PALMS+Users+Guide+-+Calculation+Parameters+(R2)

=Calculation Parameters (R2)=

The PALMS calculation contains numerous parameters organized by device and function. There is a tab for each device and with in each tab, a block for each function.

__General Information Section__

 * **Parameter name** || **Usage** ||
 * Participant || Selects one individual participant or all participants to be included in the calculation ||
 * Start Date || Earliest date to be included ||
 * End Date || Latest date to be included ||
 * Interval (in seconds) || Length of interval used to summarize the data ||
 * Result Name || Name under which the results of the calculation will be stored ||

__**GPS Tab**__
//NOT CURRENTLY USED// ||
 * **Functional block** || **Parameter name** || **Defaults** || **Usage** ||
 * Invalid values filter ||  ||   ||   ||
 * || Filter invalid || 0 || Values: 0 = filter (remove) invalid points from the calculation, //1 = mark points//, 2 = do not filter or mark ||
 * || Max speed (Km/hr) || 130 || invalid if fix has speed greater than this value ||
 * || Max change in elevation (meters) || 1000 || invalid if fix as elevation delta greater than this value over the interval ||
 * || Max change in distance (meters) || 5000 || invalid if change in distance greater than this value over interval
 * || Min change in distance (meters) || 1 || discard if change in distance is less than this value over the interval ||
 * || Max loss of signal (in seconds) || 600 || declare loss of signal when time between fixes exceeds this value ||
 * || Filter lone fixes || checked || When checked, filters fixes when the time between fixes indicates loss of signal. ||
 * Indoors detection ||  ||   ||   ||
 * || Detect indoors || checked || When checked, mark fixes as indoors or outdoors ||
 * || Max satellite ratio when indoors || 50 || Maximum ratio of satellites-used / satellites-in-view to be considered indoors. Values greater than this are marked as outdoors. ||
 * || Max SNR value when indoors || 250 || Maximum signal-noise value to be considered indoors. Values greater than this are marked as outdoors. ||
 * Apply averages to ||  ||   ||   ||
 * || Compute average speed || unchecked || When checked, computes and presents speed as a moving average over N GPS samples. ||
 * || Compute average elevation || unchecked || When checked, computes and presents elevation delta as a moving average over N GPS samples ||
 * || Number of GPS samples to average || 3 || Number of samples (N) used to compute the moving average ||
 * Location detection ||  ||   ||   ||
 * || Detect location clusters before trips || unchecked || When checked, location clusters are detected before trips detection (Trips are considered was occurring between locations. However, this does not work well in restricted geographic spaces, such as school campus and retirement communities.) ||
 * || Include trip pause locations || checked || When check, pauses occurring during a trip are included as locations. ||
 * || Trap points within location || unchecked || When checked, all GPS fixes within a given radius of the location will be set the the center of the location. ||
 * || Cluster radius (meters) || 30 || Defines radius of location in which fixes are trapped ||
 * || Min time at location || 300 || Minimum amount of time that must be spent at a location for it to be considered a location ||
 * Trip detection ||  ||   ||   ||
 * || Detect trips || checked || When checked, trips are detected, numbered and classified ||
 * || Min change in distance (meters) || 10 || Minimum distance that must be traveled over one minute to indicate the start of a trip. (Note: 1 KM/hour = 17 meters/minute) ||
 * || Min trip length (meters) || 100 || Trips less than this distance in length are not classified as trips. ||
 * || Min duration for trips (seconds) || 180 || Trips less than this duration are not classified as trips. ||
 * || Min pause time (seconds) || 180 || When duration at point exceeds this value, point is marked as a pause point. ||
 * || Max pause time (seconds) || 300 || When duration of pause exceeds this value, point is marked as a end point. ||
 * || Allow trips within a single locations. || unchecked || When checked, allow a trip to occur solely within one location. (By default, such trips are removed because such trips are hard to distinguish from GPS "noise" . ||
 * Speed cutoff values ||  ||   ||   ||
 * || Vehicle speed cutoff (KMph) || 35 || Speeds greater than this are marked as vehicle ||
 * || Bicycle speed cutoff (KMph) || 10 || Speeds greater than this are marked as bicycle ||
 * || Running speed cutoff (KMph) || 12 || Speeds greater than this are marked as running - not yet implemented ||
 * || Jogging speed cutoff (KMph) || 9 || Speeds greater than this are marked as jogging - not yet implemented ||
 * || Walking speed cutoff (KMph) || 1 || Speeds greater than this are marked as walking - not yet implemented ||
 * || Sedentary speed cutoff (KMph) || 0 || Speeds greater than this are marked as pedestrian ||

__**Accelerometer Tab**__

 * **Functional block** || **Parameter name** || **Defaults** || **Usage** ||
 * Not wearing time ||  ||   ||   ||
 * || Mark not wearing || checked || When checked, mark not wearing time ||
 * || Minutes of zeros in a row || 30 || Number of consecutive minutes of zeros that must be present for period to be marked as not wearing. ||
 * Bouts detection ||  ||   ||   ||
 * || Detect activity bouts || checked || When checked, detect bouts of activity ||
 * || Activity bout length (minutes) || 5 || Minimum duration of bout ||
 * || Activity bout upper limit (counts) || 9999 || Maximum limit of activity to be considered part of a bout ||
 * || Activity bout lower limit (counts) || 1953 || Minimum level of activity to be considered part of a bout ||
 * || Activity bout tolerance (minutes) || 2 || Number of consecutive minutes allowed outside of the activity limits that will still be considered part of a bout ||
 * Sedentary bouts detection ||  ||   ||   ||
 * || Detect sedentary bouts || checked || When checked, detect bouts of sedentary periods (non-activity) ||
 * || Sedentary bout length (minutes) || 30 || Minimum duration on sedentary bout ||
 * || Sedentary bout upper limit (counts) || 100 || Maximum level of activity to be considered sedentary ||
 * || Sedentary bout tolerance (minutes) || 1 || Number of consecutive minutes of activity allowed during sedentary bout ||
 * Cutoff values ||  ||   ||   ||
 * || Very hard (counts) || 9498 || Counts greater than this value will be classified as very hard (very vigorous) ||
 * || Hard (counts) || 5725 || Counts greater than this value and less than the above value will be classified as hard (vigorous) ||
 * || Moderate (counts) || 1953 || Counts greater than this value and less than the above value will be classified as moderate ||
 * || Light (counts) || 100 || Counts greater than this value and less than the above value will be classified as light. NOTE: Counts less than this value will be classified as sedentary. ||

**__Heart Rate Tab__**
Possible choices are: Default (220-age), Londeree, Miller, Kavonen ||
 * **Functional block** || **Parameter name** || **Defaults** || **Usage** ||
 * Include heart rate calculation ||  ||   ||   ||
 * || Include heart rate || checked || When checked, heart rate is included in calculation. ||
 * Invalid values filter ||  ||   ||   ||
 * || Filter invalid values || checked || When checked, replace invalid heart rate with moving average or last valid heart rate ||
 * || Max number replaced || 60 || Maximum number of samples that would be replaced before declaring invalid ||
 * || Min valid rate (bpm) || 40 || Minimum heart rate allowed in beats per minute ||
 * || Max valid rate (bpm) || 200 || Maximum hear rate allowed in beats per minute ||
 * Moving average ||  ||   ||   ||
 * || Compute moving average || checked || When checked, computes and presents heart rate as a moving average over N samples ||
 * || Number of samples to average || 5 || Computes moving average over this number of sample (N) ||
 * Bouts detection ||  ||   ||   ||
 * || Detect bouts || checked || If checked, detect bouts of elevated heart rate ||
 * || Bout length (minutes) || 10 || Minimum duration of bout ||
 * || Upper limit (percentage of max HR) || 100 || Maximum heart rate to be considered part of a bout ||
 * || Lower limit (percentage of max HP) || 60 || Minimum heart rate to be considered part of a bout ||
 * || Bout tolerance (minutes) || 2 || Number of consecutive minutes outside of the limits allowed in the bout ||
 * Max HR Formula ||  ||   ||   ||
 * || Max HR Formula || Default (220-age) || Formula used to compute maximum heart rate based on participant's age
 * || Default age || 30 || Age to be used when participant's age is not known ||
 * Cutoff values ||  ||   ||   ||
 * || Heart rate max effort (percentage of maximum heart rate) || 90 || Percentages greater that this number will be classified as max effort ||
 * || Heart rate anaerobic (percentage) || 80 || Percentages greater than this number and less than the above will be classified as anaerobic ||
 * || Heart rate aerobic (percentage) || 70 || Percentages greater than this number and less than the above will be classified as aerobic ||
 * || Heart rate weight control (percentage) || 60 || Percentages greater than this number and less than the above will be classified as weight control ||
 * || Heart rate moderate (percentage) || 50 || Percentages greater than this number and less than the above will be classified as moderate ||
 * || Heart rate light (percentage) || 40 || Percentages greater than this number and less than the above will be classified as light. ||
 * || Heart rate resting (percentage) || 30 || Percentages greater than this number and less than the above will be classified as resting. Percentages less that this value will be marked as invalid. ||

__**EE (Energy Expenditure) Estimate Tab**__

 * **Functional**
 * block** || **Parameter name** || **Defaults** || **Usage** ||
 * EE Formula ||  ||   ||   ||
 * || Formula || None || Select formula used to estimate energy expenditure:

None -- do not estimate EE

Device Default -- use the EE value estimated by the device's software and uploaded to PALMS (accelerometer / heart rate monitor)

Freedson -- (for ActiGraph devices only) - use Freedson formula based on counts and partipicant's weight

Work-Energy Theorem -- (for ActiGraph devices only) - use Work-Energy Theorem formula based on counts and participant's weight

Combination -- (for ActiGraph devices only) - use a combination of the Freedson and WET formula based on the combination cutoff value (see below). ||
 * || Combination Cutoff Value || 1952 || When Combination Formula is selected:

For counts below this value, use WET. For counts greater or equal to this value, use Freedson ||
 * || //Branched Equation// ||  || //Not yet implemented// ||

**__Merge Options Tab__**

 * **Functional block** || **Parameter name** || **Defaults** || **Usage** ||
 * Merge Options ||  ||   ||   ||
 * || Merge data to GPS || checked || When checked, activity and heart-rate data is aligned to the GPS timeline. Data without GPS fixes are discarded. ||
 * || Start first day at midnight || unchecked || When checked, the timeline for the first day of data starts at midnight. Otherwise, it starts at the timestamp of the first data sample. ||
 * || Insert missing fixes || checked || When checked, gaps in GPS fixes are replaced by the last valid fix. ||

Note: On 25-Jul-2013, the documentation was updated to reflect the default values. The values did NOT change. .

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