PhotosynQ Documentation

# Data Issues

We have programmed issue warnings into the default Leaf Photosynthesis MultispeQ v1.0 and Photosynthesis RIDES protocols. We recommend that users discard measurements with red warning message's, unless they are certain the measurement is accurate. Users may also program issue warnings into their own macro's for quality control.

Tip

The Leaf Photosynthesis MultispeQ v1.0 protocol also has yellow issue warnings. These are for information only and should NOT be discarded unless you are certain the measurement is bad.

Issue warnings on the android (left) and desktop (right) apps

# Common causes of issue warnings

  1. The device or leaf was not held steady throughout the measurement. This can be due to taking measurements in windy conditions or the data collector's hand shaking.
  2. The leaf did not fully cover the light guide. This is especially problematic for absorbance measurements such as relative chlorophyll content. This often results in a warning message stating that the relative chlorophyll content is either very low or out of the expected range.
  3. The leaf was dead or dying. Leaves in this condition can cause the Phi2, PhiNPQ or PhiNO values to be out of the expected range. This may be a completely valid measurement, or a measurement that should be discarded.

# Identify measurements with issue warnings in the data explorer?

  1. We have added a default panel on the dashboard labelled Data Quality - Issues that provides information about how many of the non-flagged measurements have issues. If the panel is not visible, you can add it to your dashboard by:
    • Select Add Panel in the dashboard
    • Select the data quality tab
    • Select the Show Issues button below Data Issues

Note

Only non-flagged measurements with issues will be displayed on the dashboard. Once you have flagged a measurement, it is hidden from normal data viewing and analysis unless you check the Include flagged datasets box in the Add Series tab

1. Add panel to the dashboard 2. Open the Data Quality tab from the Dialog and select the Show Issues button. 3. The panel will be added to the dashboard.

  1. In the Spreadsheet view, there is an Issues column that will display how many issues exist for a given measurement.

  2. In the single datum view, any issues will be present as a red bar above the measurement results.

1. Identifying issues in the spreadsheet (left) 2. Click on the ID in the first column to select bring up the data view. 3. See the details in the single datum view.

# Adding issue warnings to Macros

Anyone can add issue warnings to their own macro's by following the code structure below.

# Code Structure

Here is an example of how we added issue warnings to the Photosynthesis RIDES protocol for when Phi was out of the expected range (0 - 0.85).

if (fvfm <= 0) {
  danger("Phi2 is outside of expected range, please consider discarding the measurement",output);
}
else if (fvfm >=.85) {
  danger("Phi2 is outside of expected range, please consider discarding the measurement", output);
}
else {
  output["Phi2"] = MathROUND(fvfm,3);
}

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