changeLight: Residency analysis using a changepoint model

In slisovski/GeoLight: Analysis of Light Based Geolocator Data

Residency analysis using a changepoint model

Description

Function to discriminate between periods of residency and movement based on consecutive sunrise and sunset data. The calculation is based on a changepoint model (R Package changepoint: cpt.mean) to find multiple changepoints within the data.

Usage

changeLight(
  tFirst,
  tSecond,
  type,
  twl,
  quantile = 0.9,
  rise.prob = NA,
  set.prob = NA,
  days = 5,
  fixed = NULL,
  plot = TRUE,
  summary = TRUE
)

Arguments

tFirst	vector of sunrise/sunset times (e.g. 2008-12-01 08:30).
tSecond	vector of of sunrise/sunset times (e.g. 2008-12-01 17:30).
type	vector of either 1 or 2, defining tFirst as sunrise or sunset respectively.
twl	data.frame containing twilights and at least tFirst, tSecond and type (alternatively give each parameter separately).
quantile	probability threshold for stationary site selection. Higher values (above the defined quantile of all probabilities) will be considered as changes in the behavior. Argmuent will only be considered if either rise.prob and/or set.prob remain unspecified.
rise.prob	the probability threshold for sunrise: greater or equal values indicates changes in the behaviour of the individual.
set.prob	the probability threshold for sunset: higher and equal values indicates changes in the behaviour of the individual.
days	a threshold for the length of stationary period. Periods smaller than "days" will not be considered as a residency period
fixed	...
plot	logical, if TRUE a plot will be produced
summary	logical, if TRUE a summary of the results will be printed

Details

The cpt.mean from the R Package changepoint is a function to find a multiple changes in mean for data where no assumption is made on their distribution. The value returned is the result of finding the optimal location of up to Q changepoints (in this case as many as possible) using the cumulative sums test statistic.

Value

A list with probabilities for sunrise and sunset the user settings of the probabilities and the resulting stationary periods given as a vector, with the residency sites as positiv numbers in ascending order (0 indicate movement/migration).

Note

The sunrise and/or sunset times shown in the graph (if plot=TRUE) represent hours of the day. However if one or both of the twilight events cross midnight during the recording period the values will be formed to avoid discontinuity.

Author(s)

Simeon Lisovski & Tamara Emmenegger

References

Taylor, Wayne A. (2000) Change-Point Analysis: A Powerful New Tool For Detecting Changes.

M. Csorgo, L. Horvath (1997) Limit Theorems in Change-Point Analysis. Wiley.

Chen, J. and Gupta, A. K. (2000) Parametric statistical change point analysis. Birkhauser.

See Also

changepoint, cpt.mean

Examples

data(hoopoe2)
  hoopoe2$tFirst <- as.POSIXct(hoopoe2$tFirst, tz = "GMT")
  hoopoe2$tSecond <- as.POSIXct(hoopoe2$tSecond, tz = "GMT")
residency <- changeLight(hoopoe2, quantile=0.9)

slisovski/GeoLight documentation built on June 5, 2024, 4:24 p.m.