germinationmetrics (version 0.1.3)

MeanGermRate: Germination rate

Description

Compute the following metrics:

MeanGermRate

Mean germination rate () labouriau_germination_1976,labouriau_uma_1983,ranal_how_2006germinationmetrics.

VarGermRate

Variance of germination rate () labouriau_uma_1983,ranal_how_2006germinationmetrics.

SEGermRate

Standard error of germination rate () labouriau_uma_1983,ranal_how_2006germinationmetrics.

CVG

Coefficient of velocity/rate of germination or Kotowski's coefficient of velocity () kotowski_temperature_1926,nichols_two_1968,labouriau_uma_1983,scott_review_1984,bewley_seeds:_1994germinationmetrics.

GermRateRecip

Germination rate as reciprocal of median time () went_experimental_1957,labouriau_uma_1983,ranal_how_2006germinationmetrics.

Usage

MeanGermRate(germ.counts, intervals, partial = TRUE)
CVG(germ.counts, intervals, partial = TRUE)
VarGermRate(germ.counts, intervals, partial = TRUE)
SEGermRate(germ.counts, intervals, partial = TRUE)
GermRateRecip(germ.counts, intervals, partial = TRUE,
  method = c("coolbear", "farooq"))

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.

method

The method for computing median germination time. Either "coolbear" or "farooq".

Value

For MeanGermRate, the mean germination rate value as .

For VarGermTime, the variance of germination rate value as .

For SEGermTime, the standard error of germination rate as .

For CVG, the value of Coefficient of of velocity/rate of germination or Kotowski's coefficient of velocity.

For GermRateRecip, the value of germination rate as .

Details

MeanGermRate computes the mean germination rate () according to the following formula labouriau_germination_1976,labouriau_uma_1983,ranal_how_2006germinationmetrics.

Where, is the time from the start of the experiment to the th observation, is the number of seeds germinated in the th time (not the accumulated number, but the number correspondent to the th observation) and is the last time of germination.

It is the inverse of mean germination time ().

VarGermRate computes the variance of germination rate () according to the following formula labouriau_uma_1983,ranal_how_2006germinationmetrics.

Where, is the variance of germination time.

SEGermRate computes the standard error of germination time () according to the following formula labouriau_uma_1983,ranal_how_2006germinationmetrics.

Where, is the number of seeds germinated in the th time (not the accumulated number, but the number correspondent to the th observation) and is the last time of germination.

CVG computes the coefficient of velocity/rate of germination or Kotowski's coefficient of velocity () according to the following formula kotowski_temperature_1926,nichols_two_1968,labouriau_uma_1983,scott_review_1984,bewley_seeds:_1994germinationmetrics.

Where, is the time from the start of the experiment to the th observation, is the number of seeds germinated in the th time (not the accumulated number, but the number correspondent to the th observation) and is the last time of germination.

GermRateRecip computes the germination rate () as the reciprocal of the median germination time () went_experimental_1957,labouriau_uma_1983,ranal_how_2006germinationmetrics computed according to the methods of coolbear_effect_1984;textualgerminationmetrics or farooq_thermal_2005;textualgerminationmetrics as follows:

References

See Also

MeanGermTime, t50

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
#----------------------------------------------------------------------------
MeanGermRate(germ.counts = x, intervals = int)
CVG(germ.counts = x, intervals = int)
VarGermRate(germ.counts = x, intervals = int)
SEGermRate(germ.counts = x, intervals = int)
GermRateRecip(germ.counts = x, intervals = int, method = "coolbear")
GermRateRecip(germ.counts = x, intervals = int, method = "farooq")

# From cumulative germination counts
#----------------------------------------------------------------------------
MeanGermRate(germ.counts = y, intervals = int, partial = FALSE)
CVG(germ.counts = y, intervals = int, partial = FALSE)
VarGermRate(germ.counts = y, intervals = int, partial = FALSE)
SEGermRate(germ.counts = y, intervals = int, partial = FALSE)
GermRateRecip(germ.counts = y, intervals = int,
              method = "coolbear", partial = FALSE)
GermRateRecip(germ.counts = y, intervals = int,
              method = "farooq", partial = FALSE)

# }