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b/man/get_cpp_api.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/get_cpp_api.R |
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\name{get_cpp_api} |
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\alias{get_cpp_api} |
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\title{Access internal C++ rountines used in outbreaker2} |
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\usage{ |
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get_cpp_api() |
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} |
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\value{ |
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An environment containing Rcpp bindings to C++ functions used internally in |
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outbreaker2. All functions are named as cpp_[type]_[component], where 'type' |
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can be: |
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\itemize{ |
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\item 'prior': prior computation |
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\item 'll': likelihood computation |
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\item 'move': movement of parameters or augmented data |
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} |
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And where 'component' can be: |
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\itemize{ |
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\item 'mu': (parameter) mutation rate |
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\item 'pi': (parameter) reporting probability |
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\item 'lambda': (parameter) non-infectious contact rate |
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\item 'eps': (parameter) contact reporting coverage |
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\item 'alpha': (augmented data) ancestries of the cases |
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\item 'kappa': (augmented data) generation between cases on transmission |
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chains |
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\item 't_inf': (augmented data) dates of infections |
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\item 'timing_infections': (likelihood component) timing between infectors and |
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infectees |
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\item 'timing_sampling': (likelihood component) timing between infection and |
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reporting / isolation |
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\item 'timing': (likelihood component) sum of the two timing components |
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\item 'genetic': (likelihood component) genetic diversity accumulated along |
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transmission chains |
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\item 'reporting': (likelihood component) reporting of cases |
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\item 'all': (likelihood component) sum of all likelihood components |
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\item 'swap_cases': (type of movement) swap infectors and infectees on a |
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transmission tree |
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} |
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For a description of the arguments of these functions, see the Rcpp_API |
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vignette (\code{vignette("Rcpp_API", package = "outbreaker2")}). |
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} |
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\description{ |
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This function returns an environment containing all C++ functions (bound to R |
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using Rcpp) used for priors, likelihoods, and movements of parameters in |
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outbreaker2. |
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} |
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\examples{ |
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## get functions in an environment |
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api <- get_cpp_api() |
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api |
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## check content of the environment |
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ls(api) |
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## test the prior for mu |
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args(api$cpp_prior_mu) |
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config <- create_config() |
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api$cpp_prior_mu(list(mu = 0.00123), config) |
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dexp(0.00123, rate = config$prior_mu, log = TRUE) |
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} |
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\author{ |
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Thibaut Jombart (\email{thibautjombart@gmail.com}) |
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} |