data-raw/susceptibility_clinical_fraction.R

In njtierney/conmat: Builds Contact Matrices using GAMs and Population Data

# define susceptibility and clinical fraction parameters

davies_age_extended <- tibble::tribble(
  ~age,
  ~clinical_fraction,
  ~davies_original,
  ~davies_updated,
  0L,
  0.300839660771568,
  0.405243125439588,
  0.274004152218713,
  1L,
  0.297586599464828,
  0.402502562049369,
  0.274004152218713,
  2L,
  0.294208301590236,
  0.399703435419883,
  0.274004152218713,
  3L,
  0.29051957414156,
  0.396767294839426,
  0.287971835280787,
  4L,
  0.286293944054413,
  0.393631526404334,
  0.30202412593778,
  5L,
  0.281297196807437,
  0.39024837115024,
  0.315969936850741,
  6L,
  0.27532628857806,
  0.386639120630588,
  0.329807021459044,
  7L,
  0.268313789505417,
  0.382962806655906,
  0.343252033229079,
  8L,
  0.260278873472712,
  0.379457962719388,
  0.356057219950796,
  9L,
  0.25151164285796,
  0.376578047143387,
  0.368287559034645,
  10L,
  0.242623803184268,
  0.374974292206878,
  0.379898148409262,
  11L,
  0.234390556914771,
  0.37551811523472,
  0.391068420742893,
  12L,
  0.227534377060263,
  0.37914484476869,
  0.401701350527736,
  13L,
  0.222433214901116,
  0.386843956530518,
  0.412174391845095,
  14L,
  0.219262779263751,
  0.399593187250161,
  0.422423014051142,
  15L,
  0.218132212839674,
  0.418310718938954,
  0.432745312484442,
  16L,
  0.219007317855831,
  0.443686311967971,
  0.443686311967971,
  17L,
  0.221784110265796,
  0.47606573657563,
  0.47606573657563,
  18L,
  0.226235803861586,
  0.514887514579814,
  0.514887514579814,
  19L,
  0.232049453113255,
  0.558936696339759,
  0.558936696339759,
  20L,
  0.23869497040697,
  0.605235588597757,
  0.605235588597757,
  21L,
  0.245609064320696,
  0.650219777449733,
  0.650219777449733,
  22L,
  0.252316661836057,
  0.690765197596418,
  0.690765197596418,
  23L,
  0.258684635130281,
  0.725721651138198,
  0.725721651138198,
  24L,
  0.264737956231352,
  0.754821349991641,
  0.754821349991641,
  25L,
  0.270630228996984,
  0.778558441695052,
  0.778558441695052,
  26L,
  0.276553920048141,
  0.797672844392098,
  0.797672844392098,
  27L,
  0.282712455604753,
  0.813127844894791,
  0.813127844894791,
  28L,
  0.289209182915552,
  0.825738269481566,
  0.825738269481566,
  29L,
  0.296059616143947,
  0.836168846621602,
  0.836168846621602,
  30L,
  0.303031609510398,
  0.844650726312517,
  0.844650726312517,
  31L,
  0.309808598259769,
  0.851115001001754,
  0.851115001001754,
  32L,
  0.316137172162428,
  0.855475701865309,
  0.855475701865309,
  33L,
  0.322049660503632,
  0.857781939986349,
  0.857781939986349,
  34L,
  0.327702819226518,
  0.858121211564892,
  0.858121211564892,
  35L,
  0.33333773119303,
  0.85661508991501,
  0.85661508991501,
  36L,
  0.33921769995894,
  0.853396603572318,
  0.853396603572318,
  37L,
  0.345583190055924,
  0.848634916364279,
  0.848634916364279,
  38L,
  0.352532036118614,
  0.842603877145873,
  0.842603877145873,
  39L,
  0.360069544028309,
  0.83564492682245,
  0.83564492682245,
  40L,
  0.367920217958573,
  0.828315328873318,
  0.828315328873318,
  41L,
  0.375610890052003,
  0.821329042907506,
  0.821329042907506,
  42L,
  0.382952793862932,
  0.81514623794299,
  0.81514623794299,
  43L,
  0.389900935960663,
  0.810101263424909,
  0.810101263424909,
  44L,
  0.396655795866673,
  0.80631065923119,
  0.80631065923119,
  45L,
  0.403522410648723,
  0.803777247132055,
  0.803777247132055,
  46L,
  0.410814103582096,
  0.802471571141377,
  0.802471571141377,
  47L,
  0.41882378960398,
  0.80229950264122,
  0.80229950264122,
  48L,
  0.427745652062345,
  0.803146988536476,
  0.803146988536476,
  49L,
  0.43750414030479,
  0.80486784763572,
  0.80486784763572,
  50L,
  0.447844724898509,
  0.807291215530529,
  0.807291215530529,
  51L,
  0.458184144145412,
  0.810216233141427,
  0.810216233141427,
  52L,
  0.468325453638762,
  0.813567249486111,
  0.813567249486111,
  53L,
  0.478270945409754,
  0.817327682421881,
  0.817327682421881,
  54L,
  0.488330392142053,
  0.821574603669556,
  0.821574603669556,
  55L,
  0.498928943990846,
  0.826404494869757,
  0.826404494869757,
  56L,
  0.510485370318433,
  0.831897495252623,
  0.831897495252623,
  57L,
  0.523338634781543,
  0.838065466684734,
  0.838065466684734,
  58L,
  0.537642536835924,
  0.844813797692746,
  0.844813797692746,
  59L,
  0.55307493784313,
  0.851790755198216,
  0.851790755198216,
  60L,
  0.569009979460861,
  0.858489878458342,
  0.858489878458342,
  61L,
  0.58425252052942,
  0.864102749266343,
  0.864102749266343,
  62L,
  0.59815084659305,
  0.86799674664621,
  0.86799674664621,
  63L,
  0.610346875128792,
  0.869648201095943,
  0.869648201095943,
  64L,
  0.620937438784477,
  0.86870170386519,
  0.86870170386519,
  65L,
  0.630196505980292,
  0.864889588131732,
  0.864889588131732,
  66L,
  0.638485754269898,
  0.858119979544064,
  0.858119979544064,
  67L,
  0.646180255022669,
  0.848381547117261,
  0.848381547117261,
  68L,
  0.653575750264358,
  0.83591416963295,
  0.83591416963295,
  69L,
  0.660734224129279,
  0.821411784109917,
  0.821411784109917,
  70L,
  0.667578313494737,
  0.805826995276759,
  0.805826995276759,
  71L,
  0.673746895348781,
  0.790612084492718,
  0.790612084492718,
  72L,
  0.67901777760772,
  0.776773260388288,
  0.776773260388288,
  73L,
  0.683372065476387,
  0.764679929756006,
  0.764679929756006,
  74L,
  0.686855807518284,
  0.754484635842462,
  0.754484635842462,
  75L,
  0.689617752595992,
  0.745975990685674,
  0.745975990685674,
  76L,
  0.691835258172059,
  0.73879303288655,
  0.73879303288655,
  77L,
  0.693686291239087,
  0.732546839645335,
  0.732546839645335,
  78L,
  0.695335752518966,
  0.726829395297702,
  0.726829395297702,
  79L,
  0.696898868800772,
  0.721341371191107,
  0.721341371191107,
  80L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  81L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  82L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  83L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  84L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  85L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  86L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  87L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  88L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  89L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  90L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  91L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  92L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  93L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  94L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  95L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  96L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  97L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  98L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  99L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111,
  100L,
  0.698453096414112,
  0.71587836634111,
  0.71587836634111
)

use_data(davies_age_extended, compress = "xz", overwrite = TRUE)