diff --git a/inst/shiny/WQReviewGUI/www/WQReviewGUI.html b/inst/shiny/WQReviewGUI/www/WQReviewGUI.html index b0979db..6de3f96 100644 --- a/inst/shiny/WQReviewGUI/www/WQReviewGUI.html +++ b/inst/shiny/WQReviewGUI/www/WQReviewGUI.html @@ -1,18 +1,16 @@ - - - - + + - - - + - + -WQReview GUI + + +WQReview GUI User Guide @@ -43,166 +41,151 @@ - + - + - +
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Introduction

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Toolbox for discrete water-quality data review and exploration.Users are encouraged to post any bugs or comments for additional functionality on the issues page at:

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WQ-Review Issues.

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This package facilitates data review and exploration of discrete water-quality data through rapid and easy-to-use plotting functions and tabular data summaries. Data is imported with user-specified options for single or multiple sites and parameter codes using an ODBC connection to the user’s local NWIS server. A graphical user interface allows the user to easily explore their data through a variety of graphical and tabular outputs.

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Screenshot

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Requirements

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Bug reporting and enhancements

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Please report any issues with the application or R package on the issues page at:

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WQ-Review Issues.

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Additionaly, please feel free to post any suggestions or enhancement requests.

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Your participation will make this a better tool for everyone!

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Installation for stand alone application (non-R users)

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  1. Download the application at
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ftp://ftpint.usgs.gov/private/cr/co/lakewood/tmills/wqReviewSetup.exe

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  1. Run wqReviewSetup.exe and follow the installation instructions.
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DO NOT INSTALL WQ-REVIEW INTO YOUR PROGRAM FILES DIRECTORY OR THE APPLICATION WILL NOT RUN. INSTALL TO C DRIVE OR YOUR DOCUMENTS FOLDER.

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  1. Update WQ-Review to the latest version either by clicking the checkbox at the end of the setup, or by going to Startmenu->Programs->WQ-Review->Update. A command prompt window will appear and stay open until the update is complete. When the update is complete it will close with no other prompts.
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Installation for R users

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Step 1. Switch over to 32-bit R.

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R must be run in 32-bit mode to use the ODBC driver. Open R-studio and click Tools-Global Options on the top toolbar. Under “General” in the global options dialog, you will see “R version:” at the top. Click “Change” next to the R version and select “Use your machine’s default version of R (32 bit)” to change to 32-bit R. R-studio will need to restart after doing this.

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Step 2. Install the “devtools” package for installing WQ-Review directly from Github.

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Open R-studio in 32-bit mode if it is not already open and type the following command in the console:

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install.packages(c("curl","devtools"))
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This will install the devtools package on your machine.

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If an error appears about “Rtools not installed”, ignore this message, Rtools is not required for the devtools functions you will use.

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Step 3. Install the WQ-Review package from Github.

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Open R-studio in 32-bit mode if it is not already open and type the following commands in the console:

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library(devtools)
-install_github("USGS-R/WQ-Review",build_vignettes = TRUE)
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This will install the WQ-Review package as well as all other packages that WQ-Review relies on. It may take a minute to download and install the supporting packages during the first installation.

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Run the app

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The shiny app is launched by loading the WQ-Review package and running the function

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library(WQReview)
-WQReviewGUI()
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Guidance for setting up ODBC connection to NWIS

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Your database administrator or IT specialist will may need to assist for these steps.

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Step 1

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You need to setup a user Data Source Name (User DSN). On 64bit Windows 7 and 8, run “C:/Windows/SysWOW64/odbcad32.exe”.

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On 32bit Windows 7 and 8, run “C:/Windows/System32/odbcad32.exe”.

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In the User DSN tab, if you do not see a connection with the same name as your NWIS server of interest, you must add a new connection. Click “Add” on the right.

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Screenshot

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Step 2

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Scroll down until you see a driver named “Oracle in OraClient11g_home1” and click “Finish”. IF YOU DO NOT SEE THE ABOVE DRIVER LISTED, IT IS NOT INSTALLED AND YOU WILL NEED ASSISTANCE FROM AN IT SPECIALIST TO INSTALL IT, THE LINK TO GUIDANCE IS PROVIDED BELOW

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Screenshot

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Step 3

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A new dialogue will appear. Click the dropdown box next to “TNS Service Name” and select the NWIS server you would like to connect to. After selecting the server, type in the server name into the “Data Source Name” text box at the top. DO NOT ENTER A USER ID, LEAVE THIS FIELD BLANK. You are finished, click OK to close the dialogue and then click OK in the main ODBC Data Source Administrator application to close the application.

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Screenshot

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If you do not have the driver installed

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Install the Oracle client by following the instructions here:

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http://nwis.usgs.gov/IT/ORACLE/Oracle.client.installation.htm

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Then follow the instructions to setup the system DSN

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http://nwis.usgs.gov/IT/INSTRUCT/HOWTO/DB_oracle_odbc.html

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The ODBC connection must be setup for Oracle and in 32-bit mode.

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Importing Data

This will describe the process for importing data into the WQReview Graphical User Interface (GUI). We will start by importing data for a single site using predefined NWIS parameter groups. ##Load the WQReview package and open the WQReview GUI

@@ -282,7 +265,7 @@

Selecting data to plot

Global plot controls

New data threshold

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Point data in all plots can be labeled as “New” data based off of when that data was last modified using the “New data threshold” slider. Any data modified after the date indicated on the slider will be labeled as “New”. This helps identify data that has not been reviewed from historic data when the data are not displayed as a timeseries. Note that the “New data threshold” is set off of when the data were last modified for result-level plots (e.g. timeseries, seasonal, etc.) not when they were created. Sample-level plots (e.g. charge balance) are labeled new according to the sample collection date.

+

Point data in all plots can be labeled as “New” data based off of when that data was last modified using the “New data threshold” slider. Any data modified after the date indicated on the slider will be labeled as “New”. This helps identify data that has not been reviewed from historic data when the data are not displayed as a timeseries. Note that the “New data threshold” is set off of when the data were last modified for result-level plots (e.g. timeseries, seasonal, etc.) not when they were created. Sample-level plots (e.g. charge balance) are labeled new according to the sample collection date.

Record highlights

@@ -459,7 +442,7 @@

Plot controls

Ions vs conductance

This pane generates a x-y plot of sum of cations or anions vs conductance. The ratio of the sum of cations or anions vs specific conductance generally falls within a range of 0.92 - 1.24 for natural waters. The shaded region on the plot indicates this typical range. These are the values used in QWData for alert limits, see QWData documentation and references therein for further explanation.

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At many sites, there will be a roughly linear relationship between the sum of cations or anions vs. conductance. If a point falls above or below the general trend line, this is an indication that the particular group of ions is either to low or too high.

+

At many sites, there will be a roughly linear relationship between the sum of cations or anions vs. conductance. If a point falls above or below the general trend line, this is an indication that the particular group of ions is either to low or too high.

Uses

    @@ -543,7 +526,7 @@

    Tables

    This section will describe the various tables generated by the WQReview GUI. The WQ-Review GUI produces 2 general classes of tables: Auto-flag results, and data/QAQC tables. All tables can be downloaded as tab-delimited text files by clicking on the download button above each table. All tables are sortable by clicking on the header, and the number of entries per table page is adjusted using hte “show entries” dropdown. Additionally, all tables can be filtered using the search bar. Typing a value into the searchbar will search the table columns for that value and subset the table to only those rows containing the search value. For example, typing “WSQ” into the search bar will filter the table to only replicate samples.

    Auto-flagged samples

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    During data import, samples or results are auto-flagged following criteria developed by NAWQA for all water-quality data, and are defined here. For any flags comparing a current sample to historic data, the current sample is compared to all REVIEWED AND ACCEPTED data rather than prior samples in time. This is because data that have not been reviewed and accepted could themselves be problematic.

    +

    During data import, samples or results are auto-flagged following criteria developed by NAWQA for all water-quality data, and are defined at the end of this manual. For any flags comparing a current sample to historic data, the current sample is compared to all REVIEWED AND ACCEPTED data rather than prior samples in time. This is because data that have not been reviewed and accepted could themselves be problematic.

    Basic chemical flags

    This table contains basic chemical checks similar to those provided by the QWDATA unix software. The first 6 columns contain sample-level information and the remaining columns contain flags wit hthe column name coorresponding to the particular data check. If a sample fails a given data check, a flag is applied to the respective column for that sample.

    @@ -561,6 +544,53 @@

    Results flags

    Data and QAQC tables

    These tables are controlled similarly to the auto-flagged tables except that they can be generated according to site and date selection criteria. These tables include standard data tables, a wide (sample-result) and a long (by result) format table. 4 QAQC tables are also presented, including a chargebalance table, a table of replicate agreement, a summary table of blank detections, and a table comparing filtered ot unfiltered values. The last column of each of these QAQC tables contains a column with flags if a particular sample violates some standard QAQC measure. For example, a sample with a charge imbalance > 10% would get a flag in the final column of hte chargebalance table. The blank summary table is calculated on the fly given the input criteria For example, leaving the default date range (last 3 years) in the blank table input and selecting a site would summarize the blank detections for that 3 year period for that site.

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    Flag descriptions

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    SC_badLabVSField

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    The difference between Lab SC (90095) and field SC (00095) is greater than 10%

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    30.01.

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    pH lower than expected Every water-quality sample (environmental and QC) had its pH (p00400) checked for appropriate ranges. If the pH value is less than 4.5, the sample is flagged for 30.01.

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    +
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    30.02. pH higher than expected

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    Every water-quality sample (environmental and QC) had its pH (p00400) checked for appropriate ranges. If the pH value is higher than 9, the sample is flagged for 30.02.

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    +
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    30.03. Dissolved Oxygen higher than expected

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    Every water-quality sample (environmental and QC) had its dissolved oxygen (p00300) checked for appropriate ranges. If the D.O. value is higher than 25, the sample is flagged for 30.03.

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    30.11. Greater than max value in old data

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    New Environmental samples are compared to “old” environmental samples at the same site from water-year 1996 and later, for pesticides, nutrients, field parameters, and major ions. When a parameter has 5 or more “old” values at the site, and a new sample has a new maximum for that parameter, that sample and parameter are flagged for 30.11. Pesticides in Schedule 2437 which existed in the earlier schedules 2033 or 2060 (under different pcodes) are compared to the older pcodes as well as the Schedule 2437 pcodes.

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    +

    30.12. Less than min value in old data

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    New Environmental samples are compared to “old” environmental samples at the same site from water-year 1996 and later, for pesticides, nutrients, field parameters, and major ions. When a parameter has 5 or more “old” values at the site, and a new sample has a new minimum for that parameter, that sample and parameter are flagged for 30.12. Pesticides in Schedule 2437 which existed in the earlier schedules 2033 or 2060 (under different pcodes) are compared to the older pcodes as well as the Schedule 2437 pcodes.

    +
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    30.13. Schedule 2437 Pesticide hits greater than max hits in old data

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    The number of Schedule 2437 pesticide hits in new environmental samples is compared to 2437 pesticide hits in “old” environmental samples at the same site from water-year 2013 and later (the year Schedule 2437 began). When a site has 5 or more “old” pesticide samples and a new sample has a new maximum number of pesticide hits, that sample is flagged for 30.13. Only pesticides in Schedule 2437 are counted as hits.

    +
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    30.14 Less than minimum pesticide hits in old data

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    The number of Schedule 2437 pesticide hits in new environmental samples is compared to 2437 pesticide hits in “old” environmental samples at the same site from water-year 2013 and later (the year Schedule 2437 began). When a site has five or more “old” pesticide samples and a new sample has a new minimum number of pesticide hits, that sample is flagged for 30.14. Only pesticides in Schedule 2437 are counted as hits.

    +
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    30.15. Greater than 99p in old data

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    New Environmental samples are compared to “old” environmental samples at the same site from water-year 1996 and later, for pesticides, nutrients, field parameters, and major ions. When a parameter has 24 or more “old” values at the site, and a new sample has a value greater than the 99th percentile of the “old” data set for that parameter, that sample and parameter are flagged for 30.15. Pesticides in Schedule 2437 which existed in the earlier schedules 2033 or 2060 (under different pcodes) are compared to the older pcodes as well as the Schedule 2437 pcodes.

    +
    +
    +

    30.16. Less than 1p in old data

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    New Environmental samples are compared to “old” environmental samples at the same site from water-year 1996 and later, for pesticides, nutrients, field parameters, and major ions. When a parameter has 24 or more “old” values at the site, and a new sample has a value less than the 1st percentile of the “old” data set for that parameter, that sample and parameter are flagged for 30.15. Pesticides in Schedule 2437 which existed in the earlier schedules 2033 or 2060 (under different pcodes) are compared to the older pcodes as well as the Schedule 2437 pcodes.

    +
    +
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    30.21. Questionable cation-anion balance

    +

    For each environmental sample, the cation-anion percent difference was be calculated (using the same formula, but a slightly simpler procedure, than what NWIS-QWDATA uses) and compared to the value for specific conductance (P00095). The cation-anion ballance is flagged for 30.21 if any of the following conditions is true 1. specific conductance is less than or equal to 100 microsiemens/cm, AND percent difference is greater (in absolute value) than +/- 15 percent 2. specific conductance is greater than 100 and less than or equal to 1000 microsiemens/cm, AND percent difference is greater (in absolute value) than +/- 10 percent 3. specific conductance is greater than 1000 microsiemens/cm, AND percent difference is greater (in absolute value) than +/- 5 percent

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    @@ -575,5 +605,6 @@

    Data and QAQC tables

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This section will describe the various tables generated by the WQReview GUI. The WQ-Review GUI produces 2 general classes of tables: Auto-flag results, and data/QAQC tables. All tables can be downloaded as tab-delimited text files by clicking on the download button above each table. All tables are sortable by clicking on the header, and the number of entries per table page is adjusted using hte "show entries" dropdown. Additionally, all tables can be filtered using the search bar. Typing a value into the searchbar will search the table columns for that value and subset the table to only those rows containing the search value. For example, typing "WSQ" into the search bar will filter the table to only replicate samples. ##Auto-flagged samples -During data import, samples or results are auto-flagged following criteria developed by NAWQA for all water-quality data, and are defined [here](flagDescriptions.htm). For any flags comparing a current sample to historic data, the current sample is compared to all REVIEWED AND ACCEPTED data rather than prior samples in time. This is because data that have not been reviewed and accepted could themselves be problematic. +During data import, samples or results are auto-flagged following criteria developed by NAWQA for all water-quality data, and are defined at the end of this manual. For any flags comparing a current sample to historic data, the current sample is compared to all REVIEWED AND ACCEPTED data rather than prior samples in time. This is because data that have not been reviewed and accepted could themselves be problematic. ###Basic chemical flags This table contains basic chemical checks similar to those provided by the QWDATA unix software. The first 6 columns contain sample-level information and the remaining columns contain flags wit hthe column name coorresponding to the particular data check. If a sample fails a given data check, a flag is applied to the respective column for that sample. @@ -316,4 +316,41 @@ This table contains flags for evaluating number of pesticide hits in schedule 24 This table contains flags for results that are either suspisously high or low compared to historic data. ##Data and QAQC tables -These tables are controlled similarly to the auto-flagged tables except that they can be generated according to site and date selection criteria. These tables include standard data tables, a wide (sample-result) and a long (by result) format table. 4 QAQC tables are also presented, including a chargebalance table, a table of replicate agreement, a summary table of blank detections, and a table comparing filtered ot unfiltered values. The last column of each of these QAQC tables contains a column with flags if a particular sample violates some standard QAQC measure. For example, a sample with a charge imbalance > 10% would get a flag in the final column of hte chargebalance table. **The blank summary table is calculated on the fly given the input criteria** For example, leaving the default date range (last 3 years) in the blank table input and selecting a site would summarize the blank detections for that 3 year period for that site. \ No newline at end of file +These tables are controlled similarly to the auto-flagged tables except that they can be generated according to site and date selection criteria. These tables include standard data tables, a wide (sample-result) and a long (by result) format table. 4 QAQC tables are also presented, including a chargebalance table, a table of replicate agreement, a summary table of blank detections, and a table comparing filtered ot unfiltered values. The last column of each of these QAQC tables contains a column with flags if a particular sample violates some standard QAQC measure. For example, a sample with a charge imbalance > 10% would get a flag in the final column of hte chargebalance table. **The blank summary table is calculated on the fly given the input criteria** For example, leaving the default date range (last 3 years) in the blank table input and selecting a site would summarize the blank detections for that 3 year period for that site. + +##Flag descriptions +###SC_badLabVSField +The difference between Lab SC (90095) and field SC (00095) is greater than 10% + +###30.01. +pH lower than expected Every water-quality sample (environmental and QC) had its pH (p00400) checked for appropriate ranges. If the pH value is less than 4.5, the sample is flagged for 30.01. + +###30.02. pH higher than expected +Every water-quality sample (environmental and QC) had its pH (p00400) checked for appropriate ranges. If the pH value is higher than 9, the sample is flagged for 30.02. + +###30.03. Dissolved Oxygen higher than expected +Every water-quality sample (environmental and QC) had its dissolved oxygen (p00300) checked for appropriate ranges. If the D.O. value is higher than 25, the sample is flagged for 30.03. + +###30.11. Greater than max value in old data +New Environmental samples are compared to “old” environmental samples at the same site from water-year 1996 and later, for pesticides, nutrients, field parameters, and major ions. When a parameter has 5 or more “old” values at the site, and a new sample has a new maximum for that parameter, that sample and parameter are flagged for 30.11. Pesticides in Schedule 2437 which existed in the earlier schedules 2033 or 2060 (under different pcodes) are compared to the older pcodes as well as the Schedule 2437 pcodes. + +###30.12. Less than min value in old data +New Environmental samples are compared to “old” environmental samples at the same site from water-year 1996 and later, for pesticides, nutrients, field parameters, and major ions. When a parameter has 5 or more “old” values at the site, and a new sample has a new minimum for that parameter, that sample and parameter are flagged for 30.12. Pesticides in Schedule 2437 which existed in the earlier schedules 2033 or 2060 (under different pcodes) are compared to the older pcodes as well as the Schedule 2437 pcodes. + +###30.13. Schedule 2437 Pesticide hits greater than max hits in old data +The number of Schedule 2437 pesticide hits in new environmental samples is compared to 2437 pesticide hits in “old” environmental samples at the same site from water-year 2013 and later (the year Schedule 2437 began). When a site has 5 or more “old” pesticide samples and a new sample has a new maximum number of pesticide hits, that sample is flagged for 30.13. Only pesticides in Schedule 2437 are counted as hits. + +###30.14 Less than minimum pesticide hits in old data +The number of Schedule 2437 pesticide hits in new environmental samples is compared to 2437 pesticide hits in “old” environmental samples at the same site from water-year 2013 and later (the year Schedule 2437 began). When a site has five or more “old” pesticide samples and a new sample has a new minimum number of pesticide hits, that sample is flagged for 30.14. Only pesticides in Schedule 2437 are counted as hits. + +###30.15. Greater than 99p in old data +New Environmental samples are compared to “old” environmental samples at the same site from water-year 1996 and later, for pesticides, nutrients, field parameters, and major ions. When a parameter has 24 or more “old” values at the site, and a new sample has a value greater than the 99th percentile of the “old” data set for that parameter, that sample and parameter are flagged for 30.15. Pesticides in Schedule 2437 which existed in the earlier schedules 2033 or 2060 (under different pcodes) are compared to the older pcodes as well as the Schedule 2437 pcodes. + +###30.16. Less than 1p in old data +New Environmental samples are compared to “old” environmental samples at the same site from water-year 1996 and later, for pesticides, nutrients, field parameters, and major ions. When a parameter has 24 or more “old” values at the site, and a new sample has a value less than the 1st percentile of the “old” data set for that parameter, that sample and parameter are flagged for 30.15. Pesticides in Schedule 2437 which existed in the earlier schedules 2033 or 2060 (under different pcodes) are compared to the older pcodes as well as the Schedule 2437 pcodes. + +###30.21. Questionable cation-anion balance +For each environmental sample, the cation-anion percent difference was be calculated (using the same formula, but a slightly simpler procedure, than what NWIS-QWDATA uses) and compared to the value for specific conductance (P00095). The cation-anion ballance is flagged for 30.21 if any of the following conditions is true +1. specific conductance is less than or equal to 100 microsiemens/cm, AND percent difference is greater (in absolute value) than +/- 15 percent +2. specific conductance is greater than 100 and less than or equal to 1000 microsiemens/cm, AND percent difference is greater (in absolute value) than +/- 10 percent +3. specific conductance is greater than 1000 microsiemens/cm, AND percent difference is greater (in absolute value) than +/- 5 percent \ No newline at end of file