update vlab link

README.Rmd

@@ -39,7 +39,7 @@ knitr::opts_chunk$set(
 
 "The United States Department of Commerce (DOC) GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its use. DOC has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any claims against the Department of Commerce stemming from the use of its GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government."
 
-<!-- - This project code is made available through GitHub but is managed by NOAA at https://vlab.ncep.noaa.gov/redmine/projects/integrated-fisheries-toolbox/files -->
+<!-- - This project code is made available through GitHub but is managed by NOAA at https://vlab.noaa.gov/redmine/projects/integrated-fisheries-toolbox/files -->
 
   ***** *******
 
@@ -159,7 +159,7 @@ fore$Nforecastyrs
 
 However, an assessment will be conducted every 3 years and 3 years of forecasting is required. SSMSE will modify this value to the appropriate number of forecasting years.
 
-More information on using the forecast module in SS to forecast catches is available in the [Stock Synthesis users manual](https://vlab.ncep.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/4513132).
+More information on using the forecast module in SS to forecast catches is available in the [Stock Synthesis users manual](https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/4513132).
 
 
 ## Adding observation error: Specify how to sample data from the Operating model

README.md

@@ -63,7 +63,7 @@ The Department of Commerce seal and logo, or the seal and logo of a DOC
 bureau, shall not be used in any manner to imply endorsement of any
 commercial product or activity by DOC or the United States Government.”
 
-<!-- - This project code is made available through GitHub but is managed by NOAA at https://vlab.ncep.noaa.gov/redmine/projects/integrated-fisheries-toolbox/files -->
+<!-- - This project code is made available through GitHub but is managed by NOAA at https://vlab.noaa.gov/redmine/projects/integrated-fisheries-toolbox/files -->
 
 -----
 
@@ -257,7 +257,7 @@ number of forecasting years.
 
 More information on using the forecast module in SS to forecast catches
 is available in the [Stock Synthesis users
-manual](https://vlab.ncep.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/4513132).
+manual](https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/4513132).
 
 ## Adding observation error: Specify how to sample data from the Operating model
 

docs/index.html

@@ -105,7 +105,7 @@
           </div>
             <ul id = "assocaited_tools">
 
-                <li><a href="https://vlab.ncep.noaa.gov/web/stock-synthesis"><i>SS</i></a></li>
+                <li><a href="https://vlab.noaa.gov/web/stock-synthesis"><i>SS</i></a></li>
 
                 <li><a href="https://nmfs-fish-tools.github.io/DST"><i>DST</i></a></li>
 

docs/manual/SSMSE.html

@@ -265,7 +265,7 @@ <h3><span class="header-section-number">3.3.2</span> Using a custom management s
 </div>
 <div id="sampling-options" class="section level2">
 <h2><span class="header-section-number">3.4</span> Sampling options</h2>
-<p>Currently, the only available sampling option is to use the bootstrapping module within SS itself. This means specifying <code>use_SS_boot_vec = TRUE</code>. Details on how sampling is done using the bootstrapping module in SS is available in the “Bootstrap Data Files” section of the <a href="https://vlab.ncep.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view_file/11684231">SS user manual</a>.</p>
+<p>Currently, the only available sampling option is to use the bootstrapping module within SS itself. This means specifying <code>use_SS_boot_vec = TRUE</code>. Details on how sampling is done using the bootstrapping module in SS is available in the “Bootstrap Data Files” section of the <a href="https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view_file/11684231">SS user manual</a>.</p>
 <p>Users also need to specify how and which data types should be sampled for each future year in the simulation in <code>sample_struct_list</code>. <code>sample_struct_list</code> is a list of lists. The first level is a list for each scenario; then, for the scenario, there is a list of dataframes, each of which specifying which years and fleets of data should be sampled in the future as well as which standard errors or sample sizes should be used.</p>
 <p>The helper function <code>create_sample_struct()</code> can be used to help users generate the list of dataframes for a scenario. See an example of this function’s use in the <a href="#sample">simple example</a> or by typing <code>?SSMSE::create_sample_struct()</code> into the R console.</p>
 </div>

docs/manual/intro.html

@@ -195,7 +195,7 @@ <h1>
 <h1><span class="header-section-number">1</span> Introduction</h1>
 <div id="purpose" class="section level2">
 <h2><span class="header-section-number">1.1</span> Purpose</h2>
-<p>SSMSE was developed to increase the ease of using <a href="https://vlab.ncep.noaa.gov/web/stock-synthesis">Stock Synthesis</a> (SS) directly as an operating model in an Management Strategy evaluation. The approach requires a conditioned Stock Synthesis model, which is treated as the Operating Model and a Stock Synthesis model to use as the Estimation Model (EM) and to specify the Management procedure through the Stock Synthesis forecasting model.</p>
+<p>SSMSE was developed to increase the ease of using <a href="https://vlab.noaa.gov/web/stock-synthesis">Stock Synthesis</a> (SS) directly as an operating model in an Management Strategy evaluation. The approach requires a conditioned Stock Synthesis model, which is treated as the Operating Model and a Stock Synthesis model to use as the Estimation Model (EM) and to specify the Management procedure through the Stock Synthesis forecasting model.</p>
 </div>
 <div id="funs" class="section level2">
 <h2><span class="header-section-number">1.2</span> Functions in SSMSE</h2>

docs/manual/simple.html

@@ -252,7 +252,7 @@ <h2><span class="header-section-number">2.3</span> Examine the management proced
 <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">fore<span class="op">$</span>Nforecastyrs</a></code></pre></div>
 <pre><code>[1] 1</code></pre>
 <p>However, an assessment will be conducted every 3 years and 3 years of forecasting is required. SSMSE will modify this value to the appropriate number of forecasting years.</p>
-<p>More information on using the forecast module in SS to forecast catches is available in the <a href="https://vlab.ncep.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/4513132">Stock Synthesis users manual</a>.</p>
+<p>More information on using the forecast module in SS to forecast catches is available in the <a href="https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/4513132">Stock Synthesis users manual</a>.</p>
 </div>
 <div id="adding-observation-error-specify-how-to-sample-data-from-the-operating-model-sample" class="section level2">
 <h2><span class="header-section-number">2.4</span> Adding observation error: Specify how to sample data from the Operating model (#sample)</h2>

inst/bookdown/01-intro.Rmd

@@ -2,7 +2,7 @@
 
 ## Purpose
 
-SSMSE was developed to increase the ease of using [Stock Synthesis](https://vlab.ncep.noaa.gov/web/stock-synthesis) (SS) directly as an operating model in an Management Strategy evaluation. The approach requires a conditioned Stock Synthesis model, which is treated as the Operating Model and a Stock Synthesis model to use as the Estimation Model (EM) and to specify the Management procedure through the Stock Synthesis forecasting model. 
+SSMSE was developed to increase the ease of using [Stock Synthesis](https://vlab.noaa.gov/web/stock-synthesis) (SS) directly as an operating model in an Management Strategy evaluation. The approach requires a conditioned Stock Synthesis model, which is treated as the Operating Model and a Stock Synthesis model to use as the Estimation Model (EM) and to specify the Management procedure through the Stock Synthesis forecasting model. 
 
 ## Functions in SSMSE {#funs}
 

inst/bookdown/02-ex-simple.Rmd

@@ -84,7 +84,7 @@ fore$Nforecastyrs
 
 However, an assessment will be conducted every 3 years and 3 years of forecasting is required. SSMSE will modify this value to the appropriate number of forecasting years.
 
-More information on using the forecast module in SS to forecast catches is available in the [Stock Synthesis users manual](https://vlab.ncep.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/4513132).
+More information on using the forecast module in SS to forecast catches is available in the [Stock Synthesis users manual](https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view/4513132).
 
 
 ## Adding observation error: Specify how to sample data from the Operating model (#sample)

inst/bookdown/03-runSSMSE.Rmd

@@ -82,7 +82,7 @@ run_result_custom <- run_SSMSE(
 
 ## Sampling options
 
-Currently, the only available sampling option is to use the bootstrapping module within SS itself. This means specifying `use_SS_boot_vec = TRUE`. Details on how sampling is done using the bootstrapping module in SS is available in the "Bootstrap Data Files" section of the [SS user manual](https://vlab.ncep.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view_file/11684231).
+Currently, the only available sampling option is to use the bootstrapping module within SS itself. This means specifying `use_SS_boot_vec = TRUE`. Details on how sampling is done using the bootstrapping module in SS is available in the "Bootstrap Data Files" section of the [SS user manual](https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view_file/11684231).
 
 Users also need to specify how and which data types should be sampled for each future year in the simulation in `sample_struct_list`. `sample_struct_list` is a list of lists. The first level is a list for each scenario; then, for the scenario, there is a list of dataframes, each of which specifying which years and fleets of data should be sampled in the future as well as which standard errors or sample sizes should be used.
 

inst/extdata/models/cod/Report.sso

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 
 StartTime: Thu Sep 03 07:21:47 2020
 EndTime: Thu Sep 03 07:24:47 2020

inst/extdata/models/cod/control.ss

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 #_data_and_control_files: ss3.dat // em.ctl
 0  # 0 means do not read wtatage.ss; 1 means read and use wtatage.ss and also read and use growth parameters
 1  #_N_Growth_Patterns

inst/extdata/models/cod/control.ss_new

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 #_data_and_control_files: ss3.dat // control.ss
 0  # 0 means do not read wtatage.ss; 1 means read and use wtatage.ss and also read and use growth parameters
 1  #_N_Growth_Patterns (Growth Patterns, Morphs, Bio Patterns, GP are terms used interchangeably in SS)

inst/extdata/models/cod/data.ss_new

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 #_Start_time: Thu Sep 03 07:24:47 2020
 #_Number_of_datafiles: 2
 #C data file created using the SS_writedat function in the R package r4ss

inst/extdata/models/cod/starter.ss_new

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 #C starter file written by R function SS_writestarter
 #C rerun model to get more complete formatting in starter.ss_new
 #C should work with SS version: 3.30

inst/extdata/test_mod/cod_initOM_for_tests/Report.sso

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 
 StartTime: Wed Apr 08 10:52:36 2020
 EndTime: Wed Apr 08 10:52:37 2020

inst/extdata/test_mod/cod_initOM_for_tests/control.ss

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 #C file created using the SS_writectl function in the R package r4ss
 #C file write time: 2020-04-08 10:52:31
 #_data_and_control_files: ss3.dat // control.ss

inst/extdata/test_mod/cod_initOM_for_tests/data.ss

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 #_Start_time: Wed Apr 08 10:52:38 2020
 #_Number_of_datafiles: 2
 #C data file created using the SS_writedat function in the R package r4ss

inst/extdata/test_mod/cod_initOM_for_tests/starter.ss

@@ -2,7 +2,7 @@
 #Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States.
 #Foreign copyrights may apply. See copyright.txt for more information.
 #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov
-#_user_info_available_at:https://vlab.ncep.noaa.gov/group/stock-synthesis
+#_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 #C starter file written by R function SS_writestarter
 #C rerun model to get more complete formatting in starter.ss_new
 #C should work with SS version: 3.30