Merge pull request #19 from OdyOSG/develop

release candidate v0.1.8

NEWS.md

@@ -1,3 +1,7 @@
+# EHDEN HMB v0.1.8
+
+* Fix pid and std file names in cohort definitions, changes anticipated build order
+
 # EHDEN HMB v0.1.7
 
 * Correct event in time to procedure intervention

analysis/settings/baselineCharacteristics.yml

@@ -50,9 +50,9 @@ baselineCharacteristics:
       id: 21
     - name: pcos
       id: 22
-    - name: PID
+    - name: pid
       id: 23
-    - name: STD
+    - name: std
       id: 24
     - name: tamoxifen
       id: 25

docs/contribution.html

@@ -256,6 +256,8 @@ <h2 data-number="5.1" class="anchored" data-anchor-id="sending-results"><span cl
 <p>Results from this study will be loaded to a secure file transfer protocol (sftp) hosted by Bayer. Participants in the study will be provided a key and password for the sftp emailed individually. Please contact the study coordinators if you do not have the sftp credentials prior to running the study.</p>
 <section id="instructions-to-share" class="level3" data-number="5.1.1">
 <h3 data-number="5.1.1" class="anchored" data-anchor-id="instructions-to-share"><span class="header-section-number">5.1.1</span> Instructions to Share</h3>
+<section id="sftp" class="level4" data-number="5.1.1.1">
+<h4 data-number="5.1.1.1" class="anchored" data-anchor-id="sftp"><span class="header-section-number">5.1.1.1</span> SFTP</h4>
 <ol type="1">
 <li>Review that a sftp key and secret credential have been sent to your site via email</li>
 <li>Open the file <code>extras/ShareResults.R</code></li>
@@ -268,11 +270,16 @@ <h3 data-number="5.1.1" class="anchored" data-anchor-id="instructions-to-share">
 </ul></li>
 <li>Contact the study coordinators that you have successfully uploaded your results to sftp</li>
 </ol>
+</section>
+<section id="via-email" class="level4" data-number="5.1.1.2">
+<h4 data-number="5.1.1.2" class="anchored" data-anchor-id="via-email"><span class="header-section-number">5.1.1.2</span> Via email</h4>
+<p>You may also email the results to <a href="mailto:[email protected]">Martin Lavallee</a> as a zip file using the following naming convention: <code>&lt;site_id&gt;_results_&lt;date&gt;.zip</code>.</p>
 
 
 </section>
 </section>
 </section>
+</section>
 
 </main> <!-- /main -->
 <script id="quarto-html-after-body" type="application/javascript">

docs/news.html

@@ -156,7 +156,8 @@
     <h2 id="toc-title">On this page</h2>
 
   <ul>
-  <li><a href="#ehden-hmb-v0.1.7" id="toc-ehden-hmb-v0.1.7" class="nav-link active" data-scroll-target="#ehden-hmb-v0.1.7">EHDEN HMB v0.1.7</a></li>
+  <li><a href="#ehden-hmb-v0.1.8" id="toc-ehden-hmb-v0.1.8" class="nav-link active" data-scroll-target="#ehden-hmb-v0.1.8">EHDEN HMB v0.1.8</a></li>
+  <li><a href="#ehden-hmb-v0.1.7" id="toc-ehden-hmb-v0.1.7" class="nav-link" data-scroll-target="#ehden-hmb-v0.1.7">EHDEN HMB v0.1.7</a></li>
   <li><a href="#ehden-hmb-v0.1.6" id="toc-ehden-hmb-v0.1.6" class="nav-link" data-scroll-target="#ehden-hmb-v0.1.6">EHDEN HMB v0.1.6</a></li>
   <li><a href="#ehden-hmb-v0.1.5" id="toc-ehden-hmb-v0.1.5" class="nav-link" data-scroll-target="#ehden-hmb-v0.1.5">EHDEN HMB v0.1.5</a></li>
   <li><a href="#ehden-hmb-v0.1.4" id="toc-ehden-hmb-v0.1.4" class="nav-link" data-scroll-target="#ehden-hmb-v0.1.4">EHDEN HMB v0.1.4</a></li>
@@ -193,6 +194,12 @@ <h1 class="title">News</h1>
 
 </header>
 
+<section id="ehden-hmb-v0.1.8" class="level1">
+<h1>EHDEN HMB v0.1.8</h1>
+<ul>
+<li>Fix pid and std file names in cohort definitions, changes anticipated build order</li>
+</ul>
+</section>
 <section id="ehden-hmb-v0.1.7" class="level1">
 <h1>EHDEN HMB v0.1.7</h1>
 <ul>

docs/search.json

@@ -46,7 +46,7 @@
     "href": "news.html",
     "title": "News",
     "section": "",
-    "text": "EHDEN HMB v0.1.7\n\nCorrect event in time to procedure intervention\n\n\n\nEHDEN HMB v0.1.6\n\nMinor bug fix to treatment patterns analysis\nCorrect typo in functions\n\n\n\nEHDEN HMB v0.1.5\n\nCorrect bug in analysis settings (Issue #12)\nUpdate package website\nAdd yearly incidence to Incidence Analysis (Issue #13)\nAdd R scripts for data exchange and CD preview (Issue #14)\nupdate cohort definitions from Siir\n\ncopperIUDproc\ncopperIUDdrug\ndisorderOfOvary\n\n\n\n\nEHDEN HMB v0.1.4\n\nFix bug in baseline characteristics; typo in analysis settings (Issue #10)\nCorrections to the study website\n\n\n\nEHDEN HMB v0.1.3\n\nUpdate cohort definitions\n\nadd baseline procedures\nadd baseline drugs\n\nInclude procedure prevalence at baseline [-365,0]\n\n\n\nEHDEN HMB v0.1.2\n\nUpdate cohort definitions\n\nrerun drug exposure with Capr\nrerun procedures with Capr\nadd time restraints to nsaids\nadd hmb cohort without hysterectomy censor\n\nAdd secondary treatment sequence including procedures\n\n\n\nEHDEN HMB v0.1.1\n\nAdd study website\nUpdate cohort definitions for denominator\nAddition of executeStudy.R file to automate execution\nadd age strata [under 30, 30-45, 45-55]\n\n\n\nEHDEN HMB v0.1.0\n\nFirst release of study code for EHDEN HMB\n\nAdd Incidence Analysis\nAdd Baseline Characteristics\nAdd Treatment Patterns\nAdd Procedure Analysis\n\n\n\n\nEHDEN HMB v0.0.6\n\nAdd file StoreResults to upload cohort diagnostics zip to aws s3 bucket\nUpdate KeyringSetup to match Ulysses\nUpdate renv.lock to add aws.s3 and Ulysses v0.0.2\nminor correction to study task files\n\n\n\nEHDEN HMB v0.0.5\n\nAdd in renv\nminor correction to HMB cohort for cohort diagnostics\n\n\n\nEHDEN HMB v0.0.4\n\nFix errors in KeyringSetup.R file\nFix cohort diagnostics to use integer64 with id in cohortDefinitionSet\n\n\n\nEHDEN HMB v0.0.3\n\nUpdate How to run file with installation instructions for usethis and Ulysses\nFix extras/KeyringSetup.R file to correctly set up credentials and check them\nEdit startSnowflakeSession function to handle string split of workDatabaseSchema\nEdit study tasks to order snowflake start correctly and close connection at end of file\n\n\n\nEHDEN HMB v0.0.2\n\nUpdate cohort definition for HMB to fix error\nAdd cohort diagnostics script\nAdd How to Run file and key ring file\n\n\n\nEHDEN HMB v0.0.1\n\nAdd HMB cohort definition to repo\nStart preparing documentation about study\nInitialize OHDSI study\nAdd NEWS.md to"
+    "text": "EHDEN HMB v0.1.8\n\nFix pid and std file names in cohort definitions, changes anticipated build order\n\n\n\nEHDEN HMB v0.1.7\n\nCorrect event in time to procedure intervention\n\n\n\nEHDEN HMB v0.1.6\n\nMinor bug fix to treatment patterns analysis\nCorrect typo in functions\n\n\n\nEHDEN HMB v0.1.5\n\nCorrect bug in analysis settings (Issue #12)\nUpdate package website\nAdd yearly incidence to Incidence Analysis (Issue #13)\nAdd R scripts for data exchange and CD preview (Issue #14)\nupdate cohort definitions from Siir\n\ncopperIUDproc\ncopperIUDdrug\ndisorderOfOvary\n\n\n\n\nEHDEN HMB v0.1.4\n\nFix bug in baseline characteristics; typo in analysis settings (Issue #10)\nCorrections to the study website\n\n\n\nEHDEN HMB v0.1.3\n\nUpdate cohort definitions\n\nadd baseline procedures\nadd baseline drugs\n\nInclude procedure prevalence at baseline [-365,0]\n\n\n\nEHDEN HMB v0.1.2\n\nUpdate cohort definitions\n\nrerun drug exposure with Capr\nrerun procedures with Capr\nadd time restraints to nsaids\nadd hmb cohort without hysterectomy censor\n\nAdd secondary treatment sequence including procedures\n\n\n\nEHDEN HMB v0.1.1\n\nAdd study website\nUpdate cohort definitions for denominator\nAddition of executeStudy.R file to automate execution\nadd age strata [under 30, 30-45, 45-55]\n\n\n\nEHDEN HMB v0.1.0\n\nFirst release of study code for EHDEN HMB\n\nAdd Incidence Analysis\nAdd Baseline Characteristics\nAdd Treatment Patterns\nAdd Procedure Analysis\n\n\n\n\nEHDEN HMB v0.0.6\n\nAdd file StoreResults to upload cohort diagnostics zip to aws s3 bucket\nUpdate KeyringSetup to match Ulysses\nUpdate renv.lock to add aws.s3 and Ulysses v0.0.2\nminor correction to study task files\n\n\n\nEHDEN HMB v0.0.5\n\nAdd in renv\nminor correction to HMB cohort for cohort diagnostics\n\n\n\nEHDEN HMB v0.0.4\n\nFix errors in KeyringSetup.R file\nFix cohort diagnostics to use integer64 with id in cohortDefinitionSet\n\n\n\nEHDEN HMB v0.0.3\n\nUpdate How to run file with installation instructions for usethis and Ulysses\nFix extras/KeyringSetup.R file to correctly set up credentials and check them\nEdit startSnowflakeSession function to handle string split of workDatabaseSchema\nEdit study tasks to order snowflake start correctly and close connection at end of file\n\n\n\nEHDEN HMB v0.0.2\n\nUpdate cohort definition for HMB to fix error\nAdd cohort diagnostics script\nAdd How to Run file and key ring file\n\n\n\nEHDEN HMB v0.0.1\n\nAdd HMB cohort definition to repo\nStart preparing documentation about study\nInitialize OHDSI study\nAdd NEWS.md to"
   },
   {
     "objectID": "contribution.html",
@@ -74,7 +74,7 @@
     "href": "contribution.html#sending-results",
     "title": "Contribution Guidelines",
     "section": "5.1 Sending Results",
-    "text": "5.1 Sending Results\nResults from this study will be loaded to a secure file transfer protocol (sftp) hosted by Bayer. Participants in the study will be provided a key and password for the sftp emailed individually. Please contact the study coordinators if you do not have the sftp credentials prior to running the study.\n\n5.1.1 Instructions to Share\n\nReview that a sftp key and secret credential have been sent to your site via email\nOpen the file extras/ShareResults.R\nRun the R file line by line\n\nWhen running L30 you will be asked to input the sftp credentials in a prompt\nCopy and paste the credentials into the prompt\nReplace L37 with a shortname for your study site\nExecute the remaining lines\n\nContact the study coordinators that you have successfully uploaded your results to sftp"
+    "text": "5.1 Sending Results\nResults from this study will be loaded to a secure file transfer protocol (sftp) hosted by Bayer. Participants in the study will be provided a key and password for the sftp emailed individually. Please contact the study coordinators if you do not have the sftp credentials prior to running the study.\n\n5.1.1 Instructions to Share\n\n5.1.1.1 SFTP\n\nReview that a sftp key and secret credential have been sent to your site via email\nOpen the file extras/ShareResults.R\nRun the R file line by line\n\nWhen running L30 you will be asked to input the sftp credentials in a prompt\nCopy and paste the credentials into the prompt\nReplace L37 with a shortname for your study site\nExecute the remaining lines\n\nContact the study coordinators that you have successfully uploaded your results to sftp\n\n\n\n5.1.1.2 Via email\nYou may also email the results to Martin Lavallee as a zip file using the following naming convention: <site_id>_results_<date>.zip."
   },
   {
     "objectID": "howToRun.html",

documentation/contribution.qmd

@@ -64,6 +64,8 @@ Results from this study will be loaded to a secure file transfer protocol (sftp)
 
 ### Instructions to Share
 
+#### SFTP
+
 1) Review that a sftp key and secret credential have been sent to your site via email
 2) Open the file `extras/ShareResults.R`
 3) Run the R file line by line
@@ -73,3 +75,7 @@ Results from this study will be loaded to a secure file transfer protocol (sftp)
     - Execute the remaining lines
 4) Contact the study coordinators that you have successfully uploaded your results to sftp
 
+#### Via email
+
+You may also email the results to [Martin Lavallee](mailto:[email protected]) as a zip file using the following naming convention: `<site_id>_results_<date>.zip`.
+

documentation/news.qmd

@@ -2,6 +2,10 @@
 title: "News"
 ---
 
+# EHDEN HMB v0.1.8
+
+* Fix pid and std file names in cohort definitions, changes anticipated build order
+
 # EHDEN HMB v0.1.7
 
 * Correct event in time to procedure intervention