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using Rcpp) used for priors, likelihoods, and movements of parameters in |
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outbreaker2." /> |
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<div class="page-header"> |
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<h1>Access internal C++ rountines used in outbreaker2</h1> |
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<div class="hidden name"><code>get_cpp_api.Rd</code></div> |
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</div> |
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<div class="ref-description"> |
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<p>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.</p> |
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</div> |
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<pre class="usage"><span class='fu'>get_cpp_api</span><span class='op'>(</span><span class='op'>)</span></pre> |
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
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<p>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:</p> |
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<ul> |
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<li><p>'prior': prior computation</p></li> |
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<li><p>'ll': likelihood computation</p></li> |
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<li><p>'move': movement of parameters or augmented data</p></li> |
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</ul> |
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<p>And where 'component' can be:</p> |
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<ul> |
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<li><p>'mu': (parameter) mutation rate</p></li> |
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<li><p>'pi': (parameter) reporting probability</p></li> |
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<li><p>'lambda': (parameter) non-infectious contact rate</p></li> |
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<li><p>'eps': (parameter) contact reporting coverage</p></li> |
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<li><p>'alpha': (augmented data) ancestries of the cases</p></li> |
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<li><p>'kappa': (augmented data) generation between cases on transmission |
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chains</p></li> |
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<li><p>'t_inf': (augmented data) dates of infections</p></li> |
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<li><p>'timing_infections': (likelihood component) timing between infectors and |
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infectees</p></li> |
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<li><p>'timing_sampling': (likelihood component) timing between infection and |
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reporting / isolation</p></li> |
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<li><p>'timing': (likelihood component) sum of the two timing components</p></li> |
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<li><p>'genetic': (likelihood component) genetic diversity accumulated along |
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transmission chains</p></li> |
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<li><p>'reporting': (likelihood component) reporting of cases</p></li> |
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<li><p>'all': (likelihood component) sum of all likelihood components</p></li> |
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<li><p>'swap_cases': (type of movement) swap infectors and infectees on a |
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transmission tree</p></li> |
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</ul> |
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<p>For a description of the arguments of these functions, see the Rcpp_API |
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vignette (<code><a href='../articles/Rcpp_API.html'>vignette("Rcpp_API", package = "outbreaker2")</a></code>).</p> |
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<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> |
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<p>Thibaut Jombart (<a href='mailto:thibautjombart@gmail.com'>thibautjombart@gmail.com</a>)</p> |
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
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<pre class="examples"><div class='input'> |
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<span class='co'>## get functions in an environment</span> |
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<span class='va'>api</span> <span class='op'><-</span> <span class='fu'>get_cpp_api</span><span class='op'>(</span><span class='op'>)</span> |
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<span class='va'>api</span> |
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</div><div class='output co'>#> <environment: 0x000000003a142060></div><div class='input'> |
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<span class='co'>## check content of the environment</span> |
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<span class='fu'><a href='https://rdrr.io/r/base/ls.html'>ls</a></span><span class='op'>(</span><span class='va'>api</span><span class='op'>)</span> |
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</div><div class='output co'>#> [1] "cpp_ll_all" "cpp_ll_contact" |
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#> [3] "cpp_ll_genetic" "cpp_ll_reporting" |
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#> [5] "cpp_ll_timing" "cpp_ll_timing_infections" |
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#> [7] "cpp_ll_timing_sampling" "cpp_move_alpha" |
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#> [9] "cpp_move_eps" "cpp_move_kappa" |
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#> [11] "cpp_move_lambda" "cpp_move_mu" |
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#> [13] "cpp_move_pi" "cpp_move_swap_cases" |
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#> [15] "cpp_move_t_inf" "cpp_prior_all" |
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#> [17] "cpp_prior_eps" "cpp_prior_lambda" |
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#> [19] "cpp_prior_mu" "cpp_prior_pi" </div><div class='input'> |
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<span class='co'>## test the prior for mu</span> |
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<span class='fu'><a href='https://rdrr.io/r/base/args.html'>args</a></span><span class='op'>(</span><span class='va'>api</span><span class='op'>$</span><span class='va'>cpp_prior_mu</span><span class='op'>)</span> |
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</div><div class='output co'>#> function (param, config, custom_function = NULL) |
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#> NULL</div><div class='input'> |
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<span class='va'>config</span> <span class='op'><-</span> <span class='fu'><a href='create_config.html'>create_config</a></span><span class='op'>(</span><span class='op'>)</span> |
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<span class='va'>api</span><span class='op'>$</span><span class='fu'>cpp_prior_mu</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>mu <span class='op'>=</span> <span class='fl'>0.00123</span><span class='op'>)</span>, <span class='va'>config</span><span class='op'>)</span> |
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</div><div class='output co'>#> [1] -0.00123</div><div class='input'> |
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<span class='fu'><a href='https://rdrr.io/r/stats/Exponential.html'>dexp</a></span><span class='op'>(</span><span class='fl'>0.00123</span>, rate <span class='op'>=</span> <span class='va'>config</span><span class='op'>$</span><span class='va'>prior_mu</span>, log <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> |
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</div><div class='output co'>#> [1] -0.00123</div><div class='input'> |
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</div></pre> |
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<h2 data-toc-skip>Contents</h2> |
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<p>Developed by Thibaut Jombart, Finlay Campbell, Rich Fitzjohn.</p> |
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