v2.0.7.9031

- refactor: Update Shiny app text and tables, Issue \#156 - refactor: Update Shiny app exit links, Issue \#159
leppott · Feb 27, 2024 · 1df0004 · 1df0004
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ContDataQC
 Title: Quality Control (QC) of Continous Monitoring Data
-Version: 2.0.7.9029
+Version: 2.0.7.9031
 Authors@R: c(
 	person("Erik W", "Leppo", email="[email protected]",role=c("aut","cre")),
 	person("Ann","Roseberry Lincoln", role="ctb"),

diff --git a/NEWS b/NEWS
@@ -3,10 +3,17 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-02-20 16:10:16.725919
+    #> Last Update: 2024-02-27 14:17:40.109261
 
 # Version History
 
+## v2.0.7.9031
+
+2024-02-27
+
+- refactor: Update Shiny app text and tables, Issue \#156
+- refactor: Update Shiny app exit links, Issue \#159
+
 ## v2.0.7.9030
 
 2024-02-20

diff --git a/NEWS.md b/NEWS.md
@@ -3,10 +3,17 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-02-20 16:10:16.725919
+    #> Last Update: 2024-02-27 14:17:40.109261
 
 # Version History
 
+## v2.0.7.9031
+
+2024-02-27
+
+- refactor: Update Shiny app text and tables, Issue \#156
+- refactor: Update Shiny app exit links, Issue \#159
+
 ## v2.0.7.9030
 
 2024-02-20

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,6 +21,12 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## v2.0.7.9031
+2024-02-27
+
+* refactor: Update Shiny app text and tables, Issue #156
+* refactor: Update Shiny app exit links, Issue #159
+
 ## v2.0.7.9030
 2024-02-20
 

diff --git a/inst/shiny-examples/ContDataQC/external/tab_1_About.R b/inst/shiny-examples/ContDataQC/external/tab_1_About.R
@@ -15,11 +15,11 @@ function() {
                                     , includeHTML("www/RMD_HTML/App_1b_TestData.html")
                          )## tabPanel ~ END
 
-                         , tabPanel("FAQ"
+                         , tabPanel("Basic Information"
                                     , includeHTML("www/RMD_HTML/App_1c_FAQ.html")
                          )## tabPanel~ END
 
-                         , tabPanel("QC Tips"
+                         , tabPanel("Tips"
                                     ,includeHTML("www/RMD_HTML/App_1d_Tips.html")
                          )# tabPanel ~ QC Tips ~ END
 

diff --git a/inst/shiny-examples/ContDataQC/external/tab_1c_FAQ.R b/inst/shiny-examples/ContDataQC/external/tab_1c_FAQ.R
@@ -2,7 +2,7 @@
 
 function() {
 
-  tabPanel("FAQs"
+  tabPanel("Basis Info"
            , mainPanel(
              includeHTML("www/RMD_HTML/App_2FAQ.html")
 

diff --git a/inst/shiny-examples/ContDataQC/external/tab_2_DataPrep.R b/inst/shiny-examples/ContDataQC/external/tab_2_DataPrep.R
@@ -45,8 +45,8 @@ function() {
                                                       )# sidebarPanel~ END
                                                       , mainPanel(
                                                         includeHTML("www/RMD_HTML/App_2a1_HOBO.html")
-                                                        , img(src = "Fig_HOBOreformat_v1_20210617.png"
-                                                              , height = 600, width = 1000)
+                                                        # , img(src = "Fig_HOBOreformat_v1_20210617.png"
+                                                        #       , height = 600, width = 1000)
                                                       ) ## mainPanel ~ END
                                                     )# sidebarLayout~ END
                                          )## tabPanel ~ HOBO ~ END

diff --git a/inst/shiny-examples/ContDataQC/global.R b/inst/shiny-examples/ContDataQC/global.R
@@ -22,7 +22,7 @@ library(shinyjs)
 # Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:\\Rtools\\bin", sep = ";"))
 
 # Version Number
-version <- "2.0.7.9030"
+version <- "2.0.7.9031"
 
 #Maximum individual file size that can be uploaded is 70 MB
 options(shiny.maxRequestSize = 70 * 1024^2)

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd
@@ -19,15 +19,14 @@ if(boo_DEBUG==TRUE){
 
 # About ContDataQC
 
-The ContDataQC Shiny app is a free R-based tool that was developed to help water
-quality monitoring programs QC, merge and summarize continuous sensor data files
-in a standardized, more efficient way. It also has a function that allows users 
-to download U.S. Geological Survey gage data at sites and over periods of their 
-choosing. This Shiny app is linked to the ContDataQC R package, which was 
-developed by Erik W. Leppo from Tetra Tech and is 
-available on <a href="https://github.com/leppott/ContDataQC" data-once="external-links protected-links" target="_blank">GitHub<svg class="icon icon--exit is-spaced-before" role="img"> == $0 <title>Exit EPA's website</title><use href="https://www.epa.gov/themes/epa_theme/images/sprite.svg#launch"></use></svg></a>.
+The ContDataQC Shiny app is a free R-based tool that was developed to help water quality monitoring programs QC, merge and summarize continuous sensor data files in a standardized, more efficient way. It also has a function that allows users to download U.S. Geological Survey gage data at sites and over periods of their choosing. This Shiny app is linked to the ContDataQC R package, which was developed by Tetra Tech in support of the EPA and is 
+available on <a class="menu__link" href="https://github.com/leppott/ContDataQC" target="_blank">Github<span class="usa-tag external-link__tag" title="Exit EPA Website">
+                    <span aria-hidden="true">Exit</span>
+                    <span class="u-visually-hidden"> Exit EPA Website</span>
+                  </span>
+                </a>.
 
-The ContDataQC R package and Shiny app were developed with the following objectives in mind: ensure that a certain (minimum) level of QC is being performed on continuous data files; standardize and speed up data QC and reduce missed errors; and standardize data for further analysis and sharing.  ContDataQC is configured for temperature, water level, discharge, conductivity, pH, turbidity, chlorophyll-a and salinity data. Users with advanced R skills can add any other parameters that they desire by making edits to the configuration file, which can be viewed in R or in Notepad.
+The ContDataQC R package and Shiny app were developed with the following objectives in mind: ensure that a certain (minimum) level of Quality Control (QC) is being performed on continuous data files; standardize and speed up data QC and reduce missed errors; and standardize data for further analysis and sharing. ContDataQC is configured for temperature, water level, discharge, conductivity, dissolved oxygen (DO), pH, turbidity, chlorophyll-a and salinity data. Users with advanced R skills can add any other parameters that they desire by making edits to the configuration file, which can be viewed in R or in Notepad.
 
 # ContDataQC Shiny App Workflow
 
@@ -56,10 +55,10 @@ table %>%
 # Funding
 
 Development of the ContDataQC R tools has been funded by the United States 
-Environmental Protection Agency (EPA) Office of Research and Development (ORD) 
-as part of a larger project to establish Regional Monitoring Networks (RMNs) for
-freshwater streams and inland lakes. The 
-RMNs are a volunteer, collaborative effort in which entities collect long-term 
-continuous temperature and hydrologic data at targeted sites to detect changes 
+Environmental Protection Agency (EPA) Office of Research and Development (ORD) as part of a larger project to establish Regional Monitoring Networks (RMNs) for freshwater streams and inland lakes. The RMNs are a volunteer, collaborative effort in which entities collect long-term continuous temperature and hydrologic data at targeted sites to detect changes 
 over time. For more information on the RMNs, please refer to the 
-<a href="https://cfpub.epa.gov/ncea/global/recordisplay.cfm?deid=307973" data-once="external-links protected-links" target="_blank">stream Regional Monitoring Networks report<svg class="icon icon--exit is-spaced-before" role="img"> == $0 <title>Exit EPA's website</title><use href="https://www.epa.gov/themes/epa_theme/images/sprite.svg#launch"></use></svg></a>.
+<a class="menu__link" href="https://assessments.epa.gov/global/document/&deid=307973" target="_blank">stream Regional Monitoring Networks report<span class="usa-tag external-link__tag" title="Exit EPA Website">
+                    <span aria-hidden="true">Exit</span>
+                    <span class="u-visually-hidden"> Exit EPA Website</span>
+                  </span>
+                </a>.
diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd
@@ -20,11 +20,14 @@ if(boo_DEBUG==TRUE){
 }## IF ~ boo_DEBUG ~ END
 ```
 
-There are two sets of test files, one from Onset HOBO U20 water level loggers (non-vented pressure transducers) and one from a miniDOT DO sensor. Please contact us if you have example files from other sensors that you would like us to add to this website.
+Below are test files that you can download and run through the Shiny app. They are from Onset HOBO U20 water level loggers (non-vented pressure transducers) and miniDOT DO sensors. Please contact us if you have example files from other sensors that you would like us to add to this website.
 
-# Onset HOBO
-The Onset HOBO U20 files can be downloaded [here](TestData_HOBOU20_20220822.zip) [ZIP].
-The test data consist of two comma-separated values (CSV) files. The files are from the same site but cover two different time periods. You'll see two folders:
+# Test files
+* [Onset HOBO U20](TestData_HOBOU20_20220822.zip) [ZIP]
+* [miniDOT DO](TestData_miniDOT.zip) [ZIP]
+
+## Onset HOBO
+The Onset HOBO U20 test data consist of two comma-separated values (CSV) files. The files are from the same site but cover two different time periods. You'll see two folders:
 
 * **Test**
 
@@ -34,10 +37,9 @@ The test data consist of two comma-separated values (CSV) files. The files are f
 
     + This folder has the complete set of outputs for both files so that you can see examples of the QC reports and other outputs without having to run the test data through the functions yourself. 
 
-# miniDOT DO Sensors
+## miniDOT DO Sensors
 
-The miniDOT DO test files can be downloaded [here](TestData_miniDOT.zip) [ZIP].
-They are from one site and one deployment period.
+The miniDOT DO test files are from one site and one deployment period.
 You’ll see two sets of folders. Within each folder are example input and output files.
 
 * **miniDOT_concatenate** - When data are initially downloaded from miniDOT sensors, there are separate .txt files for each day (in this example, 325 individual files). Go to the **Automated Reformat – miniDOT** tab and run the **Concatenate** function to combine them all into one file. 

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1c_FAQ.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1c_FAQ.rmd
@@ -23,7 +23,11 @@ if(boo_DEBUG==TRUE){
 
 **Failure to run:** When the Shiny app fails to run, the screen will gray out and the message 'disconnected from the server' will appear. The problem typically stems from a formatting issue with the input file, in particular the Date/Time field. Check your input file, refresh the app and try again. If you still have problems, click the 'contact us' link at the bottom of this page and request assistance. Be prepared to share  a copy of your input file(s) and the error message.
 
-**Speed:** If you have a slow internet connection, you can run ContDataQC as a Shiny app on your local computer and it will likely be faster. Running it locally requires that you have R software and the ContDataQC R package installed on your computer, which can be downloaded from GitHub <a href="https://github.com/leppott/ContDataQC" data-once="external-links protected-links" target="_blank">GitHub<svg class="icon icon--exit is-spaced-before" role="img"> == $0 <title>Exit EPA's website</title><use href="https://www.epa.gov/themes/epa_theme/images/sprite.svg#launch"></use></svg></a>.
+**Speed:** If you have a slow internet connection, you can run ContDataQC as a Shiny app on your local computer and it will likely be faster. Running it locally requires that you have R software and the ContDataQC R package installed on your computer, which can be downloaded from GitHub <a class="menu__link" href="https://github.com/leppott/ContDataQC" target="_blank">GitHub<span class="usa-tag external-link__tag" title="Exit EPA Website">
+                    <span aria-hidden="true">Exit</span>
+                    <span class="u-visually-hidden"> Exit EPA Website</span>
+                  </span>
+                </a>.
 
 **Internet browsers:** This Shiny app has been tested and run successfully with Google Chrome, Firefox and Microsoft Edge. It may be compatible with other browsers but they have not been tested. Google Chrome is most frequently used. Some browsers (like Chrome and Firefox) allow users to specify what folder to download files to, which can be a time saver.
 
@@ -38,10 +42,18 @@ if(boo_DEBUG==TRUE){
 **Usability on phones:** Mobile use of this app is possible although the screen size of a phone may make it impractical.
 
 **Data summary and visualization:** The ContDataSumViz app has more summary and visualization options.
-Shiny app (beta version): <a href="https://contdataqcsumviz_containerized_stg.app.cloud.gov/" data-once="external-links protected-links" target="_blank">https://contdataqcsumviz_containerized_stg.app.cloud.gov/<svg class="icon icon--exit is-spaced-before" role="img"> == $0 <title>Exit EPA's website</title><use href="https://www.epa.gov/themes/epa_theme/images/sprite.svg#launch"></use></svg></a>
-
-R code: <a href="https://github.com/USEPA/dmap-ContDataQCSumViz" data-once="external-links protected-links" target="_blank">https://github.com/USEPA/dmap-ContDataQCSumViz<svg class="icon icon--exit is-spaced-before" role="img"> == $0 <title>Exit EPA's website</title><use href="https://www.epa.gov/themes/epa_theme/images/sprite.svg#launch"></use></svg></a>
-
+Shiny app (beta version): <a class="menu__link" href="https://contdataqcsumviz_containerized_stg.app.cloud.gov/" target="_blank">https://contdataqcsumviz_containerized_stg.app.cloud.gov/<span class="usa-tag external-link__tag" title="Exit EPA Website">
+                    <span aria-hidden="true">Exit</span>
+                    <span class="u-visually-hidden"> Exit EPA Website</span>
+                  </span>
+                </a>
+
+R code: <a class="menu__link" href="https://github.com/USEPA/dmap-ContDataQCSumViz" target="_blank">https://github.com/USEPA/dmap-ContDataQCSumViz<span class="usa-tag external-link__tag" title="Exit EPA Website">
+                    <span aria-hidden="true">Exit</span>
+                    <span class="u-visually-hidden"> Exit EPA Website</span>
+                  </span>
+                </a>
+
 **Downloading USGS gage data:**You can simultaneously download data from different USGS gages but only for the same time period.
 
-**Aggregating files with overlapping dates:** If you run the aggregate function on input files with overlapping date ranges, all records (even duplicates) are included in the output. It is up to the user to identify when these situations are occurring and remove the duplicate rows before running the files through the various functions.
+**Aggregating files with overlapping dates:** If you run the aggregate function on input files with overlapping date ranges, all records (even duplicates) are included in the output. It is up to the user to identify when these situations are occurring and remove the duplicate rows before running the files through the various functions.