Datasets
Models
Downloads: 1
Diff of
/docs/reference/create_config.html
[000000]
..
[dfe06d]
Switch to side-by-side view
--- a +++ b/docs/reference/create_config.html @@ -0,0 +1,409 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Set and check parameter settings of outbreaker — create_config • outbreaker2</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> + +<!-- Font Awesome icons --> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> + +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + + + + +<meta property="og:title" content="Set and check parameter settings of outbreaker — create_config" /> +<meta property="og:description" content="This function defines settings for outbreaker. It takes a list of named +items as input, performs various checks, set defaults where arguments are +missing, and return a correct list of settings. If no input is given, it +returns the default settings." /> + + + + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + + </head> + + <body data-spy="scroll" data-target="#toc"> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">outbreaker2</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html"> + <span class="fas fa-home fa-lg"></span> + + </a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/customisation.html">Using custom priors, likelihood, or movements in outbreaker2</a> + </li> + <li> + <a href="../articles/introduction.html">Introduction to outbreaker2</a> + </li> + <li> + <a href="../articles/overview.html">outbreaker2: package overview</a> + </li> + <li> + <a href="../articles/Rcpp_API.html">outbreaker2: Rcpp API</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">Changelog</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Set and check parameter settings of outbreaker</h1> + + <div class="hidden name"><code>create_config.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function defines settings for outbreaker. It takes a list of named +items as input, performs various checks, set defaults where arguments are +missing, and return a correct list of settings. If no input is given, it +returns the default settings.</p> + </div> + + <pre class="usage"><span class='fu'>create_config</span><span class='op'>(</span><span class='va'>...</span>, data <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span> + +<span class='co'># S3 method for outbreaker_config</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>...</th> + <td><p>further arguments to be passed to other methods</p></td> + </tr> + <tr> + <th>data</th> + <td><p>an optional list of data items as returned by +<code>outbreaker_data</code>; if provided, this allows for further checks of +the outbreaker setings.</p></td> + </tr> + <tr> + <th>x</th> + <td><p>an <code>outbreaker_config</code> object as returned by <code>create_config</code>.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>Acceptables arguments for ... are:</p> +<dl> + +<dt>init_tree</dt><dd><p>the tree used to initialize the MCMC. Can be either a +character string indicating how this tree should be computed, or a vector of +integers corresponding to the tree itself, where the i-th value corresponds +to the index of the ancestor of 'i' (i.e., <code>init.tree[i]</code> is the +ancestor of case <code>i</code>). Accepted character strings are "seqTrack" (uses +seqTrack algorithm to generate the initial tree - see function +<code>seqTrack</code> in the package <code>adegenet</code>), "random" (ancestor randomly +selected from preceding cases), and "star" (all cases coalesce to the first +case). Note that for SeqTrack, all cases should have been sequenced.</p></dd> + +<dt>init_alpha</dt><dd><p>a vector of integers indicating the initial values of +alpha, where the i-th value indicates the ancestor of case 'i'; defaults to +<code>NULL</code>, in which ancestries are defined from <code>init_tree</code>.</p></dd> + +<dt>init_kappa</dt><dd><p>a (recycled) vector of integers indicating the initial +values of kappa; defaults to 1.</p></dd> + +<dt>init_t_inf</dt><dd><p>a vector of integers indicating the initial values of +<code>t_inf</code>, i.e. dates of infection; defaults to <code>NULL</code>, in which case +the most likely <code>t_inf</code> will be determined from the delay to +reporting/symptoms distribution, and the dates of reporting/symptoms, +provided in <code>data</code>.</p></dd> + +<dt>init_mu</dt><dd><p>initial value for the mutation rates</p></dd> + +<dt>init_pi</dt><dd><p>initial value for the reporting probability</p></dd> + +<dt>init_eps</dt><dd><p>initial value for the contact reporting coverage</p></dd> + +<dt>init_lambda</dt><dd><p>initial value for the non-infectious contact rate</p></dd> + +<dt>n_iter</dt><dd><p>an integer indicating the number of iterations in the MCMC, +including the burnin period</p></dd> + + +<dt>move_alpha</dt><dd><p>a vector of logicals indicating, for each case, if the +ancestry should be estimated ('moved' in the MCMC), or not, defaulting to +TRUE; the vector is recycled if needed.</p></dd> + +<dt>move_t_inf</dt><dd><p>a vector of logicals indicating, for each case, if the +dates of infection should be estimated ('moved' in the MCMC), or not, +defaulting to TRUE; the vector is recycled if needed.</p></dd> + +<dt>move_mu</dt><dd><p>a logical indicating whether the mutation rates +should be estimated ('moved' in the MCMC), or not, all defaulting to TRUE.</p></dd> + +<dt>move_pi</dt><dd><p>a logical indicating whether the reporting probability +should be estimated ('moved' in the MCMC), or not, all defaulting to TRUE.</p></dd> + +<dt>move_eps</dt><dd><p>a logical indicating whether the contact reporting coverage +should be estimated ('moved' in the MCMC), or not at all, defaulting to +TRUE.</p></dd> + +<dt>move_lambda</dt><dd><p>a logical indicating whether the non-infectious contact +rate should be estimated ('moved' in the MCMC), or not at all, defaulting to +TRUE.</p></dd> + +<dt>move_kappa</dt><dd><p>a logical indicating whether the number of generations +between two successive cases should be estimated ('moved' in the MCMC), or +not, all defaulting to TRUE.</p></dd> + +<dt>move_pi</dt><dd><p>a logical indicating whether the reporting probability +should be estimated ('moved' in the MCMC), or not, all defaulting to TRUE.</p></dd> + +<dt>n_iter</dt><dd><p>the number of iterations of the MCMC</p></dd> + +<dt>sample_every</dt><dd><p>the frequency at which MCMC samples are retained for the +output</p></dd> + +<dt>sd_mu</dt><dd><p>the standard deviation for the Normal proposal for the mutation +rates</p></dd> + +<dt>sd_pi</dt><dd><p>the standard deviation for the Normal proposal for the reporting +probability</p></dd> + +<dt>sd_eps</dt><dd><p>the standard deviation for the Normal proposal for the +contact reporting coverage</p></dd> + +<dt>sd_lambda</dt><dd><p>the standard deviation for the Normal proposal for the +non-infectious contact rate</p></dd> + +<dt>prop_alpha_move</dt><dd><p>the proportion of ancestries to move at each iteration +of the MCMC</p></dd> + +<dt>prop_t_inf_move</dt><dd><p>the proportion of infection dates to move at each +iteration of the MCMC</p></dd> +<dt>batch_size</dt><dd><p>the size of the batch of random number pre-generated</p></dd> + +<dt>paranoid</dt><dd><p>a logical indicating if the paranoid mode should be used; +this mode is used for performing additional tests during outbreaker; it makes +computations substantially slower and is mostly used for debugging purposes.</p></dd> + +<dt>min_date</dt><dd><p>earliest infection date possible, expressed as days since the +first sampling</p></dd> + +<dt>max_kappa</dt><dd><p>an integer indicating the largest number of generations +between any two linked cases; defaults to 5</p></dd> + +<dt>prior_mu</dt><dd><p>a numeric value indicating the rate of the exponential prior +for the mutation rate 'mu'</p></dd> + +<dt>prior_pi</dt><dd><p>a numeric vector of length 2 indicating the first and second +parameter of the beta prior for the reporting probability 'pi'</p></dd> + +<dt>prior_eps</dt><dd><p>a numeric vector of length 2 indicating the first and second +parameter of the beta prior for the contact reporting coverage 'eps'</p></dd> + +<dt>prior_lambda</dt><dd><p>a numeric vector of length 2 indicating the first and +second parameter of the beta prior for the non-infectious contact rate +'lambda'</p></dd> + +<dt>ctd_directed</dt><dd><p>a logical indicating if the contact tracing data is +directed or not. If yes, the first column represents the infector and the +second column the infectee. If ctd is provided as an epicontacts objects, +directionality will be taken from there.</p></dd> + +<dt>pb</dt><dd><p>a logical indicating if a progress bar should be displayed</p></dd> + + +</dl> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <div class='dont-index'><p><code><a href='outbreaker_data.html'>outbreaker_data</a></code> to check and process data for outbreaker</p></div> + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>Thibaut Jombart (<a href='mailto:thibautjombart@gmail.com'>thibautjombart@gmail.com</a>)</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='co'>## see default settings</span> +<span class='fu'>create_config</span><span class='op'>(</span><span class='op'>)</span> +</div><div class='output co'>#> +#> +#> ///// outbreaker settings /// +#> +#> class: outbreaker_config list +#> number of items: 37 +#> +#> /// initialisation // +#> init_tree init_mu init_kappa init_pi init_eps init_lambda +#> seqTrack 1e-04 1 0.9 0.5 0.05 +#> +#> /// movements // +#> move_alpha move_swap_cases move_t_inf move_mu move_kappa +#> TRUE TRUE TRUE TRUE TRUE +#> move_pi move_eps move_lambda prop_alpha_move prop_t_inf_move +#> TRUE TRUE TRUE 0.25 0.2 +#> sd_mu sd_pi sd_eps sd_lambda +#> 1e-04 0.1 0.1 0.05 +#> +#> /// chains // +#> n_iter sample_every +#> 10000 50 +#> +#> /// priors // +#> prior_mu prior_pi1 prior_pi2 prior_eps1 prior_eps2 +#> 1 10 1 1 1 +#> prior_lambda1 prior_lambda2 +#> 1 1 +#> +#> /// imported cases // +#> find_import n_iter_import sample_every_import outlier_threshold +#> TRUE 5000 50 5 +#> +#> /// other settings // +#> paranoid min_date max_kappa ctd_directed pb +#> FALSE -10 5 FALSE FALSE </div><div class='input'> +<span class='co'>## change defaults</span> +<span class='fu'>create_config</span><span class='op'>(</span>move_alpha <span class='op'>=</span> <span class='cn'>FALSE</span>, n_iter <span class='op'>=</span> <span class='fl'>2e5</span>, sample_every <span class='op'>=</span> <span class='fl'>1000</span><span class='op'>)</span> +</div><div class='output co'>#> +#> +#> ///// outbreaker settings /// +#> +#> class: outbreaker_config list +#> number of items: 37 +#> +#> /// initialisation // +#> init_tree init_mu init_kappa init_pi init_eps init_lambda +#> seqTrack 1e-04 1 0.9 0.5 0.05 +#> +#> /// movements // +#> move_alpha move_swap_cases move_t_inf move_mu move_kappa +#> FALSE TRUE TRUE TRUE TRUE +#> move_pi move_eps move_lambda prop_alpha_move prop_t_inf_move +#> TRUE TRUE TRUE 0.25 0.2 +#> sd_mu sd_pi sd_eps sd_lambda +#> 1e-04 0.1 0.1 0.05 +#> +#> /// chains // +#> n_iter sample_every +#> 2e+05 1000 +#> +#> /// priors // +#> prior_mu prior_pi1 prior_pi2 prior_eps1 prior_eps2 +#> 1 10 1 1 1 +#> prior_lambda1 prior_lambda2 +#> 1 1 +#> +#> /// imported cases // +#> find_import n_iter_import sample_every_import outlier_threshold +#> TRUE 5000 50 5 +#> +#> /// other settings // +#> paranoid min_date max_kappa ctd_directed pb +#> FALSE -10 5 FALSE FALSE </div><div class='input'> + + +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Thibaut Jombart, Finlay Campbell, Rich Fitzjohn.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + +