v2.0.7.9030

- refactor: Text updates on most tabs of Shiny app - refactor: Remove Troubleshooting info in Shiny app, except for Console - refactor: Figures of tables to tables in Shiny app, Issue \#157
leppott · Feb 20, 2024 · 0b63a35 · 0b63a35
1 parent 137c236
commit 0b63a35
Show file tree

Hide file tree

Showing 53 changed files with 2,036 additions and 673 deletions.
diff --git a/NEWS b/NEWS
@@ -3,10 +3,18 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-01-31 18:26:09.974138
+    #> Last Update: 2024-02-20 16:10:16.725919
 
 # Version History
 
+## v2.0.7.9030
+
+2024-02-20
+
+- refactor: Text updates on most tabs of Shiny app
+- refactor: Remove Troubleshooting info in Shiny app, except for Console
+- refactor: Figures of tables to tables in Shiny app, Issue \#157
+
 ## v2.0.7.9029
 
 2024-01-31

diff --git a/NEWS.md b/NEWS.md
@@ -3,10 +3,18 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-01-31 18:26:09.974138
+    #> Last Update: 2024-02-20 16:10:16.725919
 
 # Version History
 
+## v2.0.7.9030
+
+2024-02-20
+
+- refactor: Text updates on most tabs of Shiny app
+- refactor: Remove Troubleshooting info in Shiny app, except for Console
+- refactor: Figures of tables to tables in Shiny app, Issue \#157
+
 ## v2.0.7.9029
 
 2024-01-31

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,6 +21,13 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## v2.0.7.9030
+2024-02-20
+
+* refactor: Text updates on most tabs of Shiny app
+* refactor: Remove Troubleshooting info in Shiny app, except for Console
+* refactor: Figures of tables to tables in Shiny app, Issue #157
+
 ## v2.0.7.9029
 2024-01-31
 

diff --git a/inst/shiny-examples/ContDataQC/external/tab_5_Troubleshooting.R b/inst/shiny-examples/ContDataQC/external/tab_5_Troubleshooting.R
@@ -4,22 +4,22 @@ function() {
   tabPanel("Troubleshooting"
            , mainPanel(
                tabsetPanel(type = "tabs"
-                         , tabPanel("Troubleshooting"
-                                  ,includeHTML("www/RMD_HTML/App_5a_Troubleshooting.html")
-                                  # ,tableOutput("logText")
-                                  # ,tableOutput("logTextUSGS")
-                                  # ,tags$b(textOutput("logTextMessage")
-                                  )
+                         # , tabPanel("Troubleshooting"
+                         #          ,includeHTML("www/RMD_HTML/App_5a_Troubleshooting.html")
+                         #          # ,tableOutput("logText")
+                         #          # ,tableOutput("logTextUSGS")
+                         #          # ,tags$b(textOutput("logTextMessage")
+                         #          )
 
                         , tabPanel("Console"
                                              ,includeHTML("www/RMD_HTML/App_5b_Console.html")
                                              ,tableOutput("logText")
                                              ,tableOutput("logTextUSGS")
                                              ,tags$b(textOutput("logTextMessage"))
                          )##tabPanel
-                        , tabPanel("Contact Info"
-                                   ,includeHTML("www/RMD_HTML/App_5c_Contact.html")
-                        )##tabPanel
+                        # , tabPanel("Contact Info"
+                        #            ,includeHTML("www/RMD_HTML/App_5c_Contact.html")
+                        # )##tabPanel
                )##tabsetPanel
           )##mainPanel
        )##tabPanel

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 <- "2.0.7.9029"
+version <- "2.0.7.9030"
 
 #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.html b/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.html
diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd
@@ -24,17 +24,14 @@ 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 ([email protected]) and is 
+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 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.
 
 # ContDataQC Shiny App Workflow
 
-The figure below lays out the general workflow for using the ContDataQC R tools. Items in bold blue text show functions that can be performed with ContDataQC.
-
-Want to try it yourself? Click [here](Custom_QC_Config_ECO66G20_test1.R) [R] to 
-download test files.
+The table below lays out the general workflow for using ContDataQC.
 
 ```{r}
 library(readxl)
@@ -61,9 +58,8 @@ table %>%
 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 (lead EPA scientist: Britta Bierwagen). The 
+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 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>.
diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd
@@ -20,19 +20,19 @@ 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. We are happy to add more test data to this website. If you have example files that you would like to contribute, please send them to Jen Stamp ([Jen.Stamp\@tetratech.com](mailto:[email protected]){.email}).
+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.
 
 # 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. 
+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**
 
   + The two HOBO U20 test files are in the Data0_Original folder. Go to the **Automated Reformat – Onset HOBO** tab and run both files through the reformatting function. Multiple files can be run through the function at the same time (in ‘batches’). The function reformats the files so that they are ready to run through the QC report function. Next, go to the **Main Functions-Import Files** tab, import the reformatted files, run them through the ‘QC raw data’ function (multiple files can be run through the function at the same time), check the flagged data (edit if needed),  aggregate the two QC’d CSV files with the ‘Aggregate QC’ed data’ function, and run the ‘Summary Statistics’ function to summarize the data. 
 
 * **Completed**
 
-    + 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 R tool yourself. 
+    + 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
 
@@ -42,4 +42,4 @@ You’ll see two sets of folders. Within each folder are example input and outpu
 
 * **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. 
 
-*	**miniDOT_reformat** – run the combined file through the Reformat function. The function reformats the file so that it is ready to run through the QC report function. Next, go to the Main **Functions-Import Files**s tab, import the reformatted file, run it through the ‘QC raw data’ function, and check the flagged data (edit if needed).
+*	**miniDOT_reformat** – run the combined file through the Reformat function. The function reformats the file so that it is ready to run through the QC report function. Next, go to the Main **Functions-Import Files**s tab, import the reformatted file, run it through the ‘QC raw data’ function, and check the flagged data (edit if needed).