R/gibbs_draws.R
process_I_multivariant.RdProcess incidence input for multivariant analyses with estimate_advantage
process_I_multivariant(incid, incid_imported = NULL)a multidimensional array containing values of the incidence for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension)
an optional multidimensional array containing values of the incidence of imported cases for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension). `incid - incid_imported` is therefore the incidence of locally infected cases. If `incid_imported` is NULL this means there are no known imported cases and all cases other than on those from the first time step will be considered locally infected.
a list with two elements. 1) `local` a multidimensional array containing values of the incidence of locally infected cases for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension) 2) `imported` a multidimensional array containing values of the incidence of imported cases for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension)
n_v <- 3 # 3 variants
n_loc <- 1 # 1 location
T <- 100 # 100 time steps
# constant incidence 10 per day everywhere
incid <- array(10, dim = c(T, n_loc, n_v))
process_I_multivariant(incid)
#> $local
#> , , 1
#>
#> [,1]
#> [1,] 0
#> [2,] 10
#> [3,] 10
#> [4,] 10
#> [5,] 10
#> [6,] 10
#> [7,] 10
#> [8,] 10
#> [9,] 10
#> [10,] 10
#> [11,] 10
#> [12,] 10
#> [13,] 10
#> [14,] 10
#> [15,] 10
#> [16,] 10
#> [17,] 10
#> [18,] 10
#> [19,] 10
#> [20,] 10
#> [21,] 10
#> [22,] 10
#> [23,] 10
#> [24,] 10
#> [25,] 10
#> [26,] 10
#> [27,] 10
#> [28,] 10
#> [29,] 10
#> [30,] 10
#> [31,] 10
#> [32,] 10
#> [33,] 10
#> [34,] 10
#> [35,] 10
#> [36,] 10
#> [37,] 10
#> [38,] 10
#> [39,] 10
#> [40,] 10
#> [41,] 10
#> [42,] 10
#> [43,] 10
#> [44,] 10
#> [45,] 10
#> [46,] 10
#> [47,] 10
#> [48,] 10
#> [49,] 10
#> [50,] 10
#> [51,] 10
#> [52,] 10
#> [53,] 10
#> [54,] 10
#> [55,] 10
#> [56,] 10
#> [57,] 10
#> [58,] 10
#> [59,] 10
#> [60,] 10
#> [61,] 10
#> [62,] 10
#> [63,] 10
#> [64,] 10
#> [65,] 10
#> [66,] 10
#> [67,] 10
#> [68,] 10
#> [69,] 10
#> [70,] 10
#> [71,] 10
#> [72,] 10
#> [73,] 10
#> [74,] 10
#> [75,] 10
#> [76,] 10
#> [77,] 10
#> [78,] 10
#> [79,] 10
#> [80,] 10
#> [81,] 10
#> [82,] 10
#> [83,] 10
#> [84,] 10
#> [85,] 10
#> [86,] 10
#> [87,] 10
#> [88,] 10
#> [89,] 10
#> [90,] 10
#> [91,] 10
#> [92,] 10
#> [93,] 10
#> [94,] 10
#> [95,] 10
#> [96,] 10
#> [97,] 10
#> [98,] 10
#> [99,] 10
#> [100,] 10
#>
#> , , 2
#>
#> [,1]
#> [1,] 0
#> [2,] 10
#> [3,] 10
#> [4,] 10
#> [5,] 10
#> [6,] 10
#> [7,] 10
#> [8,] 10
#> [9,] 10
#> [10,] 10
#> [11,] 10
#> [12,] 10
#> [13,] 10
#> [14,] 10
#> [15,] 10
#> [16,] 10
#> [17,] 10
#> [18,] 10
#> [19,] 10
#> [20,] 10
#> [21,] 10
#> [22,] 10
#> [23,] 10
#> [24,] 10
#> [25,] 10
#> [26,] 10
#> [27,] 10
#> [28,] 10
#> [29,] 10
#> [30,] 10
#> [31,] 10
#> [32,] 10
#> [33,] 10
#> [34,] 10
#> [35,] 10
#> [36,] 10
#> [37,] 10
#> [38,] 10
#> [39,] 10
#> [40,] 10
#> [41,] 10
#> [42,] 10
#> [43,] 10
#> [44,] 10
#> [45,] 10
#> [46,] 10
#> [47,] 10
#> [48,] 10
#> [49,] 10
#> [50,] 10
#> [51,] 10
#> [52,] 10
#> [53,] 10
#> [54,] 10
#> [55,] 10
#> [56,] 10
#> [57,] 10
#> [58,] 10
#> [59,] 10
#> [60,] 10
#> [61,] 10
#> [62,] 10
#> [63,] 10
#> [64,] 10
#> [65,] 10
#> [66,] 10
#> [67,] 10
#> [68,] 10
#> [69,] 10
#> [70,] 10
#> [71,] 10
#> [72,] 10
#> [73,] 10
#> [74,] 10
#> [75,] 10
#> [76,] 10
#> [77,] 10
#> [78,] 10
#> [79,] 10
#> [80,] 10
#> [81,] 10
#> [82,] 10
#> [83,] 10
#> [84,] 10
#> [85,] 10
#> [86,] 10
#> [87,] 10
#> [88,] 10
#> [89,] 10
#> [90,] 10
#> [91,] 10
#> [92,] 10
#> [93,] 10
#> [94,] 10
#> [95,] 10
#> [96,] 10
#> [97,] 10
#> [98,] 10
#> [99,] 10
#> [100,] 10
#>
#> , , 3
#>
#> [,1]
#> [1,] 0
#> [2,] 10
#> [3,] 10
#> [4,] 10
#> [5,] 10
#> [6,] 10
#> [7,] 10
#> [8,] 10
#> [9,] 10
#> [10,] 10
#> [11,] 10
#> [12,] 10
#> [13,] 10
#> [14,] 10
#> [15,] 10
#> [16,] 10
#> [17,] 10
#> [18,] 10
#> [19,] 10
#> [20,] 10
#> [21,] 10
#> [22,] 10
#> [23,] 10
#> [24,] 10
#> [25,] 10
#> [26,] 10
#> [27,] 10
#> [28,] 10
#> [29,] 10
#> [30,] 10
#> [31,] 10
#> [32,] 10
#> [33,] 10
#> [34,] 10
#> [35,] 10
#> [36,] 10
#> [37,] 10
#> [38,] 10
#> [39,] 10
#> [40,] 10
#> [41,] 10
#> [42,] 10
#> [43,] 10
#> [44,] 10
#> [45,] 10
#> [46,] 10
#> [47,] 10
#> [48,] 10
#> [49,] 10
#> [50,] 10
#> [51,] 10
#> [52,] 10
#> [53,] 10
#> [54,] 10
#> [55,] 10
#> [56,] 10
#> [57,] 10
#> [58,] 10
#> [59,] 10
#> [60,] 10
#> [61,] 10
#> [62,] 10
#> [63,] 10
#> [64,] 10
#> [65,] 10
#> [66,] 10
#> [67,] 10
#> [68,] 10
#> [69,] 10
#> [70,] 10
#> [71,] 10
#> [72,] 10
#> [73,] 10
#> [74,] 10
#> [75,] 10
#> [76,] 10
#> [77,] 10
#> [78,] 10
#> [79,] 10
#> [80,] 10
#> [81,] 10
#> [82,] 10
#> [83,] 10
#> [84,] 10
#> [85,] 10
#> [86,] 10
#> [87,] 10
#> [88,] 10
#> [89,] 10
#> [90,] 10
#> [91,] 10
#> [92,] 10
#> [93,] 10
#> [94,] 10
#> [95,] 10
#> [96,] 10
#> [97,] 10
#> [98,] 10
#> [99,] 10
#> [100,] 10
#>
#>
#> $imported
#> , , 1
#>
#> [,1]
#> [1,] 10
#> [2,] 0
#> [3,] 0
#> [4,] 0
#> [5,] 0
#> [6,] 0
#> [7,] 0
#> [8,] 0
#> [9,] 0
#> [10,] 0
#> [11,] 0
#> [12,] 0
#> [13,] 0
#> [14,] 0
#> [15,] 0
#> [16,] 0
#> [17,] 0
#> [18,] 0
#> [19,] 0
#> [20,] 0
#> [21,] 0
#> [22,] 0
#> [23,] 0
#> [24,] 0
#> [25,] 0
#> [26,] 0
#> [27,] 0
#> [28,] 0
#> [29,] 0
#> [30,] 0
#> [31,] 0
#> [32,] 0
#> [33,] 0
#> [34,] 0
#> [35,] 0
#> [36,] 0
#> [37,] 0
#> [38,] 0
#> [39,] 0
#> [40,] 0
#> [41,] 0
#> [42,] 0
#> [43,] 0
#> [44,] 0
#> [45,] 0
#> [46,] 0
#> [47,] 0
#> [48,] 0
#> [49,] 0
#> [50,] 0
#> [51,] 0
#> [52,] 0
#> [53,] 0
#> [54,] 0
#> [55,] 0
#> [56,] 0
#> [57,] 0
#> [58,] 0
#> [59,] 0
#> [60,] 0
#> [61,] 0
#> [62,] 0
#> [63,] 0
#> [64,] 0
#> [65,] 0
#> [66,] 0
#> [67,] 0
#> [68,] 0
#> [69,] 0
#> [70,] 0
#> [71,] 0
#> [72,] 0
#> [73,] 0
#> [74,] 0
#> [75,] 0
#> [76,] 0
#> [77,] 0
#> [78,] 0
#> [79,] 0
#> [80,] 0
#> [81,] 0
#> [82,] 0
#> [83,] 0
#> [84,] 0
#> [85,] 0
#> [86,] 0
#> [87,] 0
#> [88,] 0
#> [89,] 0
#> [90,] 0
#> [91,] 0
#> [92,] 0
#> [93,] 0
#> [94,] 0
#> [95,] 0
#> [96,] 0
#> [97,] 0
#> [98,] 0
#> [99,] 0
#> [100,] 0
#>
#> , , 2
#>
#> [,1]
#> [1,] 10
#> [2,] 0
#> [3,] 0
#> [4,] 0
#> [5,] 0
#> [6,] 0
#> [7,] 0
#> [8,] 0
#> [9,] 0
#> [10,] 0
#> [11,] 0
#> [12,] 0
#> [13,] 0
#> [14,] 0
#> [15,] 0
#> [16,] 0
#> [17,] 0
#> [18,] 0
#> [19,] 0
#> [20,] 0
#> [21,] 0
#> [22,] 0
#> [23,] 0
#> [24,] 0
#> [25,] 0
#> [26,] 0
#> [27,] 0
#> [28,] 0
#> [29,] 0
#> [30,] 0
#> [31,] 0
#> [32,] 0
#> [33,] 0
#> [34,] 0
#> [35,] 0
#> [36,] 0
#> [37,] 0
#> [38,] 0
#> [39,] 0
#> [40,] 0
#> [41,] 0
#> [42,] 0
#> [43,] 0
#> [44,] 0
#> [45,] 0
#> [46,] 0
#> [47,] 0
#> [48,] 0
#> [49,] 0
#> [50,] 0
#> [51,] 0
#> [52,] 0
#> [53,] 0
#> [54,] 0
#> [55,] 0
#> [56,] 0
#> [57,] 0
#> [58,] 0
#> [59,] 0
#> [60,] 0
#> [61,] 0
#> [62,] 0
#> [63,] 0
#> [64,] 0
#> [65,] 0
#> [66,] 0
#> [67,] 0
#> [68,] 0
#> [69,] 0
#> [70,] 0
#> [71,] 0
#> [72,] 0
#> [73,] 0
#> [74,] 0
#> [75,] 0
#> [76,] 0
#> [77,] 0
#> [78,] 0
#> [79,] 0
#> [80,] 0
#> [81,] 0
#> [82,] 0
#> [83,] 0
#> [84,] 0
#> [85,] 0
#> [86,] 0
#> [87,] 0
#> [88,] 0
#> [89,] 0
#> [90,] 0
#> [91,] 0
#> [92,] 0
#> [93,] 0
#> [94,] 0
#> [95,] 0
#> [96,] 0
#> [97,] 0
#> [98,] 0
#> [99,] 0
#> [100,] 0
#>
#> , , 3
#>
#> [,1]
#> [1,] 10
#> [2,] 0
#> [3,] 0
#> [4,] 0
#> [5,] 0
#> [6,] 0
#> [7,] 0
#> [8,] 0
#> [9,] 0
#> [10,] 0
#> [11,] 0
#> [12,] 0
#> [13,] 0
#> [14,] 0
#> [15,] 0
#> [16,] 0
#> [17,] 0
#> [18,] 0
#> [19,] 0
#> [20,] 0
#> [21,] 0
#> [22,] 0
#> [23,] 0
#> [24,] 0
#> [25,] 0
#> [26,] 0
#> [27,] 0
#> [28,] 0
#> [29,] 0
#> [30,] 0
#> [31,] 0
#> [32,] 0
#> [33,] 0
#> [34,] 0
#> [35,] 0
#> [36,] 0
#> [37,] 0
#> [38,] 0
#> [39,] 0
#> [40,] 0
#> [41,] 0
#> [42,] 0
#> [43,] 0
#> [44,] 0
#> [45,] 0
#> [46,] 0
#> [47,] 0
#> [48,] 0
#> [49,] 0
#> [50,] 0
#> [51,] 0
#> [52,] 0
#> [53,] 0
#> [54,] 0
#> [55,] 0
#> [56,] 0
#> [57,] 0
#> [58,] 0
#> [59,] 0
#> [60,] 0
#> [61,] 0
#> [62,] 0
#> [63,] 0
#> [64,] 0
#> [65,] 0
#> [66,] 0
#> [67,] 0
#> [68,] 0
#> [69,] 0
#> [70,] 0
#> [71,] 0
#> [72,] 0
#> [73,] 0
#> [74,] 0
#> [75,] 0
#> [76,] 0
#> [77,] 0
#> [78,] 0
#> [79,] 0
#> [80,] 0
#> [81,] 0
#> [82,] 0
#> [83,] 0
#> [84,] 0
#> [85,] 0
#> [86,] 0
#> [87,] 0
#> [88,] 0
#> [89,] 0
#> [90,] 0
#> [91,] 0
#> [92,] 0
#> [93,] 0
#> [94,] 0
#> [95,] 0
#> [96,] 0
#> [97,] 0
#> [98,] 0
#> [99,] 0
#> [100,] 0
#>
#>
#> attr(,"class")
#> [1] "incid_multivariant"