v2.0.7.9021

* refactor: Add text for tab references instead of links

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ContDataQC
 Title: Quality Control (QC) of Continous Monitoring Data
-Version: 2.0.7.9020
+Version: 2.0.7.9021
 Authors@R: c(
 	person("Erik W", "Leppo", email="[email protected]",role=c("aut","cre")),
 	person("Ann","Roseberry Lincoln", role="ctb"),

NEWS.rmd

@@ -21,6 +21,11 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## v2.0.7.9021
+2023-09-15
+
+* refactor: Add text for tab references instead of links
+
 ## v2.0.7.9020
 2023-09-14
 

inst/shiny-examples/ContDataQC/external/tab_3_MainFunc.R

@@ -13,7 +13,7 @@ function(){
                           , tabPanel("Run Functions"
                                      , sidebarLayout(
                                        sidebarPanel(
-                                         p("1. Upload customized QC test thresholds if desired; otherwise, the default thresholds will be used.")
+                                         p("1. Upload customized QC test thresholds ('Main - QC Thresholds - Upload Custom Thresholds' tab) if desired; otherwise, the default thresholds ('Main - QC Threholds - Default' tab) will be used.")
                                          , p("2. Confirm correct configuration file is being used.")
                                          , p(textOutput("fn_input_display_config_main"))
                                          , p("3. Upload input files.")

inst/shiny-examples/ContDataQC/rmd/App_2a_FormattingFiles.rmd

@@ -37,7 +37,7 @@ Input files need to be formatted a specific way in order for the Shiny app and R
 
 *	Advanced R users can add new parameters (beyond the ones show in the table below) to the configuration file.
 
-*	Optional fields include rowID, logger ID (serial number) and discrete measurements. Discrete (in situ) measurements can be entered for any parameter (just add ‘Discrete’ to the beginning of the column heading; for example, ‘Discrete Air Temp C’). The discrete data point will be included in the time series plots that are generated when the user runs the QC function. If using Onset HOBO sensors, you can save time by using the automated reformat function 
+*	Optional fields include rowID, logger ID (serial number) and discrete measurements. Discrete (in situ) measurements can be entered for any parameter (just add ‘Discrete’ to the beginning of the column heading; for example, ‘Discrete Air Temp C’). The discrete data point will be included in the time series plots that are generated when the user runs the QC function. If using Onset HOBO sensors, you can save time by using the automated reformat function ('Data Preparation - Automated Formatting - HOBOware reformat' tab). 
 
 
 ## Data Formattting Information

inst/shiny-examples/ContDataQC/rmd/App_2b_OrganizingFiles.rmd

@@ -62,3 +62,5 @@ table2a %>%
   kbl() %>% 
   kable_styling(full_width = F, position = "left")
 ```
+
+Click [here](EXAMPLE_AccuracyCheckWkst.xlsx) to download example Accuracy Check worksheet.

inst/shiny-examples/ContDataQC/rmd/App_3a1_About.rmd

@@ -19,7 +19,7 @@ if(boo_DEBUG==TRUE){
 
 # Workflow
 
-1.	**Select QC flag test thresholds.** Use the default thresholds or upload a customized configuration file. If you have one or more years of continuous data for a site, we encourage you to evaluate the performance of the QC test thresholds for each parameter at that site and customize the configuration file if needed. Click here for tips on evaluating thresholds. To learn how to edit thresholds, click here.
+1.	**Select QC flag test thresholds.** Use the default thresholds ('Main - QC Thresholds - Default' tab) or upload a customized configuration file ('Main - QC Thresholds - Upload Custom Thresholds' tab). If you have one or more years of continuous data for a site, we encourage you to evaluate the performance of the QC test thresholds for each parameter at that site and customize the configuration file if needed. Click 'Main - QC Thresholds - Evaluate Thresholds' tab for tips on evaluating thresholds. To learn how to edit thresholds, click 'Main - QC Thresholds - Edit Thresholds' tab.
 
 2.	**Check the configuration file name.** Make sure the correct configuration file has been uploaded prior to running the QC reports.
 
@@ -34,5 +34,5 @@ After running each function, users must unzip/extract the files or else the file
 Time-saver tip: some internet browsers, like Google Chrome and Mozilla Firefox, allow users to change settings so that users can select which folder to download files to (versus files going to the default Download folder). Click [here](GoogleChrome_TimesaverTips.pdf) for instructions on how to set this up in Chrome. With Mozilla Firefox, go to Settings > General > Files and Applications > Check box for “always ask where to save files.”
 
 Some users may prefer to use the R code instead of the Shiny app. 
-For more information, see the ‘Advanced’ tab 
+For more information, see the ‘About - Advanced’ tab 
 

inst/shiny-examples/ContDataQC/rmd/App_3a2_QCReports.rmd

@@ -41,7 +41,7 @@ this button.
 
 8.	Review each set of files, check flagged data points, do visual checks on the
 time series plots, and decide if and how to make corrections. For tips on the QC
-process, see the ‘QC tips’ subtab. 
+process, see the ‘About - QC tips’ subtab. 
 
 The Data Quality Control Report is organized into four main sections, starting 
 with an overall summary followed by summaries for each parameter:
@@ -72,5 +72,5 @@ change how they handled a correction.
 
 Currently there are no automated corrections programmed into the QC function. 
 The user must make the changes manually. For tips on the QC process, see the 
-‘QC tips’ subtab. 
+‘About - QC tips’ subtab. 
 

inst/shiny-examples/ContDataQC/ui.R

@@ -25,7 +25,7 @@ tab_5b_Console    <- source("external/tab_5b_Console.R", local = TRUE)$value
 
 shinyUI(
   # VERSION, 1, current [non-EPA] ----
-  navbarPage("Continuous data QC, summary, and statistics - v2.0.7.9020",
+  navbarPage("Continuous data QC, summary, and statistics - v2.0.7.9021",
              theme = shinytheme("spacelab")
              ,tab_1_About()
              #,tab_1a_Overview()

inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a_FormattingFiles.html

@@ -28,7 +28,8 @@ <h1>Formatting Files</h1>
 heading; for example, ‘Discrete Air Temp C’). The discrete data point
 will be included in the time series plots that are generated when the
 user runs the QC function. If using Onset HOBO sensors, you can save
-time by using the automated reformat function</p></li>
+time by using the automated reformat function (‘Data Preparation -
+Automated Formatting - HOBOware reformat’ tab).</p></li>
 </ul>
 <div id="data-formattting-information" class="section level2">
 <h2>Data Formattting Information</h2>

inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2b_OrganizingFiles.html

@@ -103,7 +103,7 @@ <h3>Folder descriptions</h3>
 An important QC check (which we call an ‘accuracy check’) involves
 comparing in situ measurements taken during site visits to the closest
 sensor measurement(s). We recommend keeping an accuracy check worksheet
-in this folder (click here to download an example worksheet).
+in this folder (click link at bottom to download an example worksheet).
 </td>
 </tr>
 <tr>
@@ -174,5 +174,7 @@ <h3>Folder descriptions</h3>
 </tr>
 </tbody>
 </table>
+<p>Click <a href="EXAMPLE_AccuracyCheckWkst.xlsx">here</a> to download
+example Accuracy Check worksheet.</p>
 </div>
 </div>

inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a1_About.html

@@ -5,12 +5,14 @@
 <h1>Workflow</h1>
 <ol style="list-style-type: decimal">
 <li><p><strong>Select QC flag test thresholds.</strong> Use the default
-thresholds or upload a customized configuration file. If you have one or
-more years of continuous data for a site, we encourage you to evaluate
-the performance of the QC test thresholds for each parameter at that
-site and customize the configuration file if needed. Click here for tips
-on evaluating thresholds. To learn how to edit thresholds, click
-here.</p></li>
+thresholds (‘Main - QC Thresholds - Default’ tab) or upload a customized
+configuration file (‘Main - QC Thresholds - Upload Custom Thresholds’
+tab). If you have one or more years of continuous data for a site, we
+encourage you to evaluate the performance of the QC test thresholds for
+each parameter at that site and customize the configuration file if
+needed. Click ‘Main - QC Thresholds - Evaluate Thresholds’ tab for tips
+on evaluating thresholds. To learn how to edit thresholds, click ‘Main -
+QC Thresholds - Edit Thresholds’ tab.</p></li>
 <li><p><strong>Check the configuration file name.</strong> Make sure the
 correct configuration file has been uploaded prior to running the QC
 reports.</p></li>
@@ -37,5 +39,5 @@ <h1>Workflow</h1>
 to save files.”</p></li>
 </ol>
 <p>Some users may prefer to use the R code instead of the Shiny app. For
-more information, see the ‘Advanced’ tab</p>
+more information, see the ‘About - Advanced’ tab</p>
 </div>

inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a2_QCReports.html

@@ -31,7 +31,7 @@ <h3>QC reports</h3>
 code).</p></li>
 <li><p>Review each set of files, check flagged data points, do visual
 checks on the time series plots, and decide if and how to make
-corrections. For tips on the QC process, see the ‘QC tips’
+corrections. For tips on the QC process, see the ‘About - QC tips’
 subtab.</p></li>
 </ol>
 <p>The Data Quality Control Report is organized into four main sections,
@@ -63,5 +63,5 @@ <h3>QC reports</h3>
 correction.</p>
 <p>Currently there are no automated corrections programmed into the QC
 function. The user must make the changes manually. For tips on the QC
-process, see the ‘QC tips’ subtab.</p>
+process, see the ‘About - QC tips’ subtab.</p>
 </div>