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| a | b/R/RcppExports.R | ||
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| 1 | # Generated by using Rcpp::compileAttributes() -> do not edit by hand |
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| 2 | # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 |
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| 3 | |||
| 4 | cpp_are_possible_ancestors <- function(t_inf, i) { |
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| 5 | .Call(`_outbreaker2_cpp_are_possible_ancestors`, t_inf, i) |
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| 6 | } |
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| 7 | |||
| 8 | cpp_sample1 <- function(x) { |
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| 9 | .Call(`_outbreaker2_cpp_sample1`, x) |
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| 10 | } |
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| 11 | |||
| 12 | cpp_pick_possible_ancestor <- function(t_inf, i) { |
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| 13 | .Call(`_outbreaker2_cpp_pick_possible_ancestor`, t_inf, i) |
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| 14 | } |
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| 15 | |||
| 16 | cpp_find_descendents <- function(alpha, i) { |
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| 17 | .Call(`_outbreaker2_cpp_find_descendents`, alpha, i) |
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| 18 | } |
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| 19 | |||
| 20 | cpp_find_local_cases <- function(alpha, i) { |
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| 21 | .Call(`_outbreaker2_cpp_find_local_cases`, alpha, i) |
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| 22 | } |
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| 23 | |||
| 24 | cpp_swap_cases <- function(param, i) { |
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| 25 | .Call(`_outbreaker2_cpp_swap_cases`, param, i) |
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| 26 | } |
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| 27 | |||
| 28 | cpp_get_n_mutations <- function(data, i, j) { |
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| 29 | .Call(`_outbreaker2_cpp_get_n_mutations`, data, i, j) |
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| 30 | } |
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| 31 | |||
| 32 | cpp_lookup_sequenced_ancestor <- function(data, param, i) { |
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| 33 | .Call(`_outbreaker2_cpp_lookup_sequenced_ancestor`, data, param, i) |
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| 34 | } |
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| 35 | |||
| 36 | cpp_ll_genetic <- function(data, param, i = NULL, custom_function = NULL) { |
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| 37 | .Call(`_outbreaker2_cpp_ll_genetic`, data, param, i, custom_function) |
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| 38 | } |
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| 39 | |||
| 40 | cpp_ll_timing_infections <- function(data, param, i = NULL, custom_function = NULL) { |
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| 41 | .Call(`_outbreaker2_cpp_ll_timing_infections`, data, param, i, custom_function) |
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| 42 | } |
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| 43 | |||
| 44 | cpp_ll_timing_sampling <- function(data, param, i = NULL, custom_function = NULL) { |
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| 45 | .Call(`_outbreaker2_cpp_ll_timing_sampling`, data, param, i, custom_function) |
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| 46 | } |
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| 47 | |||
| 48 | cpp_ll_reporting <- function(data, param, i = NULL, custom_function = NULL) { |
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| 49 | .Call(`_outbreaker2_cpp_ll_reporting`, data, param, i, custom_function) |
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| 50 | } |
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| 51 | |||
| 52 | cpp_ll_contact <- function(data, param, i = NULL, custom_function = NULL) { |
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| 53 | .Call(`_outbreaker2_cpp_ll_contact`, data, param, i, custom_function) |
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| 54 | } |
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| 55 | |||
| 56 | cpp_ll_timing <- function(data, param, i = NULL, custom_functions = NULL) { |
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| 57 | .Call(`_outbreaker2_cpp_ll_timing`, data, param, i, custom_functions) |
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| 58 | } |
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| 59 | |||
| 60 | cpp_ll_all <- function(data, param, i = NULL, custom_functions = NULL) { |
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| 61 | .Call(`_outbreaker2_cpp_ll_all`, data, param, i, custom_functions) |
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| 62 | } |
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| 63 | |||
| 64 | cpp_move_mu <- function(param, data, config, custom_ll = NULL, custom_prior = NULL) { |
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| 65 | .Call(`_outbreaker2_cpp_move_mu`, param, data, config, custom_ll, custom_prior) |
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| 66 | } |
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| 67 | |||
| 68 | cpp_move_pi <- function(param, data, config, custom_ll = NULL, custom_prior = NULL) { |
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| 69 | .Call(`_outbreaker2_cpp_move_pi`, param, data, config, custom_ll, custom_prior) |
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| 70 | } |
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| 71 | |||
| 72 | cpp_move_eps <- function(param, data, config, custom_ll = NULL, custom_prior = NULL) { |
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| 73 | .Call(`_outbreaker2_cpp_move_eps`, param, data, config, custom_ll, custom_prior) |
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| 74 | } |
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| 75 | |||
| 76 | cpp_move_lambda <- function(param, data, config, custom_ll = NULL, custom_prior = NULL) { |
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| 77 | .Call(`_outbreaker2_cpp_move_lambda`, param, data, config, custom_ll, custom_prior) |
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| 78 | } |
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| 79 | |||
| 80 | cpp_move_t_inf <- function(param, data, list_custom_ll = NULL) { |
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| 81 | .Call(`_outbreaker2_cpp_move_t_inf`, param, data, list_custom_ll) |
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| 82 | } |
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| 83 | |||
| 84 | cpp_move_alpha <- function(param, data, list_custom_ll = NULL) { |
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| 85 | .Call(`_outbreaker2_cpp_move_alpha`, param, data, list_custom_ll) |
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| 86 | } |
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| 87 | |||
| 88 | cpp_move_swap_cases <- function(param, data, list_custom_ll = NULL) { |
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| 89 | .Call(`_outbreaker2_cpp_move_swap_cases`, param, data, list_custom_ll) |
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| 90 | } |
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| 91 | |||
| 92 | cpp_move_kappa <- function(param, data, config, list_custom_ll = NULL) { |
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| 93 | .Call(`_outbreaker2_cpp_move_kappa`, param, data, config, list_custom_ll) |
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| 94 | } |
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| 95 | |||
| 96 | cpp_prior_mu <- function(param, config, custom_function = NULL) { |
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| 97 | .Call(`_outbreaker2_cpp_prior_mu`, param, config, custom_function) |
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| 98 | } |
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| 99 | |||
| 100 | cpp_prior_pi <- function(param, config, custom_function = NULL) { |
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| 101 | .Call(`_outbreaker2_cpp_prior_pi`, param, config, custom_function) |
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| 102 | } |
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| 103 | |||
| 104 | cpp_prior_eps <- function(param, config, custom_function = NULL) { |
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| 105 | .Call(`_outbreaker2_cpp_prior_eps`, param, config, custom_function) |
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| 106 | } |
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| 107 | |||
| 108 | cpp_prior_lambda <- function(param, config, custom_function = NULL) { |
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| 109 | .Call(`_outbreaker2_cpp_prior_lambda`, param, config, custom_function) |
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| 110 | } |
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| 111 | |||
| 112 | cpp_prior_all <- function(param, config, custom_functions = NULL) { |
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| 113 | .Call(`_outbreaker2_cpp_prior_all`, param, config, custom_functions) |
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| 114 | } |
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| 115 |