germinationmetrics (version 0.1.3)

GermSynchrony: Synchrony and uncertainty of germination

Description

Compute the following metrics:

GermSynchrony

Synchrony of germination ( index) primack_longevity_1985,ranal_how_2006germinationmetrics.

GermUncertainty

Synchronization index () or Uncertainty of the germination process () or Informational entropy () shannon_mathematical_1948,labouriau_germination_1976,labouriau_uma_1983germinationmetrics.

Usage

GermSynchrony(germ.counts, intervals, partial = TRUE)
GermUncertainty(germ.counts, intervals, partial = TRUE)

Arguments

germ.counts

Germination counts at each time interval. Can be partial or cumulative as specified in the argument partial.

intervals

The time intervals.

partial

logical. If TRUE, germ.counts is considered as partial and if FALSE, it is considered as cumulative. Default is TRUE.

Value

For GermUncertainty, the value of uncertainty of germination process.

For GermSynchrony, the value of synchrony of germination.

Details

GermSynchrony computes the value of synchrony of germination ( index) as follows primack_longevity_1985,ranal_how_2006germinationmetrics.

Where, is the partial combination of the two germinated seeds from among , the number of seeds germinated on the th time (estimated as ) and is the partial combination of the two germinated seeds from among the total number of seeds germinated at the final count, assuming that all seeds that germinated did so simultaneously.

GermUncertainty computes the value of synchronization index () or uncertainty of the germination process () or informational entropy () as follows shannon_mathematical_1948,labouriau_germination_1976,labouriau_uma_1983germinationmetrics.

Where, is the relative frequency of germination (estimated as ), is the number of seeds germinated on the th time and is the last day of observation.

References

See Also

CUGerm

Examples

# NOT RUN {
x <- c(0, 0, 0, 0, 4, 17, 10, 7, 1, 0, 1, 0, 0, 0)
y <- c(0, 0, 0, 0, 4, 21, 31, 38, 39, 39, 40, 40, 40, 40)
int <- 1:length(x)

# From partial germination counts
#----------------------------------------------------------------------------
GermSynchrony(germ.counts = x, intervals = int)
GermUncertainty(germ.counts = x, intervals = int)

# From cumulative germination counts
#----------------------------------------------------------------------------
GermSynchrony(germ.counts = y, intervals = int, partial = FALSE)
GermUncertainty(germ.counts = y, intervals = int, partial = FALSE)

# }