2.0.7.9019

- refactor: Edits to Shiny tabs
leppott · Sep 14, 2023 · 9666e56 · 9666e56
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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: 2.0.7.9018
+Version: 2.0.7.9019
 Authors@R: c(
 	person("Erik W", "Leppo", email="Erik.Leppo@tetratech.com",role=c("aut","cre")),
 	person("Ann","Roseberry Lincoln", role="ctb"),

diff --git a/NEWS b/NEWS
@@ -3,10 +3,16 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2023-09-13 13:56:12.588924
+    #> Last Update: 2023-09-14 16:55:51.688632
 
 # Version History
 
+## v2.0.7.9019
+
+2023-09-14
+
+- refactor: Edits to Shiny tabs
+
 ## v2.0.7.9018
 
 2023-09-13

diff --git a/NEWS.md b/NEWS.md
@@ -3,10 +3,16 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2023-09-13 13:56:12.588924
+    #> Last Update: 2023-09-14 16:55:51.688632
 
 # Version History
 
+## v2.0.7.9019
+
+2023-09-14
+
+- refactor: Edits to Shiny tabs
+
 ## v2.0.7.9018
 
 2023-09-13

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,6 +21,11 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## v2.0.7.9019
+2023-09-14
+
+* refactor: Edits to Shiny tabs
+
 ## v2.0.7.9018
 2023-09-13
 

diff --git a/inst/shiny-examples/ContDataQC/external/tab_3_MainFunc.R b/inst/shiny-examples/ContDataQC/external/tab_3_MainFunc.R
@@ -10,31 +10,12 @@ function(){
 
               tabsetPanel(type = "tabs"
 
-                          , tabPanel("About"
-                          , tabsetPanel(type = "tabs"
-                                           , tabsetPanel(type="tabs"
-                                                        ,tabPanel("Run functions"
-                                                                  , includeHTML("www/RMD_HTML/App_3a1_About.html")
-                                                                  , img(src = "Fig_Rpackage_v1_20210617.png"
-                                                                        , height = 500, width = 800)
-                                                        ) # tabPanel ~ Run Functions ~ END
-                                                        , tabPanel("QC Reports"
-                                                                   , includeHTML("www/RMD_HTML/App_3a2_QCReports.html"))
-                                                        , tabPanel("Aggregate"
-                                                                   , includeHTML("www/RMD_HTML/App_3a3_Aggregate.html"))
-                                                        , tabPanel("Summary Stats"
-                                                                   , includeHTML("www/RMD_HTML/App_3a4_SummaryStats.html"))
-
-                                            ) # tabsetPanel ~ END
-
-                                       )## tabsetPanel
-                           )##tabPanel ~ About
-
-                          , tabPanel("Import Files"
+                          , tabPanel("Run Functions"
                                      , sidebarLayout(
                                        sidebarPanel(
                                          p("1. Upload customized QC test thresholds if desired; otherwise, the default thresholds will be used.")
                                          , p("2. Confirm correct configuration file is being used.")
+                                         , p(textOutput("fn_input_display_config"))
                                          , p("3. Upload input files.")
                                          #The selected input file
                                          #Tool tip code from https://stackoverflow.com/questions/16449252/tooltip-on-shiny-r
@@ -105,6 +86,24 @@ function(){
 
                           , tab_3c_QCThresh()
 
+                          , tabPanel("Instructions"
+                                     , tabsetPanel(type = "tabs"
+                                                   , tabsetPanel(type="tabs"
+                                                                 ,tabPanel("Workflow"
+                                                                           , includeHTML("www/RMD_HTML/App_3a1_About.html")
+                                                                 ) # tabPanel ~ Run Functions ~ END
+                                                                 , tabPanel("QC Reports"
+                                                                            , includeHTML("www/RMD_HTML/App_3a2_QCReports.html"))
+                                                                 , tabPanel("Aggregate"
+                                                                            , includeHTML("www/RMD_HTML/App_3a3_Aggregate.html"))
+                                                                 , tabPanel("Summary Stats"
+                                                                            , includeHTML("www/RMD_HTML/App_3a4_SummaryStats.html"))
+
+                                                   ) # tabsetPanel ~ END
+
+                                     )## tabsetPanel
+                          )##tabPanel ~ About
+
                           # , tabPanel("Advanced?"
                           #            )##tabPanel ~ Adv
 

diff --git a/inst/shiny-examples/ContDataQC/external/tab_3c_QCThresh.R b/inst/shiny-examples/ContDataQC/external/tab_3c_QCThresh.R
@@ -30,7 +30,7 @@ function() {
                            , br()
 
                            #Only shows the "Default configuration" button after a user-selected file has been used
-                           ,tags$div(title = "Click to use default configuration data"
+                           ,tags$div(title = "Click to use default configuration file"
                                      ,uiOutput('ui.defaultConfig'))
                          )# sidebarPanel~ END
                          , mainPanel(
@@ -98,19 +98,19 @@ function() {
                                      , p(paste("Test if data point exceeds a user defind"
                                                , "threshold."))
                                      , fluidRow(
-                                        column(width = 3,
+                                        column(width = sizeThreshEdit,
                                                 numericInput(inputId = "GR_Fail_Max"
                                                              , label = "Fail (Hi)"
                                                              , value = "1"))
-                                       ,column(width = 3,
+                                       ,column(width = sizeThreshEdit,
                                               numericInput(inputId = "GR_Fail_Min"
                                                            , label = "Fail (Lo)"
                                                            , value = "1"))
-                                       , column(width = 3,
+                                       , column(width = sizeThreshEdit,
                                                numericInput(inputId = "GR_Sus_Max"
                                                             , label = "Suspect (Hi)"
                                                             , value = "1"))
-                                       , column(width = 3,
+                                       , column(width = sizeThreshEdit,
                                                numericInput(inputId = "GR_Sus_Min"
                                                             , label = "Suspect (Lo)"
                                                             , value = "1"))
@@ -120,11 +120,11 @@ function() {
                                      , p(paste("Test if data point exceeds a user defined"
                                                ,"threshold relative to the previous data point."))
                                      , fluidRow(
-                                       column(width = 3,
+                                       column(width = sizeThreshEdit,
                                               numericInput(inputId = "Spike_Fail"
                                                            , label = "Fail"
                                                            , value = "1"))
-                                       ,column(width = 3,
+                                       ,column(width = sizeThreshEdit,
                                                numericInput(inputId = "Spike_Sus"
                                                             , label = "Suspect"
                                                             , value = "1"))
@@ -135,11 +135,11 @@ function() {
                                                ,"standard deviations from the previous"
                                                ,"data points over a user defined time period."))
                                      , fluidRow(
-                                       column(width = 3,
+                                       column(width = sizeThreshEdit,
                                               numericInput(inputId = "RoC_SDs"
                                                            , label = "SDs"
                                                            , value = "1"))
-                                       ,column(width = 3,
+                                       ,column(width = sizeThreshEdit,
                                                numericInput(inputId = "RoC_Hrs"
                                                             , label = "Hours"
                                                             , value = "1"))
@@ -150,15 +150,15 @@ function() {
                                                ,"threshold from previous data points over"
                                                ,"a user defined range."))
                                      , fluidRow(
-                                       column(width = 3,
+                                       column(width = sizeThreshEdit,
                                               numericInput(inputId = "Flat_Fail"
                                                            , label = "Fail"
                                                            , value = "1"))
-                                       ,column(width = 3,
+                                       ,column(width = sizeThreshEdit,
                                                numericInput(inputId = "Flat_Sus"
                                                             , label = "Suspect"
                                                             , value = "1"))
-                                       ,column(width = 3,
+                                       ,column(width = sizeThreshEdit,
                                                numericInput(inputId = "Flat_Toler"
                                                             , label = "Tolerance"
                                                             , value = "1"))

diff --git a/inst/shiny-examples/ContDataQC/global.R b/inst/shiny-examples/ContDataQC/global.R
@@ -36,6 +36,9 @@ if (exists("ContData.env", mode = "environment") == FALSE) {
          , local = TRUE)
 }## exists ~ END
 
+# Other ----
+sizeThreshEdit <- 4
+
 # Functions ----
 
 ##Extracts properties of the input spreadsheets

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd
@@ -37,6 +37,7 @@ Want to try it yourself? Click [here](Custom_QC_Config_ECO66G20_test1.R) to
 download test files.
 
 ![ContDataQC Shiny App workflow](RMD_Images/1.1_Fig1_About_20230828.jpg){width=95%}
+
 # Funding
 
 Development of the ContDataQC R tools has been funded by the United States 

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd
@@ -28,13 +28,15 @@ The test data consist of two comma-separated values (CSV) files. The files are f
 
 * **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**
+  + 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. 
 
 # miniDOT DO Sensors
 
-The miniDOT DO test files can be downloaded [here](TestData_HOBOU20_20220822.zip).
+The miniDOT DO test files can be downloaded [here](TestData_miniDOT.zip).
 They are from one site and one deployment period.
 You’ll see two sets of folders. Within each folder are example input and output files.
 

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1c_FAQ.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1c_FAQ.rmd
@@ -27,7 +27,7 @@ A: No, only internet access is required.
 
 A: Yes, if you have R software installed on your computer, you can run ContDataQC as a Shiny app on your local computer and it will likely be faster.
 
-The Shiny app is availabe as part of the ContDataQC R package.  The <a href="https://github.com/leppott/ContDataQC" target="_blank">GitHub</a> includes
+The Shiny app is available as part of the ContDataQC R package.  The <a href="https://github.com/leppott/ContDataQC" target="_blank">GitHub</a> includes
 install directions for R.
 
 **Q: What internet browsers is this website compatible with?**

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1f_RelatedApps.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1f_RelatedApps.rmd
@@ -40,7 +40,7 @@ GitHub: https://github.com/mnsentinellakes/logger_processing
 
 Primary contact: [tim.martin\@state.mn.us](mailto:tim.martin@state.mn.us){.email}
 
-#### LakeMonitoR, for summarizing and visualizing QC’d continuous vertical profile data for lakes. 
+### LakeMonitoR, for summarizing and visualizing QC’d continuous vertical profile data for lakes. 
 
 Several of its outputs are based on the rLakeAnalyzer R package.
 
@@ -52,7 +52,7 @@ Primary point of contact: [Erik.Leppo\@tetratech.com](mailto:Erik.Leppo@tetratec
 
 ### Regional Monitoring Network (RMN) protocol documents for deploying continuous temperature, water level or DO sensors and time lapse cameras in streams or lakes.
 
-Shiny app: nalms.shinyapps.io/RMN_Documents/
+Shiny app: <a href="https://nalms.shinyapps.io/RMN_Documents/" target="_blank">https://nalms.shinyapps.io/RMN_Documents/</a> 
 
 Primary contact: [Jen.Stamp\@tetratech.com](mailto:Jen.Stamp@tetratech.com){.email}
 

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2a2_miniDOT1.Rmd b/inst/shiny-examples/ContDataQC/rmd/App_2a2_miniDOT1.Rmd
@@ -31,13 +31,12 @@ function; or 2) the **PME java app** that comes with the logger.
 
 ## Additional Notes
 
-*	Want to try it yourself? Click [here](SiteX_20230828.zip) to 
+*	Want to try it yourself? Click [here](TestData_miniDOT.zip) to 
 download miniDOT DO test files.
 
 *	Why are the DO saturation values all NA? This occurs when no inputs are 
-provided to calculate DO percent saturation.  To avoid issues with the main 
-ContDataQC QC function any field with all NA's is when the miniDOT file is
-created.
+provided to calculate DO percent saturation.  For more information, please see 
+miniDOT manual or contact the miniDOT support team.
 
 ## Examples
 

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2a3_miniDOT2.Rmd b/inst/shiny-examples/ContDataQC/rmd/App_2a3_miniDOT2.Rmd
@@ -46,13 +46,12 @@ ready to run through the QC report function.
 
 ## Additional Notes
 
--   Want to try it yourself? Click [here](SiteX_20230828.zip) to
+-   Want to try it yourself? Click [here](TestData_miniDOT.zip) to
     download miniDOT DO test files.
 
--   Why are the DO saturation values all NA? This occurs when no inputs
-    are provided to calculate DO percent saturation. To avoid issues
-    with the main ContDataQC QC function any field with all NA's is when
-    the miniDOT file is created.
+*	Why are the DO saturation values all NA? This occurs when no inputs are 
+provided to calculate DO percent saturation.  For more information, please see 
+miniDOT manual or contact the miniDOT support team.
 
 ## Examples
 

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2cz_DiscreteData.rmd b/inst/shiny-examples/ContDataQC/rmd/App_2cz_DiscreteData.rmd
@@ -23,6 +23,6 @@ if(boo_DEBUG==TRUE){
 
 Discrete (in situ) measurements can be entered for any parameter. This needs to be done manually after the input file has been formatted (for example, after a HOBO file has been run through the Reformat function). Just add a new column into the input file and use the following naming scheme for the column heading: parameter name and units, with ‘Discrete’ at the beginning (for example, ‘Discrete Air Temp C’). The discrete data point(s) will be included in the time series plots in the Word or html QC reports that are generated when the user runs the QC function (below is an example). 
 
-Discrete measurements are important for validating your data, and in some cases, can be used to correct for sensor drift. Accuracy checks are comparisons of discrete or in situ measurements taken in the lab and/or in the field with sensor measurements from the closest date/time. The sensor measurement should be within the accuracy quoted by the manufacturer (e.g., ±0.2°C if you are using the Onset HOBO proV2 sensor). Click [configuration file](EXAMPLE_AccuracyCheckWkst.xlsx) to download an example of an accuracy check worksheet being kept by an RMN partner.
+Discrete measurements are important for validating your data, and in some cases, can be used to correct for sensor drift. Accuracy checks are comparisons of discrete or in situ measurements taken in the lab and/or in the field with sensor measurements from the closest date/time. The sensor measurement should be within the accuracy quoted by the manufacturer (e.g., ±0.2°C if you are using the Onset HOBO proV2 sensor). Click [here](EXAMPLE_AccuracyCheckWkst.xlsx) to download an example of an accuracy check worksheet being kept by an RMN partner.
 
 ![Example QC plot with discrete data](RMD_Images/2.3_Discrete_Fig1_20230828.jpg)
diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3a1_About.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3a1_About.rmd
@@ -17,9 +17,7 @@ if(boo_DEBUG==TRUE){
 }## IF ~ boo_DEBUG ~ END
 ```
 
-# Main Functions
-
-_Workflow_
+# 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.
 
@@ -35,3 +33,6 @@ _Workflow_
 After running each function, users must unzip/extract the files or else the files won’t be seen as an option to upload for the next step. After files are unzipped, new folders will automatically appear and the original zipped files can be deleted if desired.
 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 
+
diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3c4_QCThresh_Edit.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3c4_QCThresh_Edit.rmd
@@ -53,12 +53,16 @@ R. If you cannot install R on your computer, we recommend use Notepad or
 (some people prefer Notepad++ because it has color-coding).
 
 
-### Option 2, use the interactive functions shown left and below.
+### Option 2, use the interactive functions.
 
 * Select a parameter using the drop-down menu (upper left box)
 
 * Edit thresholds using the boxes below
 
+* After you make changes for each parameter, click ‘save changes’ as you go 
+(otherwise when you switch to a different parameter, it won’t save the changes 
+you made to the previous parameter)  
+
 * Save changes (for each parameter)
 
 * Download custom thresholds file