-
Notifications
You must be signed in to change notification settings - Fork 10
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* refactor: Update Thresholds tab order * refactor: Add text to Main - Import tab
- Loading branch information
Showing
18 changed files
with
320 additions
and
16,029 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Large diffs are not rendered by default.
Oops, something went wrong.
15,913 changes: 0 additions & 15,913 deletions
15,913
inst/shiny-examples/ContDataQC/data/7392-354869-base_noQ_noPctSat.csv
This file was deleted.
Oops, something went wrong.
Empty file.
Empty file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes.
File renamed without changes.
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
25 changes: 25 additions & 0 deletions
25
inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c2_QCThresh_Upload.html
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
|
|
||
|
|
||
|
|
||
| <div id="upload-custom-thresholds" class="section level2"> | ||
| <h2>Upload Custom Thresholds</h2> | ||
| <p>Click the ‘Browse’ button (to the left) and select the desired | ||
| customized configuration file. The status bar will tell you when the | ||
| file has been uploaded. A new button will appear that gives you the | ||
| option of returning to the default configuration file. Do not click this | ||
| unless you change your mind and n o longer want to use the customized | ||
| file.</p> | ||
| <p>Go to the ‘Main Functions’ tab; verify that the correct configuration | ||
| file has been uploaded (by checking the file name); select the desired | ||
| input file(s); run them through the QC function. Save the output to the | ||
| desired location. Open the Word or html QC report and scroll to the | ||
| ‘Thresholds, Quick Reference’ table (in the middle section of the | ||
| report). Verify that the correct thresholds were used.</p> | ||
| <p>Be aware that each time you close and reopen the Shiny app, it will | ||
| automatically revert back to the default configuration file. Also – | ||
| remember the sequencing! If you forget to upload the customized | ||
| configuration file prior to running the QC function, it will use the | ||
| default thresholds.</p> | ||
| <p>Want to try this yourself? Click <a href="Custom_QC_Config_ECO66G20_test1.R">here</a> to download a test | ||
| file.</p> | ||
| </div> |
24 changes: 24 additions & 0 deletions
24
inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c3_QCThresh_Eval.html
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
|
|
||
|
|
||
|
|
||
| <div id="evaluate-thresholds" class="section level2"> | ||
| <h2>Evaluate Thresholds</h2> | ||
| <p>If you have one or more years of continuous data for a site, we | ||
| strongly encourage you to evaluate the performance of the QC test | ||
| thresholds for each parameter at that site and customize the | ||
| configuration file if needed.</p> | ||
| <p>Click <a href="EvaluateThresholds.zip">here</a> for instructions on | ||
| how to generate pivot tables and plots to evaluate thresholds for the | ||
| Unrealistic values (‘Gross range’) and Spike tests.</p> | ||
| <p>Another option is to use R code written by Tim Martin (Minnesota DNR) | ||
| to generate statistical outputs that can help inform thresholds for all | ||
| four QC tests. Click <a href="TimMartin_R_ThresholdEval.zip">here</a> to | ||
| download the R scripts and instructions.</p> | ||
| <p>To aid with documentation of the threshold evaluation process, click | ||
| <a href="ThresholdsCheckWorksheet_20220826.xlsx">here</a> to download an | ||
| Excel worksheet that lists the default thresholds for each parameter and | ||
| has a column where you can enter the customized values for a given site | ||
| as well as rationale for making the changes. When doing this, make sure | ||
| you consider what units you are using (as well as what the defaults | ||
| are), since units have a large effect on thresholds.</p> | ||
| </div> |
111 changes: 111 additions & 0 deletions
111
inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c4_QCThresh_Edit.html
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
|
|
||
|
|
||
|
|
||
| <div id="edit-thresholds" class="section level2"> | ||
| <h2>Edit Thresholds</h2> | ||
| <p>Click <a href="EditingQCtestThresholds_20220117.pdf">here</a> for | ||
| instructions on how to edit thresholds and create customized | ||
| configuration files. There are two options (see below). For either | ||
| option, save the customized configuration file in a folder that is easy | ||
| to find so that you can reuse the file each time you QC data for that | ||
| site. It is helpful to include the StationID and other relevant | ||
| information in the file name (for example, if thresholds are customized | ||
| for a particular season).</p> | ||
| <p>After you save the file, go to the ‘upload custom thresholds’ tab, | ||
| browse to the custom thresholds file, upload the file and then, under | ||
| ‘Main functions’, generate the QC reports. If you forget the upload | ||
| step, the default QC thresholds will be used.</p> | ||
| <div id="option-1-download-the-default-configuration-file-open-the-file-in-r-or-notepad-make-edits-and-save." class="section level3"> | ||
| <h3>Option 1, download the default configuration file, open the file in | ||
| R or Notepad++, make edits and save.</h3> | ||
| <p>Configuration files can be downloaded here -</p> | ||
| <ul> | ||
| <li><p><a href="Config_default.zip">Default</a>, with hydrologic | ||
| parameters in feet</p></li> | ||
| <li><p><a href="Config_Lakes_meters.zip">Hydrologic parameters in | ||
| meters</a> Navigate to the ‘QC tests and calculations’ section. Edit | ||
| thresholds as desired. Save the file.</p></li> | ||
| </ul> | ||
| <p>When you download the configuration file(s), you will see two types | ||
| of files: an R file (.R) and a text (.txt) file for users who do not | ||
| have R installed on their computer. You can download R from this | ||
| website: | ||
| <a href="https://cran.r-project.org" target="_blank">https://cran.r-project.org</a>. | ||
| You may also want to download | ||
| <a href="https://www.rstudio.com/products/rstudio/download/" target="_blank">RStudio</a>, | ||
| which is a separate program but is a useful code editor and interface | ||
| (IDE) for R. If you cannot install R on your computer, we recommend use | ||
| Notepad or | ||
| <a href="https://notepad-plus-plus.org/downloads" target="_blank">Notepad++</a> | ||
| (some people prefer Notepad++ because it has color-coding).</p> | ||
| </div> | ||
| <div id="option-2-use-the-interactive-functions-shown-left-and-below." class="section level3"> | ||
| <h3>Option 2, use the interactive functions shown left and below.</h3> | ||
| <ul> | ||
| <li><p>Select a parameter using the drop-down menu (upper left | ||
| box)</p></li> | ||
| <li><p>Edit thresholds using the boxes below</p></li> | ||
| <li><p>Save changes (for each parameter)</p></li> | ||
| <li><p>Download custom thresholds file</p></li> | ||
| </ul> | ||
| <table> | ||
| <caption>Default Units</caption> | ||
| <thead> | ||
| <tr class="header"> | ||
| <th align="left">Parameter</th> | ||
| <th align="left">Units</th> | ||
| </tr> | ||
| </thead> | ||
| <tbody> | ||
| <tr class="odd"> | ||
| <td align="left">Temperature</td> | ||
| <td align="left">Celsius</td> | ||
| </tr> | ||
| <tr class="even"> | ||
| <td align="left">Sensor depth and water level</td> | ||
| <td align="left">feet</td> | ||
| </tr> | ||
| <tr class="odd"> | ||
| <td align="left">Discharge</td> | ||
| <td align="left">ft3/s</td> | ||
| </tr> | ||
| <tr class="even"> | ||
| <td align="left">Dissolved oxygen</td> | ||
| <td align="left">mg/L</td> | ||
| </tr> | ||
| <tr class="odd"> | ||
| <td align="left">DO pctsat</td> | ||
| <td align="left">%</td> | ||
| </tr> | ||
| <tr class="even"> | ||
| <td align="left">Conductivity</td> | ||
| <td align="left">uS/cm</td> | ||
| </tr> | ||
| <tr class="odd"> | ||
| <td align="left">Pressure</td> | ||
| <td align="left">psi</td> | ||
| </tr> | ||
| <tr class="even"> | ||
| <td align="left">pH</td> | ||
| <td align="left">SU</td> | ||
| </tr> | ||
| <tr class="odd"> | ||
| <td align="left">Turbidity</td> | ||
| <td align="left">NTU</td> | ||
| </tr> | ||
| <tr class="even"> | ||
| <td align="left">Salinity</td> | ||
| <td align="left">ppt</td> | ||
| </tr> | ||
| <tr class="odd"> | ||
| <td align="left">Chlorophylla</td> | ||
| <td align="left">g/cm3</td> | ||
| </tr> | ||
| </tbody> | ||
| </table> | ||
| <p>If you do not want to use the default units, you will need to use | ||
| Option 1.</p> | ||
| <p>Acknowledgment: Tim Martin (MN DNR) wrote the R code that we used for | ||
| the interactive functions below.</p> | ||
| </div> | ||
| </div> |