From 3268853b3a9f12fa9fe0b25ec65f41be4655a9c8 Mon Sep 17 00:00:00 2001
From: Marlena Bannick <mnorwood@uw.edu>
Date: Tue, 16 Nov 2021 16:20:28 -0800
Subject: [PATCH] updated documentation for q

---
 R/estimators.R                            | 1 +
 R/external-study-sim.R                    | 2 +-
 docs/pkgdown.yml                          | 2 +-
 docs/reference/assay.properties.nsim.html | 4 ++--
 docs/reference/get.snapshot.html          | 6 +++++-
 man/assay.properties.nsim.Rd              | 2 +-
 man/get.snapshot.Rd                       | 4 +++-
 7 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/R/estimators.R b/R/estimators.R
index d17c0b9..0a6aac0 100644
--- a/R/estimators.R
+++ b/R/estimators.R
@@ -60,6 +60,7 @@ var.log.to.var <- function(estimate, variance) (estimate ** 2) * variance
 #' @param n Total number of observations (\eqn{n_n + n_p = n})
 #' @param mu Mean window period (in years, not days)
 #' @param mu_var Variance of the estimator for mean window period.
+#' @param q Fraction of positives that were given recency test, defaults to 1
 #'   If \eqn{\mu} is known, input 0.
 #' @return Returns a list of the estimate and the variance for \eqn{\lambda}.
 #' @examples
diff --git a/R/external-study-sim.R b/R/external-study-sim.R
index a066e5a..9b57cd7 100644
--- a/R/external-study-sim.R
+++ b/R/external-study-sim.R
@@ -259,7 +259,7 @@ assay.properties.est <- function(study, bigT, tau, last_point=TRUE){
 #'
 #' The external study data for mean window and MDRI is available here from
 #' Duong et al. 2015:
-#' # https://doi.org/10.1371/journal.pone.0114947.s001
+#' https://doi.org/10.1371/journal.pone.0114947.s001
 #'
 #' @export
 #' @param n_sims Number of simulations
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index b75c61b..b1ff318 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.10.1
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2021-11-17T00:12Z
+last_built: 2021-11-17T00:19Z
 
diff --git a/docs/reference/assay.properties.nsim.html b/docs/reference/assay.properties.nsim.html
index cea58fd..4229bd8 100644
--- a/docs/reference/assay.properties.nsim.html
+++ b/docs/reference/assay.properties.nsim.html
@@ -44,7 +44,7 @@
 infection, and false recent rate (FRR) based on external study data. — assay.properties.nsim" />
 <meta property="og:description" content="The external study data for mean window and MDRI is available here from
 Duong et al. 2015:
-# https://doi.org/10.1371/journal.pone.0114947.s001" />
+https://doi.org/10.1371/journal.pone.0114947.s001" />
 
 
 
@@ -116,7 +116,7 @@ <h1>Function that simulates the mean window period, mean duration of recent
     <div class="ref-description">
     <p>The external study data for mean window and MDRI is available here from
 Duong et al. 2015:
-# https://doi.org/10.1371/journal.pone.0114947.s001</p>
+https://doi.org/10.1371/journal.pone.0114947.s001</p>
     </div>
 
     <pre class="usage"><span class='fu'>assay.properties.nsim</span><span class='op'>(</span>
diff --git a/docs/reference/get.snapshot.html b/docs/reference/get.snapshot.html
index 183828d..3d1f04b 100644
--- a/docs/reference/get.snapshot.html
+++ b/docs/reference/get.snapshot.html
@@ -145,7 +145,11 @@ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arg
     </tr>
     <tr>
       <th>mu_var</th>
-      <td><p>Variance of the estimator for mean window period.
+      <td><p>Variance of the estimator for mean window period.</p></td>
+    </tr>
+    <tr>
+      <th>q</th>
+      <td><p>Fraction of positives that were given recency test, defaults to 1
 If \(\mu\) is known, input 0.</p></td>
     </tr>
     </table>
diff --git a/man/assay.properties.nsim.Rd b/man/assay.properties.nsim.Rd
index cae4db5..5c18910 100644
--- a/man/assay.properties.nsim.Rd
+++ b/man/assay.properties.nsim.Rd
@@ -41,7 +41,7 @@ A list of estimated mean window period \eqn{\mu} and its variance,
 \description{
 The external study data for mean window and MDRI is available here from
 Duong et al. 2015:
-# https://doi.org/10.1371/journal.pone.0114947.s001
+https://doi.org/10.1371/journal.pone.0114947.s001
 }
 \examples{
 set.seed(0)
diff --git a/man/get.snapshot.Rd b/man/get.snapshot.Rd
index a75214d..9c7de96 100644
--- a/man/get.snapshot.Rd
+++ b/man/get.snapshot.Rd
@@ -17,7 +17,9 @@ get.snapshot(n_r, n_n, n_p, n, mu, mu_var, q = 1)
 
 \item{mu}{Mean window period (in years, not days)}
 
-\item{mu_var}{Variance of the estimator for mean window period.
+\item{mu_var}{Variance of the estimator for mean window period.}
+
+\item{q}{Fraction of positives that were given recency test, defaults to 1
 If \eqn{\mu} is known, input 0.}
 }
 \value{