R/sim_funs.R
make_jac.Rd
construct Jacobian matrix for ICU model (not quite complete: doesn't include flows to R)
make_jac(params, state = NULL)
parameter vector
state vector (named)
Other classic_macpan:
add_d_log()
,
add_updated_vaxrate()
,
aggregate_agecats()
,
calibrate_comb()
,
calibrate()
,
check_age_cat_compatibility()
,
check_contact_rate_setting()
,
col_multiply()
,
condense_age()
,
condense_params_vax()
,
condense_state()
,
condense_vax()
,
dev_is_tikz()
,
do_step()
,
expand_params_age()
,
expand_params_desc_age()
,
expand_params_desc_variant()
,
expand_params_desc_vax()
,
expand_params_mistry()
,
expand_params_variant()
,
expand_params_vax()
,
expand_state_age()
,
expand_state_vax()
,
expand_stateval_testing()
,
fix_pars()
,
fix_stored()
,
forecast_ensemble()
,
forecast_sim()
,
getData()
,
get_GI_moments()
,
get_Gbar()
,
get_R0()
,
get_doses_per_day()
,
get_evec()
,
get_kernel_moments()
,
get_opt_pars()
,
get_r()
,
invlink_trans()
,
make_betavec()
,
make_beta()
,
make_ratemat()
,
make_state()
,
make_test_wtsvec()
,
make_vaxrate()
,
mk_Nvec()
,
mk_agecats()
,
mk_contact_rate_setting()
,
mk_mistry_Nvec()
,
mk_pmat()
,
mk_vaxcats()
,
mle_fun()
,
non_expanded_states
,
rExp()
,
read_params()
,
repair_names_age()
,
restore()
,
run_sim_ageify()
,
run_sim_break()
,
run_sim_loglin()
,
run_sim_mobility()
,
run_sim_range()
,
run_sim()
,
show_ratemat()
,
testify()
,
texify()
,
trans_state_vars()
,
update_contact_rate_setting()
,
update_foi()
,
update_params_mistry()
,
vis_model()
,
write_params()
params <- read_params("ICU1.csv")
state <- make_state(params[["N"]],E0=params[["E0"]], use_eigvec=FALSE)
## state[c("E","Ia","Ip","Im","Is")] <- 1
state[["E"]] <- 1
J <- make_jac(params,state)
J["S","S"]
#> [1] 0
Jr <- J[1:6,1:6]
round(Jr,3)
#> to
#> from S E Ia Ip Im Is
#> S 0 0.000 -0.667 -1.000 -1.000 -1.000
#> E 0 -0.192 0.667 1.000 1.000 1.000
#> Ia 0 0.064 -0.143 0.000 0.000 0.000
#> Ip 0 0.128 0.000 -2.000 0.000 0.000
#> Im 0 0.000 0.000 1.912 -0.143 0.000
#> Is 0 0.000 0.000 0.088 0.000 -0.175
eigen(Jr)$values
#> [1] -1.9941503 -0.5979562 0.2558539 -0.1737373 -0.1428571 0.0000000
make_jac(params)
#> to
#> from S E Ia Ip Im Is H H2 ICUs
#> S 0 0.00000000 -0.6666667 -1.000 -1.0000000 -1.00000000 0.0 0.0 0.00
#> E 0 -0.19230769 0.6666667 1.000 1.0000000 1.00000000 0.0 0.0 0.00
#> Ia 0 0.06410256 -0.1428571 0.000 0.0000000 0.00000000 0.0 0.0 0.00
#> Ip 0 0.12820513 0.0000000 -2.000 0.0000000 0.00000000 0.0 0.0 0.00
#> Im 0 0.00000000 0.0000000 1.912 -0.1428571 0.00000000 0.0 0.0 0.00
#> Is 0 0.00000000 0.0000000 0.088 0.0000000 -0.17482517 0.0 0.0 0.00
#> H 0 0.00000000 0.0000000 0.000 0.0000000 0.13286713 -0.1 0.0 0.00
#> H2 0 0.00000000 0.0000000 0.000 0.0000000 0.00000000 0.0 -0.2 0.05
#> ICUs 0 0.00000000 0.0000000 0.000 0.0000000 0.02097902 0.0 0.0 -0.05
#> ICUd 0 0.00000000 0.0000000 0.000 0.0000000 0.02097902 0.0 0.0 0.00
#> D 0 0.00000000 0.0000000 0.000 0.0000000 0.00000000 0.0 0.0 0.00
#> R 0 0.00000000 0.1428571 0.000 0.1428571 0.00000000 0.1 0.2 0.00
#> X 0 0.00000000 0.0000000 0.000 0.0000000 0.00000000 0.0 0.0 0.00
#> V 0 0.00000000 0.0000000 0.000 0.0000000 0.00000000 0.0 0.0 0.00
#> to
#> from ICUd D R X V
#> S 0.000 0 0 0 0
#> E 0.000 0 0 0 0
#> Ia 0.000 0 0 0 0
#> Ip 0.000 0 0 0 0
#> Im 0.000 0 0 0 0
#> Is 0.000 0 0 0 0
#> H 0.000 0 0 0 0
#> H2 0.000 0 0 0 0
#> ICUs 0.000 0 0 0 0
#> ICUd -0.125 0 0 0 0
#> D 0.125 0 0 0 0
#> R 0.000 0 0 0 0
#> X 0.000 0 0 0 0
#> V 0.000 0 0 0 0