-
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: 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
- Loading branch information
Showing
53 changed files
with
2,036 additions
and
673 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
168 changes: 0 additions & 168 deletions
168
inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.html
This file was deleted.
Oops, something went wrong.
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 |
---|---|---|
|
@@ -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>. |
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 |
---|---|---|
|
@@ -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). |
Oops, something went wrong.