LabAnalyst X SPECIAL menu

LabAnalyst X. has five menus, plus on-line instructions in the "Special" menu and three functions in the "LabAnalyst X" menu.  FILE  EDIT  ANALYZE VIEW  SCRIPTS   SPECIAL Simple math STP adjustment Altitude & pressure pO2 estimation Metabolic allometry Ventilation Julian date calculator Closed system respirometry Help window

The SPECIAL menu contains several utility routines useful in respirometry (STP conversion, altitude and pressure calculations, a metabolism estimates routine, a routine to compute ventilation) and a simple calculator.

  SIMPLE MATH CALCULATOR...     This is an elementary math calculator (addition, subtraction, multiplication, division) with a few frequently-used functions (logs, square roots, etc.) and some specialized keys for interchanging time units (division and multiplication by 60 and 24).  If you have previously computed a mean value with an ANALYZE menu operation, you can transfer that mean to the calculator for additional manipulation (note that this does not work for regression slopes).  The 'store X value...' button lets you save the result for use as a scaling factor in subsequent ANALYZE operations.  Clicking this button opens the scaling factors window.  Click on any channel's "*" or "÷" button, and the current X-value will appear in the first edit field (the multiplication or division factor) for that channel.

For addition, subtraction, multiplication, and division the calculator works in a simple RPN mode.  Enter the first number in the X-value edit field, hit 'return' and enter the second number, and then hit the '+', '-', '*', or '/ ' key.  The result will appear in the X-value field.

STP ADJUSTMENT...     This window contains a small calculator for adjusting a measured flow rate to conditions of standard temperature and pressure (STP).  STP conversion is necessary for gas exchange calculations.  Although the gas exchange routines will perform an STP adjustment, this window's algorithm is more versatile:

• You can select either a measure of uncorrected flow rate (in ml/min) or a cumulative volume (ml) over a measured time period (seconds).  The latter method is most useful for dry volume meters, bubble meters, etc. 
• In addition to barometric pressure, you can account for any internal pressure within the gas flow meter (which may occur if you are using relatively high flow rates and/or small-diameter tubing).  Internal pressure can be in units of torr, PSI (pounds/square inch), KPa (Kilopascals), or mm of water (if you are using a water manometer). 
• You can adjust the calibration temperature of your flow instrument.  Most such devices are calibrated for a temperature of zero °C, but some (like Singer dry volume meters) may be calibrated for 20 °C or other temperatures. 

Oher functions...

• The 'add to sum' button adds the current value into an internal register that is used to compute an average value (displayed with the 'show average' button).  These functions correctly account for whether the display is set for standard cubic centimeters/min (SCCM) or standard liters per minute (SLPM). 
• The 'store flowrate' button saves the currently displayed STP flow rate as the default flow rate for gas exchange calculations (in units of SCCM).  Either an averaged flow rate or an individually-computed value are accepted, and the display setting (SCCM or SLPM) is taken into account.  In addition to saving STP flow, this button also stores a barometric pressure of 760 torr and a meter temperature of 0 °C (this is necessary to retain the accuracy of the STP conversion when computing gas exchange).

  EXPRESSION EVALUATOR...     This routine lets you write a mathematical expression, enter numeric values for the expression variables, and have the computer solve it. The program parses the expression into components and performs the operations. The expression evaluator understands the following symbols (upper or lower case entries are OK):

• Simple operators: + - * / ^ ( )
• Complex operators: EXP, LOG or LN, LOG10, SIN, COS, TAN, ATN or ATAN, ABS, INT, SQR (square), SQRT (square root)
• Two special variables (i.e., channels) named "X" and "Y", chosen with push-buttons (see image below)
• PI (or the equivalent Greek letter)
• Numbers (such as 5, -3.1889, and 1e-10)
• If you wish you can add a comment at the end of your expression, delineated with the " ` " character.

Some general considerations:

• The 'Show instructions...' button displays the same list of permissable symbols and operations shown above. You'll need to click it again to switch off the instructions.
• The 'Check expression' button does a preliminary parsing of the expression and indicates if there are any syntax errors (in the above example, this button has been clicked).
• The 'Evaluate' button processes the channel data according to the expression in the upper left window. The transformed data are re-written to the main plot area. If any errors are found (see below), a warming message is shown.

NOTE: This routine will only 'catch' errors in the basic numeric expression. It may not detect invalid or meaningless math operations that may be attempted when data are processed, such as division by zero, or taking the log or a non-integer exponent of a negative number. If such situations occur, results may be unpredicatable. The algorithm does find most such errors during processing, however.

The underlying code for the expression evaluator was very largely developed by Robert Purves.  I 'borrowed' it -- with his permission -- and made some modifications for LabAnalyst.  But Robert P. deserves all the credit.

  ALTITUDE & PRESSURE...     This option computes an estimate of mean atmospheric pressure as a function of altitude, or vice versa.  It is based on a polynomial approximation of the International Standard Atmosphere equation, obtained from the Smithsonian Meteorological Tables. (as a rough approximation, pressure decreases by 50% for every 5500 meter increase in altitude).  The results should be accurate within 1-2% of actual pressure or altitude, unless weather conditions are really unusual.  Nevertheless, if you use this calculator, you need to keep a few caveats in mind:

• Due to approximation (and rounding errors), the algorithm is not completely reversible (for example, the estimated pressure for an altitude of 2200 meters is 581 torr, but the estimated altitude for a pressure of 581 torr is 2204 meters). 
• The results are estimated mean values and do not account for local pressure fluctuations arising from weather changes. 
• The calculator cannot account for any pressure differential inside your system.  For example, if you use a positive-pressure ("push") respirometry system, the pressure inside the plumbing -- and hence, inside your flow meter -- will be slightly higher than atmospheric.  The opposite is true for a negative-pressure ("pull") flow arrangement.  If you want to be compulsive, you might consider using a water manometer or some other pressure gauge to measure the pressure differential and add that to atmospheric pressure during STP calculations.  In most cases, the pressure differential will be small relative to total atmospheric pressure.
• Accuracy will decrease for altitudes above about 9000 meters (or pressures less than about 230 torr).
• The newest versions let you use kilopascals (kPa) for pressure units, in addition to torr.
• The 'store pressure' button will save the current value of barometric pressure.

  pO2 ESTIMATION... You can use this calculator to determine the partial pressure of oxygen (pO₂) -- or any other gas species in a mixture -- from ambient temperature, ambient pressure (in the gas phase), fractional concentration of the gas species of interest in a dry gas mix, and the percent saturation of water vapor (i.e., relative humidity) in the gas phase. Oxygen (or other gases) are diluted by water vapor, and the degree of that dilution depends on RH and temperature.

In the example at right, pressure is sea level standard atmospheric pressure(760 torr), temperature is the typical mammalian body temperature (37 °C), etc. Note that at this temperature the saturation vapor pressure of water is about 47.6 torr (this is not affected by the total pressure in the system).

Other considerations for this calculator:

• The calculated pO₂ value is applicable for the gas phase, and also for dissolved oxygen, as long as the solution is fully saturated with O₂. 
• The default pressure (torr or kilopascals, kPa) is obtained from the current data file; the default temperature is 37 °C, and the default fractional gas concentration is .2095 (20.95%, the normal oxygen content of dry atmospheric air). 

   METABOLIC ALLOMETRY...     Use this somewhat specialized utility to make estimates of an animal's resting metabolism, based on its size and taxonomic affiliation.  The initial popup menu contains some very generalized equations, and also allows you to switch to submenus for specific taxa (arthropods, fish, birds, mammals, etc.).  For most taxa, several different equations are available (from different literature sources, which are described in the 'help' field to the right).  You can also pick the desired output units.  The energy equivalence of metabolism (joules per ml of oxygen consumed) can be set with the 'O2 heat equivalence' selection in the "Respirometry" submenu (EDIT menu); the default value is 20.1 joules/ml.  The mass coefficient in the allometric equation ('a' value) is adjusted to reflect whatever output unit is in use.  Results can be stored for later use.

This example shows an estimate of the resting metabolic rate (RMR) of a 37.3 g nestling bird, in units of ml O₂/min.  The equation was derived from a paper published by W. Weathers and R. Siegel (the full citation would be visible if the edit field on the right was scrolled).  Note that the mass coefficient ('a' value) and mass exponent are shown and can be edited.  Also, it is possible to make corrections for the effect of body temperature by making the appropriate adjustments to the value of actual T_b and Q10 (in this example, the 'base' T_b, from which the equation was derived, is equal to the actual T_b so no temperature correction occurs).  After changing values in the edit fields, click the 'calculate' button to display the new results.

   VENTILATION...     This rather arcane calculator is for studies of ventilation (breathing dynamics) using open-flow plethysmography systems.  It will compute tidal volume (V_t, the volume of gas inspired with each breath), minute volume (V_min, the total volume of gas inspired each minute), and oxygen extraction (EO₂, the fraction of inspired oxygen that is absorbed from tidal gas).

To support these calculations -- which are largely based on the small pressure fluctuations induced by the warming and wetting of tidal air -- you need to provide a number of variables.  Several of these are self-explanatory (at least if you know something about respiratory physiology).  Abbreviations for some of the more obscure ones are: VO₂, the rate of oxygen consumption, T_b and T_a (body and air temperature), delta-P (pressure gradient between the metabolism chamber and ambient barometric pressure, in mm of water), RH (relative humidity in the metabolism chamber), calibration vol (the volume of gas injected during system calibrations), calibration volts (mean peak height of calibration deflections), calibration gain (signal amplification during calibrations), sample volts (mean peak height of individual breaths in the breathing record), sample gain (signal amplification when recording breathing).  You can use the 'waveform analysis' routines in the ANALYSIS menu to obtain breathing frequeny, calibration volts, and sample volts from recorded breathing records.

In this fairly typical example, the animal (a mouse) breathed about 6.3 times per second (not unusual for a small mammal in cold conditions) and had a tidal volume of 0.248 ml and a minute volume of about 94 ml/min.  The oxygen extraction was about 26.5%. Although there is a lot of data to enter, the program makes it as easy as possible.;  Most values are remembered between successive uses of the calculator, so you only have to change a few edit fields (like VO₂, frequency, and sample volts).  You can tab (or hit return) to move between successive edit fields.

   JULIAN DATE CALCULATOR...     This simple calculator will provide the Julian date (days since December 31) for a combination of date, month, and year.   It should account for leap years.

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