GermSynchrony: Synchrony and uncertainty of germination

Description Usage Arguments Details Value References See Also Examples

View source: R/GermSynchrony.R

Description

Compute the following metrics:

GermSynchrony

Synchrony of germination (\mjseqnZ index) \insertCiteprimack_longevity_1985,ranal_how_2006germinationmetrics.

GermUncertainty

Synchronization index (\mjseqn\overlineE) or Uncertainty of the germination process (\mjseqnU) or Informational entropy (\mjseqnH) \insertCiteshannon_mathematical_1948,labouriau_germination_1976,labouriau_uma_1983germinationmetrics.

\loadmathjax

Usage

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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.

Details

GermSynchrony computes the value of synchrony of germination (\mjseqnZ index) as follows \insertCiteprimack_longevity_1985,ranal_how_2006germinationmetrics.

\mjsdeqn

Z=\frac\sum_i=1^kC_N_i,2C_\Sigma N_i,2

Where, \mjseqnC_N_i,2 is the partial combination of the two germinated seeds from among \mjseqnN_i, the number of seeds germinated on the \mjseqnith time interval (estimated as \mjseqnC_N_i,2=\fracN_i(N_i-1)2), and \mjseqnC_\Sigma 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 (\mjseqn\overlineE) or uncertainty of the germination process (\mjseqnU) or informational entropy (\mjseqnH) as follows \insertCiteshannon_mathematical_1948,labouriau_germination_1976,labouriau_uma_1983germinationmetrics.

\mjsdeqn\overline

E = -\sum_i=1^kf_i\log_2f_i

Where, \mjseqnf_i is the relative frequency of germination (estimated as \mjseqnf_i=\fracN_i\sum_i=1^kN_i), \mjseqnN_i is the number of seeds germinated on the \mjseqnith time interval, and \mjseqnk is the total number of time intervals.

Value

For GermUncertainty, the value of uncertainty of germination process.

For GermSynchrony, the value of synchrony of germination.

References

\insertAllCited

See Also

CUGerm

Examples

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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)

germinationmetrics documentation built on Feb. 17, 2021, 5:09 p.m.