R/simulate_sutherland_model.R
simulate_sutherland_model.RdFunction to run multiple simulations of the Sutherland et al. Estimation Model
simulate_sutherland_model(list_annual_TB_decrease = list(TB_decrease_as_matrix(sutherland_TB_decrease), TB_decrease_as_matrix(sutherland_TB_decrease)), list_incidence_rates = list(sutherland_incidence_rates, sutherland_incidence_rates), list_percentage_year_one = rep(0.764, 2), list_sym_lag = list(2, 2), cores = 1, ...)
| list_annual_TB_decrease | A list of annual TB decreases with each element as specified for
the |
|---|---|
| list_incidence_rates | A list of incidence rates with each element as specified for the |
| list_percentage_year_one | A list of percentage secondary notifications in the first year
with each element as specified for the |
| cores | The number of cores to use, defaults to one |
| ... | Additional parameters to pass to |
A list of simulations for each of the outputs of sutherland_model.
simulate_sutherland_model(cores = 1)#> $`Table 2 - Estimated risk of developing notified TB` #> $`Table 2 - Estimated risk of developing notified TB`[[1]] #> Aged 13 in Unvaccinated Vaccinated #> [1,] 1969 370 1800 #> [2,] 1974 680 2400 #> [3,] 1979 1000 4000 #> [4,] 1984 1700 6500 #> [5,] 1989 2700 10000 #> [6,] 1994 4300 17000 #> [7,] 1999 6900 27000 #> [8,] 2004 11000 43000 #> [9,] 2009 18000 68000 #> #> $`Table 2 - Estimated risk of developing notified TB`[[2]] #> Aged 13 in Unvaccinated Vaccinated #> [1,] 1969 370 1800 #> [2,] 1974 680 2400 #> [3,] 1979 1000 4000 #> [4,] 1984 1700 6500 #> [5,] 1989 2700 10000 #> [6,] 1994 4300 17000 #> [7,] 1999 6900 27000 #> [8,] 2004 11000 43000 #> [9,] 2009 18000 68000 #> #> #> $`Table 3 - Estimated of no. of TB notifications prevented` #> $`Table 3 - Estimated of no. of TB notifications prevented`[[1]] #> Vac at age 13 Notifications prevented in 15 years #> [1,] 1969 218 #> [2,] 1974 106 #> [3,] 1979 71 #> [4,] 1984 44 #> [5,] 1989 28 #> [6,] 1994 17 #> [7,] 1999 11 #> [8,] 2004 7 #> [9,] 2009 4 #> Vacs to prevent one notification in 15 years #> [1,] 460 #> [2,] 940 #> [3,] 1400 #> [4,] 2200 #> [5,] 3600 #> [6,] 5800 #> [7,] 9300 #> [8,] 15000 #> [9,] 24000 #> #> $`Table 3 - Estimated of no. of TB notifications prevented`[[2]] #> Vac at age 13 Notifications prevented in 15 years #> [1,] 1969 218 #> [2,] 1974 106 #> [3,] 1979 71 #> [4,] 1984 44 #> [5,] 1989 28 #> [6,] 1994 17 #> [7,] 1999 11 #> [8,] 2004 7 #> [9,] 2009 4 #> Vacs to prevent one notification in 15 years #> [1,] 460 #> [2,] 940 #> [3,] 1400 #> [4,] 2200 #> [5,] 3600 #> [6,] 5800 #> [7,] 9300 #> [8,] 15000 #> [9,] 24000 #> #> #> $`Table 4 - Estimated no. of TB notifications prevented by Schools BCG scheme` #> $`Table 4 - Estimated no. of TB notifications prevented by Schools BCG scheme`[[1]] #> 15-19 years 20-24 years 25-29 years #> 1969 449 345 171 #> 1974 207 211 123 #> 1979 175 150 87 #> 1984 96 82 48 #> 1989 47 40 24 #> 1994 31 26 15 #> 1999 19 16 10 #> 2004 12 10 6 #> 2009 8 6 4 #> #> $`Table 4 - Estimated no. of TB notifications prevented by Schools BCG scheme`[[2]] #> 15-19 years 20-24 years 25-29 years #> 1969 449 345 171 #> 1974 207 211 123 #> 1979 175 150 87 #> 1984 96 82 48 #> 1989 47 40 24 #> 1994 31 26 15 #> 1999 19 16 10 #> 2004 12 10 6 #> 2009 8 6 4 #> #> #> $`Table 4 - Total notifcations prevented each year` #> $`Table 4 - Total notifcations prevented each year`[[1]] #> 1983 1988 1993 1998 2003 2008 2013 #> 558 369 217 119 69 44 27 #> #> $`Table 4 - Total notifcations prevented each year`[[2]] #> 1983 1988 1993 1998 2003 2008 2013 #> 558 369 217 119 69 44 27 #> #> #> $`Table 5 - Total notifications if the scheme continues` #> $`Table 5 - Total notifications if the scheme continues`[[1]] #> 1983 1988 1993 1998 2003 2008 2013 #> 463 296 166 91 52 33 22 #> #> $`Table 5 - Total notifications if the scheme continues`[[2]] #> 1983 1988 1993 1998 2003 2008 2013 #> 463 296 166 91 52 33 22 #> #> #> $`Table 5 - Primary additional notifications` #> $`Table 5 - Primary additional notifications`[[1]] #> 1973 1978 1983 1988 1993 1998 2003 2008 2013 #> 1971 0 207 387 369 217 119 69 44 27 #> 1976 0 0 175 246 217 119 69 44 27 #> 1981 0 0 0 96 130 119 69 44 27 #> 1986 0 0 0 0 47 71 69 44 27 #> 1991 0 0 0 0 0 31 46 44 27 #> 1996 0 0 0 0 0 0 19 29 27 #> 2001 0 0 0 0 0 0 0 12 18 #> 2006 0 0 0 0 0 0 0 0 8 #> 2011 0 0 0 0 0 0 0 0 0 #> #> $`Table 5 - Primary additional notifications`[[2]] #> 1973 1978 1983 1988 1993 1998 2003 2008 2013 #> 1971 0 207 387 369 217 119 69 44 27 #> 1976 0 0 175 246 217 119 69 44 27 #> 1981 0 0 0 96 130 119 69 44 27 #> 1986 0 0 0 0 47 71 69 44 27 #> 1991 0 0 0 0 0 31 46 44 27 #> 1996 0 0 0 0 0 0 19 29 27 #> 2001 0 0 0 0 0 0 0 12 18 #> 2006 0 0 0 0 0 0 0 0 8 #> 2011 0 0 0 0 0 0 0 0 0 #> #> #> $`Table 5 - Secondary additional notifications` #> $`Table 5 - Secondary additional notifications`[[1]] #> 1978 1983 1988 1993 1998 2003 2008 2013 #> 1971 59 209 290 238 138 77 46 29 #> 1976 0 50 154 180 138 77 46 29 #> 1981 0 0 28 83 96 77 46 29 #> 1986 0 0 0 13 43 54 46 29 #> 1991 0 0 0 0 9 28 34 29 #> 1996 0 0 0 0 0 5 18 21 #> 2001 0 0 0 0 0 0 3 11 #> 2006 0 0 0 0 0 0 0 2 #> 2011 0 0 0 0 0 0 0 0 #> #> $`Table 5 - Secondary additional notifications`[[2]] #> 1978 1983 1988 1993 1998 2003 2008 2013 #> 1971 59 209 290 238 138 77 46 29 #> 1976 0 50 154 180 138 77 46 29 #> 1981 0 0 28 83 96 77 46 29 #> 1986 0 0 0 13 43 54 46 29 #> 1991 0 0 0 0 9 28 34 29 #> 1996 0 0 0 0 0 5 18 21 #> 2001 0 0 0 0 0 0 3 11 #> 2006 0 0 0 0 0 0 0 2 #> 2011 0 0 0 0 0 0 0 0 #> #> #> $`Table 5 - Secondary additional notifcations reduced to Sutherland for clarity` #> $`Table 5 - Secondary additional notifcations reduced to Sutherland for clarity`[[1]] #> 1993 1998 2003 2008 2013 #> 1986 13 43 54 46 29 #> 1991 0 9 28 34 29 #> 1996 0 0 5 18 21 #> #> $`Table 5 - Secondary additional notifcations reduced to Sutherland for clarity`[[2]] #> 1993 1998 2003 2008 2013 #> 1986 13 43 54 46 29 #> 1991 0 9 28 34 29 #> 1996 0 0 5 18 21 #> #> #> $`Table 5 - Total secondary notifications all time` #> $`Table 5 - Total secondary notifications all time`[[1]] #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 1086 674 359 185 100 44 14 2 0 #> #> $`Table 5 - Total secondary notifications all time`[[2]] #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 1086 674 359 185 100 44 14 2 0 #> #> #> $`Table 5 - Total Effects of ending the schools BCG scheme` #> $`Table 5 - Total Effects of ending the schools BCG scheme`[[1]] #> 1983 1988 1993 1998 2003 2008 2013 #> 1971 1059 955 621 348 198 123 78 #> 1976 688 696 563 348 198 123 78 #> 1981 463 420 379 306 198 123 78 #> 1986 463 296 226 205 175 123 78 #> 1991 463 296 166 131 126 111 78 #> 1996 463 296 166 91 76 80 70 #> 2001 463 296 166 91 52 48 51 #> 2006 463 296 166 91 52 33 32 #> 2011 463 296 166 91 52 33 22 #> #> $`Table 5 - Total Effects of ending the schools BCG scheme`[[2]] #> 1983 1988 1993 1998 2003 2008 2013 #> 1971 1059 955 621 348 198 123 78 #> 1976 688 696 563 348 198 123 78 #> 1981 463 420 379 306 198 123 78 #> 1986 463 296 226 205 175 123 78 #> 1991 463 296 166 131 126 111 78 #> 1996 463 296 166 91 76 80 70 #> 2001 463 296 166 91 52 48 51 #> 2006 463 296 166 91 52 33 32 #> 2011 463 296 166 91 52 33 22 #> #> #> $`Total additional notifications` #> $`Total additional notifications`[[1]] #> 1983 1988 1993 1998 2003 2008 2013 #> 1971 596 659 455 257 146 90 56 #> 1976 225 400 397 257 146 90 56 #> 1981 0 124 213 215 146 90 56 #> 1986 0 0 60 114 123 90 56 #> 1991 0 0 0 40 74 78 56 #> 1996 0 0 0 0 24 47 48 #> 2001 0 0 0 0 0 15 29 #> 2006 0 0 0 0 0 0 10 #> 2011 0 0 0 0 0 0 0 #> #> $`Total additional notifications`[[2]] #> 1983 1988 1993 1998 2003 2008 2013 #> 1971 596 659 455 257 146 90 56 #> 1976 225 400 397 257 146 90 56 #> 1981 0 124 213 215 146 90 56 #> 1986 0 0 60 114 123 90 56 #> 1991 0 0 0 40 74 78 56 #> 1996 0 0 0 0 24 47 48 #> 2001 0 0 0 0 0 15 29 #> 2006 0 0 0 0 0 0 10 #> 2011 0 0 0 0 0 0 0 #> #> #> $`Total additional notifications all time` #> $`Total additional notifications all time`[[1]] #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 11295 7855 4220 2215 1240 595 220 50 0 #> #> $`Total additional notifications all time`[[2]] #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 11295 7855 4220 2215 1240 595 220 50 0 #> #> #> $total_primary_additional #> $total_primary_additional[[1]] #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 6160 4485 2425 1290 740 375 150 40 0 #> #> $total_primary_additional[[2]] #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 6160 4485 2425 1290 740 375 150 40 0 #> #> #> $total_secondary_additional #> $total_secondary_additional[[1]] #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 5960 3720 2010 1075 615 310 125 30 0 #> #> $total_secondary_additional[[2]] #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 5960 3720 2010 1075 615 310 125 30 0 #> #>