From 8dc679ed07a03efa0b9d461ae4c66bf5a004d526 Mon Sep 17 00:00:00 2001 From: Erik Leppo Date: Wed, 31 Jan 2024 14:17:07 -0500 Subject: [PATCH] v2.0.7.9026 - refactor: Move version number from title to about, Issue \#161 - refactor: Add file identifiers to download links, Issue \#160 --- DESCRIPTION | 4 +- NEWS | 9 +- NEWS.md | 9 +- NEWS.rmd | 6 + data-raw/ProcessRMD_Gibbs_ShinyHTML.R | 78 +- .../ContDataQC/external/tab_1_About.R | 1 + inst/shiny-examples/ContDataQC/global.R | 3 + .../ContDataQC/rmd/App_1a_Overview.rmd | 2 +- .../ContDataQC/rmd/App_1b_TestData.rmd | 4 +- .../ContDataQC/rmd/App_1d_Tips.rmd | 18 +- .../ContDataQC/rmd/App_1e_Advanced.rmd | 2 +- .../ContDataQC/rmd/App_2a1_HOBO.rmd | 10 +- .../ContDataQC/rmd/App_2a2_miniDOT1.Rmd | 2 +- .../ContDataQC/rmd/App_2a3_miniDOT2.Rmd | 2 +- .../ContDataQC/rmd/App_2a_FormattingFiles.rmd | 2 +- .../ContDataQC/rmd/App_2b_OrganizingFiles.rmd | 4 +- .../ContDataQC/rmd/App_2c_NamingFiles.rmd | 2 +- .../ContDataQC/rmd/App_2cz_DiscreteData.rmd | 2 +- .../ContDataQC/rmd/App_3a1_About.rmd | 2 +- .../ContDataQC/rmd/App_3a2_QCReports.rmd | 2 +- .../ContDataQC/rmd/App_3a3_Aggregate.rmd | 2 +- .../ContDataQC/rmd/App_3a4_SummaryStats.rmd | 2 +- .../rmd/App_3c1_QCThresh_Defaults.rmd | 6 +- .../rmd/App_3c2_QCThresh_Upload.rmd | 2 +- .../ContDataQC/rmd/App_3c3_QCThresh_Eval.rmd | 6 +- .../ContDataQC/rmd/App_3c4_QCThresh_Edit.rmd | 6 +- inst/shiny-examples/ContDataQC/ui.R | 1014 ++++++++--------- .../www/RMD_HTML/App_1a_Overview.html | 2 +- .../www/RMD_HTML/App_1b_TestData.html | 12 +- .../ContDataQC/www/RMD_HTML/App_1d_Tips.html | 43 +- .../www/RMD_HTML/App_1e_Advanced.html | 2 +- .../ContDataQC/www/RMD_HTML/App_2a1_HOBO.html | 14 +- .../www/RMD_HTML/App_2a2_miniDOT1.html | 2 +- .../www/RMD_HTML/App_2a3_miniDOT2.html | 2 +- .../www/RMD_HTML/App_2a_FormattingFiles.html | 2 +- .../www/RMD_HTML/App_2b_OrganizingFiles.html | 12 +- .../www/RMD_HTML/App_2c_NamingFiles.html | 4 +- .../www/RMD_HTML/App_2cz_DiscreteData.html | 6 +- .../www/RMD_HTML/App_3a1_About.html | 4 +- .../www/RMD_HTML/App_3a2_QCReports.html | 8 +- .../www/RMD_HTML/App_3a3_Aggregate.html | 2 +- .../www/RMD_HTML/App_3a4_SummaryStats.html | 4 +- .../RMD_HTML/App_3c1_QCThresh_Defaults.html | 9 +- .../www/RMD_HTML/App_3c2_QCThresh_Upload.html | 2 +- .../www/RMD_HTML/App_3c3_QCThresh_Eval.html | 23 +- .../www/RMD_HTML/App_3c4_QCThresh_Edit.html | 10 +- 46 files changed, 715 insertions(+), 650 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b215285..88ed4bc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ContDataQC Title: Quality Control (QC) of Continous Monitoring Data -Version: 2.0.7.9025 +Version: 2.0.7.9026 Authors@R: c( person("Erik W", "Leppo", email="Erik.Leppo@tetratech.com",role=c("aut","cre")), person("Ann","Roseberry Lincoln", role="ctb"), @@ -42,5 +42,5 @@ Remotes: tsangyp/StreamThermal, jasonelaw/iha StagedInstall: no -RoxygenNote: 7.3.0 +RoxygenNote: 7.3.1 Config/testthat/edition: 3 diff --git a/NEWS b/NEWS index 918ffdc..7a0f380 100644 --- a/NEWS +++ b/NEWS @@ -3,10 +3,17 @@ NEWS-ContDataQC - #> Last Update: 2024-01-25 12:04:12.540163 + #> Last Update: 2024-01-31 14:12:04.111378 # Version History +## v2.0.7.9026 + +2024-01-31 + +- refactor: Move version number from title to about, Issue \#161 +- refactor: Add file identifiers to download links, Issue \#160 + ## v2.0.7.9025 2024-01-25 diff --git a/NEWS.md b/NEWS.md index 918ffdc..7a0f380 100644 --- a/NEWS.md +++ b/NEWS.md @@ -3,10 +3,17 @@ NEWS-ContDataQC - #> Last Update: 2024-01-25 12:04:12.540163 + #> Last Update: 2024-01-31 14:12:04.111378 # Version History +## v2.0.7.9026 + +2024-01-31 + +- refactor: Move version number from title to about, Issue \#161 +- refactor: Add file identifiers to download links, Issue \#160 + ## v2.0.7.9025 2024-01-25 diff --git a/NEWS.rmd b/NEWS.rmd index 2c5ef12..eedd9cc 100644 --- a/NEWS.rmd +++ b/NEWS.rmd @@ -21,6 +21,12 @@ cat(paste0("Last Update: ",Sys.time())) # Version History +## v2.0.7.9026 +2024-01-31 + +* refactor: Move version number from title to about, Issue #161 +* refactor: Add file identifiers to download links, Issue #160 + ## v2.0.7.9025 2024-01-25 diff --git a/data-raw/ProcessRMD_Gibbs_ShinyHTML.R b/data-raw/ProcessRMD_Gibbs_ShinyHTML.R index 5607d91..233ad01 100644 --- a/data-raw/ProcessRMD_Gibbs_ShinyHTML.R +++ b/data-raw/ProcessRMD_Gibbs_ShinyHTML.R @@ -4,10 +4,68 @@ # 2022-09-16 #~~~~~~~~~~~~~~ +# AUTO, RMD 2 HTML ---- +# EWL, 2024-01-31 +# Render RMD to HTML and move to www # Packages # libary(rmarkdown) +# Files +myFiles <- list.files(path = "inst/shiny-examples/ContDataQC/rmd" + , pattern = "^App_" + , full.names = TRUE) + +# Loop over files + + +# Render as HTML +path_shiny_www <- file.path("inst" + , "shiny-examples" + , "ContDataQC" + , "www" + , "RMD_HTML") + + +for (i in myFiles) { + # file name w/o extension + #i_fn <- tools::file_path_sans_ext(basename(i)) + # save to HTML + rmarkdown::render(input = i + , output_dir = path_shiny_www) +}## FOR ~ i + +shell.exec(normalizePath(path_shiny_www)) + + +# MANUAL, Move Knitted HTML ---- +# Knit to HTML manually +# Move those HTML files to www + +path_rmd <- file.path("inst", "shiny-examples", "ContDataQC", "rmd") +path_shiny_www <- file.path("inst", "shiny-examples", "ContDataQC", "www", "RMD_HTML") + +# open folder +shell.exec(normalizePath(path_rmd)) + +# Copy +myFile <- list.files(path = path_rmd + , pattern = "^App_.+\\.html$" + , full.names = TRUE) +file.copy(myFile + , file.path(path_shiny_www, basename(myFile)) + , overwrite = TRUE) +# Delete +unlink(myFile) + + + + +# OLD code ---- +# +# Packages +# libary(rmarkdown) + # # Files # path_rmd <- "data-raw/rmd" # myFiles <- list.files(path = path_rmd @@ -33,23 +91,3 @@ # }## FOR ~ i # # shell.exec(normalizePath(path_shiny_www)) - -#______________________________ -# Knit to HTML manually - -path_rmd <- file.path("inst", "shiny-examples", "ContDataQC", "rmd") -path_shiny_www <- file.path("inst", "shiny-examples", "ContDataQC", "www", "RMD_HTML") - -# open folder -shell.exec(normalizePath(path_rmd)) - -# Copy -myFile <- list.files(path = path_rmd - , pattern = "^App_.+\\.html$" - , full.names = TRUE) -file.copy(myFile - , file.path(path_shiny_www, basename(myFile)) - , overwrite = TRUE) -# Delete -unlink(myFile) - diff --git a/inst/shiny-examples/ContDataQC/external/tab_1_About.R b/inst/shiny-examples/ContDataQC/external/tab_1_About.R index 52e4f20..318eca9 100644 --- a/inst/shiny-examples/ContDataQC/external/tab_1_About.R +++ b/inst/shiny-examples/ContDataQC/external/tab_1_About.R @@ -7,6 +7,7 @@ function() { tabsetPanel(type = "tabs" , tabPanel("Overview" + , p(paste0("Version ", version, ".")) , includeHTML("www/RMD_HTML/App_1a_Overview.html") )## tabPanel ~ END diff --git a/inst/shiny-examples/ContDataQC/global.R b/inst/shiny-examples/ContDataQC/global.R index c403af5..12038d6 100644 --- a/inst/shiny-examples/ContDataQC/global.R +++ b/inst/shiny-examples/ContDataQC/global.R @@ -21,6 +21,9 @@ library(shinyjs) # #access Window's zipping abilities # Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:\\Rtools\\bin", sep = ";")) +# Version Number +version <- "2.0.7.9026" + #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 index b99bccd..ae7e96c 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_1a_Overview.rmd @@ -33,7 +33,7 @@ The ContDataQC R package and Shiny app were developed with the following objecti 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) to +Want to try it yourself? Click [here](Custom_QC_Config_ECO66G20_test1.R) [R] to download test files. ![ContDataQC Shiny App workflow](RMD_Images/1.1_Fig1_About_20230828.jpg){width=95%} diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd index a4913c5..cf9f7ca 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd @@ -23,7 +23,7 @@ if(boo_DEBUG==TRUE){ 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:Jen.Stamp@tetratech.com){.email}). # Onset HOBO -The Onset HOBO U20 files can be downloaded [here](TestData_HOBOU20_20220822.zip). +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. * **Test** @@ -36,7 +36,7 @@ The test data consist of two comma-separated values (CSV) files. The files are f # miniDOT DO Sensors -The miniDOT DO test files can be downloaded [here](TestData_miniDOT.zip). +The miniDOT DO test files can be downloaded [here](TestData_miniDOT.zip) [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_1d_Tips.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1d_Tips.rmd index 148cbfb..42d208a 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_1d_Tips.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_1d_Tips.rmd @@ -40,21 +40,21 @@ people using the data decide whether to remove questionable measurements from their analysis. * Document that you checked each point flagged as ‘F’ and ‘S’ by adding a data -qualifier to the Comment column. Click [here](DataQualifiers_20220210.xlsx) to +qualifier to the Comment column. Click [here](DataQualifiers_20220210.xlsx) [XLSX] to download the list of data qualifiers currently being used by RMN partners. * Leave missing data cells blank. ## Workflow -Click [here](Workflow_QC_report_20220824.pdf) for recommendations on a workflow +Click [here](Workflow_QC_report_20220824.pdf) [PDF] for recommendations on a workflow for reviewing the QC reports. If you have a backlog of data files from multiple deployments and are wondering -how to most efficiently QC the files, [here](Workflow_DataPileup_20220824.pdf) +how to most efficiently QC the files, [here](Workflow_DataPileup_20220824.pdf) [PDF] is a recommended workflow. -Click [here](SiteVisitChecklist.zip) for a site visit checklist to help ensure +Click [here](SiteVisitChecklist.zip) [ZIP] for a site visit checklist to help ensure that you do not forget to document information that is important for the data QC process. @@ -64,12 +64,12 @@ Some people have had problems with air and water sensors being out of sync ( e.g., one records at 11:00 and the other records at 11:07). If you are deploying air and water sensors at a site, make sure they are recording at the same time. This will make data processing faster and easier. If you are using Onset HOBO -sensors, click [here](HOBO_ConfigLaunch_20170803.pdf) for tips on configuring +sensors, click [here](HOBO_ConfigLaunch_20170803.pdf) [PDF] for tips on configuring them in a way that ensures they will record at the same time. Another issue that sometimes occurs is data overlap (where more than one file has measurements covering part of the same time periods). If you are using Onset -HOBO sensors, click [here](HOBO_DataDownload_20170823.pdf) for procedures to +HOBO sensors, click [here](HOBO_DataDownload_20170823.pdf) [PDF] for procedures to follow during data download to clear sensor memory and avoid overlapping data. ## Accuracy checks @@ -79,20 +79,20 @@ 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). Accuracy checks are used to validate your data, and in some cases, correct for sensor drift. Click -[here](EXAMPLE_AccuracyCheckWkst.xlsx) to download an example of an accuracy +[here](EXAMPLE_AccuracyCheckWkst.xlsx) [XLSX] to download an example of an accuracy check worksheet being kept by an RMN partner. ## Visual checks of time series plots Visual checks of time series plots are an important part of the QC process. -Click [here](PlotQC_WatchList_20220824.pdf) to see a compilation of patterns to +Click [here](PlotQC_WatchList_20220824.pdf) [PDF] to see a compilation of patterns to watch for when interpreting the plots. They include ice cover, beaver activity, leaf packs, dewatering, and dead batteries. We will continue to add slides to this as we receive materials. ## Checking sensor data against other data sources -This is optional but encouraged if time permits. Click [here](Daymet_Wx_Gage.zip) for instructional +This is optional but encouraged if time permits. Click [here](Daymet_Wx_Gage.zip) [ZIP] for instructional materials from David Smith (Kentucky Division of Water) on how he has been downloading data from nearby weather stations and USGS gages, as well as modeled air temperature and precipitation data from Daymet ( diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1e_Advanced.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1e_Advanced.rmd index 3d471a4..c5a5f3f 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_1e_Advanced.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_1e_Advanced.rmd @@ -31,7 +31,7 @@ and generate outputs for each input file that matches the criteria. Users with intermediate to advanced-level R skills can customize the settings (e.g., add new parameters, change units, change file naming and formatting requirements, change the format of one of the QC reports from Word to html or -PDF) by editing a plain text [configuration file](Config_default.zip). Users +PDF) by editing a plain text [configuration file](Config_default.zip) [ZIP]. Users have more flexibility using the Shiny app versus R package when it comes to setting directories and file naming schemes because they can browse to the desired input file(s). diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2a1_HOBO.rmd b/inst/shiny-examples/ContDataQC/rmd/App_2a1_HOBO.rmd index 0fcec0b..e330c26 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_2a1_HOBO.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_2a1_HOBO.rmd @@ -23,13 +23,13 @@ The HOBOware reformat function is for data files from Onset HOBO sensors. It con HOBO sensor files must first be opened with HOBOware software, then processed and exported as CSV files. If you follow these instructions, you will be able to run them through the reformat function without manipulation - -* [HOBOware default settings](HOBOware_DefaultSettings_20220824.pdf) +* [HOBOware default settings](HOBOware_DefaultSettings_20220824.pdf) [PDF] -* [Temperature (proV2)](HOBOware_Temperature_20220825.pdf) +* [Temperature (proV2)](HOBOware_Temperature_20220825.pdf) [PDF] -* [Water level (U20 series)](HOBOware_WaterLevel_U20_20220824.pdf) +* [Water level (U20 series)](HOBOware_WaterLevel_U20_20220824.pdf) [PDF] -* [Dissolved oxygen (U26)](HOBOware_DO_20220824.pdf) +* [Dissolved oxygen (U26)](HOBOware_DO_20220824.pdf) [PDF] ### Instructions @@ -47,7 +47,7 @@ HOBO sensor files must first be opened with HOBOware software, then processed an * Unzip/extract the file(s) or else the files won’t be seen as an option to upload to the QC report function (Main Functions - QC raw data). After file is unzipped, a new folder called ‘HOBO’ will appear. The original zipped file 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.” +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) [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.” Your files are now ready to be run through the QC function! Below are examples of what HOBO U20 CSV files look like before and after they are run through the reformat function. The reformat function does the following - diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2a2_miniDOT1.Rmd b/inst/shiny-examples/ContDataQC/rmd/App_2a2_miniDOT1.Rmd index db2a1e7..f53727a 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_2a2_miniDOT1.Rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_2a2_miniDOT1.Rmd @@ -31,7 +31,7 @@ function; or 2) the **PME java app** that comes with the logger. ## Additional Notes -* Want to try it yourself? Click [here](TestData_miniDOT.zip) to +* Want to try it yourself? Click [here](TestData_miniDOT.zip) [ZIP] to download miniDOT DO test files. * Why are the DO saturation values all NA? This occurs when no inputs are diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2a3_miniDOT2.Rmd b/inst/shiny-examples/ContDataQC/rmd/App_2a3_miniDOT2.Rmd index 042bade..70bf691 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_2a3_miniDOT2.Rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_2a3_miniDOT2.Rmd @@ -46,7 +46,7 @@ ready to run through the QC report function. ## Additional Notes -- Want to try it yourself? Click [here](TestData_miniDOT.zip) to +- Want to try it yourself? Click [here](TestData_miniDOT.zip) [ZIP] to download miniDOT DO test files. * Why are the DO saturation values all NA? This occurs when no inputs are diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2a_FormattingFiles.rmd b/inst/shiny-examples/ContDataQC/rmd/App_2a_FormattingFiles.rmd index 4604019..e543908 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_2a_FormattingFiles.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_2a_FormattingFiles.rmd @@ -29,7 +29,7 @@ Input files need to be formatted a specific way in order for the Shiny app and R * There are two required fields: SiteID; and “Date Time” (with Date and Time combined into one field). -* If using the default [configuration file](Config_default.zip), column names must match the capitalization, spelling and symbology shown in the table below (for example, R will not recognize ‘sensor depth ft’; it needs to be ‘Sensor Depth ft’) +* If using the default [configuration file](Config_default.zip) [ZIP], column names must match the capitalization, spelling and symbology shown in the table below (for example, R will not recognize ‘sensor depth ft’; it needs to be ‘Sensor Depth ft’) * Either periods or spaces in the column headings are acceptable. For example, in the table below, air temperature is shown as ‘’Air Temp C’ but it can also be entered as ‘Air.Temp.C’. diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2b_OrganizingFiles.rmd b/inst/shiny-examples/ContDataQC/rmd/App_2b_OrganizingFiles.rmd index f516869..6019715 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_2b_OrganizingFiles.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_2b_OrganizingFiles.rmd @@ -24,7 +24,7 @@ we recommend setting up folders as shown below as a starting point. Folders and files can be customized as you gain more experience. The files should be backed up regularly and accessible to other members of your data management team. -Click [here](SiteX_20230828.zip) to download a zipped file with a +Click [here](SiteX_20230828.zip) [ZIP] to download a zipped file with a ready-made set of (empty) folders. Put the file in the desired location, unzip it and then replace ‘SiteX’ with the appropriate site name. @@ -63,4 +63,4 @@ table2a %>% kable_styling(full_width = F, position = "left") ``` -Click [here](EXAMPLE_AccuracyCheckWkst.xlsx) to download example Accuracy Check worksheet. +Click [here](EXAMPLE_AccuracyCheckWkst.xlsx) [XLSX] to download example Accuracy Check worksheet. diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2c_NamingFiles.rmd b/inst/shiny-examples/ContDataQC/rmd/App_2c_NamingFiles.rmd index 3909dab..8303c89 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_2c_NamingFiles.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_2c_NamingFiles.rmd @@ -57,7 +57,7 @@ Depth can include decimals (for example, 0.1M is ok) and does not need to include leading zeros (either 01M or 1M are acceptable). Units can be upper or lower case (M or m), and abbreviated (M) or spelled out (meters). You can change the double-dash separator if desired by customizing the -[configuration file](Config_default.zip) (for example, you could change it to a +[configuration file](Config_default.zip) [ZIP] (for example, you could change it to a tilde ~). If you are using the Shiny app and have more than one type of sensor deployed at diff --git a/inst/shiny-examples/ContDataQC/rmd/App_2cz_DiscreteData.rmd b/inst/shiny-examples/ContDataQC/rmd/App_2cz_DiscreteData.rmd index 29460dc..3da06f8 100644 --- 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 [here](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) [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 index d4be5fa..c878ac1 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_3a1_About.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_3a1_About.rmd @@ -31,7 +31,7 @@ if(boo_DEBUG==TRUE){ 6. **The user can run the aggregated file through the Summary Statistics function** to generate CSV files with an assortment of summary statistics (e.g., min, median, max, quartiles) and a PDF with time series plots for each parameter. 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.” +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) [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 ‘About - Advanced’ tab diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3a2_QCReports.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3a2_QCReports.rmd index 0efabf4..05154aa 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_3a2_QCReports.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_3a2_QCReports.rmd @@ -37,7 +37,7 @@ this button. 6. Unzip/extract the file(s). After file is unzipped, a new folder called ‘data’ will appear, which contains QC reports that have ‘QC_’ as the prefix in the file name. The original zipped file can be deleted if desired. -7. Open the QC reports. There are two types of outputs: a Word document Data Quality Control Report and a comma-delimited (.csv) spreadsheet. The reports include results from the ‘flag’ tests (gross, spike, rate of change and flat line), missing data checks and time series plots. Click [here](Example_QCreports.zip) to download an example of a QC output. If users prefer a Hypertext Markup Language (HTML) report instead of Word, they can change the format in the configuration file (this requires some familiarity with R code). +7. Open the QC reports. There are two types of outputs: a Word document Data Quality Control Report and a comma-delimited (.csv) spreadsheet. The reports include results from the ‘flag’ tests (gross, spike, rate of change and flat line), missing data checks and time series plots. Click [here](Example_QCreports.zip) [ZIP] to download an example of a QC output. If users prefer a Hypertext Markup Language (HTML) report instead of Word, they can change the format in the configuration file (this requires some familiarity with R code). 8. Review each set of files, check flagged data points, do visual checks on the time series plots, and decide if and how to make corrections. For tips on the QC diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3a3_Aggregate.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3a3_Aggregate.rmd index 25bd0ab..df97e91 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_3a3_Aggregate.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_3a3_Aggregate.rmd @@ -30,4 +30,4 @@ Shiny app instructions 5. Unzip/extract the file(s). After file is unzipped, a new folder called ‘data’ will appear. If a ‘data’ folder already exists, outputs will go into that folder. The aggregate reports have ‘DATA_’ as the prefix in the file name. The original zipped file can be deleted if desired. -6. Open and review the aggregated reports. As with the QC output, there are two types of outputs: a Word document Data Quality Control Report and a comma-delimited (.csv) spreadsheet. Click [here](Example_Aggregate.zip) to download an example of an Aggregate output. If users prefer a Hypertext Markup Language (HTML) report instead of Word, they can change the format in the configuration file (this requires some familiarity with R code). +6. Open and review the aggregated reports. As with the QC output, there are two types of outputs: a Word document Data Quality Control Report and a comma-delimited (.csv) spreadsheet. Click [here](Example_Aggregate.zip) [ZIP] to download an example of an Aggregate output. If users prefer a Hypertext Markup Language (HTML) report instead of Word, they can change the format in the configuration file (this requires some familiarity with R code). diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3a4_SummaryStats.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3a4_SummaryStats.rmd index 413fea8..17f43ad 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_3a4_SummaryStats.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_3a4_SummaryStats.rmd @@ -38,5 +38,5 @@ appear in the lower right corner. 6. Open and review the summary statistics reports. There should be two sets of CSV files and a PDF with time series plots for each parameter. One of the CSVs has daily means and the other has a wider range of summary statistics (e.g., -min, median, max, quartiles). Click [here](Example_SumStats.zip) to download an +min, median, max, quartiles). Click [here](Example_SumStats.zip) [ZIP] to download an example of a Summary Stats output. diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3c1_QCThresh_Defaults.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3c1_QCThresh_Defaults.rmd index 1d03bc7..1356a22 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_3c1_QCThresh_Defaults.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_3c1_QCThresh_Defaults.rmd @@ -48,7 +48,7 @@ table3a1 %>% The 'flag' tests were selected based on the following references: - U.S. Integrated Ocean Observing System, 2017. Manual for the Use of Real-Time Oceanographic Data Quality Control Flags, Version 1.1. 43 pp. -https://cdn.ioos.noaa.gov/media/2017/12/QARTOD-Data-Flags-Manual_Final_version1.1.pdf +https://cdn.ioos.noaa.gov/media/2017/12/QARTOD-Data-Flags-Manual_Final_version1.1.pdf [PDF] - Wagner, R.J., Boulger, R.W., Oblinger, C.J., Smith, B.A., 2006. Guidelines and Standard Procedures for Continuous Water-quality Monitors: Station Operation, Record Computation, and Data Reporting. U.S. Geological Survey Techniques and Methods 1-D3, 51 pp. þ 8 attachments. http://pubs.water.usgs.gov/tm1d3. @@ -69,9 +69,9 @@ Units are an important consideration as well. The default configuration puts hyd Configuration files can be downloaded here: -- [Default](Config_default.zip), with hydrologic parameters in feet +- [Default](Config_default.zip) [ZIP], with hydrologic parameters in feet -- [Customized](Config_Lakes_meters.zip), with hydrologic parameters in meters +- [Customized](Config_Lakes_meters.zip) [ZIP], with hydrologic parameters in meters This table shows the default QC test thresholds for each parameter as of 2023-08-28. diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3c2_QCThresh_Upload.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3c2_QCThresh_Upload.rmd index 1bebba9..596edce 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_3c2_QCThresh_Upload.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_3c2_QCThresh_Upload.rmd @@ -32,5 +32,5 @@ automatically revert back to the default configuration file. Also – remember t sequencing! If you forget to upload the customized configuration file prior to running the QC function, it will use the default thresholds. -Want to try this yourself? Click [here](Custom_QC_Config_ECO66G20_test1.R) to +Want to try this yourself? Click [here](Custom_QC_Config_ECO66G20_test1.R) [R] to download a test file. diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3c3_QCThresh_Eval.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3c3_QCThresh_Eval.rmd index 30af1b1..7b5f0f9 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_3c3_QCThresh_Eval.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_3c3_QCThresh_Eval.rmd @@ -23,16 +23,16 @@ 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. -Click [here](EvaluateThresholds.zip) for instructions on how to generate pivot +Click [here](EvaluateThresholds.zip) [ZIP] for instructions on how to generate pivot tables and plots to evaluate thresholds for the Unrealistic values ('Gross range') and Spike tests. 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 [here](TimMartin_R_ThresholdEval.zip) to download the R scripts and +tests. Click [here](TimMartin_R_ThresholdEval.zip) [ZIP] to download the R scripts and instructions. -To aid with documentation of the threshold evaluation process, click [here](ThresholdsCheckWorksheet_20220826.xlsx) to download an Excel worksheet +To aid with documentation of the threshold evaluation process, click [here](ThresholdsCheckWorksheet_20220826.xlsx) [XLSX] 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 diff --git a/inst/shiny-examples/ContDataQC/rmd/App_3c4_QCThresh_Edit.rmd b/inst/shiny-examples/ContDataQC/rmd/App_3c4_QCThresh_Edit.rmd index 9a176ce..756fac4 100644 --- a/inst/shiny-examples/ContDataQC/rmd/App_3c4_QCThresh_Edit.rmd +++ b/inst/shiny-examples/ContDataQC/rmd/App_3c4_QCThresh_Edit.rmd @@ -19,7 +19,7 @@ if(boo_DEBUG==TRUE){ ## Edit Thresholds -Click [here](EditingQCtestThresholds_20220117.pdf) for instructions on how to +Click [here](EditingQCtestThresholds_20220117.pdf) [PDF] 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 @@ -36,9 +36,9 @@ thresholds will be used. Configuration files can be downloaded here - -* [Default](Config_default.zip), with hydrologic parameters in feet +* [Default](Config_default.zip) [ZIP], with hydrologic parameters in feet -* [Hydrologic parameters in meters](Config_Lakes_meters.zip) +* [Hydrologic parameters in meters](Config_Lakes_meters.zip) [ZIP] Navigate to the ‘QC tests and calculations’ section. Edit thresholds as desired. Save the file. When you download the configuration file(s), you will see two types of files: an diff --git a/inst/shiny-examples/ContDataQC/ui.R b/inst/shiny-examples/ContDataQC/ui.R index 17a2015..55229c3 100644 --- a/inst/shiny-examples/ContDataQC/ui.R +++ b/inst/shiny-examples/ContDataQC/ui.R @@ -23,23 +23,23 @@ tab_5b_Console <- source("external/tab_5b_Console.R", local = TRUE)$value #tab_9_Status <- source("external/tab_9_Status.R", local = TRUE)$value -# shinyUI( -# # VERSION, 1, current [non-EPA] ---- -# navbarPage("Continuous data QC, summary, and statistics - v2.0.7.9024", -# theme = shinytheme("spacelab") -# ,tab_1_About() -# #,tab_1a_Overview() -# #,tab_1c_FAQ() -# , tab_2_DataPrep() -# , tab_3_MainFunc() -# #,tab_3c_QCThresh() -# , tab_4_USGSgage() -# , tab_5_Troubleshooting() -# #,tab_5b_Console() -# #,tab_x_TestData() -# #,tab_9_Status() -# )## navbarPage ~ END -# )## shinyUI ~ END +shinyUI( + # VERSION, 1, current [non-EPA] ---- + navbarPage("Continuous data QC, summary, and statistics", + theme = shinytheme("spacelab") + ,tab_1_About() + #,tab_1a_Overview() + #,tab_1c_FAQ() + , tab_2_DataPrep() + , tab_3_MainFunc() + #,tab_3c_QCThresh() + , tab_4_USGSgage() + , tab_5_Troubleshooting() + #,tab_5b_Console() + #,tab_x_TestData() + #,tab_9_Status() + )## navbarPage ~ END +)## shinyUI ~ END # shinyUI( # # VERSION, 0, old ---- @@ -66,494 +66,494 @@ tab_5b_Console <- source("external/tab_5b_Console.R", local = TRUE)$value # VERSION, EPA Template ---- # 2022-09-15 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -shinyUI( - fluidPage( - tags$html(class = "no-js", lang="en"), - tags$head( - HTML( - " - - - " - ), - tags$meta(charset="utf-8"), - tags$meta(property="og:site_name", content="US EPA"), - #tags$link(rel = "stylesheet", type = "text/css", href = "css/uswds.css"), - tags$link(rel = "stylesheet", type = "text/css", href = "https://cdnjs.cloudflare.com/ajax/libs/uswds/3.0.0-beta.3/css/uswds.min.css", integrity="sha512-ZKvR1/R8Sgyx96aq5htbFKX84hN+zNXN73sG1dEHQTASpNA8Pc53vTbPsEKTXTZn9J4G7R5Il012VNsDEReqCA==", crossorigin="anonymous", referrerpolicy="no-referrer"), - tags$meta(property="og:url", content="https://www.epa.gov/themes/epa_theme/pattern-lab/.markup-only.html"), - tags$link(rel="canonical", href="https://www.epa.gov/themes/epa_theme/pattern-lab/.markup-only.html"), - tags$link(rel="shortlink", href="https://www.epa.gov/themes/epa_theme/pattern-lab/.markup-only.html"), - tags$meta(property="og:url", content="https://www.epa.gov/themes/epa_theme/pattern-lab/.markup-only.html"), - tags$meta(property="og:image", content="https://www.epa.gov/sites/all/themes/epa/img/epa-standard-og.jpg"), - 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' - ), - - # Site Footer - HTML( - '
- - - - - - - - ' - ) - ) # END fluidPage -)## shinyUI +# shinyUI( +# fluidPage( +# tags$html(class = "no-js", lang="en"), +# tags$head( +# HTML( +# " +# +# +# " +# ), +# tags$meta(charset="utf-8"), +# tags$meta(property="og:site_name", content="US EPA"), +# #tags$link(rel = "stylesheet", type = "text/css", href = "css/uswds.css"), +# tags$link(rel = "stylesheet", type = "text/css", href = "https://cdnjs.cloudflare.com/ajax/libs/uswds/3.0.0-beta.3/css/uswds.min.css", integrity="sha512-ZKvR1/R8Sgyx96aq5htbFKX84hN+zNXN73sG1dEHQTASpNA8Pc53vTbPsEKTXTZn9J4G7R5Il012VNsDEReqCA==", crossorigin="anonymous", referrerpolicy="no-referrer"), +# tags$meta(property="og:url", content="https://www.epa.gov/themes/epa_theme/pattern-lab/.markup-only.html"), +# tags$link(rel="canonical", href="https://www.epa.gov/themes/epa_theme/pattern-lab/.markup-only.html"), +# tags$link(rel="shortlink", href="https://www.epa.gov/themes/epa_theme/pattern-lab/.markup-only.html"), +# tags$meta(property="og:url", content="https://www.epa.gov/themes/epa_theme/pattern-lab/.markup-only.html"), +# tags$meta(property="og:image", content="https://www.epa.gov/sites/all/themes/epa/img/epa-standard-og.jpg"), +# tags$meta(property="og:image:width", content="1200"), +# tags$meta(property="og:image:height", content="630"), +# tags$meta(property="og:image:alt", content="U.S. Environmental Protection Agency"), +# tags$meta(name="twitter:card", content="summary_large_image"), +# tags$meta(name="twitter:image:alt", content="U.S. Environmental Protection Agency"), +# tags$meta(name="twitter:image:height", content="600"), +# tags$meta(name="twitter:image:width", content="1200"), +# tags$meta(name="twitter:image", content="https://www.epa.gov/sites/all/themes/epa/img/epa-standard-twitter.jpg"), +# tags$meta(name="MobileOptimized", content="width"), +# tags$meta(name="HandheldFriendly", content="true"), +# tags$meta(name="viewport", content="width=device-width, initial-scale=1.0"), +# tags$meta(`http-equiv`="x-ua-compatible", content="ie=edge"), +# tags$script(src = "js/pattern-lab-head-script.js"), +# # _update title ---- +# tags$title('ContDataQC | US EPA'), +# tags$link(rel="icon", type="image/x-icon", href="https://www.epa.gov/themes/epa_theme/images/favicon.ico"), +# tags$meta(name="msapplication-TileColor", content="#FFFFFF"), +# tags$meta(name="msapplication-TileImage", content="https://www.epa.gov/themes/epa_theme/images/favicon-144.png"), +# tags$meta(name="application-name", content=""), +# tags$meta(name="msapplication-config", content="https://www.epa.gov/themes/epa_theme/images/ieconfig.xml"), +# tags$link(rel="apple-touch-icon-precomposed", sizes="196x196", href="https://www.epa.gov/themes/epa_theme/images/favicon-196.png"), +# tags$link(rel="apple-touch-icon-precomposed", sizes="152x152", href="https://www.epa.gov/themes/epa_theme/images/favicon-152.png"), +# tags$link(rel="apple-touch-icon-precomposed", sizes="144x144", href="https://www.epa.gov/themes/epa_theme/images/favicon-144.png"), +# tags$link(rel="apple-touch-icon-precomposed", sizes="120x120", href="https://www.epa.gov/themes/epa_theme/images/favicon-120.png"), +# tags$link(rel="apple-touch-icon-precomposed", sizes="114x114", href="https://www.epa.gov/themes/epa_theme/images/favicon-114.png"), +# tags$link(rel="apple-touch-icon-precomposed", sizes="72x72", href="https://www.epa.gov/themes/epa_theme/images/favicon-72.png"), +# tags$link(rel="apple-touch-icon-precomposed", href="https://www.epa.gov/themes/epa_theme/images/favicon-180.png"), +# tags$link(rel="icon", href="https://www.epa.gov/themes/epa_theme/images/favicon-32.png", sizes="32x32"), +# tags$link(rel="preload", href="https://www.epa.gov/themes/epa_theme/fonts/source-sans-pro/sourcesanspro-regular-webfont.woff2", as="font", crossorigin="anonymous"), +# tags$link(rel="preload", href="https://www.epa.gov/themes/epa_theme/fonts/source-sans-pro/sourcesanspro-bold-webfont.woff2", as="font", crossorigin="anonymous"), +# tags$link(rel="preload", href="https://www.epa.gov/themes/epa_theme/fonts/merriweather/Latin-Merriweather-Bold.woff2", as="font", crossorigin="anonymous"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/ajax-progress.module.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/autocomplete-loading.module.css?r6lsex" ), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/js.module.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/sticky-header.module.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/system-status-counter.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/system-status-report-counters.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/system-status-report-general-info.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/tabledrag.module.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/tablesort.module.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/core/themes/stable/css/system/components/tree-child.module.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/themes/epa_theme/css/styles.css?r6lsex"), +# tags$link(rel="stylesheet", media="all", href="https://www.epa.gov/themes/epa_theme/css-lib/colorbox.min.css?r6lsex"), +# +# tags$script(src = 'https://cdnjs.cloudflare.com/ajax/libs/uswds/3.0.0-beta.3/js/uswds-init.min.js'), +# #fix container-fluid that boostrap RShiny uses +# tags$style(HTML( +# '.container-fluid { +# padding-right: 0; +# padding-left: 0; +# margin-right: 0; +# margin-left: 0; +# } +# .tab-content { +# margin-right: 30px; +# margin-left: 30px; +# }' +# )) +# ), +# tags$body( +# class="path-themes not-front has-wide-template", id="top", +# tags$script( +# src = 'https://cdnjs.cloudflare.com/ajax/libs/uswds/3.0.0-beta.3/js/uswds.min.js' +# ) +# ), +# +# # Site Header +# HTML( +# ' +# +# +# +# +# +#
+#
+#
+#
+#
+#
+# U.S. flag +#
+#
+#

An official website of the United States government

+# +#
+# +#
+#
+#
+#
+#
+# Dot gov +#
+#

+# Official websites use .gov +#
A .gov website belongs to an official government organization in the United States. +#

+#
+#
+#
+# HTTPS +#
+#

+# Secure .gov websites use HTTPS +#
A lock () or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites. +#

+#
+#
+#
+#
+#
+#
+#
+#
+# +#
+#
+#
+#
+#
+#
+#
+# +# +#
+#
+#
+#
+# +# +# +# +# +# +# +# +# +# +#
+#
+#
+#
+#
+#
+# +#
+#
+#
' +# ), +# +# # Individual Page Header +# HTML( +# '
+#
+#
+#
+#
+#
+#
+# Contact Us +#
+#
+#
' +# ), +# +# # _Insert your UI code here ---- +# # ## Begin example UI code +# # titlePanel("Hello Shiny!"), +# # sidebarLayout +# # ( +# # sidebarPanel +# # ( +# # sliderInput +# # ( +# # "obs", +# # "Number of observations:", +# # min = 0, +# # max = 1000, +# # value = 500 +# # ) +# # ), +# # mainPanel +# # ( +# # plotOutput("distPlot") +# # ) +# # ) +# # ## End example UI code +# +# # IMPORTANT! For a navbar page, you will need to place the header and footer inside the navbar section (as shown below) - +# # you will then want to comment out lines 201-213 and lines 254-263 +# navbarPage( +# title = h2("Continuous data QC, summary, and statistics - v2.0.7.9025"), +# #theme= shinytheme("spacelab"), +# header = HTML( +# '
+#
+#
+#
+#
+#
+#
+# Contact Us +#
+#
+#
' +# ), +# footer = HTML( +# '
+#
+#
+#
+#

Contact Us to ask a question, provide feedback, or report a problem.

+#
+#
+#
' +# ), +# tab_1_About(), +# #,tab_1a_Overview() +# #,tab_1c_FAQ() +# tab_2_DataPrep(), +# tab_3_MainFunc(), +# #,tab_3c_QCThresh() +# tab_4_USGSgage(), +# tab_5_Troubleshooting(), +# #,tab_5b_Console() +# #,tab_x_TestData() +# #,tab_9_Status() +# +# # tab_1Overview(), +# # tab_2FAQ(), +# # tab_3DataPrep(), +# # tab_4QCThresh(), +# # tab_5MainFunc(), +# # tab_6USGSgage(), +# # tab_7TestData(), +# # tab_8Console(), +# # #tab_9Status(), +# ), +# +# # Individual Page Footer +# HTML( +# '
+#
+#
+#
+#

Contact Us to ask a question, provide feedback, or report a problem.

+#
+#
+#
' +# ), +# +# # Site Footer +# HTML( +# '
+# +# +# +# +# +# +# +# ' +# ) +# ) # END fluidPage +# )## shinyUI diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1a_Overview.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1a_Overview.html index 3f94f82..d2e68d7 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1a_Overview.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1a_Overview.html @@ -26,7 +26,7 @@

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 to download test +

Want to try it yourself? Click here [R] to download test files.

ContDataQC Shiny App workflow diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1b_TestData.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1b_TestData.html index d5b2d15..4aae6cc 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1b_TestData.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1b_TestData.html @@ -8,9 +8,9 @@ Stamp ().

Onset HOBO

-

The Onset HOBO U20 files can be downloaded here. 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 Onset HOBO U20 files can be downloaded here [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.

  • Test

      @@ -36,9 +36,9 @@

      Onset HOBO

miniDOT DO Sensors

-

The miniDOT DO test files can be downloaded here. 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.

+

The miniDOT DO test files can be downloaded here [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.

  • miniDOT_concatenate - When data are initially downloaded from miniDOT sensors, there are separate .txt files for each diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1d_Tips.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1d_Tips.html index 212e08f..57741aa 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1d_Tips.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1d_Tips.html @@ -22,21 +22,21 @@

    Data corrections

    and do not delete. Let the people using the data decide whether to remove questionable measurements from their analysis.

  • Document that you checked each point flagged as ‘F’ and ‘S’ by -adding a data qualifier to the Comment column. Click here to download the list of -data qualifiers currently being used by RMN partners.

    • +adding a data qualifier to the Comment column. Click here [XLSX] to download the list +of data qualifiers currently being used by RMN partners.

  • Leave missing data cells blank.

Workflow

-

Click here for +

Click here [PDF] for recommendations on a workflow for reviewing the QC reports.

If you have a backlog of data files from multiple deployments and are -wondering how to most efficiently QC the files, here is a recommended +wondering how to most efficiently QC the files, here [PDF] is a recommended workflow.

-

Click here for a site visit -checklist to help ensure that you do not forget to document information -that is important for the data QC process.

+

Click here [ZIP] for a site +visit checklist to help ensure that you do not forget to document +information that is important for the data QC process.

Sensor configuration

@@ -44,12 +44,13 @@

Sensor configuration

sync ( e.g., one records at 11:00 and the other records at 11:07). If you are deploying air and water sensors at a site, make sure they are recording at the same time. This will make data processing faster and -easier. If you are using Onset HOBO sensors, click here for tips on configuring -them in a way that ensures they will record at the same time.

+easier. If you are using Onset HOBO sensors, click here [PDF] for tips on +configuring them in a way that ensures they will record at the same +time.

Another issue that sometimes occurs is data overlap (where more than one file has measurements covering part of the same time periods). If -you are using Onset HOBO sensors, click here for procedures to follow -during data download to clear sensor memory and avoid overlapping +you are using Onset HOBO sensors, click here [PDF] for procedures to +follow during data download to clear sensor memory and avoid overlapping data.

@@ -59,24 +60,24 @@

Accuracy checks

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). Accuracy checks are used to validate your data, and -in some cases, correct for sensor drift. Click here to download an example of -an accuracy check worksheet being kept by an RMN partner.

+in some cases, correct for sensor drift. Click here [XLSX] to download an +example of an accuracy check worksheet being kept by an RMN partner.

Visual checks of time series plots

Visual checks of time series plots are an important part of the QC -process. Click here to see a -compilation of patterns to watch for when interpreting the plots. They -include ice cover, beaver activity, leaf packs, dewatering, and dead -batteries. We will continue to add slides to this as we receive +process. Click here [PDF] to +see a compilation of patterns to watch for when interpreting the plots. +They include ice cover, beaver activity, leaf packs, dewatering, and +dead batteries. We will continue to add slides to this as we receive materials.

Checking sensor data against other data sources

-

This is optional but encouraged if time permits. Click here for instructional materials from -David Smith (Kentucky Division of Water) on how he has been downloading -data from nearby weather stations and USGS gages, as well as modeled air -temperature and precipitation data from Daymet ( +

This is optional but encouraged if time permits. Click here [ZIP] for instructional materials +from David Smith (Kentucky Division of Water) on how he has been +downloading data from nearby weather stations and USGS gages, as well as +modeled air temperature and precipitation data from Daymet ( https://daymet.ornl.gov/getdata ), and comparing those data to sensor measurements as part of his QC process.

diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1e_Advanced.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1e_Advanced.html index a025ab6..c801ba2 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1e_Advanced.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1e_Advanced.html @@ -16,7 +16,7 @@

Advanced

Users with intermediate to advanced-level R skills can customize the settings (e.g., add new parameters, change units, change file naming and formatting requirements, change the format of one of the QC reports from -Word to html or PDF) by editing a plain text configuration file. Users have more +Word to html or PDF) by editing a plain text configuration file [ZIP]. Users have more flexibility using the Shiny app versus R package when it comes to setting directories and file naming schemes because they can browse to the desired input file(s).

diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a1_HOBO.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a1_HOBO.html index 143b3ca..ffdc2b4 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a1_HOBO.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a1_HOBO.html @@ -14,13 +14,13 @@

HOBOware Reformat

manipulation -

Instructions

@@ -47,8 +47,8 @@

Instructions

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 for instructions on how -to set this up in Chrome. With Mozilla Firefox, go to Settings > +Download folder). Click here [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.”

Your files are now ready to be run through the QC function! Below are diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a2_miniDOT1.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a2_miniDOT1.html index dfa86d4..94aa5c8 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a2_miniDOT1.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a2_miniDOT1.html @@ -32,7 +32,7 @@

Concatenate Instructions

Additional Notes

    -

  • Want to try it yourself? Click here to download miniDOT DO test +

  • Want to try it yourself? Click here [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. For more diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a3_miniDOT2.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a3_miniDOT2.html index 29f4499..6c2067a 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a3_miniDOT2.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a3_miniDOT2.html @@ -31,7 +31,7 @@

    Instructions

    Additional Notes

      -

    • Want to try it yourself? Click here to download miniDOT DO test +

    • Want to try it yourself? Click here [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. For more diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a_FormattingFiles.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a_FormattingFiles.html index 9cab5e9..1c27849 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a_FormattingFiles.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2a_FormattingFiles.html @@ -12,7 +12,7 @@

      Formatting Files

    • There are two required fields: SiteID; and “Date Time” (with Date and Time combined into one field).

    • If using the default configuration -file, column names must match the capitalization, spelling and +file [ZIP], column names must match the capitalization, spelling and symbology shown in the table below (for example, R will not recognize ‘sensor depth ft’; it needs to be ‘Sensor Depth ft’)

    • Either periods or spaces in the column headings are acceptable. diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2b_OrganizingFiles.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2b_OrganizingFiles.html index ef27000..9672085 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2b_OrganizingFiles.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2b_OrganizingFiles.html @@ -8,10 +8,10 @@

      Organizing Files

      point. Folders and files can be customized as you gain more experience. The files should be backed up regularly and accessible to other members of your data management team.

      -

      Click here to download a zipped file -with a ready-made set of (empty) folders. Put the file in the desired -location, unzip it and then replace ‘SiteX’ with the appropriate site -name.

      +

      Click here [ZIP] to download a +zipped file with a ready-made set of (empty) folders. Put the file in +the desired location, unzip it and then replace ‘SiteX’ with the +appropriate site name.

      You have more flexibility with file organization when using the Shiny app vs R package. With the Shiny app, it is not necessary to name the folders exactly as shown below because you can browse to the desired @@ -174,7 +174,7 @@

      Folder descriptions

      -

      Click here to download -example Accuracy Check worksheet.

      +

      Click here [XLSX] to +download example Accuracy Check worksheet.

diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2c_NamingFiles.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2c_NamingFiles.html index da1a578..229b977 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2c_NamingFiles.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2c_NamingFiles.html @@ -33,8 +33,8 @@

Naming Files

need to include leading zeros (either 01M or 1M are acceptable). Units can be upper or lower case (M or m), and abbreviated (M) or spelled out (meters). You can change the double-dash separator if desired by -customizing the configuration file (for -example, you could change it to a tilde ~).

+customizing the configuration file +[ZIP] (for example, you could change it to a tilde ~).

If you are using the Shiny app and have more than one type of sensor deployed at the same depth (for example, both a DO and temperature sensor at 2M), you can put the sensor type in the second part of the diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2cz_DiscreteData.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2cz_DiscreteData.html index c08879d..f9e02a0 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2cz_DiscreteData.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_2cz_DiscreteData.html @@ -18,9 +18,9 @@

Discrete Data

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 to -download an example of an accuracy check worksheet being kept by an RMN -partner.

+sensor). Click here [XLSX] +to download an example of an accuracy check worksheet being kept by an +RMN partner.

Example QC plot with discrete data
Example QC plot with discrete data
diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a1_About.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a1_About.html index 0a59c46..b21bd45 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a1_About.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a1_About.html @@ -33,8 +33,8 @@

Workflow

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 for instructions on how -to set this up in Chrome. With Mozilla Firefox, go to Settings > +default Download folder). Click here [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.”

diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a2_QCReports.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a2_QCReports.html index 2ee33d1..7e526ea 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a2_QCReports.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a2_QCReports.html @@ -24,10 +24,10 @@

QC reports

document Data Quality Control Report and a comma-delimited (.csv) spreadsheet. The reports include results from the ‘flag’ tests (gross, spike, rate of change and flat line), missing data checks and time -series plots. Click here to download -an example of a QC output. If users prefer a Hypertext Markup Language -(HTML) report instead of Word, they can change the format in the -configuration file (this requires some familiarity with R +series plots. Click here [ZIP] to +download an example of a QC output. If users prefer a Hypertext Markup +Language (HTML) report instead of Word, they can change the format in +the configuration file (this requires some familiarity with R code).

  • Review each set of files, check flagged data points, do visual checks on the time series plots, and decide if and how to make diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a3_Aggregate.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a3_Aggregate.html index 1c660a6..2db29ab 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a3_Aggregate.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a3_Aggregate.html @@ -24,7 +24,7 @@

    Aggregate

    desired.

  • Open and review the aggregated reports. As with the QC output, there are two types of outputs: a Word document Data Quality Control -Report and a comma-delimited (.csv) spreadsheet. Click here to download an example of an +Report and a comma-delimited (.csv) spreadsheet. Click here [ZIP] to download an example of an Aggregate output. If users prefer a Hypertext Markup Language (HTML) report instead of Word, they can change the format in the configuration file (this requires some familiarity with R code).

    • diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a4_SummaryStats.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a4_SummaryStats.html index 43971b4..6f39df0 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a4_SummaryStats.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3a4_SummaryStats.html @@ -25,7 +25,7 @@

    Summary Statistics

    two sets of CSV files and a PDF with time series plots for each parameter. One of the CSVs has daily means and the other has a wider range of summary statistics (e.g., min, median, max, quartiles). Click -here to download an example of a -Summary Stats output.

    +here [ZIP] to download an example of +a Summary Stats output.

    diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c1_QCThresh_Defaults.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c1_QCThresh_Defaults.html index b48f741..c55c301 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c1_QCThresh_Defaults.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c1_QCThresh_Defaults.html @@ -64,7 +64,8 @@

    Flag test descriptions

  • U.S. Integrated Ocean Observing System, 2017. Manual for the Use of Real-Time Oceanographic Data Quality Control Flags, Version 1.1. 43 pp. -https://cdn.ioos.noaa.gov/media/2017/12/QARTOD-Data-Flags-Manual_Final_version1.1.pdf

    • +https://cdn.ioos.noaa.gov/media/2017/12/QARTOD-Data-Flags-Manual_Final_version1.1.pdf +[PDF]

  • Wagner, R.J., Boulger, R.W., Oblinger, C.J., Smith, B.A., 2006. Guidelines and Standard Procedures for Continuous Water-quality Monitors: Station Operation, Record Computation, and Data Reporting. @@ -96,10 +97,10 @@

    Flag test descriptions

    tests lose relevance.

    Configuration files can be downloaded here:

      -

    • Default, with hydrologic +

    • Default [ZIP], with hydrologic parameters in feet

      • -

    • Customized, with hydrologic -parameters in meters

      • +

    • Customized [ZIP], with +hydrologic parameters in meters

    This table shows the default QC test thresholds for each parameter as of 2023-08-28.

    diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c2_QCThresh_Upload.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c2_QCThresh_Upload.html index ca64b32..bd67a84 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c2_QCThresh_Upload.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c2_QCThresh_Upload.html @@ -20,6 +20,6 @@

    Upload Custom Thresholds

    remember the sequencing! If you forget to upload the customized configuration file prior to running the QC function, it will use the default thresholds.

    -

    Want to try this yourself? Click here to download a test +

    Want to try this yourself? Click here [R] to download a test file.

    • diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c3_QCThresh_Eval.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c3_QCThresh_Eval.html index 3e957d4..4b21554 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c3_QCThresh_Eval.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c3_QCThresh_Eval.html @@ -7,18 +7,19 @@

    Evaluate Thresholds

    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.

    -

    Click here for instructions on -how to generate pivot tables and plots to evaluate thresholds for the -Unrealistic values (‘Gross range’) and Spike tests.

    +

    Click here [ZIP] for +instructions on how to generate pivot tables and plots to evaluate +thresholds for the Unrealistic values (‘Gross range’) and Spike +tests.

    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 here to -download the R scripts and instructions.

    +four QC tests. Click here +[ZIP] to download the R scripts and instructions.

    To aid with documentation of the threshold evaluation process, click -here 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.

    +here [XLSX] 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.

    diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c4_QCThresh_Edit.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c4_QCThresh_Edit.html index 843cd66..0679789 100644 --- a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c4_QCThresh_Edit.html +++ b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_3c4_QCThresh_Edit.html @@ -3,8 +3,8 @@

    Edit Thresholds

    -

    Click here for -instructions on how to edit thresholds and create customized +

    Click here [PDF] +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 @@ -20,11 +20,11 @@

    Option 1, download the default configuration file, open the file in R or Notepad++, make edits and save.

    Configuration files can be downloaded here -

      -

    • Default, with hydrologic +

    • Default [ZIP], with hydrologic parameters in feet

    • Hydrologic parameters in -meters Navigate to the ‘QC tests and calculations’ section. Edit -thresholds as desired. Save the file.

      • +meters [ZIP] Navigate to the ‘QC tests and calculations’ section. +Edit thresholds as desired. Save the file.

    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