PALMS+User's+Guide+-+Calculation+Parameters+(R4)

=Calculation Parameters (R4)=

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**__
Details on the operation of the GPS processing algorithms and a discussion on selecting GPS parameters can be found on this page.

(was 70 in June beta release) || Max percentage of a trip's fixes that are allowed to occur indoors. When this value is exceeded, the trip is considered invalid (because it was generated by GPS noise) and is removed. If you want to allow trips that occur entirely indoors, then set this value to 100. ||
 * **Functional block** || **Parameter name** || **Default Value** || **Usage** ||
 * Loss of signal ||  ||   ||   ||
 * || Max duration allowed (in seconds) || 600 || Maximum amount of time between GPS fixes allowed to occur before loss-of-signal (LOS) is declared. For durations less than this value, the previous good GPS fixed is assumed. ||
 * || Remove lone fixes || checked || When checked, "lone" fixes are removed. A lone fix is one that occurs after LOS is declared. ||
 * Invalid values filter ||  ||   ||   ||
 * || Filter invalid fixes || checked || When checked, filter (remove) invalid points from the calculation. ||
 * || Max speed (Km/hr) || 130 || Consider fix invalid if speed greater than this value ||
 * || Max change in elevation (meters) || 1000 || Consider fix invalid if elevation delta greater than this value over the interval ||
 * || Min change in distance required over 3 fixes (meters) || 10 || Discard fix if change in distance between fix 1 and fix 3 is less than this value. Indicates a forwards and backwards movement that typically is cause by GPS jitter. ||
 * Indoors detection ||  ||   ||   ||
 * || Detect indoors || checked || When checked, mark fixes as indoors or outdoors if additional satellite information has been recorded by the GPS. ||
 * || 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. Default is for Qstarz GPS ||
 * Trip detection ||  ||   ||   ||
 * || Min distance traveled over one minute (meters) || 34 || 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 trip duration (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. ||
 * || Max % of trip allowed within a single location || 90 || Max percentage of a trip's fixes that are allowed to occur within a single location. When this value is exceeded, the trip is considered invalid (because it was generated by GPS noise) and is removed. If you want to allow trips to occur within a single location, then set this value to 100. ||
 * || Max % of trip allowed indoors || 50
 * || Remove indoor points from trip starts and ends || checked || When checked, points estimated to be indoors are removed from the starts and ends of trips. A trip starts when it has been detected that the participant exited a building and ends when a person has entered a building.

Trips which are 100% indoors will be removed unless the value above is set to 100%. ||
 * Location detection ||  ||   ||   ||
 * || Include trip pauses as locations || unchecked || When check, pauses occurring during a trip are included as locations. ||
 * || Trap indoor points within location || checked || When checked, stationary indoor GPS fixes within a given radius of the location will be set to the center of the location. ||
 * || Trap outdoor points within location || checked || When checked, stationary outdoor GPS fixes within a given radius of the location will be set to the center of the location.

NOTE: When both are checked, stationary points will be trapped. GPS does not need to have collected indoor / outdoor information. ||
 * || Trap points that are part of a trip || unchecked || When checked, also include GPS fixes that are part of a trip. ||
 * || Allow locations without trips || unchecked || When checked, locations may be identified that are not associated with a trip. ||
 * || Reset location numbers for each participant || unchecked || When checked, location numbers are reset for each participant. When unchecked, location numbers will be the same for all participants in a calculation. ||
 * || Cluster radius (meters) || 30 || Defines radius of location in which fixes are trapped ||
 * || Min time at location (seconds) || 0 || Minimum amount of time that must be spent at a location for it to be considered a location.

NOTE: Changing this value may also remove locations established by first and last GPS fixes, since the duration at those locations is often small. || NOTE: If you know there is no bicycle travel in the study, set the bicycle and vehicle cutoffs to the same value (typically 5-10) ||
 * Mode of transportation ||  ||   ||   ||
 * || Vehicle speed cutoff (KMph) || 25 || Speeds greater than this are marked as vehicle ||
 * || Bicycle speed cutoff (KMph) || 10 || Speeds greater than this are marked as bicycle
 * || Walk speed cutoff (KMph) || 1 || Speeds greater than this are marked as pedestrian ||
 * || Percentile of speed samples to consider || 90 || Above comparisons are made at this percentile. If set to 90%, then the speed at the 90th percentile will be used to classify the mode of transportation. This prevents mis-classifications based on erroneous speeds caused by GPS noise. ||
 * || Classification segment length (in meters) || 30 || Minimum length of a trip segment used to classify mode transportation. ||
 * Compute averages ||  ||   ||   ||
 * || 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 ||

__**Accelerometer Tab**__
(**Note: Cut-off values will need to be changed. See discussion below.)** || Source: [] J Sci Med Sport. 2011 Sep;14(5):411-6. Epub 2011 May 25.Validation and comparison of ActiGraph activity monitors.Sasaki JE, John D, Freedson PS.
 * **Functional block** || **Parameter name** || **Default**
 * Value** || **Usage** ||
 * Accelerometer calculations ||  ||   ||   ||
 * || Include accelerometer || checked || When checked, accelerometer data will be processed. (Un-check if you are only interested in GPS processing. It will reduce the run time of the calculation,) ||
 * || Use vector magnitude (if available) || unchecked || When checked, vector magnitude values will be used in place of axis 1 count data.
 * Not wearing time ||  ||   ||   ||
 * || Mark not wearing || checked || When checked, non-wearing time will be marked with a value of -2 ||
 * || 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. ||
 * NOTE:** Defaults for cutoff values are those for single axis Actigraphs. If //"Use vector magnitude"// is checked above, the cutoff values must be changed.
 * Vector magnitude cuttoff values || Very hard || 9642 ||
 * || Hard || 6167 ||
 * || Moderate || 2690 ||
 * || Light || 100 ||

**__Heart Rate Tab__**
Possible choices are: Default (220-age), Londeree, Miller, Kavonen ||
 * **Functional block** || **Parameter name** || **Default**
 * Value** || **Usage** ||
 * Heart rate calculation ||  ||   ||   ||
 * || Include heart rate || checked || When checked, heart rate is included in calculation. ||
 * Invalid values filter ||  ||   ||   ||
 * || Replace invalid values || checked || When checked, replace invalid heart rate with last valid heart rate (or the moving average if computed) ||
 * || Max duration of invalid time (in seconds) || 120 || Maximum number of seconds that would be replaced before declaring invalid ||
 * || Min valid rate (bpm) || 40 || Minimum heart rate allowed in beats per minute ||
 * || Max valid rate (bpm) || 220 || 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 seconds ||
 * || Number of seconds to average || 30 || Computes moving average over this number of seconds (N) ||
 * || Replace invalid samples with moving averages || checked || When checked, replace invalid samples with moving average value (instead of the last valid heart-rate) ||
 * Bouts detection ||  ||   ||   ||
 * || Detect bouts of elevated heart rate || checked || If checked, detect bouts of elevated heart rate ||
 * || Bout duration (minutes) || 10 || Minimum duration of bout ||
 * || Upper limit (percentage of max HR) || 100 || Maximum percentage to be considered part of a bout ||
 * || Lower limit (percentage of max HP) || 60 || Minimum percentage 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 || 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 (defaults to 30) ||
 * 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**__
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). Actigraph Vector Magnitude || For counts below this value, use WET. For counts greater or equal to this value, use Freedson ||
 * **Functional**
 * block** || **Parameter name** || **Default**
 * Value** || **Usage** ||
 * EE Formula ||  ||   ||   ||
 * || Formula || None || Select formula used to estimate energy expenditure:
 * || Combination Cutoff Value ||  || When Combination Formula is selected:

**__Lux Options Tab__**

 * **Functional block** || **Parameter name** || **Default**
 * Values** || **Usage** ||
 * Lux classification cutoff values ||  ||   ||   ||
 * || Direct sunlight || 32000 || Values greater than this are considered to be in direct sunlight ||
 * || Full daylight || 10000 || Values greater than this and less than the above value are considered to be in full daylight ||
 * || Overcast || 500 || Values greater than this and less than the above value are considered to be an overcast day. ||
 * || Indoors (commercial buildings) || 300 || Values greater than this and less than the above value are considered to be indoors a commercial building. ||
 * || Indoors (home) || 50 || Values greater than this and less than the above value are considered to be indoors a residential building. ||
 * || Twilight || 5 || Values greater than this and less than the above value are considered to be outdoors at twilight. ||

**__Merge Options Tab__**

 * **Functional block** || **Parameter name** || **Default**
 * Values** || **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. ||
 * Missing GPS Fixes ||  ||   ||   ||
 * || Insert missing fixes || checked || When checked, gaps in GPS fixes are replaced by the last valid fix. ||
 * || Insert until a max duration || unchecked || When checked, continue inserting missing fixes until the max duration (specified below) is reached. ||
 * || Max number of seconds to insert || 600 || Max number of seconds to replace missing fixes with last valid fix. After this duration is reached, the location is marked as unknown. ||
 * Mark Events ||  ||   || Events are marked and the event number incremented when a change in the participant's activity occurs. The options below allow you to determine which changes are to be marked as events. Events provide a convenient way of scanning a large result set for major changes. ||
 * || Mark trips || checked || When checked, trip starts and trip ends are marked as events. ||
 * || Mark pause points || checked || When checked, the start and stop of pauses that occur within a trip are marked as events. ||
 * || Mark location changes || checked || When checked, a change in the location number is marked as an event. ||
 * || Mark activity bouts || checked || When checked, the start and end of an activity bout is marked as an event. ||
 * || Mark sedentary bouts || checked || When checked, the start and end of a sedentary bout is marked as an event. ||
 * || Mark sedentary bouts || checked || When checked, the start and end of a sedentary bout is marked as an event. ||

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