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Co-Authored-By: Claudio Moroni <[email protected]> Co-Authored-By: Pietro Monticone <[email protected]>
UniTo-SEPI · Jan 18, 2023 · d36c84d · d36c84d
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diff --git a/data/parameters/README.md b/data/parameters/README.md
diff --git a/.../parameters/delays/A_R/Time_AR_Davies.csv → ...meters/time-delays/A_R/Time_AR_Davies.csv b/.../parameters/delays/A_R/Time_AR_Davies.csv → ...meters/time-delays/A_R/Time_AR_Davies.csv
diff --git a/data/parameters/delays/A_R/Time_AR_Knock.csv → ...ameters/time-delays/A_R/Time_AR_Knock.csv b/data/parameters/delays/A_R/Time_AR_Knock.csv → ...ameters/time-delays/A_R/Time_AR_Knock.csv
diff --git a/data/parameters/delays/D_N/Time_DN_ECDC.csv → ...rameters/time-delays/D_N/Time_DN_ECDC.csv b/data/parameters/delays/D_N/Time_DN_ECDC.csv → ...rameters/time-delays/D_N/Time_DN_ECDC.csv
diff --git a/...Empirical_Delay_Distributions_Zardini.csv → ...Empirical_Delay_Distributions_Zardini.csv b/...Empirical_Delay_Distributions_Zardini.csv → ...Empirical_Delay_Distributions_Zardini.csv
diff --git a/...Empirical_Delay_Distributions_Zardini.txt → ...Empirical_Delay_Distributions_Zardini.txt b/...Empirical_Delay_Distributions_Zardini.txt → ...Empirical_Delay_Distributions_Zardini.txt
diff --git a/data/parameters/delays/H/Time_H_Davies.csv → ...arameters/time-delays/H/Time_H_Davies.csv b/data/parameters/delays/H/Time_H_Davies.csv → ...arameters/time-delays/H/Time_H_Davies.csv
diff --git a/data/parameters/delays/H/Time_H_Docherty.csv → ...ameters/time-delays/H/Time_H_Docherty.csv b/data/parameters/delays/H/Time_H_Docherty.csv → ...ameters/time-delays/H/Time_H_Docherty.csv
diff --git a/data/parameters/delays/H/Time_H_ECDC.csv → .../parameters/time-delays/H/Time_H_ECDC.csv b/data/parameters/delays/H/Time_H_ECDC.csv → .../parameters/time-delays/H/Time_H_ECDC.csv
diff --git a/data/parameters/delays/H/Time_H_Fonfria.csv → ...rameters/time-delays/H/Time_H_Fonfria.csv b/data/parameters/delays/H/Time_H_Fonfria.csv → ...rameters/time-delays/H/Time_H_Fonfria.csv
diff --git a/data/parameters/delays/H/Time_H_Hall.csv → .../parameters/time-delays/H/Time_H_Hall.csv b/data/parameters/delays/H/Time_H_Hall.csv → .../parameters/time-delays/H/Time_H_Hall.csv
diff --git a/data/parameters/delays/H/Time_H_Rees.csv → .../parameters/time-delays/H/Time_H_Rees.csv b/data/parameters/delays/H/Time_H_Rees.csv → .../parameters/time-delays/H/Time_H_Rees.csv
diff --git a/data/parameters/delays/H/Time_H_Trentini.csv → ...ameters/time-delays/H/Time_H_Trentini.csv b/data/parameters/delays/H/Time_H_Trentini.csv → ...ameters/time-delays/H/Time_H_Trentini.csv
diff --git a/data/parameters/delays/H/Time_H_Zardini.csv → ...rameters/time-delays/H/Time_H_Zardini.csv b/data/parameters/delays/H/Time_H_Zardini.csv → ...rameters/time-delays/H/Time_H_Zardini.csv
diff --git a/...ers/delays/H/Time_H_Zardini_Empirical.csv → ...ime-delays/H/Time_H_Zardini_Empirical.csv b/...ers/delays/H/Time_H_Zardini_Empirical.csv → ...ime-delays/H/Time_H_Zardini_Empirical.csv
diff --git a/data/parameters/delays/H_D/Time_HD_Knock.csv → ...ameters/time-delays/H_D/Time_HD_Knock.csv b/data/parameters/delays/H_D/Time_HD_Knock.csv → ...ameters/time-delays/H_D/Time_HD_Knock.csv
diff --git a/.../parameters/delays/H_D/Time_HD_Linton.csv → ...meters/time-delays/H_D/Time_HD_Linton.csv b/.../parameters/delays/H_D/Time_HD_Linton.csv → ...meters/time-delays/H_D/Time_HD_Linton.csv
diff --git a/data/parameters/delays/H_D/Time_HD_Nair.csv → ...rameters/time-delays/H_D/Time_HD_Nair.csv b/data/parameters/delays/H_D/Time_HD_Nair.csv → ...rameters/time-delays/H_D/Time_HD_Nair.csv
diff --git a/data/parameters/delays/H_D/Time_HD_Salje.csv → ...ameters/time-delays/H_D/Time_HD_Salje.csv b/data/parameters/delays/H_D/Time_HD_Salje.csv → ...ameters/time-delays/H_D/Time_HD_Salje.csv
diff --git a/...arameters/delays/H_ICU/Time_HICU_ECDC.csv → ...ters/time-delays/H_ICU/Time_HICU_ECDC.csv b/...arameters/delays/H_ICU/Time_HICU_ECDC.csv → ...ters/time-delays/H_ICU/Time_HICU_ECDC.csv
diff --git a/...arameters/delays/H_ICU/Time_HICU_Hall.csv → ...ters/time-delays/H_ICU/Time_HICU_Hall.csv b/...arameters/delays/H_ICU/Time_HICU_Hall.csv → ...ters/time-delays/H_ICU/Time_HICU_Hall.csv
diff --git a/...rameters/delays/H_ICU/Time_HICU_Knock.csv → ...ers/time-delays/H_ICU/Time_HICU_Knock.csv b/...rameters/delays/H_ICU/Time_HICU_Knock.csv → ...ers/time-delays/H_ICU/Time_HICU_Knock.csv
diff --git a/...eters/delays/H_ICU/Time_HICU_Trentini.csv → .../time-delays/H_ICU/Time_HICU_Trentini.csv b/...eters/delays/H_ICU/Time_HICU_Trentini.csv → .../time-delays/H_ICU/Time_HICU_Trentini.csv
diff --git a/...meters/delays/H_ICU/Time_HICU_Zardini.csv → ...s/time-delays/H_ICU/Time_HICU_Zardini.csv b/...meters/delays/H_ICU/Time_HICU_Zardini.csv → ...s/time-delays/H_ICU/Time_HICU_Zardini.csv
diff --git a/...ays/H_ICU/Time_HICU_Zardini_Empirical.csv → ...ays/H_ICU/Time_HICU_Zardini_Empirical.csv b/...ays/H_ICU/Time_HICU_Zardini_Empirical.csv → ...ays/H_ICU/Time_HICU_Zardini_Empirical.csv
diff --git a/data/parameters/delays/H_R/Time_HR_Knock.csv → ...ameters/time-delays/H_R/Time_HR_Knock.csv b/data/parameters/delays/H_R/Time_HR_Knock.csv → ...ameters/time-delays/H_R/Time_HR_Knock.csv
diff --git a/data/parameters/delays/H_R/Time_HR_Nair.csv → ...rameters/time-delays/H_R/Time_HR_Nair.csv b/data/parameters/delays/H_R/Time_HR_Nair.csv → ...rameters/time-delays/H_R/Time_HR_Nair.csv
diff --git a/data/parameters/delays/I/Time_I_ECDC.csv → .../parameters/time-delays/I/Time_I_ECDC.csv b/data/parameters/delays/I/Time_I_ECDC.csv → .../parameters/time-delays/I/Time_I_ECDC.csv
diff --git a/data/parameters/delays/I/Time_I_Knock.csv → ...parameters/time-delays/I/Time_I_Knock.csv b/data/parameters/delays/I/Time_I_Knock.csv → ...parameters/time-delays/I/Time_I_Knock.csv
diff --git a/...parameters/delays/ICU/Time_ICU_Davies.csv → ...eters/time-delays/ICU/Time_ICU_Davies.csv b/...parameters/delays/ICU/Time_ICU_Davies.csv → ...eters/time-delays/ICU/Time_ICU_Davies.csv
diff --git a/...rameters/delays/ICU/Time_ICU_Docherty.csv → ...ers/time-delays/ICU/Time_ICU_Docherty.csv b/...rameters/delays/ICU/Time_ICU_Docherty.csv → ...ers/time-delays/ICU/Time_ICU_Docherty.csv
diff --git a/data/parameters/delays/ICU/Time_ICU_ECDC.csv → ...ameters/time-delays/ICU/Time_ICU_ECDC.csv b/data/parameters/delays/ICU/Time_ICU_ECDC.csv → ...ameters/time-delays/ICU/Time_ICU_ECDC.csv
diff --git a/...arameters/delays/ICU/Time_ICU_Fonfria.csv → ...ters/time-delays/ICU/Time_ICU_Fonfria.csv b/...arameters/delays/ICU/Time_ICU_Fonfria.csv → ...ters/time-delays/ICU/Time_ICU_Fonfria.csv
diff --git a/data/parameters/delays/ICU/Time_ICU_Hall.csv → ...ameters/time-delays/ICU/Time_ICU_Hall.csv b/data/parameters/delays/ICU/Time_ICU_Hall.csv → ...ameters/time-delays/ICU/Time_ICU_Hall.csv
diff --git a/data/parameters/delays/ICU/Time_ICU_Rees.csv → ...ameters/time-delays/ICU/Time_ICU_Rees.csv b/data/parameters/delays/ICU/Time_ICU_Rees.csv → ...ameters/time-delays/ICU/Time_ICU_Rees.csv
diff --git a/...rameters/delays/ICU/Time_ICU_Trentini.csv → ...ers/time-delays/ICU/Time_ICU_Trentini.csv b/...rameters/delays/ICU/Time_ICU_Trentini.csv → ...ers/time-delays/ICU/Time_ICU_Trentini.csv
diff --git a/...arameters/delays/ICU/Time_ICU_Zardini.csv → ...ters/time-delays/ICU/Time_ICU_Zardini.csv b/...arameters/delays/ICU/Time_ICU_Zardini.csv → ...ters/time-delays/ICU/Time_ICU_Zardini.csv
diff --git a/...delays/ICU/Time_ICU_Zardini_Empirical.csv → ...delays/ICU/Time_ICU_Zardini_Empirical.csv b/...delays/ICU/Time_ICU_Zardini_Empirical.csv → ...delays/ICU/Time_ICU_Zardini_Empirical.csv
diff --git a/...arameters/delays/ICU_D/Time_ICUD_ECDC.csv → ...ters/time-delays/ICU_D/Time_ICUD_ECDC.csv b/...arameters/delays/ICU_D/Time_ICUD_ECDC.csv → ...ters/time-delays/ICU_D/Time_ICUD_ECDC.csv
diff --git a/...arameters/delays/ICU_D/Time_ICUD_Hall.csv → ...ters/time-delays/ICU_D/Time_ICUD_Hall.csv b/...arameters/delays/ICU_D/Time_ICUD_Hall.csv → ...ters/time-delays/ICU_D/Time_ICUD_Hall.csv
diff --git a/...rameters/delays/ICU_D/Time_ICUD_Knock.csv → ...ers/time-delays/ICU_D/Time_ICUD_Knock.csv b/...rameters/delays/ICU_D/Time_ICUD_Knock.csv → ...ers/time-delays/ICU_D/Time_ICUD_Knock.csv
diff --git a/...arameters/delays/ICU_R/Time_ICUR_Hall.csv → ...ters/time-delays/ICU_R/Time_ICUR_Hall.csv b/...arameters/delays/ICU_R/Time_ICUR_Hall.csv → ...ters/time-delays/ICU_R/Time_ICUR_Hall.csv
diff --git a/...meters/delays/ICU_WD/Time_ICUWD_Knock.csv → ...s/time-delays/ICU_WD/Time_ICUWD_Knock.csv b/...meters/delays/ICU_WD/Time_ICUWD_Knock.csv → ...s/time-delays/ICU_WD/Time_ICUWD_Knock.csv
diff --git a/...meters/delays/ICU_WR/Time_ICUWR_Knock.csv → ...s/time-delays/ICU_WR/Time_ICUWR_Knock.csv b/...meters/delays/ICU_WR/Time_ICUWR_Knock.csv → ...s/time-delays/ICU_WR/Time_ICUWR_Knock.csv
diff --git a/...s/Incubation/Incubation_Period_Backer.csv → ...s/Incubation/Incubation_Period_Backer.csv b/...s/Incubation/Incubation_Period_Backer.csv → ...s/Incubation/Incubation_Period_Backer.csv
diff --git a/...ys/Incubation/Incubation_Period_Banka.csv → ...ys/Incubation/Incubation_Period_Banka.csv b/...ys/Incubation/Incubation_Period_Banka.csv → ...ys/Incubation/Incubation_Period_Banka.csv
diff --git a/...elays/Incubation/Incubation_Period_Bi.csv → ...elays/Incubation/Incubation_Period_Bi.csv b/...elays/Incubation/Incubation_Period_Bi.csv → ...elays/Incubation/Incubation_Period_Bi.csv
diff --git a/...ays/Incubation/Incubation_Period_ECDC.csv → ...ays/Incubation/Incubation_Period_ECDC.csv b/...ays/Incubation/Incubation_Period_ECDC.csv → ...ays/Incubation/Incubation_Period_ECDC.csv
diff --git a/.../Incubation/Incubation_Period_Fonfria.csv → .../Incubation/Incubation_Period_Fonfria.csv b/.../Incubation/Incubation_Period_Fonfria.csv → .../Incubation/Incubation_Period_Fonfria.csv
diff --git a/...elays/Incubation/Incubation_Period_Hu.csv → ...elays/Incubation/Incubation_Period_Hu.csv b/...elays/Incubation/Incubation_Period_Hu.csv → ...elays/Incubation/Incubation_Period_Hu.csv
diff --git a/...ys/Incubation/Incubation_Period_Knock.csv → ...ys/Incubation/Incubation_Period_Knock.csv b/...ys/Incubation/Incubation_Period_Knock.csv → ...ys/Incubation/Incubation_Period_Knock.csv
diff --git a/...ys/Incubation/Incubation_Period_Lauer.csv → ...ys/Incubation/Incubation_Period_Lauer.csv b/...ys/Incubation/Incubation_Period_Lauer.csv → ...ys/Incubation/Incubation_Period_Lauer.csv
diff --git a/...elays/Incubation/Incubation_Period_Li.csv → ...elays/Incubation/Incubation_Period_Li.csv b/...elays/Incubation/Incubation_Period_Li.csv → ...elays/Incubation/Incubation_Period_Li.csv
diff --git a/...s/Incubation/Incubation_Period_Linton.csv → ...s/Incubation/Incubation_Period_Linton.csv b/...s/Incubation/Incubation_Period_Linton.csv → ...s/Incubation/Incubation_Period_Linton.csv
diff --git a/.../Incubation/Incubation_Period_McAloon.csv → .../Incubation/Incubation_Period_McAloon.csv b/.../Incubation/Incubation_Period_McAloon.csv → .../Incubation/Incubation_Period_McAloon.csv
diff --git a/...ys/Incubation/Incubation_Period_Zhang.csv → ...ys/Incubation/Incubation_Period_Zhang.csv b/...ys/Incubation/Incubation_Period_Zhang.csv → ...ys/Incubation/Incubation_Period_Zhang.csv
diff --git a/...rs/delays/Latent/Latent_Period_Davies.csv → ...me-delays/Latent/Latent_Period_Davies.csv b/...rs/delays/Latent/Latent_Period_Davies.csv → ...me-delays/Latent/Latent_Period_Davies.csv
diff --git a/...rameters/delays/Median_Times_Palmieri.csv → ...ers/time-delays/Median_Times_Palmieri.csv b/...rameters/delays/Median_Times_Palmieri.csv → ...ers/time-delays/Median_Times_Palmieri.csv
diff --git a/.../parameters/delays/P_S/Time_PS_Davies.csv → ...meters/time-delays/P_S/Time_PS_Davies.csv b/.../parameters/delays/P_S/Time_PS_Davies.csv → ...meters/time-delays/P_S/Time_PS_Davies.csv
diff --git a/...parameters/delays/S_D/Time_SD_Fonfria.csv → ...eters/time-delays/S_D/Time_SD_Fonfria.csv b/...parameters/delays/S_D/Time_SD_Fonfria.csv → ...eters/time-delays/S_D/Time_SD_Fonfria.csv
diff --git a/data/parameters/delays/S_D/Time_SD_Knock.csv → ...ameters/time-delays/S_D/Time_SD_Knock.csv b/data/parameters/delays/S_D/Time_SD_Knock.csv → ...ameters/time-delays/S_D/Time_SD_Knock.csv
diff --git a/.../parameters/delays/S_D/Time_SD_Linton.csv → ...meters/time-delays/S_D/Time_SD_Linton.csv b/.../parameters/delays/S_D/Time_SD_Linton.csv → ...meters/time-delays/S_D/Time_SD_Linton.csv
diff --git a/...arameters/delays/S_D/Time_SD_Trentini.csv → ...ters/time-delays/S_D/Time_SD_Trentini.csv b/...arameters/delays/S_D/Time_SD_Trentini.csv → ...ters/time-delays/S_D/Time_SD_Trentini.csv
diff --git a/...parameters/delays/S_D/Time_SD_Zardini.csv → ...eters/time-delays/S_D/Time_SD_Zardini.csv b/...parameters/delays/S_D/Time_SD_Zardini.csv → ...eters/time-delays/S_D/Time_SD_Zardini.csv
diff --git a/.../delays/S_D/Time_SD_Zardini_Empirical.csv → ...-delays/S_D/Time_SD_Zardini_Empirical.csv b/.../delays/S_D/Time_SD_Zardini_Empirical.csv → ...-delays/S_D/Time_SD_Zardini_Empirical.csv
diff --git a/data/parameters/delays/S_H/Time_SH_Bi.csv → ...parameters/time-delays/S_H/Time_SH_Bi.csv b/data/parameters/delays/S_H/Time_SH_Bi.csv → ...parameters/time-delays/S_H/Time_SH_Bi.csv
diff --git a/...arameters/delays/S_H/Time_SH_D_Linton.csv → ...ters/time-delays/S_H/Time_SH_D_Linton.csv b/...arameters/delays/S_H/Time_SH_D_Linton.csv → ...ters/time-delays/S_H/Time_SH_D_Linton.csv
diff --git a/data/parameters/delays/S_H/Time_SH_ECDC.csv → ...rameters/time-delays/S_H/Time_SH_ECDC.csv b/data/parameters/delays/S_H/Time_SH_ECDC.csv → ...rameters/time-delays/S_H/Time_SH_ECDC.csv
diff --git a/...parameters/delays/S_H/Time_SH_Fonfria.csv → ...eters/time-delays/S_H/Time_SH_Fonfria.csv b/...parameters/delays/S_H/Time_SH_Fonfria.csv → ...eters/time-delays/S_H/Time_SH_Fonfria.csv
diff --git a/data/parameters/delays/S_H/Time_SH_Hall.csv → ...rameters/time-delays/S_H/Time_SH_Hall.csv b/data/parameters/delays/S_H/Time_SH_Hall.csv → ...rameters/time-delays/S_H/Time_SH_Hall.csv
diff --git a/data/parameters/delays/S_H/Time_SH_Li.csv → ...parameters/time-delays/S_H/Time_SH_Li.csv b/data/parameters/delays/S_H/Time_SH_Li.csv → ...parameters/time-delays/S_H/Time_SH_Li.csv
diff --git a/...arameters/delays/S_H/Time_SH_R_Linton.csv → ...ters/time-delays/S_H/Time_SH_R_Linton.csv b/...arameters/delays/S_H/Time_SH_R_Linton.csv → ...ters/time-delays/S_H/Time_SH_R_Linton.csv
diff --git a/...arameters/delays/S_H/Time_SH_Trentini.csv → ...ters/time-delays/S_H/Time_SH_Trentini.csv b/...arameters/delays/S_H/Time_SH_Trentini.csv → ...ters/time-delays/S_H/Time_SH_Trentini.csv
diff --git a/...parameters/delays/S_H/Time_SH_Zardini.csv → ...eters/time-delays/S_H/Time_SH_Zardini.csv b/...parameters/delays/S_H/Time_SH_Zardini.csv → ...eters/time-delays/S_H/Time_SH_Zardini.csv
diff --git a/.../delays/S_H/Time_SH_Zardini_Empirical.csv → ...-delays/S_H/Time_SH_Zardini_Empirical.csv b/.../delays/S_H/Time_SH_Zardini_Empirical.csv → ...-delays/S_H/Time_SH_Zardini_Empirical.csv
diff --git a/data/parameters/delays/S_H/Time_SH_Zhang.csv → ...ameters/time-delays/S_H/Time_SH_Zhang.csv b/data/parameters/delays/S_H/Time_SH_Zhang.csv → ...ameters/time-delays/S_H/Time_SH_Zhang.csv
diff --git a/...meters/delays/S_ICU/Time_SICU_Fonfria.csv → ...s/time-delays/S_ICU/Time_SICU_Fonfria.csv b/...meters/delays/S_ICU/Time_SICU_Fonfria.csv → ...s/time-delays/S_ICU/Time_SICU_Fonfria.csv
diff --git a/...meters/delays/S_ICU/Time_SICU_Zardini.csv → ...s/time-delays/S_ICU/Time_SICU_Zardini.csv b/...meters/delays/S_ICU/Time_SICU_Zardini.csv → ...s/time-delays/S_ICU/Time_SICU_Zardini.csv
diff --git a/...ays/S_ICU/Time_SICU_Zardini_Empirical.csv → ...ays/S_ICU/Time_SICU_Zardini_Empirical.csv b/...ays/S_ICU/Time_SICU_Zardini_Empirical.csv → ...ays/S_ICU/Time_SICU_Zardini_Empirical.csv
diff --git a/data/parameters/delays/S_N/Time_SN_Zhang.csv → ...ameters/time-delays/S_N/Time_SN_Zhang.csv b/data/parameters/delays/S_N/Time_SN_Zhang.csv → ...ameters/time-delays/S_N/Time_SN_Zhang.csv
diff --git a/data/parameters/delays/S_P/Time_SP_Hu.csv → ...parameters/time-delays/S_P/Time_SP_Hu.csv b/data/parameters/delays/S_P/Time_SP_Hu.csv → ...parameters/time-delays/S_P/Time_SP_Hu.csv
diff --git a/...parameters/delays/S_P/Time_SP_Zardini.csv → ...eters/time-delays/S_P/Time_SP_Zardini.csv b/...parameters/delays/S_P/Time_SP_Zardini.csv → ...eters/time-delays/S_P/Time_SP_Zardini.csv
diff --git a/.../delays/S_P/Time_SP_Zardini_Empirical.csv → ...-delays/S_P/Time_SP_Zardini_Empirical.csv b/.../delays/S_P/Time_SP_Zardini_Empirical.csv → ...-delays/S_P/Time_SP_Zardini_Empirical.csv
diff --git a/data/parameters/delays/S_Q/Time_SQ_Bi.csv → ...parameters/time-delays/S_Q/Time_SQ_Bi.csv b/data/parameters/delays/S_Q/Time_SQ_Bi.csv → ...parameters/time-delays/S_Q/Time_SQ_Bi.csv
diff --git a/...parameters/delays/S_Q_D/Time_SQD_ECDC.csv → ...eters/time-delays/S_Q_D/Time_SQD_ECDC.csv b/...parameters/delays/S_Q_D/Time_SQD_ECDC.csv → ...eters/time-delays/S_Q_D/Time_SQD_ECDC.csv
diff --git a/.../parameters/delays/S_R/Time_SR_Davies.csv → ...meters/time-delays/S_R/Time_SR_Davies.csv b/.../parameters/delays/S_R/Time_SR_Davies.csv → ...meters/time-delays/S_R/Time_SR_Davies.csv
diff --git a/...parameters/delays/S_R/Time_SR_Fonfria.csv → ...eters/time-delays/S_R/Time_SR_Fonfria.csv b/...parameters/delays/S_R/Time_SR_Fonfria.csv → ...eters/time-delays/S_R/Time_SR_Fonfria.csv
diff --git a/...arameters/delays/S_R/Time_SR_Trentini.csv → ...ters/time-delays/S_R/Time_SR_Trentini.csv b/...arameters/delays/S_R/Time_SR_Trentini.csv → ...ters/time-delays/S_R/Time_SR_Trentini.csv
diff --git a/data/parameters/delays/S_T/Time_ST_Bi.csv → ...parameters/time-delays/S_T/Time_ST_Bi.csv b/data/parameters/delays/S_T/Time_ST_Bi.csv → ...parameters/time-delays/S_T/Time_ST_Bi.csv
diff --git a/data/parameters/delays/S_T/Time_ST_ECDC.csv → ...rameters/time-delays/S_T/Time_ST_ECDC.csv b/data/parameters/delays/S_T/Time_ST_ECDC.csv → ...rameters/time-delays/S_T/Time_ST_ECDC.csv
diff --git a/...parameters/delays/S_T/Time_ST_Fonfria.csv → ...eters/time-delays/S_T/Time_ST_Fonfria.csv b/...parameters/delays/S_T/Time_ST_Fonfria.csv → ...eters/time-delays/S_T/Time_ST_Fonfria.csv
diff --git a/data/parameters/delays/S_T/Time_ST_Hu.csv → ...parameters/time-delays/S_T/Time_ST_Hu.csv b/data/parameters/delays/S_T/Time_ST_Hu.csv → ...parameters/time-delays/S_T/Time_ST_Hu.csv
diff --git a/data/parameters/delays/S_T/Time_ST_Zhang.csv → ...ameters/time-delays/S_T/Time_ST_Zhang.csv b/data/parameters/delays/S_T/Time_ST_Zhang.csv → ...ameters/time-delays/S_T/Time_ST_Zhang.csv
diff --git a/...ters/delays/Serial/Serial_Interval_Bi.csv → ...time-delays/Serial/Serial_Interval_Bi.csv b/...ters/delays/Serial/Serial_Interval_Bi.csv → ...time-delays/Serial/Serial_Interval_Bi.csv
diff --git a/...delays/Serial/Serial_Interval_Fonfria.csv → ...delays/Serial/Serial_Interval_Fonfria.csv b/...delays/Serial/Serial_Interval_Fonfria.csv → ...delays/Serial/Serial_Interval_Fonfria.csv
diff --git a/...ters/delays/Serial/Serial_Interval_Hu.csv → ...time-delays/Serial/Serial_Interval_Hu.csv b/...ters/delays/Serial/Serial_Interval_Hu.csv → ...time-delays/Serial/Serial_Interval_Hu.csv
diff --git a/...elays/Serial/Serial_Interval_Nishiura.csv → ...elays/Serial/Serial_Interval_Nishiura.csv b/...elays/Serial/Serial_Interval_Nishiura.csv → ...elays/Serial/Serial_Interval_Nishiura.csv
diff --git a/data/parameters/delays/T_H/Time_TH_Zhang.csv → ...ameters/time-delays/T_H/Time_TH_Zhang.csv b/data/parameters/delays/T_H/Time_TH_Zhang.csv → ...ameters/time-delays/T_H/Time_TH_Zhang.csv
diff --git a/data/parameters/delays/W_D/Time_WD_Knock.csv → ...ameters/time-delays/W_D/Time_WD_Knock.csv b/data/parameters/delays/W_D/Time_WD_Knock.csv → ...ameters/time-delays/W_D/Time_WD_Knock.csv
diff --git a/data/parameters/delays/W_R/Time_WR_Knock.csv → ...ameters/time-delays/W_R/Time_WR_Knock.csv b/data/parameters/delays/W_R/Time_WR_Knock.csv → ...ameters/time-delays/W_R/Time_WR_Knock.csv
diff --git a/data/parameters/transition-rates/Asymptomatic_Fraction_Ng.csv b/data/parameters/transition-rates/Asymptomatic_Fraction_Ng.csv
@@ -0,0 +1,5 @@
+Distribution, Setting, Mean, 95%_CI_Lower, 95%_CI_Upper
+ , Home, 0.28, 0.18, 0.38
+ , ocial, 0.35, 0.16, 0.55
+ , Work, 0.36, 0.13, 0.60
+ , All, 0.36, 0.27, 0.45
diff --git a/data/parameters/transition-rates/Asymptomatic_Symptomatic_Ratio_Ng.csv b/data/parameters/transition-rates/Asymptomatic_Symptomatic_Ratio_Ng.csv
@@ -0,0 +1,5 @@
+Distribution, Setting, Mean, 95%_CI_Lower, 95%_CI_Upper
+ , Home, 0.39, 0.23, 0.62
+ , Social, 0.58, 0.20, 1.20
+ , Work, 0.61, 0.15, 1.47
+ , All, 0.57, 0.36, 0.83
diff --git a/data/parameters/transition-rates/CFR/CFR_Zardini.csv b/data/parameters/transition-rates/CFR/CFR_Zardini.csv
@@ -0,0 +1,10 @@
+Sex,Age,Mean,95%CI_Lower,95%CI_Upper
+All,0-14,0.000,0.000,0.128
+All,15-19,0.000,0.000,0.522
+All,20-39,0.000,0.000,0.062
+All,40-59,0.008,0.000,0.043
+All,60-69,0.015,0.000,0.082
+All,70-79,0.130,0.049,0.263
+All,80+,0.109,0.036,0.236
+Female,All,0.020,0.005,0.050
+Male,All,0.051,0.024,0.095
diff --git a/data/parameters/transition-rates/Critical_Fraction/Critical_Fraction_ECDC.csv b/data/parameters/transition-rates/Critical_Fraction/Critical_Fraction_ECDC.csv
@@ -0,0 +1,2 @@
+Prior_Mean, Lower_Bound, Upper_Bound
+1, 0.2, 2
diff --git a/data/parameters/transition-rates/Critical_Fraction/Critical_Fraction_Zardini.csv b/data/parameters/transition-rates/Critical_Fraction/Critical_Fraction_Zardini.csv
@@ -0,0 +1,10 @@
+Sex, Age, Mean, 95%CI_Lower, 95%CI_Upper
+All,0-14,0.000,0.000,0.026
+All,15-19,0.000,0.000,0.161
+All,20-39,0.009,0.001,0.033
+All,40-59,0.006,0.001,0.020
+All,60-69,0.011,0.001,0.038
+All,70-79,0.050,0.018,0.105
+All,80+,0.068,0.023,0.153
+Female,All,0.008,0.003,0.020
+Male,All,0.023,0.012,0.039
diff --git a/data/parameters/transition-rates/Home_Testing_Fraction_ECDC.csv b/data/parameters/transition-rates/Home_Testing_Fraction_ECDC.csv
@@ -0,0 +1,2 @@
+Prior_Mean, Lower_Bound, Upper_Bound
+0.05, NA, NA
diff --git a/data/parameters/transition-rates/PCR_Positive_Infected_Ng.csv b/data/parameters/transition-rates/PCR_Positive_Infected_Ng.csv
@@ -0,0 +1,5 @@
+Distribution, Setting, Mean, 95%_CI_Lower, 95%_CI_Upper
+ , Home, 0.85, 0.74, 0.94
+ , Social, 0.75, 0.52, 0.93
+ , Work, 0.66, 0.41, 0.90
+ , All, 0.79, 0.68, 0.88
diff --git a/data/parameters/transition-rates/PCR_Symptomatic_Ng.csv b/data/parameters/transition-rates/PCR_Symptomatic_Ng.csv
@@ -0,0 +1,5 @@
+Distribution, Setting, Mean, 95%_CI_Lower, 95%_CI_Upper
+ , Home, 0.84, 0.79, 0.89
+ , Social, 0.71, 0.63, 0.79
+ , Work, 0.65, 0.54, 0.75
+ , All, 0.75, 0.70, 0.79
diff --git a/data/parameters/transition-rates/Serology_Fraction_Ng.csv b/data/parameters/transition-rates/Serology_Fraction_Ng.csv
@@ -0,0 +1,5 @@
+Distribution, Setting, Mean, 95%_CI_Lower, 95%_CI_Upper
+ , Home, 0.30, 0.28, 0.32
+ , Social, 0.12, 0.11, 0.13
+ , Work, 0.09, 0.08, 0.10
+ , All, 0.15, 0.14, 0.16
diff --git a/data/parameters/transition-rates/Serology_Positive_Infected_Ng.csv b/data/parameters/transition-rates/Serology_Positive_Infected_Ng.csv
@@ -0,0 +1,5 @@
+Distribution, Setting, Mean, 95%_CI_Lower, 95%_CI_Upper
+ , Home, 0.98, 0.96, 1.00
+ , Social, 0.98, 0.96, 1.00
+ , Work, 0.98, 0.96, 1.00
+ , All, 0.98, 0.96, 1.00
diff --git a/data/parameters/transition-rates/Severe_Fraction_ECDC.csv b/data/parameters/transition-rates/Severe_Fraction_ECDC.csv
@@ -0,0 +1,2 @@
+Prior_Mean, Lower_Bound, Upper_Bound
+1, 0.2, 2
diff --git a/data/parameters/transition-rates/Susceptibility/Susceptibility_Consensus_Davies.csv b/data/parameters/transition-rates/Susceptibility/Susceptibility_Consensus_Davies.csv
@@ -0,0 +1,9 @@
+Age,Susceptibility_Mean,Susceptibility_Quantile_2.5%,Susceptibility_Quantile_25%,Susceptibility_Quantile_50%,Susceptibility_Quantile_75%,Susceptibility_Quantile_97.5%
+0–9,0.40,0.25,0.34,0.39,0.45,0.57
+10-19, 0.38, 0.27, 0.33, 0.38,0.42,0.53
+20-29, 0.79, 0.59, 0.72, 0.79,0.86,0.96
+30-39, 0.86, 0.69, 0.81, 0.87,0.92,0.98
+40-49, 0.80, 0.61, 0.74, 0.80,0.86,0.96
+50–59, 0.82, 0.63, 0.76, 0.82,0.88,0.97
+60–69, 0.88, 0.70, 0.83, 0.89,0.93,0.99
+≥70, 0.74, 0.56, 0.68, 0.74, 0.80,0.90
diff --git a/data/parameters/transition-rates/Susceptibility/Susceptibility_Hu.csv b/data/parameters/transition-rates/Susceptibility/Susceptibility_Hu.csv
@@ -0,0 +1,4 @@
+Age,Mean
+0-14,0.58
+15-64,1
+65+,1.65
diff --git a/data/parameters/transition-rates/Susceptibility/Susceptibility_Marziano.txt b/data/parameters/transition-rates/Susceptibility/Susceptibility_Marziano.txt
diff --git a/data/parameters/transition-rates/Susceptibility/Susceptibility_Zhang.csv b/data/parameters/transition-rates/Susceptibility/Susceptibility_Zhang.csv
@@ -0,0 +1,5 @@
+Age    , Regression_Model , OR_Mean, OR_95%CI_Lower, OR_95%CI_Upper, p_value
+0-14   , GLMM, 0.34, 0.24, 0.49, <0.0001
+15-64  , GLMM, 1   ,     ,     , 
+65+    , GLMM, 1.47, 1.12, 1.92, 0.0045
+Unknown, GLMM, 0.42, 0.17, 0.90, 0.0413
diff --git a/data/parameters/transition-rates/Symptomatic_Uninfected_Ng.csv b/data/parameters/transition-rates/Symptomatic_Uninfected_Ng.csv
@@ -0,0 +1,5 @@
+Distribution, Setting, Mean, 95%_CI_Lower, 95%_CI_Upper
+ , Home, 0.26, 0.24, 0.29
+ , Social, 0.17, 0.15, 0.19
+ , Work, 0.21, 0.18, 0.25
+ , All, 0.20, 0.18, 0.22
diff --git a/data/parameters/transition-rates/Transmissibility/README.md b/data/parameters/transition-rates/Transmissibility/README.md
@@ -0,0 +1,8 @@
+## Transmissibility Estimates 
+
+| File | References | 
+| :---- | :---- | 
+| [Transmissibility_Ng](https://github.com/InPhyT/ComputationalEpidemiologyProject/blob/main/Data/CSV/2020/Parameters/Transition_Rates/Transmissibility/Transmissibility_Ng.csv) | [Ng et al. (02-11-2020)](https://doi.org/10.1038/s41586-020-2405-7) |
+| [Transmissibility_ECDC](https://github.com/InPhyT/ComputationalEpidemiologyProject/blob/main/Data/CSV/2020/Parameters/Transition_Rates/Transmissibility_ECDC.csv) | [ECDC (23-11-2020)](https://www.ecdc.europa.eu/sites/default/files/documents/covid-forecasts-modelling-november-2020.pdf) |
+| [Transmissibility_Setting_Thompson](https://github.com/InPhyT/ComputationalEpidemiologyProject/blob/main/Data/CSV/2020/Parameters/Transition_Rates/Transmissibility/Transmissibility_Setting_Thompson.csv) | [Thompson et al. (09-02-2021)](https://doi.org/10.1093/cid/ciab100) |
+| [Transmissibility_Status_Thompson](https://github.com/InPhyT/ComputationalEpidemiologyProject/blob/main/Data/CSV/2020/Parameters/Transition_Rates/Transmissibility/Transmissibility_Status_Thompson.csv) | [Thompson et al. (09-02-2021)](https://doi.org/10.1093/cid/ciab100) |
diff --git a/data/parameters/transition-rates/Transmissibility/Transmissibility_Davies.csv b/data/parameters/transition-rates/Transmissibility/Transmissibility_Davies.csv
@@ -0,0 +1,10 @@
+Age, Mean
+0-4, 0.61
+5-10, 0.61
+11-17, 0.61
+18-29, 0.64
+30-39, 0.67
+40-49, 0.70
+50-59, 0.75
+60-69, 0.82
+70+, 0.85
diff --git a/data/parameters/transition-rates/Transmissibility/Transmissibility_ECDC.csv b/data/parameters/transition-rates/Transmissibility/Transmissibility_ECDC.csv
@@ -0,0 +1,2 @@
+Prior_Mean, Lower_Bound, Upper_Bound
+0.05, 0.01, 0.1
diff --git a/data/parameters/transition-rates/Transmissibility/Transmissibility_Marziano.csv b/data/parameters/transition-rates/Transmissibility/Transmissibility_Marziano.csv
@@ -0,0 +1,2 @@
+Mean,95%CI_Lower,95%CI_Upper
+0.0148, 0.0126, 0.0167
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Prior_Mean, Lower_Bound, Upper_Bound
		1, 0.2, 2
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Prior_Mean, Lower_Bound, Upper_Bound
		0.05, NA, NA
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Prior_Mean, Lower_Bound, Upper_Bound
		0.05, 0.01, 0.1
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Mean,95%CI_Lower,95%CI_Upper
		0.0148, 0.0126, 0.0167