View source: R/GermSynchrony.R
GermSynchrony | R Documentation |
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.
GermSynchrony(germ.counts, intervals, partial = TRUE)
GermUncertainty(germ.counts, intervals, partial = TRUE)
germ.counts |
Germination counts at each time interval. Can be partial
or cumulative as specified in the argument |
intervals |
The time intervals. |
partial |
logical. If |
GermSynchrony
computes the value of synchrony of germination
(\mjseqnZ index) as follows
\insertCiteprimack_longevity_1985,ranal_how_2006germinationmetrics.
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.
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.
For GermUncertainty
, the value of uncertainty of germination
process in \mjseqn\mathrmbit.
For GermSynchrony
, the value of synchrony of germination.
CUGerm
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)
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