R/sutherland_model.R
sutherland_model.RdSutherland et al. Model to Estimate Impact of Ending the BCG School Scheme
sutherland_model(Data = sutherland_data, incidence_rates = sutherland_incidence_rates, Rates.Per = 1e+05, Cohort.Length = 5, Data.start = 1969, Annual.TB.Decrease.Yearly = TB_decrease_as_matrix(sutherland_TB_decrease), Percentage.Year.One = NULL, trans_params = sutherland_trans_params(), Sym.Lag = 2, update_chains = FALSE)
| Data | Data used by Sutherland et al. analysis. See |
|---|---|
| incidence_rates | A list of Incidence rates (per 100,000) for the BCG vaccinated and unvaccinated population.
See |
| Rates.Per | The number of people by which to produce rates, defaults to 100,000 as in Sutherland et al. |
| Cohort.Length | Numeric, the lengh of time spent in each cohort, defaults to 5 years as in Sutherland et al. |
| Data.start | Numeric, the year the first data point originates, defaults to 1969 as in Sutherland et al. |
| Annual.TB.Decrease.Yearly | Matrix of average yearly decreases in TB with each column representing an age group (15-19, 20-24, 25-29).
Row names must be the year, starting from |
| Percentage.Year.One | Numeric, the percentage of a generation that occur in the first year.
Fitted via, |
| trans_params | A funciton for estimating the transmission parameters (expected total secondary notifications,
the size of the first generation, and the average interval between a primary case and all secondary cases). Defailts to
|
| Sym.Lag | Numeric, the generation time between infection and symtoms. Must be smaller or equal to the |
| update_chains | Logical, defaults to |
A list of tables reproducing the results presented in Sutherland et al. The final table estimates the total number of additional cases from ending the shcheme. In order to provide a complete estimate each 5 year estimate has been multiplied by the cohort length. In addition the primary additional impacts and total secondary notifications arising from each year are also output based on paper revisions.
sutherland_model(Percentage.Year.One = 0.764)#> $`Table 2 - Estimated risk of developing notified TB` #> 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` #> 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` #> 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` #> 1983 1988 1993 1998 2003 2008 2013 #> 558 369 217 119 69 44 27 #> #> $`Table 5 - Total notifications if the scheme continues` #> 1983 1988 1993 1998 2003 2008 2013 #> 463 296 166 91 52 33 22 #> #> $`Table 5 - Primary additional notifications` #> 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` #> 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` #> 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` #> 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` #> 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` #> 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` #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 11295 7855 4220 2215 1240 595 220 50 0 #> #> $total_primary_additional #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 6160 4485 2425 1290 740 375 150 40 0 #> #> $total_secondary_additional #> 1971 1976 1981 1986 1991 1996 2001 2006 2011 #> 5960 3720 2010 1075 615 310 125 30 0 #>