From 483a1e70790457626e3bc03cc1dbc461660350aa Mon Sep 17 00:00:00 2001
From: bretscm2 <michael.bretscher@roche.com>
Date: Tue, 15 Nov 2022 10:56:37 +0000
Subject: [PATCH] updating side

---
 R/calc_rwPFS.R                    | 2 +-
 docs/articles/real_world_PFS.html | 8 +++-----
 docs/pkgdown.yml                  | 4 ++--
 docs/reference/calc_rwPFS.html    | 2 +-
 man/calc_rwPFS.Rd                 | 2 +-
 vignettes/real_world_PFS.Rmd      | 2 +-
 6 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/R/calc_rwPFS.R b/R/calc_rwPFS.R
index ed18270..98124ac 100644
--- a/R/calc_rwPFS.R
+++ b/R/calc_rwPFS.R
@@ -49,7 +49,7 @@
 #'
 #'If rwPFS could not be calculated, the \code{rwpfs<label>_event_type} will be set to "Missing", and all other columns will contain missing values.
 #'This can be due to one of the following reasons: missing \code{.last_progression_abstraction_date} <= \code{.start_date}, missing \code{.last_activity_date} or <= \code{.start_date}, \code{.last_progression_abstraction_date} <= \code{.start_date},
-#'or \code{.death_date} <= \code{.start_date} (this can happen because death dates are rounded to mid-month in Flatiron).
+#'or \code{.death_date} <= \code{.start_date} (this can happen when death dates are rounded for anonymization purposes).
 #'
 #' @import rlang
 #' @import dplyr
diff --git a/docs/articles/real_world_PFS.html b/docs/articles/real_world_PFS.html
index 6236371..b69f721 100644
--- a/docs/articles/real_world_PFS.html
+++ b/docs/articles/real_world_PFS.html
@@ -78,7 +78,7 @@
       <h1 data-toc-skip>Real-world Progression-free Survival (rwPFS)</h1>
                         <h4 data-toc-skip class="author">Michael Bretscher</h4>
             
-            <h4 data-toc-skip class="date">2022-05-16</h4>
+            <h4 data-toc-skip class="date">2022-11-15</h4>
       
       
       <div class="hidden name"><code>real_world_PFS.Rmd</code></div>
@@ -107,7 +107,7 @@ <h1 id="background-on-rwpfs">Background on rwPFS<a class="anchor" aria-label="an
 <p>Whether or not <strong>PFS</strong> and <strong>rwPFS</strong> endpoints are <strong>equivalent</strong> and can be used for comparing drug efficacy across two data sets (real-world and clinical trial) may depend on type of cancer, drug category, real-world database, and other factors. While attempts should be made to understand and ensure quality of data collection in the real-world data, this will likely never be perfect. Consequently, empirical confirmation of the equivalence of rwPFS and PFS will be needed. This can be done by replicating trial arms and comparing rwPFS and trial PFS outcomes <span class="citation">(Mhatre et al. 2022; Ton et al. 2022)</span>, across indications and drug categories.</p>
 </blockquote>
 <div class="section level2">
-<h2 id="algorithm-for-calculating-rwpfs-using-flatiron-data">Algorithm for calculating rwPFS using Flatiron data<a class="anchor" aria-label="anchor" href="#algorithm-for-calculating-rwpfs-using-flatiron-data"></a>
+<h2 id="algorithm-for-calculating-rwpfs">Algorithm for calculating rwPFS<a class="anchor" aria-label="anchor" href="#algorithm-for-calculating-rwpfs"></a>
 </h2>
 <p>Figure 1 in <span class="citation">Mhatre et al. (2022)</span> illustrates the important elements required for calculating a rwPFS endpoint:</p>
 <ul>
@@ -433,9 +433,7 @@ <h2 id="using-different-subsets-of-progression-events">Using different subsets o
 <span class="co">#&gt; Warning in compare_rwPFS(., .labels = c("_all_events", "_discard_le_14d", : 8</span>
 <span class="co">#&gt; Patients with missing rwPFS were found and removed</span>
 <span class="co">#&gt; Warning: `select_()` was deprecated in dplyr 0.7.0.</span>
-<span class="co">#&gt; Please use `select()` instead.</span>
-<span class="co">#&gt; <span style="color: #555555;">This warning is displayed once every 8 hours.</span></span>
-<span class="co">#&gt; <span style="color: #555555;">Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.</span></span></code></pre></div>
+<span class="co">#&gt; Please use `select()` instead.</span></code></pre></div>
 <table class="table">
 <colgroup>
 <col width="21%">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 73f25e0..758c038 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,9 +1,9 @@
-pandoc: 2.14.0.3
+pandoc: 2.11.4
 pkgdown: 2.0.1
 pkgdown_sha: ~
 articles:
   real_world_PFS: real_world_PFS.html
-last_built: 2022-05-16T12:34Z
+last_built: 2022-11-15T10:55Z
 urls:
   reference: https://phcanalytics.github.io/RwPFS/reference
   article: https://phcanalytics.github.io/RwPFS/articles
diff --git a/docs/reference/calc_rwPFS.html b/docs/reference/calc_rwPFS.html
index 11f841b..81579a7 100644
--- a/docs/reference/calc_rwPFS.html
+++ b/docs/reference/calc_rwPFS.html
@@ -139,7 +139,7 @@ <h2>Value</h2>
 
 </dl><p>If rwPFS could not be calculated, the <code>rwpfs&lt;label&gt;_event_type</code> will be set to "Missing", and all other columns will contain missing values.
 This can be due to one of the following reasons: missing <code>.last_progression_abstraction_date</code> &lt;= <code>.start_date</code>, missing <code>.last_activity_date</code> or &lt;= <code>.start_date</code>, <code>.last_progression_abstraction_date</code> &lt;= <code>.start_date</code>,
-or <code>.death_date</code> &lt;= <code>.start_date</code> (this can happen because death dates are rounded to mid-month in Flatiron).</p>
+or <code>.death_date</code> &lt;= <code>.start_date</code> (this can happen when death dates are rounded for anonymization purposes).</p>
     </div>
 
     <div id="ref-examples">
diff --git a/man/calc_rwPFS.Rd b/man/calc_rwPFS.Rd
index 1a23af6..69fa7b9 100644
--- a/man/calc_rwPFS.Rd
+++ b/man/calc_rwPFS.Rd
@@ -73,7 +73,7 @@ Returns a data frame with the following new data columns added:
 
 If rwPFS could not be calculated, the \code{rwpfs<label>_event_type} will be set to "Missing", and all other columns will contain missing values.
 This can be due to one of the following reasons: missing \code{.last_progression_abstraction_date} <= \code{.start_date}, missing \code{.last_activity_date} or <= \code{.start_date}, \code{.last_progression_abstraction_date} <= \code{.start_date},
-or \code{.death_date} <= \code{.start_date} (this can happen because death dates are rounded to mid-month in Flatiron).
+or \code{.death_date} <= \code{.start_date} (this can happen when death dates are rounded for anonymization purposes).
 }
 \description{
 Calculates the real-world PFS (rwPFS) endpoint given information on follow-up period, progression-, and death dates.
diff --git a/vignettes/real_world_PFS.Rmd b/vignettes/real_world_PFS.Rmd
index 8c3988c..654585e 100644
--- a/vignettes/real_world_PFS.Rmd
+++ b/vignettes/real_world_PFS.Rmd
@@ -84,7 +84,7 @@ Because of these differences, it appears sensible to speak of "real-world PFS" (
 
 
 
-## Algorithm for calculating rwPFS using Flatiron data 
+## Algorithm for calculating rwPFS
 
 
 Figure 1 in @rwPFS_OAK illustrates the important elements required for calculating a rwPFS endpoint: