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computeDensity

Source: R/computeDensity.R
computeDensity.Rd

This function will estimate the density (expressed as #objects / km3) based on the observations in your database. Note that this function only works properly on Birdscan MR1 database versions >= 1.7.0.4 as the variable feature37.speed is required for the density calculation.

Usage

computeDensity(
  dbName,
  echoes,
  classSelection,
  altitudeRange,
  altitudeBinSize,
  timeRange,
  timeBinDuration_sec,
  timeZone,
  sunriseSunset,
  sunOrCivil = "civil",
  crepuscule = "nauticalSolar",
  protocolData,
  visibilityData,
  manualBlindTimes = NULL,
  saveBlindTimes = FALSE,
  blindTimesOutputDir = getwd(),
  blindTimeAsMtrZero = NULL,
  propObsTimeCutoff = 0,
  computePerDayNight = FALSE,
  computePerDayCrepusculeNight = FALSE,
  computeAltitudeDistribution = TRUE
)

Arguments

dbName

Character string, containing the name of the database you are processing

echoes

dataframe with the echo data from the data list created with extractDbData() or a subset of it created by the function

classSelection

character string vector with all classes which should be used to calculate the density. The density and number of Echoes will be calculated for each class as well as for all classes together.

altitudeRange

numeric vector of length 2 with the start and end of the altitude range in meter a.g.l.

altitudeBinSize

numeric, size of the altitude bins in meter.

timeRange

Character vector of length 2, with start and end of time range, formatted as "%Y-%m-%d %H:%M"

timeBinDuration_sec

duration of timeBins in seconds (numeric). for values <= 0 a duration of 1 hour will be set

timeZone

time zone in which the time bins should be created as string, e.g. "Etc/GMT0"

sunriseSunset

dataframe with sunrise/sunset, and civil and nautical dawn/dusk. Computed with twilight().

sunOrCivil

sunrise/sunset or civil dawn/dusk used to split day and night. Supported values: "sun" or "civil". Default: "civil"

crepuscule

optional character variable, Set to “nauticalSolar” to use the time between nautical dusk/dawn and sunrise/sunset times to define the crepuscular period, or to "nauticalCivil" to use the time between nautical and civil dusk/dawn to define the crepuscular period, or to "civilSolar" to use the time between civil dusk/dawn and sunrise/sunset times to define the crepuscular period. Default is "nauticalSolar".

protocolData

dataframe with the protocol data from the data list created by extractDbData() or a subset of it created by the function filterProtocolData().

visibilityData

dataframe with the visibility data from the data list created by extractDbData().

manualBlindTimes

dataframe with the manual blind times created by the function loadManualBlindTimes().

saveBlindTimes

Logical, determines whether to save the blind times to a file. Default: False.

blindTimesOutputDir

Character string containing the path to save the blind times to. Default: 'your-working-directory'

blindTimeAsMtrZero

character string vector with the blind time types which should be treated as observation time with MTR zero.

propObsTimeCutoff

numeric between 0 and 1. Time bins with a proportional observation time smaller than propObsTimeCutoff are set to NA.

computePerDayNight

logical, TRUE: density is computed per day and night. The time bins of each day and night will be combined and the mean density is computed for each day and night. The spread (first and third Quartile) for each day and night are also computed. The spread is dependent on the chosen time bin duration/amount of time bins; When FALSE: density is computed for each time bin. This option computes the density for each time bin defined in the time bin dataframe. The time bins that were split due to sunrise/sunset during the time bin will be combined to one bin.

computePerDayCrepusculeNight

logical, TRUE: density is computed per crepusculeMorning, day, crepusculeEvening, and night. The time bins of each of these diel phases will be combined and the mean density is computed for each phase. The spread (first and third Quartile) for each phase is also computed. The spread is dependent on the chosen time bin duration/amount of time bins; When FALSE: density is computed for each time bin. This option computes the density for each time bin defined in the time bin dataframe. The time bins that were split due to sunrise/sunset during the time bin will be combined to one bin. Default = FALSE.

computeAltitudeDistribution

logical, TRUE: compute the mean height and altitude distribution of density for the pre-defined quantiles 0.05, 0.25, 0.5, 0.75, 0.95

Value

Density

See also

Other manipulation functions: addDayNightInfoPerEcho(), computeMTR(), convertTimeZone(), createVPTS(), filterSpeedFeature37(), mergeVisibilityAndManualBlindTimes(), reclassToBats(), twilight()

Author

Birgen Haest, Fabian Hertner, Baptiste Schmid

Examples