Using SoilFluxPro Software

SoilFluxPro™ SoftwareInstruction Manual

SoilFluxPro™

Using SoilFluxPro Softwarefor Soil Gas Flux Data

LI-COR Biosciences4647 Superior StreetLincoln, Nebraska 68504Phone: +1-402-467-3576Toll free: 800-447-3576 (U.S. and Canada)[email protected]

Regional Offices

LI-COR Biosciences GmbHSiemensstraße 25A61352 Bad HomburgGermanyPhone: +49 (0) 6172 17 17 [email protected]

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LI-COR Distributor Network:www.licor.com/envdistributors

NoticeThe information in this document is subject to change without notice.

LI-COR MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING BUT NOTLIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULARPURPOSE. LI-COR shall not be held liable for errors contained herein or for incidental or consequential damages in con-nection with the furnishing, performance, or use of this material.

This document contains proprietary information, which is protected by copyright. All rights are reserved. No part of thisdocument may be photocopied, reproduced, or translated to another language without prior written consent of LI-COR,Inc.

LI-COR and SoilFluxPro™ are trademarks of LI-COR, Inc. in the United States and other countries. Google Earth is atrademark of Google LLC. Microsoft and Windows are registered trademarks of the Microsoft Corporation. All other trade-marks and registered trademarks are property of their respective owners.

Printing History© Copyright 2021, LI-COR, Inc. All rights reserved.Publication Number: 977-17711 Rev 7Created on: Wednesday, December 1, 2021.

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Contents

Section 1. Getting to know SoilFluxPro

Interface tour 1-1File Management bar 1-2Data Interaction bar 1-3Summary view 1-4Details bar 1-5Menu bar 1-5

Opening a file in SoilFluxPro Software 1-6

Section 2. Data Interaction bar

Display 2-1Measured variables 2-2Metadata 2-4Flux variables 2-5

Recompute 2-7Fit 2-7Metadata 2-11Guidance 2-12

Transform 2-13Transforming a variable 2-14Favorites 2-18

Repair 2-20Remove 2-21Statistics 2-23

Section 3. Details bar

Log 3-1Details 3-1Chart 3-2

Creating a chart 3-2Grouping by test 3-8Interacting with a chart 3-11Favorites 3-12

Section 4. File Management bar

Saving data 4-1Exporting data 4-2Importing data 4-3

General 4-3Metadata 4-4Date & Time 4-5How to import 4-6Favorites 4-7

Mapping data 4-8Creating a .kml file 4-8Adding or editing a marker 4-11

Viewing data on Google Earth™ 4-13

Appendix A. Data dictionary

Appendix B. Supported units

Appendix C. Index

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Section 1.Getting to know SoilFluxPro

SoilFluxPro Software is an application designed to view and analyze soil gas fluxdata using continuous measurements generated by the following instruments:l LI-8250 Multiplexerl 8200-01S Smart Chamberl 6800-09 Soil CO2 Flux Chamber for the LI-6800 Portable Photosynthesis Systeml LI-8100A Automated Soil CO2 Flux Systeml LI-8150 Multiplexer

This section provides an overview of the SoilFluxPro Software interface and cap-abilities.

Interface tourSoilFluxPro Software opens to a main screen made up of four subsections shown inFigure 1-1 on the next page.

1-1Using SoilFluxPro


Figure 1-1. The SoilFluxPro main screen and its subsections: File Management bar (1),Data Interaction bar (2), Summary view (3), and Details bar (4).

File Management barThe File Management bar is where you can open, save, export, and create .kml filesto view your data in the Google Earth™ mapping service. This bar also contains thecut, copy, paste, and delete buttons for observations.

l Open opens .82z, .81x, and .json observation files to be viewed and worked within SoilFluxPro Software. Each file includes raw time series data and metadatathat provides observation context.

l Save saves either the observations you have selected or all observations to achosen location as a new set of .82z files.

l Export takes summary data from the files loaded in SoilFluxPro Software andexports it as one combined .csv file.

1-2 Using SoilFluxPro

l Import lets you import time series data from stand-alone LI-78xx Trace Gas Ana-lyzers and third-party gas analyzers (when used with a LI-COR soil gas flux sys-tem) for use in SoilFluxPro.

l Map uses GPS location data to export a .kml file which can be viewed in theGoogle Earth™ mapping service.

The following tools will allow you to combine or remove observations within a FileGroup.

l Cut cuts the selected observations to the clipboard.l Copy copies the selected observations to the clipboard.l Paste pastes observations from the clipboard to the Summary view.l Remove Observation removes the selected observations from the Summary

view.

Data Interaction barThe Data Interaction bar contains the primary tools you will use to interact with andrevise data from your observations. This is also where you can load different .82z filegroups that you have opened in SoilFluxPro Software.

l File Group is where observations from opened files are organized. This pane dis-plays the name of the file and the range of start and end times for the obser-vations in that file.

l Recompute lets you adjust parameters used in the flux calculation, such as startand stop time. Any adjustments automatically recompute the flux in real timeand chart the raw times series data for an observation. Guidance can be used tooptimize your settings using analysis tools.

l Transform allows you to apply a mathematical function to a variable in the data-set or to compute something new using one or more variables. This will then cre-ate a new column or replace an existing one with the transformed data.

l Repair lets you replace a bad chamber temperature reading on a port with onefrom another port. This may be necessary if there is a bad temperature sensor orif the sensor has become damaged.


1-3Data Interaction bar


l Remove allows you to remove data from a data file that may not be relevant orto reduce the file size. This will not overwrite the data in the existing .82z file.

l Statistics provides statistics for a single observation or a range of observations.l Display allows you to choose what variables are displayed for the observations in

the Summary view.

Summary viewAn observation includes the entire time that a port is selected and active, includingpurge times and measurements. The Summary view shows all the observations youhave loaded from a particular file group. This view shows the Measured, Metadata,and Flux variables you have selected from the Display pane.

The Summary view includes a header made up of 3 lines.

l The device that is the source of the measurement (e.g., LI-8250)l A label that defines the variable name (e.g., Pressure) and the type (e.g., Mean)l The units for the variable (e.g., kPa)

Table 1-1 below shows the different devices you may encounter in SoilFluxPro. For acomplete list of the variables and units seen in SoilFluxPro, see the Data dictionaryon page A-1 and Supported units on page B-1.

Device Label in SoilFluxPro Corresponding Device

LI-8250 LI-8250 Multiplexer8250-01 8250-01 Extension ManifoldLI-8200 Smart ChamberLI-8100A LI-8100A Automated Soil CO2 Flux SystemLI-8150 LI-8150 MultiplexerLI-6800 LI-6800 Portable Photosynthesis SystemCHAMBER See Table 1-2 on the facing pageLI-870 LI-870 CO2/H2O AnalyzerLI-7810 LI-7810 CH4/CO2/H2O Trace Gas AnalyzerLI-7815 LI-7815 CO2/H2O Trace Gas AnalyzerLI-7820 LI-7820 N2O/H2O Trace Gas AnalyzerUser-Defined Device Name Imported third-party or standalone gas analyzerTRANSFORMED Created when using the Transform tool

Table 1-1. SoilFluxPro device labels and their corresponding devices.


Device Labelin SoilFluxPro

Possible Associated Chambers

LI-8250 8200-104 Opaque Long-Term Chamber, 8200-104C Clear Long-TermChamber, or digital custom chamber

LI-8200 Smart ChamberLI-8100A andLI-8150

8100-104 Opaque Long-Term Chamber, 8100-104C Clear Long-TermChamber, 8100-102 10 cm Survey Chamber, 8100-103 20 cm SurveyChamber, flasks, or custom chamber

LI-6800 6800-09 Soil CO2 Flux Chamber

Table 1-2. SoilFluxPro device labels and their possible associated chambers.

Details barThe Details bar provides a variety of tools to show details and chart data from obser-vations or to view a log of activity in SoilFluxPro Software.

l Log opens a pane that shows a running log of the operations you have per-formed since opening SoilFluxPro. The log will also record any errors youreceive.

l Chart lets you make charts for all observations or selected observations using thex and y axis parameters you specify. You can save chart configurations for easyaccess later and all charts can be saved as an image.

l Details provides the raw time series data for a selected observation.

Menu barThe Menu bar is found in the upper left-hand corner of SoilFluxPro Software andincludes three sections.l Filel Sample Filel Help

File

File includes an option called Open Directory. For details on using this feature, seeOpen Directory on page 1-7.


1-5Details bar


Sample File

Sample File provides some sample datasets to familiarize yourself with the featuresand capabilities of SoilFluxPro Software.

Help

Help provides you with the resources you need to get the most out of SoilFluxPro.l About tells you which version of SoilFluxPro you have installed.l View SoilFluxPro Guide provides you with a direct link to this manual for future

reference.l Support for SoilFluxPro will take you directly to the SoilFluxPro support site

where you can get the latest software, see frequently asked questions, and accessrelated resources.

l Check for Updates will see if there is a newer version of SoilFluxPro availablefor you to install.

Opening a file in SoilFluxPro SoftwareBefore exploring how to analyze and visualize your data, you will first need to opena data file. SoilFluxPro Software can open files individually or from an entire .ziparchive.

To open a file in SoilFluxPro Software:

1 From the main screen click Open. This opens a dialog box for your computer.

2 Navigate to the location of your .zip archive or individual file.

3 Select the file and click Open.

4 SoilFluxPro will extract the observations and open them in the Summary view.

Alternatively, you can drag files from their destination and drop them intoSoilFluxPro Software without using the Open button.

Note: The name of the File Group defaults to the filename of either the .ziparchive, the file, or the first file selected in a series.


Opening multiple filesYou can select multiple files and .zip archives from the dialog box (or drag and dropmultiple files) by using Ctrl + click to select each. This will open all files into asingle file group in the Summary view.

Open Directory

Under File is an option called Open Directory. Open Directory will open a dialogbox where you can navigate to a directory and have SoilFluxPro search for and openany .82z, .81x, or .json files within that directory. Files can be opened in a new FileGroup (using the directory name as the File Group name) or in an existing one.


1-7Opening a file in SoilFluxPro Software



Section 2.Data Interaction bar

The Data Interaction bar contains the primary tools you will use to interact with andrevise data from your observations. This is also where you can load different filegroups that you have opened in SoilFluxPro Software.

DisplayClicking on Display in SoilFluxPro Software will open the Display pane. The Dis-play pane lets you select which variables you would like to see displayed in the Sum-mary view. The variables are separated into three categories: Measured, Metadata,and Flux. For a complete list of the variables seen in SoilFluxPro, see the Data dic-tionary on page A-1.

Figure 2-1. Variables are separated into three categories: Measured, Metadata, and Flux.



Measured variablesMeasured variables are any variable measured by a device, such as pressure, tem-perature, or raw gas measurement. Under the Measured drop-down, variables arecategorized by the device they originated from (e.g., LI-8250, LI-7810, etc.).

Figure 2-2. Variables are categorized by the device where they originated.


Expanding the drop-down for a device will list all the variables measured by thatdevice with an initial value, mean, and range checkbox. Select the checkbox of thevariable and the type you would like to have added to the Summary view.l Initial Value is the intercept of a linear fit to the first ten seconds of data.l Mean is the mean value between time zero and the end of the observation.l Range is the difference between the minimum and maximum values observed

between time zero and the end of the observation.

Figure 2-3. Variables for the LI-7810 CH4/CO2/H2O Trace Gas Analyzer.

New columns are added by default to the end of the Summary view. You can movea column by clicking on the column header and dragging it to a new location.


2-3Measured variables


MetadataMetadata provide context and required inputs to the observation, such as port num-ber, collar height, and start time. Under the Metadata drop-down, there are generalmetadata, which apply to the entire observation, and metadata that are device spe-cific.

Figure 2-4. Metadata include general (1) and device-specific (2) variables.

Selecting metadata from the drop-down will add the metadata as a column to theSummary view. New columns are added by default to the end of the Summary view.You can move a column by clicking on the column header and dragging it to a newlocation.


Flux variablesUnder the Flux drop-down, flux variables are categorized by device and gas species.Devices that measure multiple gases, such as the LI-7810 CH4/CO2/H2O Trace GasAnalyzer, may include a computed flux for each gas depending on how you haveconfigured your system.

Figure 2-5. Flux variables include computed fluxes from every gas measured by each device.


2-5Flux variables


Each gas includes general flux metadata, such as deadband and stop time, as well asindividual flux calculations for exponential and linear fits.

Figure 2-6. Flux variables include general flux metadata (1) and individual flux cal-culations for exponential (2) and linear (3) fits.

Clicking on a flux variable will add a column to the Summary view. New columnsare added by default to the end of the Summary view. You can move a column byclicking on the column header and dragging it to a new location.

Flux columns are given a header unique to the fit and variable you select. The deviceand units will remain the same as their Measured variable counterparts, however,the label will now begin with an F. For instance, adding a CH4 flux from the LI-7810 CH4/CO2/H2O Trace Gas Analyzers Exponential drop-down will add a columnwith the label FCH4 Dry. If you added the CV of this flux the label would read FCH4Dry cv. Fluxes from the Linear drop-down are distinguished by also including Lin inthe label.


RecomputeRecompute allows you to use revised parameters, such as deadband, stop time, or sys-tem volume, in your flux calculations and includes tools for optimization. Anyadjustments automatically recompute the flux in real time.

Note: When two or more observations are selected, no graph is displayed underFit and Guidance is not available. If no observations are selected, any changesmade in Recompute will be automatically applied to all observations.

FitFit lets you change the variables used in flux calculations.

To use the Fit tool:

1 Choose whether you would like to use one of the existing fluxes or to Add New Flux. Add NewFlux allows you to choose a new flux gas from a list of all measured gases by device.

2 Select which device and which gas flux you will be recomputing.

3 Select the observations you would like to work with.


2-7Recompute


Note: Selected Observations refers to observations that you have selected in theSummary view. You can tell which observations you have selected, as they will behighlighted in the Summary view. You can select observations individually byclicking on them, or you can use Ctrl + click to select multiple individualobservations or Shift + click to select all observations in a range.

4 Update one of the variables, such as Deadband. Update any additional variables as needed.

l Temperature Source allows you to change the source of the temperature measurementused in the flux calculation.

l Deadband is the period from complete chamber closing until steady mixing is achieved andthe measurement begins. This is usually about 10 to 30 seconds but can vary and should beoptimized using the Start Analysis tool (see Guidance on page 2-12).

l Stop Time is the length of data used for the flux computation after the deadband. This canvary based on site conditions and should be optimized using the Stop Analysis tool (see Guid-ance on page 2-12).

l Dilution Source lets you define the instrument that provided the water vapor measurementused in the dilution correction.

5 Click Apply. To undo any changes you have made and return to the default settings click Revert.

Note: Revert only works on Selected observations. Any changes made to All obser-vations cannot be undone using Revert.

Single observations

If you are working with a single observation, additional features, including a fit tableand chart, are available.


Options

These options appear when you have a single observation selected and affect theinformation displayed on the chart.

l Force C0 allows you to force the initial gas concentration to whatever value youwant using the blue line on the chart. Usually, C0 (the starting value) is determ-ined from the initial value. You can manually override this by checking this boxand then clicking and dragging the blue line to your chosen concentration.

l Include t < 0 updates the chart to include regressions and any datapoints col-lected prior to the chamber fully closing.

l Show measured data displays the measured datapoints for an observation.l Show exponential regression plots the concentration against time and expo-

nential fit.l Show linear regression plots the concentration against time and linear fit.

Chart

The chart gives a visual representation of the flux for a specific observation. You canadjust the deadband (green line), stop time (red line), and C0 (blue line if you havechecked Force C0) by clicking and dragging them to a new location. When yourelease the mouse button, the data are fit linearly and exponentially with the resultsshown in the fit table above the chart.


2-9Fit


Fit table

The Fit table provides calculations for a number of different variables.

Variable Definition

C0 Initial dilution-corrected gas measurementCx Asymptote parameter from exponential fita Rate constant exponential coefficientt0 Time zerodC/dt Initial rate of change in dilution-corrected gas mole fractionSE of dC/dt Standard error of dC/dt for the fitr2 r2 value for the fitFlux Calculated fluxFlux CV Coefficient of variation of the fit for the flux

Table 2-1. Variable definitions for the Fit table.


MetadataMetadata allows you to update the volume or measurements of various componentsto ensure you have the correct Total Volume used to calculate your soil gas fluxes.The Total Volume field itself cannot be changed by the user but must be changed byupdating a device component.

To use the Metadata tool:

1 Select the observations you would like to update a measurement for.

2 Choose one of the device drop-downs.

3 Update one of the components, such as Collar Height, with the new measurement. Update anyadditional variables as needed.

4 Click Apply.


2-11Metadata


The Total Volume will update using the new measurement data for all flux cal-culations on the chosen observation(s). The Revert button will return all Metadatacomponent measurements to their original settings.

Note: The Area (cm2) field under CHAMBER includes a drop-down for area units.This drop-down allows you to change between area- and mass-based fluxes.Changing between area- or mass-based fluxes will affect the entire dataset as youmay only apply a single flux type to a File Group.

GuidanceGuidance provides various assessment tools to help you optimize your flux cal-culations. Guidance provides a graph that updates as you change parameters.

Note: Guidance only works on one observation at a time. If you have not selectedan observation (or have more than one selected) in the Summary view, the Guid-ance drop-down will remain inactive.


To use the Guidance tool:

1 Select which Variable you would like to assess. Variables match the list of flux calculations andare sorted by the analyzer that provided the measurement and the gas species.

2 Choose a Guidance Type.

l Start Analysis shows flux as a function of start time (given the current stop time) and canhelp you identify where the deadband needs to be set.

l Stop Analysis shows flux as a function of stop time (given the current start time) and canhelp you identify if your observations should be shorter or longer.

l Slope Analysis shows the slope of an exponential fit of data in a moving band between thecurrent start and stop times. In general, try to work in the region where this changes linearly.

l Fit Error shows how much variation there is in a flux.

3 Choose the Interval (s) to determine the step by which the time frame moves.

TransformTransform allows you to apply a mathematical function to a variable in the datasetfor all or specific observations. You can also compute something new using one ormore variables.

Data can be mathematically transformed using one of the following functions:

2-1

2-2

2-3

2-4

2-5

In these equations, Z is the output of the transformation, such as a new variable or areplaced variable, a, b, and c are user-entered constants, and X and Y are existing vari-ables used as inputs to the transformation. X and Y can be the same as Z, but theycan also be any other value in the observation.


2-13Transform


In addition to the above equations, SoilFluxPro Software includes four other built-intransformations specific to LI-8100A systems: three soil moisture transformationsand one soil temperature transformation. Each equation is named for the sensor itwill be used with and assumes that the signal from the soil moisture sensor has beenlogged in volts.

The Decagon_EC-5 transformation uses a 3rd order polynomial, and the twoDeltaT_ML3 transformations use a 6th order polynomial. The coefficients are shownin Table 2-2 below.

Name a b c d e f g

Decagon EC-5 -0.612 1.16 -0.314 - - - -DeltaT ML3(Mineral)

-0.071 0.735 0.75 -8.759 21.838 21.998 8.097

DeltaT ML3(Organic)

-0.039 0.802 0.819 -9.556 23.823 23.997 8.833

Table 2-2. The coefficients for soil moisture transformations.

The 8150-203 Thermistor option provides the following soil temperature trans-formation:

2-6

where

2-7

and a = 1.1259 × 10−3, b = 2.3459 × 10−4, and c = 8.6329 × 10−8.

Transforming a variableTo transform a variable:

1 Choose a function from the Function drop-down.

Note: Depending on the function you choose, you may not have a Y Variable or ac Value in later steps.


2 Select or deselect the Create New Column box as needed. This will create a new variablecolumn labeled "variable name" Transformed using the function, values, and units you enter.If you do not create a new column, you will need to overwrite an existing data column.

3 Select whether to transform the variable for all or specific observations.


4 Choose an X Variable and Y Variable. These will be the variables that are transformed. Vari-ables in the drop-down are sorted by device.


2-15Transforming a variable


5 Choose an X Type and a Y Type.

6 Enter an a Value, b Value, and c Value to be used in the function from step 1.


7 Give the column a New Column Name or you can use the default one provided by SoilFluxProSoftware.

8 Provide an Instrument Name or you can use the default name provided by SoilFluxProSoftware.

9 Add the Units for your transformed variable.

10 Click PREVIEW to see if the function is performing as expected.

11 Make any adjustments (if any) necessary, then click APPLY FUNCTION.


2-17Transforming a variable


A new device will appear under the Measured variables based on the InstrumentName you chose.

FavoritesAdd your Transform settings as a favorite to be applied to other datasets later.

Adding a favorite

Adding a favorite takes just a few steps. Once you have entered your settings as youwant them, click ADD TO FAVORITES at the bottom of the page.

You will receive a notification that your favorite has been added.


The Function you selected will become the name of the favorite using the X Variableand a/b Values you input.

Applying a favorite

To apply a favorite that you have saved, open the Favorites tab.

Select the favorite you would like to apply from the Favorite drop-down. ClickAPPLY FAVORITE.

The settings will load in the Settings tab.

Note: To delete a favorite, select the favorite from the Favorite drop-down andclick DELETE FAVORITE.


2-19Favorites


RepairThe Repair pane is where you can replace a bad chamber temperature reading onone port using a good reading from another port. This may be necessary if the tem-perature thermistor on a chamber is malfunctioning or damaged. Repairing a badtemperature reading will interpolate the new reading based on time.

To repair your temperature readings:

1 Select the observations you would like to repair the reading for.


2 Choose the port number that needs the reading replaced.

3 Choose the port number that will provide the replacement readings.

When the port includes an 8250-01 Extension Manifold, the port numbers will show up in a port-port combination. For example, if port 1 had an extension manifold that also had chambers onports 1, 3, and 5, the port numbers displayed would be: 1-1, 1-3, and 1-5.

4 Click REPAIR DATA.

You will receive a notification at the bottom of the page if the repair was successful.


RemoveThe Remove pane allows you to remove specific variable (columns) data from thedata.csv file that may not be relevant or to reduce the file size. However, Removewill not allow you to remove observations (rows) and removing data will not over-write the existing file. To remove observations, use the Remove Observation but-ton or, with the observations selected, you can press the Delete key.

To remove data:

1 Select the observations you would like to remove the data from.


2 Choose the variables you would like removed from the variable list. The variables are sorted bydevice.


2-21Remove


3 Click REMOVE CHOSEN. You may need to scroll through the variable list to find this button.

SoilFluxPro will then remove the selected variables from your dataset. If youremoved variables from all observations, the column will be removed. If youremoved variables from selected observations, the variables for those observationswill be replaced with a value of -9999.


StatisticsThe Statistics pane calculates statistics (mean, minimum, maximum, and standarddeviation) for your data. Statistics can be generated for all observations or a selectedrange of observations. Statistics can be provided using the variables you currentlyhave loaded in the Summary view or from a list of different variables you select.

To generate statistics:

1 Select the observations you would like to generate statistics for.


2 Choose which variables you would like statistics on.

Same as Displayed will use the variables you have currently loaded in the Summary view.

Other allows you to select the specific variables that will be used in the statistics. The variablesavailable are organized the same way as those described in Display on page 2-1.

3 Click GENERATE STATISTICS.


2-23Statistics


A new window will open with your statistics. From this window, you can Save...your statistics as a .csv file or you can Copy to Clipboard to copy the statistics andpaste them into another application.


Section 3.Details bar

The Details bar provides a variety of tools to show details and chart data from obser-vations or to view a log of your activity in SoilFluxPro Software.

LogThe Log pane shows a running, timestamped history of operations that you have per-formed since opening SoilFluxPro. The log will also show any warnings, errors, ormessages you have received.

DetailsSelecting the Details pane provides you with the raw time series data for a singleobservation. Details include all variables measured by all devices for each second ofthe observation. The variables on this page use a header structure similar to the onedescribed in Summary view on page 1-4.



Note: Not all observations will display the same variables. The columns in Detailsare based on the maximum variable set. If an observation does not have the samevariable as another observation, you will see a value of -9999.

The Details pane is read only; you cannot move or sort the columns. However, youcan save this data as a .csv file to view it in another application. To save the details ofan observation, click on the Save icon in the upper right corner.

Figure 3-1. The Details pane shows raw, second-by-second time series observation data.Details can be saved using the Save icon in the upper right corner.

This will open a dialog box. Select the destination where you would like to save thefile, enter a name for the file, and click Save. You will receive a notification at thebottom of the page that the file was saved.

ChartSoilFluxPro Software supports many charting features. The Chart pane enables youto generate charts for the dataset you have loaded. You can create charts for all orspecific observations using any variable for the x-axis and y-axis. The variables avail-able are organized the same way as those described in Display on page 2-1.

Creating a chartTo create a chart:

1 Select the observations you would like to have charted.



2 Provide a Chart Title.

3 Choose a Legend Location.


3-3Creating a chart


4 Choose an X-Axis Variable by clicking on the Add button. This field will remember the last x-axis variable you had active, so you may see a variable there when you open the Chart pane.

Navigate to the variable you would like to add and click Confirm.


5 Add Y-Axis variables by clicking on the Add button.

Navigate to the variable you would like to add and click Confirm.Y-axis variables include a num-ber of settings that can be applied to your chart.


3-5Creating a chart


l Symbol lets you choose from a number of different symbols to represent observations on achart. This is useful when using two y-axis variables.

l Axis determines on which side of the chart the variable units will appear.l Style provides three options for how observations will be displayed on the chart: as a scatter

plot, as a line chart, or as a scatter plot with a linear fit to the data.l Group By allows you to group observations by Observation or Group By Tests Below.

When grouped by observation, each observation appears in a different color and as a separateentry in the legend. Group By Tests Below is discussed in more detail under Grouping by teston page 3-8.

Note: You may have more than one y-axis variable in your chart. Distinguishthem by choosing different symbols. To remove a y-axis variable, click the Delete

Y-Axis variable button next to that variable.

6 Click GENERATE CHART or GENERATE CHART IN POPUP.

Your chart will appear either in the empty pane next to the chart settings or in apopup window.


Figure 3-2. The chart as it appears in the empty pane next to the chart settings.

Figure 3-3. The chart as it appears in a popup window.


3-7Creating a chart


Grouping by testGrouping can also be done by one or more tests. Grouping by test lets you organizeor sort how plotted data appear in your chart. For example, you could sort the data-points in Figure 3-3 on the previous page by port number to visualize fluxes by port.To group by test follow the steps in Creating a chart on page 3-2 to step 5, then:

1 Under the Y-Axis select Group By Tests Below.

2 Choose a Group By Variable. For this example, we will use Port from under theMetadata >LI-8250 drop-down.

To group by the port numbers on an 8250-01 Extension Manifold, you will need to use the ded-icated Metadata variable called Chamber. This variable will bring up a list of mul-tiplexer/extension manifold port number combinations for you to choose from.

3 Select an Interpret as option. In this case, Port would be an integer.

4 Choose a Test to set the conditions for the test grouping. These options allow you set conditionson how your datapoints will be plotted. G is for the Group By Variable you selected in step 2 and Zwill be entered in step 5.

l G is a member of set Z will include/exclude G (the variable) if it is one of the Z values. Thisis the Test we will use for this example.

l G < Z will include/exclude G if it is less than Z.l G <= Z will include/exclude G if it is less than or equal to Z.l G == Z will include/exclude G if it is equal to Z.l G >= Z will include/exclude G if it is greater than or equal to Z.l G > Z will include/exclude G if it is greater than Z.l G not already in a group will capture any datapoints that do not meet any other criteria.


5 Indicate the value Z represents in theWhere Z = field. Separate multiple values with a space. Forthis example, we would like to see datapoints from each port. Z would then need to correspond tothe port number. So, we enter Z as 1 2 3 4 5 6 7 8 because this system has a chamber onall eight ports.

6 Select whether to Include in Group Named or Exclude from any group. If you chooseInclude in Group Named, you will need to enter a name for the group. You can provide anyname you like but if you add an asterisk (*) after the name, SoilFluxPro will automatically create anew group for each value of G. For instance, we will enter the name as Port *. This will add anew group (color-coded) for each port.

7 Click ADD TEST. This will add the test for SoilFluxPro to reference when generating the chart.


3-9Grouping by test


When you click GENERATE CHART or GENERATE CHART IN POPUP you will nowsee your datapoints grouped by port number as seen in Figure 3-4 below.

Figure 3-4. A chart of CO2 fluxes grouped by port number.


Interacting with a chartCharts offer a few tools for working with them.

Zoom in

The Zoom In button allows you to zoom in on a specific portion of the chartyou would like to see more closely—especially where datapoints can be tightlygrouped. When you click the Zoom In button, your cursor will turn into a reticle.Click and drag the reticle across the region you would like to zoom in on. You canzoom multiple times.

Figure 3-5. Click and drag the reticle over the region you would like to zoom in on.

Zoom out

The Zoom Out button will go back one level on the zoom. If you have onlyzoomed in once, the view will return to 100% zoom.

Arrow Keys

When charting raw data from a single observation, the up and down arrow keys onyour keyboard allow you to cycle through observations.


3-11Interacting with a chart


Datapoint hover

Hovering your cursor over a datapoint will display details about that datapoint inthe upper left corner. This is useful for getting details about outlying datapoints.

Figure 3-6. Hovering your cursor over a datapoint will display details about that datapoint.

Save image

Clicking on the Save As Image button will save the current view of the chart as a.png file to the destination you choose.

FavoritesSoilFluxPro can save Chart settings and Tests you use frequently as favorites. Favor-ites let you quickly apply a chart setting to other datasets later. There are a few pre-defined chart favorites that can be selected but there are no predefined tests.

Adding a favorite

Adding a favorite takes just a few steps. Once you have entered your settings as youwant them, click ADD TO FAVORITES or ADD TEST SET TO FAVORITES at the bot-tom of the page.



The Chart Title or test conditions you provided will be used as the name of the favor-ite.

Applying a favorite

To apply a favorite that you have saved or one of the predefined charts, open theFavorites tab.


3-13Favorites


Select the favorite you would like to apply from the Chart Favorites or Test Favoritedrop-down.

Click APPLY FAVORITE.

The chart will generate in the empty pane automatically. If you'd like to generatethe chart in a popup, go back to the Settings tab and click GENERATE CHART INPOPUP.

Note: To delete a favorite, select the favorite from the Chart Favorite or TestFavorite drop-down and click DELETE FAVORITE.


Section 4.File Management bar

The File Management bar is where you can open, save, export, import, and create.kml files to view your data in the Google Earth™ mapping service. This bar alsocontains the cut, copy, paste, and delete buttons for observations.

Saving dataSoilFluxPro Software lets you save observations of your loaded File Group into afresh archive of .82z files. Saving data will not overwrite existing files but makes aseparate archive. The new archive includes the changes you have made inSoilFluxPro, including recomputed, transformed, repaired, and removed data.

To save data in SoilFluxPro, click Save in the File Management bar.

Select the observations you would like to save and click Save.

This will open a dialog box. Select the destination where you would like to save thearchive, enter a name for the .zip archive, and click Save. You will receive a noti-fication at the bottom of the page that the data was saved.



Exporting dataExporting data from SoilFluxPro Software lets you take the summary data of yourloaded File Group and export it as a .csv file to be opened in Microsoft Excel or stat-istical analysis software. You can export data using the variables you currently haveloaded in the Summary view or you can select particular variables from a list of allvariables.

To export a file in SoilFluxPro, click Export in the File Management bar.

Select the observations and columns you would like to export. Same as View willuse the same variables you currently have loaded in the Summary view. Other willallow you to tailor which variables to export from a list of all variables. Click Export.

This will open a dialog box. Select the destination where you would like to exportthe summary data, enter a name for the .csv file, and click Save.

You will receive a notification at the bottom of the page that the data was exported.


Importing dataImporting data lets you import time series data from stand-alone LI-78xx Trace GasAnalyzers and third-party gas analyzers (when used with a LI-COR soil gas flux sys-tem) for use in SoilFluxPro.

Imported analyzer data is resampled to align its sampling time and frequency withthe soil data where it will be imported. Alignment is accomplished by interpolationbetween the datapoints on either side of the record that are nearest in time.

Note: To import a file you must first have opened a .82z, .81x, or .json file thatcorresponds in time and was collected in parallel with the data to be imported.

The Import window can be broken down into three field sections: General,Metadata, and Date & Time.

General

1 File Format is based on the type of analyzer you will be importing data from. Available optionsare LI-78xx (for LI-COR Trace Gas Analyzers), General Purpose, LGR, Aerodyne, Gasmet, andPicarro.

2 Favorite Import Settings keeps a list of favorite settings you have added so that you can applythem quickly.

3 ADD FILES opens a file explorer where you can select your gas analyzer files from your computeror a storage device connected to your computer.

Note: If you have files stored in more than one directory, you will need to ADDFILES multiple times.

4 The Variable Selection pane lets you choose which variables you would like to import intoSoilFluxPro.

Note: Only numerical data may be imported.


4-3Importing data


Metadata

1 H2O Source defines the instrument variable that should be referenced for the water vapor meas-urement used in the dilution correction.

2 Device Name assigns the name under which all of the analyzer data will be grouped afterimporting.

3 Tube Length is the length of the tubing that runs between the analyzer and the multiplexer,chamber, or other device. The Tube Length may be zero, but it usually is not.

4 Analyzer Volume is the volume of the internal components of the analyzer and must be greaterthan zero.

5 Serial Number (optional) sets the serial number of your analyzer.

6 Firmware (optional) records the version of firmware your analyzer was running at the time of themeasurements.

Note: For LI-COR LI-78xx Trace Gas Analyzers you will not need to provide theH2O Source, Device Name, Analyzer Volume, Serial Number, or Firmware asthese are known.


Date & Time

Note: Depending on your File Format, you may not be able change many of thesefields because they are known.

1 Columns determines whether the Date Time and Time labels described below will be Com-bined or Separate.

2 DateTime Label defines the label used to reference the date (and time if combined).

3 Date Format provides the format used in the Date Time Label.

4 Time Label defines the label used to reference the time (if separated from date).

5 Time Format provides the format used in the Time Label

6 Delimiter defines what delimiter is used when reading the file. SoilFluxPro can read files withtab, comma, or space delimiters.

7 Adjust time of imported data by adjusts the time of imported data to coordinate it with datafrom .82z, .81x, or .json files.


4-5Date & Time


How to importTo import a file into SoilFluxPro:

1 Open a .82z, .81x, or .json file (see Opening a file in SoilFluxPro Software on page 1-6).

2 Click Import in the File Management bar.

3 Choose your File Format based on your analyzer.

4 ADD FILES from your computer.

5 Select which variables you would like to include and set the units as is appropriate for each vari-able. You can also select which variables you would like to receive a flux calculation for. Flux cal-culations can be added later if they are not done during Import, but the variables necessary to dosomust be imported.

Any variables with the Flux box checked will also need you to provide a Deadband, Stop time,and to choose whether the flux will be computed for aWet gas or a Dry gas. The choice of a wetor dry gas determines how dilution is done on the flux calculation.

l A dry gas means the H2O Source will only be used to provide the H2O initial value.l A wet gas means the H2O Source will be used for the H2O initial value and to convert each gas

measurement to a dry mixing ratio.

With LI-78xx Trace Gas Analyzers, many variables are preconfigured and do not need to be set.


6 Set the H2O Source.

Note: H2O Source is linked to the variables in the Variable Selection pane. Youmust set the units for your H2O source to the correct mole fraction for the sourceto be used in the dilution correction.

7 Provide a Device Name.

8 Enter the Tube Length and Analyzer Volume.

9 Provide the device Serial Number and Firmware.

10 For most analyzers you will not need to provide a DateTime Label, Date Format, Time Label,Time Format, or Delimiter. However, if you are using a General Purpose analyzer, you will needto provide these fields.

11 Set the number of seconds to Adjust time of imported data by if needed.

12 Click Import.

Note: Before clicking Import, consider if this is an analyzer you will be using fre-quently. If so, it might be useful to save these setting with the ADDTO FAVORITES button to quickly apply these same settings later.

13 Save the combined data set to a new set of .82z files (see Saving data on page 4-1).

FavoritesAdd your Import settings as a favorite to be applied later.

Adding a favorite

Adding a favorite takes just a few steps. Once you have entered your settings, clickADD TO FAVORITES at the bottom of the page and give the favorite a name.


The name you provided will become the name of the favorite.


4-7Favorites


Applying a favorite

To apply a favorite that you have saved, click the Favorite Import Settings drop-down.

Select the favorite you would like to apply and click APPLY FAVORITE.

Note: To delete a favorite, select the favorite from the Favorite Import Settingsdrop-down and click DELETE FAVORITE.

Mapping dataIf GPS data is contained in an observation, a .kml file can be created for visu-alization using Google Earth™ mapping service. The Map tool uses summary dataand associates a geographic location to it using location data from the file.

Creating a .kml fileTo map your data to a .kml file:

1 Decide which observations you would like to map from the Summary view.

You can select observations individually by clicking on them, or you can use Ctrl + click toselect multiple individual observations or Shift + click to select all observations in a range.If you would like to map all observations, press Ctrl + A to select all observations in the Sum-mary view.

2 ClickMap in the File Management bar.


3 Give the file a KML Doc Name and KML Doc Description.

4 Select the observation ID to be included in the .kml file. You can select observations individuallyusing the checkbox next to them or select them all with the global checkbox at the top.


4-9Creating a .kml file


5 Choose which markers will be included in your .kml file. Several predefined markers are included.You can edit the predefined markers according to your needs. You can also create a new markerby copying one of the existing markers or by clicking ADD MARKER. See Adding or editing amarker on the facing page for more information.

6 Select how you would like data grouped under the Group By drop-down. If you have many obser-vations, you may need to scroll down to find this menu.


7 Click EXPORT.

This will open a dialog box. Select the destination where you would like to exportto, enter a name for the .kml file, and click Save. You will receive a notification atthe bottom of the page that the KML file was saved.

Adding or editing a markerYou may need to add or edit markers according to your goals. SoilFluxPro Softwareallows you to edit markers or create new markers.

Adding a marker

You can add a marker by clicking the ADD MARKER button or by clicking the CopyMarker icon of the marker you would like to copy.

Copying a marker will create a new marker of the same name and you can adjustthe settings as you need to. ADD MARKER will provide you with an incompletemarker and you will need to enter settings from scratch. We will use an incompletemarker as an example.


4-11Adding or editing a marker


1 Give the marker a Name and Label to identify it.

2 Choose aMarker type from the drop-down. There are several to choose from and some have anadditional drop-down to further distinguish the marker.

l Point (icon) will tag locations using a point marker. This type requires you to selectanother Marker type. Pin will use a green pushpin to mark locations. A and B will mark loc-ations with an inverted teardop marker labeled A or B.

l Point (column) will insert a 3D column (if you have checked 3D Height) proportional to theflux at the location. This type requires you to selectMarker column size.

l Path lets you view the path of the measurement. With 3D Height checked, the path alsoprovides a height that is computed from the soil gas flux at each point.

l Polygon will map an area of interest using location data.

3 Description Item #1 and Description Item #2 allow you to select which variable data youwould like to have mapped, such as CO2 or CH4 flux. You will also provide a Point Set #1 orPoint Set #2 for each of these variables as either the Initial Value,Mean, Range, or All.

4 Choose an Instrument for GPS Data. This defaults to the LI-8250 Multiplexer but if you haveentered a GPS location to your chambers, these locations can be used to provide a more diversemap.

5 Toggle 3D Height. Some markers, such as columns, benefit from using a 3D Height proportionalto the flux to provide a visualization of flux.


6 Select a Line color, Line width, and Surface Color.

Editing a marker

To edit a marker, open the drop-down of the marker you would like to edit andchange the settings as needed.

Viewing data on Google Earth™To view your data using the Google Earth™ mapping service:

1 Create a .kml file with your observation data using the steps in Creating a .kml file on page 4-8.

2 In your browser, go to google.com/earth.

3 Click Launch Earth.

4 Open the Projects tab in the sidebar.

5 Expand the Open drop-down and select Import KML file from computer.

6 This will open a dialog box. Navigate to the .kml file you would like to open and select Open.

Google Earth™ will then load the .kml file and map your data.


4-13Viewing data on Google Earth™

https://www.google.com/earth



A-1Using SoilFluxPro

Appendix A.Data dictionary

The data dictionary describes variable names from the files and how those variablesare displayed in SoilFluxPro.

LI-8250 Multiplexer variables

User Interfacevariable

Units Data file variable Description

DOY DOY Decimal day of year at start of measurement

Date Time YYYY-MM-DDHH:MM:SS

Combined date and time timestamps

Date YYYYMMDD DATE Timestamp of year-month-day

Time HHMMSS TIME Timestamp of hours-minutes-seconds

Temperature C T_CASE Internal temperature of the multiplexer

Pressure kPa PA Atmospheric pressure

PressureTemperature

C T_PA Atmospheric pressure sensor temperature

Pump PositivePressure

kPa PUMP_POSITIVE_PRESSURE

Pressure sensor on the positive pressure sideof the sampling pump

Pump NegativePressure

kPa PUMP_NEGATIVE_PRESSURE

Pressure sensor on the negative pressureside of the sampling pump

Flow L M-1 FLOW Flow rate through the LI-8250 Multiplexer tothe active port.

Pump Time H PUMP_TIME Hours of sampling pump operation

Table A-1. LI-8250 Multiplexer Measured definitions. The device for these variables will be LI-8250.




Pump Setpoint PUMP_SETPOINT Drive setting for the sampling pump

Pump Current A PUMP_CURRENT Current draw by the sampling pump

SubsamplePressure

kPa SUB_PRESSURE Ambient to subsample loop pressuredifferential

Subsample Flow L M-1 SUB_FLOW Flow through the subsample loop

VSO FlowSetpoint

VSO_FLOW_SETPOINT Drive setting for the variable value on theinlet side of the subsample loop

VSO PressureSetpoint

VSO_PRESSURE_SETPOINT

Drive setting for the variable value on theoutlet side of the subsample loop

Port n Current A PORTn_CURRENT Current draw through the port number listed

Solenoid Current A SOL_CURRENT Current supplied to valves and VSOs

12 VDC Current A 12VDC_CURRENT Current draw on the 12 VDC power outputsupply

Voltage V VIN Input voltage to multiplexer

Voltage Out V VOUT Output voltage on the nominal 24 VDCsupply

VSO FlowControl Voltage

V Flow control voltage to VSO

VSO PressureControl Voltage

V Pressure control voltage to VSO

5 VDC Voltage V 5VDC_VOLTAGE 5 V supply voltage

12 VDC Voltage V 12VDC_VOLTAGE 12 V supply voltage

Flow Pressure kPa FLOW_PRESSURE Pressure measurement used to determineflow rate

Subsample FlowPressure

kPa SUB_FLOW_PRESSURE Pressure measurement used to determinesubsample flow rate

Latitude ° LATITUDE Latitude reported by GPS

Longitude ° LONGITUDE Longitude reported by GPS

Table A-1. LI-8250 Multiplexer Measured definitions. The device for these variables will be LI-8250.(...continued)

A-2 Using SoilFluxPro



Satellites SATELLITES Number of satellites

Altitude m ALTITUDE Altitude reported by GPS

Table A-1. LI-8250 Multiplexer Measured definitions. The device for these variables will be LI-8250.(...continued)



Volume cm3 VOLUME Device volume

Serial Number SERIAL_NUMBER Device serial number

Firmware FIRMWARE Device firmware version

Port Label PORT_LABEL User entered description associated with theport

Port PORT Port number the observation was made on

Latitude ° LATITUDE Multiplexer latitude in decimal degrees

Longitude ° LONGITUDE Multiplexer longitude in decimal degrees

Table A-2. LI-8250 Multiplexer Metadata definitions. The device for these variables will be LI-8250.For a list of Metadata variables common to all LI-COR devices, see Table A-23 on page A-16.


A-3Appendix A. Data dictionary


8250-01 Extension Manifold variables



Temperature C T_CASE Internal temperature of the extension manifold

Pump Time H PUMP_TIME Hours of sampling pump operation

Pump Setpoint PUMP_SETPOINT Drive setting for the sampling pump

Pump Current A PUMP_CURRENT Current draw by the sampling pump

Port n Current A PORTn_CURRENT Current draw through the port number listed

Solenoid Current A SOL_CURRENT Current supplied to valves and VSOs

Voltage V VIN Input voltage to multiplexer

12VDC_VOLTAGE

V 12VDC_VOLTAGE 12 V supply voltage

5VDC_VOLTAGE V 5VDC_VOLTAGE 5 V supply voltage

3.3VDC_VOLTAGE

V 3.3VDC_VOLTAGE 3.3 V supply voltages

Diagnostic DIAG_CODE Diagnostic flag bits

Table A-3. 8250-01 Extension Manifold data definitions. The DEVICE for these variables will be 8250-01.







Tube Length cm TUBE_LENGTH Volume of extension tubing

Table A-4. 8250-01 Extension Manifold Metadata definitions. The device for these variables will be8250-01.. For a list of Metadata variables common to all LI-COR devices, see Table A-23 onpage A-16.


8200-01S Smart Chamber variables







PressureTemperature

C T_PA Atmospheric pressure sensor temperature

Altitude m ALTITUDE Altitude reported by GPS

Satellites SATELLITES Number of satellites

Table A-5. 8200-01S Smart Chamber Measured definitions. The device for these variables will be LI-8200.



Elapsed Time s Elapsed time since the chamber has closed

Temperature C TA Chamber air temperature

TS_1 C TS_1 Soil temperature from the thermocoupleprobe

EC_2 # EC_2 Electrical conductivity from the StevensHydraProbe in S m-1

SWC_2 m3m-3 SWC_2 Soil moisture from the Stevens HydraProbe

TS_2 C TS_2 Soil temperature from the StevensHydraProbe

Table A-6. 8200-01S Smart Chamber Measured definitions. The device for these variables will beCHAMBER.








Rep REP Replicate for repeated observations

Remark REMARK Remark

Label LABEL Measurement label

Table A-7. 8200-01S Smart Chamber Metadata definitions. The device for these variables will be LI-8200. For a list of Metadata variables common to all LI-COR devices, see Table A-23 on page A-16.






Collar Height cm COLLAR_HEIGHT Collar height

Area cm2 AREA Soil area


Park PARK_POSITION Chamber park position

Latitude ° LATITUDE Chamber latitude in decimal degrees

Longitude ° LONGITUDE Chamber longitude in decimal degrees

Table A-8. 8200-01S Smart Chamber Metadata definitions. The device for these variables will beCHAMBER. For a list of Metadata variables common to all LI-COR devices, see Table A-23 onpage A-16.


LI-COR long-term chamber variables





BoardTemperature

C TB Chamber control board temperature

Voltage V VIN Chamber input voltage

Motor Current A MOTOR_CURRENT Current draw by chamber drive motor

State STATE There are eight chamber states:

1 = closing

2 = opening

3 = parking

4 = manual move

5 = closed

6 = open

7 = parked

8 = unknown

Diagnostic DIAGNOSTIC Diagnostic value indicating the quality of thedata and state of the instrument

Table A-9. LI-COR chamber Measured definitions. The device for these variables will be CHAMBER.Depending on configuration, there may be other variables in this group as defined by the user.







Serial Number SERIAL_NUMBER Device serial number or chamber type




Closing Time s CLOSE_TIME Time it took the chamber to close

Tube Length cm TUBE_LENGTH Length of tubing associated with thechamber used to calculate total volume

Park Position ° PARK Chamber park position



Table A-10. LI-COR chamber Metadata definitions. The device for these variables will be CHAMBER.For a list of Metadata variables common to all LI-COR devices, see Table A-23 on page A-16.


LI-6800 Portable Photosynthesis System and 6800-09 Soil CO2Flux Chamber variables






CO2 μmol mol-1 CO2 Carbon dioxide mole fraction

CO2 Dry μmol mol-1 CO2_DRY Carbon dioxide dry mixing ratio

H2O mmol mol-1 H2O Water vapor mole fraction


Date YYYYMMDD DATE Timestamp of year-month-day

Time HHMMSS TIME Timestamp of hours-minutes-seconds

Table A-11. LI-6800 Portable Photosynthesis System and 6800-09 Soil CO2 Flux Chamber Measureddefinitions. The device for these variables will be LI-6800.




SWC m3m-3 SWC Soil moisture from the Stevens HydraProbe


TS C TS Soil temperature from the StevensHydraProbe

State STATE

Table A-12. LI-6800 Portable Photosynthesis System and 6800-09 Soil CO2 Flux Chamber Measureddefinitions. The device for these variables will be CHAMBER.









Label LABEL Measurement label

Table A-13. LI-6800 Portable Photosynthesis System and 6800-09 Soil CO2 Flux Chamber Metadatadefinitions. The device for these variables will be LI-6800. For a list of Metadata variables common toall LI-COR devices, see Table A-23 on page A-16.









Park PARK_POSITION Chamber park position



Table A-14. LI-6800 Portable Photosynthesis System and 6800-09 Soil CO2 Flux Chamber Metadatadefinitions. The device for these variables will be CHAMBER. For a list of Metadata variablescommon to all LI-COR devices, see Table A-23 on page A-16.


LI-870 CO2/H2O Analyzer variables






Cell Temperature C T_CELL Optical bench temperature

Cell Pressure kPa PA_CELL Pressure in the optical bench

CO2 Absorption CO2_ABS Absorption by carbon dioxide

H2O Absorption H2O_ABS Absorption by water vapor

Dewpoint C Dew point temperature

Voltage V VIN Input voltage to the LI-870

Flow L M-1 FLOW Flow rate through the LI-870

Table A-15. LI-870 CO2/H2O Analyzer Measured definitions. The device for these variables will beLI-870.






Tube Length cm TUBE_LENGTH Length of tubing associated with theanalyzer used to calculate total volume

Table A-16. LI-870 Metadata definitions. The device for these variables will be LI-870. For a list ofMetadata variables common to all LI-COR devices, see Table A-23 on page A-16.




LI-78xx Trace Gas Analyzer variables



Diagnostic DIAGNOSTIC Diagnostic value indicating the quality of thedata and state of the instrument

CO2 Dry μmol mol-1 CO2_DRY Carbon dioxide dry mixing ratio (LI-7810 andLI-7815 only)


CH4 Dry nmol mol-1 CH4_DRY Methane dry mixing ratio (LI-7810 only)

N2O Dry nmol mol-1 N2O_DRY Nitrous oxide dry mixing ratio (LI-7820 only)

CavityTemperature

C T_CAVITY Optical cavity temperature

Cavity Pressure kPa PA_CAVITY Optical cavity pressure

Laser Pressure kPa PA_LASER_PHASE Pressure used to control the laser phase

LaserTemperature

C T_LASER Temperature of the laser

Residual RESIDUAL Residual of absorption spectrum fit

Ring Down μs RING_DOWN Ring down time

EnclosureTemperature

C T_THERMAL_ENCLOSURE

Temperature of the optical cavity enclosure

Phase Error PHASE_ERROR Error between setpoint and actual laserphase in counts

ShiftTemperature

C T_LASER_SHIFT Difference between factory set lasertemperature and operating lasertemperature

Voltage V VIN Input voltage to the LI-78xx

Table A-17. LI-78xx Trace Gas Analyzer Measured definitions. The device for these variables will beLI-7810, LI-7815, or LI-7820.







Tube Length cm TUBE_LENGTH Length of tubing associated with theanalyzer used to calculate total volume

Table A-18. LI-78xx Metadata definitions. The device for these variables will be LI-7810, LI-7815, orLI-7820. For a list of Metadata variables common to all LI-COR devices, see Table A-23 on page A-16.




LI-8100A Automated Soil CO2 Flux System and LI-8150Multiplexer variables




Date YYYY-MM-DDHH:MM:SS






Cell Temperature C T_CELL Optical bench temperature

RH % RH Relative humidity

BoardTemperature

C T_BOARD Control board temperature

Voltage V VIN Input voltage to LI-8100A

CO2 Absorption CO2_ABS Absorption by carbon dioxide

H2O Absorption H2O_ABS Absorption by water vapor

Hour H HOUR Hour of the day

CO2 Raw RAWCO2 Raw CO2 signal

CO2 RawReference

RAWCO2REF Optical amplitude of CO2 channel

H2O Raw RAWH2O Raw H2O signal

H2O RawReference

RAWH2OREF Optical amplitude of H2O channel

Table A-19. LI-8100A Automated Soil CO2 Flux System Measured definitions. The device for thesevariables will be LI-8100.




Flow L M-1 FLOW Flow rate through the LI-8150 Multiplexer tothe active port.

Table A-20. LI-8150 Multiplexer Measured definitions. The device for these variables will be LI-8150.







Comment COMMENT

Table A-21. LI-8100A Automated Soil CO2 Flux System Metadata definitions. The device for thesevariables will be LI-8100. For a list of Metadata variables common to all devices, see Table A-23 on thenext page.





Latitude ° LATITUDE Multiplexer latitude in decimal degrees

Longitude ° LONGITUDE Multiplexer longitude in decimal degrees

Table A-22. LI-8150 Multiplexer Metadata definitions. The device for these variables will be LI-8150.For a list of Metadata variables common to all LI-COR devices, see Table A-23 on the next page.




Metadata variables



Start Time YYYYMMDDHHMMSS

TIMESTAMP_START Timestamp at the start of an observation

Total Volume cm3 VOLUME_TOTAL Total volume used in flux calculations

Prepurge s PREPURGE Prepurge length

ObservationLength

s OBSERVATION Observation length

Post Purge s POST_PURGE Post purge length

Horizontal HORIZONTAL Numerical value of H from chamber's HVRfield

Vertical VERTICAL Numerical value of V from chamber's HVRfield

Table A-23. All LI-COR devices share the metadata variables shown below.


Flux variables



Deadband s DEADBAND Deadband length

Stop Time s STOP_TIME Length of data used for the flux computation

Replicate REPLICATE Numerical value of R from the chamber'sHVR field

Dilution Source DILUTION_SOURCE Name of the device that provided the watervapor measurement used for dilutioncorrection (NONE for a dry gas)

Dilution Units DILUTION_UNIT Units of water vapor measurement (NONEfor a dry gas)

Gas GAS Name of the gas species the flux wascomputed for

Gas Source GAS_SOURCE Name of the device that measured the gasfor which the flux was computed

Temperature TEMPERATURE Label of the temperature measurement usedin flux calculation

TemperatureSource

T_SOURCE Device of temperature measurement used influx calculation

Table A-24. Flux variable definitions. The device for these variables will reflect the analyzer used andgas measured.





Units Description

Flux nmol m-2 s-1 Area-based flux of gas species based on exponential fit

Flux nmol kg-1 s-1 Mass-based flux of gas species based on exponential fit

dC/dt nmol mol-1 s-1 Slope used to compute flux

R2 Regression coefficient of fit to accumulation curve

CV Coefficient of variation for flux calculation

C0 nmol mol-1 Gas concentration at time zero

Cx nmol mol-1 Asymptotic gas concentration

a Curvature parameter of exponential fit

T0 s Time zero for fitting accumulation curve

SEI Standard error for the intercept

SES Standard error for the slope

Table A-25. Exponential flux calculation variable definitions. The device for these variables willreflect the analyzer used and gas measured. The nmol units vary depending on the units the gas wasmeasured in (e.g., nmol, μmol, or mmol).


Units Description

Flux nmol m-2 s-1 Area-based flux of gas species based on linear fit

Flux nmol kg-1 s-1 Mass-based flux of gas species based on linear fit

dC/dt nmol mol-1 s-1 Slope used to compute flux

R2 Regression coefficient of fit to accumulation curve

CV Coefficient of variation for flux calculation

SE Standard error

SSN Normalized sum of squares

Table A-26. Linear flux calculation variable. The device for these variables will reflect the analyzerused and gas measured. The nmol units vary depending on the units the gas was measured in (e.g.,nmol, μmol, or mmol).


B-1Using SoilFluxPro

Appendix B.Supported units

Table B-1 below provides a complete listing of the units supported in SoilFluxProand their formats. The table includes how each unit is displayed in SoilFluxPro(User interface unit), how it is written in the data file (File unit), and a descriptionof the unit.

User interface unit File unit Description

% % Percent‰ permil Permilμs us Microseconds s SecondM M MinuteH H HourYYYYMMDDHHMM YYYYMMDDHHMM Date: year, month, day, hour, minutekg kg Kilogramsg g GramsK K KelvinC C CelsiusPa Pa PascalhPa hPa HectopascalkPa kPa KilopascalV V VoltsA A Ampsm m Meterscm cm Centimetersmm mm MillimetersW W Watts

Table B-1. A complete listing of all units supported in SoilFluxPro

Appendix B. Supported units

User interface unit File unit Description

J J JoulesL L Litersnmol nmol Nanomolesμmol umol Micromolesmmol mmol Millimolesmol mol Moles° degrees Decimal degreesnmol mol-1 nmol+1mol-1 Nanomoles per moleμmol mol-1 umol+1mol-1 Micromoles per mole

mmol mol-1 mmol+1mol-1 Millimoles per mole

nmol mol-1 s-1 nmol+1s-1mol-1 Nanomoles per mole dry air persecond

μmol mol-1 s-1 umol+1s-1mol-1 Micromoles per mole dry air persecond

mmol mol-1 s-1 mmol+1s-1mol-1 Millimoles per mole dry air persecond

nmol m-2 s-1 nmol+1m-2s-1 Nanomoles per meter square persecond

μmol m-2 s-1 umol+1m-2s-1 Micromoles per meter square persecond

mmol m-2 s-1 mmo+1m-2s-1 Millimoles per meter square persecond

Wm-2 W+1m-2 Watts per meter squaremm2 mm+2 Square millimeterscm2 cm+2 Square centimetersm2 m+2 Square meterscm3 cm+3 Cubic centimetersm s-1 M+1s-1 Meters per secondL M-1 L+1M-1 Liters per minuteM-1 M-1 Per minutem3m-3 m+3m-3 Cubic meters per cubic meter

# Dimensionless unit number

Table B-1. A complete listing of all units supported in SoilFluxPro (...continued)

B-2 Using SoilFluxPro

Appendix C.Index

Cchamber, 1-4variable, A-7, A-8

chart, 1-5, 3-2create, 3-2favorites, 3-12add, 3-12apply, 3-13

group by test, 3-8interacting, 3-11recompute, 2-9

Ddataexport, 4-2import, 4-3interaction bar, 1-3, 2-1map, 4-8view, 4-13

recompute, 2-7remove, 2-21save, 4-1variable, A-1

deadband, 2-8deletecolumn, 2-21row, 2-21

details, 3-1bar, 1-5, 3-1

device, 1-4display, 1-3, 2-1

Eexport, 1-2data, 4-2

extension manifoldvariable, A-4

Ffavoriteschart, 3-12add, 3-12apply, 3-13

graph, 3-12add, 3-12apply, 3-13

import, 4-7add, 4-7apply, 4-8

test, 3-12add, 3-12apply, 3-13

transform, 2-18add, 2-18apply, 2-19

file82z, 1-6group, 1-3management, 1-2

3Appendix C. Index

management bar, 1-2, 4-1open, 1-6variable, A-1zip, 1-6

fitrecompute, 2-7table, 2-10

fluxrecompute, 2-7variable, 1-4, 2-1, 2-5, A-17, A-18

GGoogle Earth, 1-2, 4-1, 4-8view, 4-13

graph, 1-5, 3-2create, 3-2favorites, 3-12add, 3-12apply, 3-13

group by test, 3-8interacting, 3-11recompute, 2-9

group by test, 3-8guidance, 2-12

Hheader, 1-4history, 3-1

Iimportdata, 4-3favorites, 4-7add, 4-7apply, 4-8

initial value, 2-3instrument, 1-4introduction, 1-1

Llabel, 1-4LI-6800variable, A-9, A-10

LI-7810, 1-4variable, A-12, A-13

LI-7820, 1-4variable, A-12, A-13

LI-8100Avariable, A-14, A-15

LI-8150variable, A-15

LI-8250, 1-4variable, A-1, A-3

LI-870, 1-4variable, A-11

log, 1-5, 3-1

Mmain screen, 1-1map, 1-2, 4-1add marker, 4-11data, 4-8view, 4-13

edit marker, 4-13maximum, 2-23mean, 2-3, 2-23measuredvariable, 1-4, 2-1, 2-2chamber, A-7LI-6800, A-9LI-7810, A-12LI-7820, A-12LI-8100A, A-14LI-8250, A-1LI-870, A-11multiplexer, A-1, A-14Smart Chamber, A-5

menubar, 1-5

metadatarecompute, 2-11variable, 1-4, 2-1, 2-4, A-16chamber, A-8LI-6800, A-10LI-7810, A-13LI-7820, A-13

Appendix C. Index

4 Using SoilFluxPro

LI-8100A, A-15LI-8150, A-15LI-8250, A-3LI-870, A-11multiplexer, A-3Smart Chamber, A-6

minimum, 2-23multiplexer, 1-4variable, A-1, A-3, A-14, A-15

Oobservationcopy, 1-3cut, 1-3paste, 1-3recompute, 2-8remove, 2-21

open82z, 1-2file, 1-6zip, 1-2

Rrange, 2-3recompute, 1-3, 2-7chart, 2-9fit, 2-7flux, 2-7graph, 2-9metadata, 2-11observation, 2-8

removecolumn, 2-21data, 1-3, 2-21observation, 2-21row, 2-21

repairtemperature, 1-3, 2-20

Ssave, 1-2data, 4-1

Smart Chambervariable, A-5, A-6

standard deviation, 2-23statistics, 1-3, 2-23stop time, 2-8summary view, 1-4, 2-1

Ttemperaturerepair, 1-3, 2-20source, 2-8

testfavorites, 3-12add, 3-12apply, 3-13

tourinterface, 1-1

Trace Gas Analyzervariable, A-12, A-13

transform, 1-3, 1-4, 2-13favorites, 2-18add, 2-18apply, 2-19

variable, 2-14

Uunits, 1-4supported, B-1

Vvariable, A-1chamber, A-7, A-8details, 3-1diplay, 1-3display, 2-1extension manifold, A-4flux, 1-4, 2-1, 2-5, A-17, A-18LI-6800, A-9, A-10LI-7810, A-12, A-13LI-7820, A-12, A-13LI-8100A, A-14, A-15LI-8150, A-15LI-8250, A-1, A-3

Appendix C. Index

5Appendix C. Index

LI-870, A-11measured, 1-4, 2-1, 2-2metadata, 1-4, 2-1, 2-4, A-16multiplexer, A-1, A-3, A-14, A-15Smart Chamber, A-5, A-6Trace Gas Analyzer, A-12, A-13transform, 2-14

Appendix C. Index

6 Using SoilFluxPro

C

M

Y

CM

MY

CY

CMY

K

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