PALMS+Users+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** ||= **Default Value** || **Usage** ||
 * Participant ||= All participants || Selects one individual participant or all participants to be included in the calculation ||
 * Start Date ||= 01/01/2008 || Earliest date to be included ||
 * End Date ||= 12/21/2012 || Latest date to be included ||
 * Interval (in seconds) ||= 30 || Length of interval used to summarize the data ||
 * Result Name ||= must be supplied || Name under which the results of the calculation will be stored ||

__**GPS Tab**__
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) ||
 * **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 ||
 * || Max change in distance (meters) || 5000 ||  || Consider fix invalid if change in distance greater than this value over interval ||
 * || Min change in distance (meters) || 1 ||  || discard fix if change in distance is less than this value over the interval ||
 * 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. (Used when SNR information is not available) ||
 * || 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 ||
 * Trip detection ||  ||   ||   ||   ||
 * || Detect trips || checked ||  || When checked, trips are detected, numbered and classified ||
 * || 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. ||
 * || 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" . ||
 * Location detection ||  ||   ||   ||   ||
 * || Include trip pause locations || unchecked ||  || When check, pauses occurring during a trip are included as locations. ||
 * || Trap points within location || checked ||  || When checked, stationary GPS fixes within a given radius of the location will be set the the center of the location. ||
 * || Trap points that are part of a trip || checked ||  || When checked, also include GPS fixes that are part of a trip. NOTE: above option must also be checked for this option to take effect. ||
 * || Reset location numbers for each participant || unchecked ||  || When checked, location numbers are reset for each participant. ||
 * || Cluster radius (meters) || 30 ||  || Defines radius of location in which fixes are trapped ||
 * || Min time at location (seconds) || 300 ||  || Minimum amount of time that must be spent at a location for it to be considered a location ||
 * 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
 * || Pedestrian 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 95%, then the speed at the 95th percentile will be used to classify the mode of transportation. This prevents miss-classifications based on erroneous speeds caused by GPS noise. ||

__**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.) ||
 * || 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, 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) || 1952 ||  || Minimum level of activity to be considered part of a bout (default is for moderate and above levels of activity) ||
 * || 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 cutoff 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 moving average or last valid heart rate ||
 * || 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 || 120 ||  || 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 ||
 * 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** || **Default**
 * value** ||  || **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).

Actigraph Vector Magnitude -- (for ActiGraph devices reporting vector magnitude) || For counts below this value, use WET. For counts greater or equal to this value, use Freedson ||
 * || Combination Cutoff Value || 1952 ||  || When Combination Formula is selected:

**__Merge Options Tab__**

 * **Functional block** || **Parameter name** || **Default**
 * value** ||  || **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. ||
 * || 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. ||