Metawards Wave04

Emulation tests for MetaWards

Model description (parameters etc. ) are here

Based on Code from James Salter.

Code for this notebook is here

Warning: call dbDisconnect() when finished working with a connection

Emulating cumulative deaths in hostpital (cumHD) in the community (cumCD) at the beginning of lockdown

The DiceKriging Emulator fit for log(deaths) looks good. Leave-one-out isn’t a great measure, but it’s a start.

Week 12 cumulative Hospital deaths Leave-one-out plots

Week 12 cumulative community deaths Leave-one-out plots

Normalise input space and re-fit to produce some sensitivity analyses

one-at-a-time sensitivity for cumulative hospital deaths

one-at-a-time sensitivity for cumulative community deaths

FAST99 sensitivity analysis of Saltelli et al (1999)

Call:
fast99(model = NULL, factors = colnames(X_norm), n = 3000, q = "qunif",     q.arg = list(min = 0, max = 1))

Model runs: 45000 

Estimations of the indices:
                first order total order
R0             2.585428e-02 0.035929466
TE             8.449869e-03 0.012916688
TP             5.232931e-03 0.009794117
TI1            2.755023e-03 0.005637028
TI2            4.424181e-04 0.002651128
nuA            2.146632e-03 0.004908428
ns             3.161063e-03 0.006554266
p_home_weekend 2.465234e-05 0.002252227
alphaTH        1.251016e-02 0.014628540
etaTH          3.012345e-02 0.032340747
alphaEP        4.749904e-02 0.049844993
alphaI1D       4.128630e-04 0.002730804
alphaHD        6.479151e-01 0.665511700
alphaI1H       4.060805e-02 0.042927247
eta            1.532206e-01 0.155485294

Call:
fast99(model = NULL, factors = colnames(X_norm), n = 3000, q = "qunif",     q.arg = list(min = 0, max = 1))

Model runs: 45000 

Estimations of the indices:
                first order  total order
R0             2.863806e-02 0.0362205113
TE             7.500666e-03 0.0101285630
TP             8.205312e-03 0.0097800745
TI1            1.751677e-03 0.0032319492
TI2            1.808647e-04 0.0009642045
nuA            1.960271e-03 0.0031444349
ns             2.630065e-03 0.0041243613
p_home_weekend 2.258216e-04 0.0010491636
alphaTH        1.813378e-05 0.0007295074
etaTH          1.559330e-04 0.0008386092
alphaEP        4.130470e-02 0.0423746633
alphaI1D       8.163022e-01 0.8302459638
alphaHD        7.783550e-06 0.0011500901
alphaI1H       7.638476e-04 0.0041380489
eta            7.532251e-02 0.0764951926

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