phenocamr (version 1.1.5)

transition_dates: Calculates transition dates for a PhenoCam time series

Description

Segments of a PhenoCam time series and calculates threshold based transition dates for all segments. This function is rarely called stand alone and `phenophases()` should be preferred when evaluating PhenoCam time series.

Usage

transition_dates(
  data,
  lower_thresh = 0.1,
  middle_thresh = 0.25,
  upper_thresh = 0.5,
  percentile = 90,
  penalty = 0.5,
  seg_length = 14,
  reverse = FALSE,
  plot = FALSE
)

Value

Transition date estimates in UNIX time, including uncertainties and the threshold values estimated for each section of a time series.

Arguments

data

a PhenoCam data file or data structure

lower_thresh

the minimum threshold used (default = 0.1)

middle_thresh

the middle threshold used (default = 0.25)

upper_thresh

the maximum threshold used (default = 0.5)

percentile

time series percentiles to process (mean, 50, 75, 90)

penalty

how sensitive is the algorithm, lower is more sensitve (< 1 )

seg_length

minimum length of a segment to be evaluated

reverse

flip the direction of the processing

plot

plot for debugging purposes

Examples

if (FALSE) {
# download demo data
download_phenocam(site = "harvard$",
                  veg_type = "DB",
                  roi_id = "1000",
                  frequency = "3")

# read the data and calculate transition dates
df <- read_phenocam(file.path(tempdir(),"harvard_DB_1000_3day.csv"))
my_dates <- transition_dates(df,
                            lower_thresh = 0.1,
                            middle_thresh = 0.25,
                            upper_thresh = 0.5,
                            percentile = 90,
                            reverse = FALSE,
                            plot = FALSE)
}