germinationmetrics (version 0.1.8)

GermSynchrony: Synchrony and uncertainty of germination

Description

Compute the following metrics:

GermSynchrony

Synchrony of germination (Z index) primack_longevity_1985,ranal_how_2006germinationmetrics.

GermUncertainty

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

Usage

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

Value

For GermUncertainty, the value of uncertainty of germination process in bit.

For GermSynchrony, the value of synchrony of germination.

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.

Details

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

Z=_i=1^kC_N_i,2C_ N_i,2

Where, C_N_i,2 is the partial combination of the two germinated seeds from among N_i, the number of seeds germinated on the ith time interval (estimated as C_N_i,2=N_i(N_i-1)2), and C_ N_i,2 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 (E) or uncertainty of the germination process (U) or informational entropy (H) as follows shannon_mathematical_1948,labouriau_germination_1976,labouriau_uma_1983germinationmetrics.

E = -_i=1^kf_i_2f_i

Where, f_i is the relative frequency of germination (estimated as f_i=N_i_i=1^kN_i), N_i is the number of seeds germinated on the ith time interval, and k is the total number of time intervals.

References

See Also

CUGerm

Examples

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)