/CYAY6MY/protocol_CYAY6MY_data.csv

data/sim_best_model/CYAY6MY/protocol_CYAY6MY_parTab.csv

data/sim_best_model/CYAY6MY/protocol_CYAY6MY_plot.png

data/sim_best_model/CYAY6MY/weekly_CYAY6MY_data.csv

data/sim_best_model/CYAY6MY/weekly_CYAY6MY_parTab.csv

data/sim_best_model/CYAY6MY/weekly_CYAY6MY_plot.png

data/sim_best_model/CYTY6BN/3days_CYTY6BN_data.csv

data/sim_best_model/CYTY6BN/3days_CYTY6BN_parTab.csv

data/sim_best_model/CYTY6BN/3days_CYTY6BN_plot.png

data/sim_best_model/CYTY6BN/protocol_CYTY6BN_data.csv

data/sim_best_model/CYTY6BN/protocol_CYTY6BN_parTab.csv

data/sim_best_model/CYTY6BN/protocol_CYTY6BN_plot.png

data/sim_best_model/CYTY6BN/weekly_CYTY6BN_data.csv

data/sim_best_model/CYTY6BN/weekly_CYTY6BN_parTab.csv

data/sim_best_model/CYTY6BN/weekly_CYTY6BN_plot.png

data/sim_best_model/CYTY6BY/3days_CYTY6BY_data.csv

data/sim_best_model/CYTY6BY/3days_CYTY6BY_parTab.csv

data/sim_best_model/CYTY6BY/3days_CYTY6BY_plot.png

data/sim_best_model/CYTY6BY/protocol_CYTY6BY_data.csv

data/sim_best_model/CYTY6BY/protocol_CYTY6BY_parTab.csv

data/sim_best_model/CYTY6BY/protocol_CYTY6BY_plot.png

data/sim_best_model/CYTY6BY/weekly_CYTY6BY_data.csv

data/sim_best_model/CYTY6BY/weekly_CYTY6BY_parTab.csv

data/sim_best_model/CYTY6BY/weekly_CYTY6BY_plot.png

data/sim_best_model/CYTY6MY/3days_CYTY6MY_data.csv

data/sim_best_model/CYTY6MY/3days_CYTY6MY_parTab.csv

data/sim_best_model/CYTY6MY/3days_CYTY6MY_plot.png

data/sim_best_model/CYTY6MY/protocol_CYTY6MY_data.csv

data/sim_best_model/CYTY6MY/protocol_CYTY6MY_parTab.csv

data/sim_best_model/CYTY6MY/protocol_CYTY6MY_plot.png

data/sim_best_model/CYTY6MY/weekly_CYTY6MY_data.csv

data/sim_best_model/CYTY6MY/weekly_CYTY6MY_parTab.csv

data/sim_best_model/CYTY6MY/weekly_CYTY6MY_plot.png

data/single_exposure/sim/sim_biphasic_fixed_CNAN3BN_data.csv

data/single_exposure/sim/sim_biphasic_fixed_CNAN3BN_parTab.csv

data/single_exposure/sim/sim_biphasic_fixed_CNAN3BN_plot.png

data/single_exposure/sim/sim_biphasic_full_CNAN3BN_data.csv

data/single_exposure/sim/sim_biphasic_full_CNAN3BN_parTab.csv

data/single_exposure/sim/sim_biphasic_full_CNAN3BN_plot.png

data/single_exposure/sim/sim_frequent_10_data.csv

data/single_exposure/sim/sim_frequent_3_data.csv

data/single_exposure/sim/sim_monophasic_fixed_CNAN3MN_data.csv

data/single_exposure/sim/sim_monophasic_fixed_CNAN3MN_parTab.csv

data/single_exposure/sim/sim_monophasic_fixed_CNAN3MN_plot.png

data/single_exposure/sim/sim_monophasic_full_CNAN3MN_data.csv

data/single_exposure/sim/sim_monophasic_full_CNAN3MN_parTab.csv

data/single_exposure/sim/sim_monophasic_full_CNAN3MN_plot.png

data/single_exposure/sim/sim_protocol_3_data.csv

data/single_exposure/sim/sim_weekly_3_data.csv

data/single_exposure/single_real_data.csv

inputs/.goutputstream-MZC8WZ

inputs/exposureTabs/A_exposureTab.csv

inputs/exposureTabs/B_exposureTab.csv

inputs/exposureTabs/C_exposureTab.csv

inputs/exposureTabs/D_exposureTab.csv

inputs/exposureTabs/E_exposureTab.csv

inputs/exposureTabs/F_exposureTab.csv

inputs/free_tp/E_parTab.csv

inputs/free_tp/G_parTab.csv

inputs/lower_tp/E_parTab.csv

inputs/lower_tp/G_parTab.csv

inputs/parTabs/A_parTab.csv

inputs/parTabs/B_parTab.csv

inputs/parTabs/C_parTab.csv

inputs/parTabs/D_parTab.csv

inputs/parTabs/E_parTab.csv

inputs/parTabs/F_parTab.csv

inputs/parTabs/G_parTab.csv

inputs/parTabs/H_parTab.csv

inputs/parTabs/I_parTab.csv

inputs/run_key.csv

inputs/run_tracker_all.csv

inputs/run_tracker_all_sim.csv

inputs/run_tracker_sim_best_models.csv

inputs/single_exposure/exposureTab_single.csv

inputs/single_exposure/parTab_basic.csv

inputs/single_exposure/parTab_basic_fixed_biphasic.csv

inputs/single_exposure/parTab_basic_fixed_monophasic.csv

inputs/single_exposure/run_tracker_single.csv

inputs/single_exposure/run_tracker_single_sim.csv

inst/doc/images/param_tab_1.png

inst/doc/images/param_tab_2.png

inst/doc/images/param_tab_3.png

inst/doc/model_fitting.Rmd

inst/doc/model_fitting.html

inst/doc/paramViewer.Rmd

inst/doc/paramViewer.html

inst/shiny-examples/paramViewer/Parameters/.~lock.exposureTab_full.csv#

inst/shiny-examples/paramViewer/Parameters/antigenicDistTab.csv

inst/shiny-examples/paramViewer/Parameters/old/A.csv

inst/shiny-examples/paramViewer/Parameters/old/B.csv

inst/shiny-examples/paramViewer/Parameters/old/base.R

inst/shiny-examples/paramViewer/Parameters/old/exposureTab_base.csv

inst/shiny-examples/paramViewer/Parameters/old/exposureTab_full.csv

inst/shiny-examples/paramViewer/Parameters/old/exposureTab_full2.csv

inst/shiny-examples/paramViewer/Parameters/old/exposureTab_full_priming.csv

inst/shiny-examples/paramViewer/Parameters/old/exposureTest2.csv

inst/shiny-examples/paramViewer/Parameters/old/full.R

inst/shiny-examples/paramViewer/Parameters/old/parTab_base.csv

inst/shiny-examples/paramViewer/Parameters/old/parTab_full.csv

inst/shiny-examples/paramViewer/Parameters/old/parTab_full2.csv

inst/shiny-examples/paramViewer/Parameters/old/test2.csv

inst/shiny-examples/paramViewer/Parameters/old/testExposureTab.csv

inst/shiny-examples/paramViewer/Parameters/old/testParTab.csv

inst/shiny-examples/paramViewer/cr_management.R inst/shiny-examples/paramViewer/cr_table.R inst/shiny-examples/paramViewer/exposure_management.R inst/shiny-examples/paramViewer/exposure_table.R inst/shiny-examples/paramViewer/exposure_table_management.R inst/shiny-examples/paramViewer/global_parameters.R inst/shiny-examples/paramViewer/helpers.R inst/shiny-examples/paramViewer/plots.R inst/shiny-examples/paramViewer/server.R inst/shiny-examples/paramViewer/tmp.R inst/shiny-examples/paramViewer/ui.R man/add_noise.Rd man/add_noise_serosolver.Rd man/calc_deviance.Rd man/calc_post_mean.Rd man/calc_post_var.Rd man/calculate_BIC.Rd man/calculate_DIC.Rd man/calculate_WAIC.Rd man/calculate_lik_matrix.Rd man/calculate_loo.Rd man/calculate_x.Rd man/convert_options_to_runName.Rd man/convert_runName_to_options.Rd man/create_data.Rd man/create_model_func.Rd man/create_model_group_func.Rd man/create_model_group_func_cpp.Rd man/exampleExposureTab.Rd man/exampleParTab.Rd man/exposure_times.Rd man/ferret_titres.Rd man/fromUnitScale.Rd man/generate_prediction_intervals.Rd man/get_best_pars.Rd man/get_index_pars.Rd man/get_titre_labels.Rd man/model_func.Rd man/model_func_group_cpp.Rd man/model_func_groups.Rd man/model_trajectory.Rd man/model_trajectory_cpp.Rd man/mvr_proposal.Rd man/norm_error.Rd man/obs_error.Rd man/obs_likelihood.Rd man/parTab_modification.Rd man/parameter_descriptions.Rd man/plot_single_fit.Rd man/posterior_func_group_cpp.Rd man/protect.Rd man/read_ferret_data.Rd man/run_MCMC.Rd man/scaletuning.Rd man/toUnitScale.Rd man/univ_proposal.Rd scripts/analyses/convergence_check_funcs.R scripts/analyses/generate_run_key.R scripts/analyses/model_comparison_functions.R scripts/analyses/par_table_formatting.R

scripts/cluster/.goutputstream-L91BZZ

scripts/cluster/cluster_setup_pt.R scripts/cluster/full_run_paralleltemp.R scripts/cross_validation/all_analyses_cv.R scripts/cross_validation/all_analyses_cv_convergence.R scripts/figures/Figure1_single_exposure_traj.R scripts/figures/Figure3_trajectories.R scripts/figures/Figure4_densities_and_tables.R scripts/figures/Figure_sim_single_exposure_traj.R scripts/figures/Supp_Figures.R scripts/figures/error_figure_plot.R

scripts/figures/infection_times.csv

scripts/figures/plotting_help.R scripts/figures/sim_best_densities.R scripts/figures/tp_sensitivity.R scripts/free_tp/free_tp_analyses.R scripts/free_tp/run_submission_free_tp.R scripts/lower_tp/lower_pt_analyses.R scripts/lower_tp/run_submission_lower_tp.R scripts/main_analyses/all_analyses.R scripts/main_analyses/fit_predictors.R scripts/main_analyses/run_submission_pt.R scripts/readme_code.R scripts/residuals/get_residuals.R

scripts/residuals/residual_file_README.docx

scripts/residuals/residuals.R scripts/sim_best_models/run_submission_best.R scripts/sim_best_models/sim_best_models.R scripts/sim_best_models/sim_best_models_analyses.R scripts/sim_best_models/sim_recover_runname.R scripts/single_exposure/real_single_exposure_analysis.R scripts/single_exposure/run_submission_single.R scripts/single_exposure/sim_recover_single.R scripts/single_exposure/sim_single_exposure_analysis.R scripts/single_exposure/simulate_single_exposure_data.R

src/.gitignore

src/RcppExports.cpp

src/helper.cpp

src/model.cpp

src/model.h

src/posterior.cpp

tests/testthat.R tests/testthat/test.R

vignettes/images/param_tab_1.png

vignettes/images/param_tab_2.png

vignettes/images/param_tab_3.png

vignettes/model_fitting.Rmd

vignettes/model_fitting.html

vignettes/paramViewer.Rmd

vignettes/paramViewer.html

jameshay218/antibodyKinetics documentation built on Nov. 8, 2019, 11 a.m.