MeanGermRate: Germination rate

Description Usage Arguments Details Value References See Also Examples

View source: R/MeanGermRate.R

Description

Compute the following metrics:

MeanGermRate

Mean germination rate (\mjseqn\overlineV) \insertCitelabouriau_germination_1976,labouriau_uma_1983,ranal_how_2006germinationmetrics.

VarGermRate

Variance of germination rate (\mjseqns_V^2) \insertCitelabouriau_uma_1983,ranal_how_2006germinationmetrics.

SEGermRate

Standard error of germination rate (\mjseqns_\overlineV) \insertCitelabouriau_uma_1983,ranal_how_2006germinationmetrics.

CVG

Coefficient of velocity/rate of germination or Kotowski's coefficient of velocity (\mjseqnCVG) \insertCitekotowski_temperature_1926,nichols_two_1968,labouriau_uma_1983,scott_review_1984,bewley_seeds_1994germinationmetrics.

GermRateRecip

Germination rate as reciprocal of median time (\mjseqnv_50) \insertCitewent_experimental_1957,labouriau_uma_1983,ranal_how_2006germinationmetrics.

\loadmathjax

Usage

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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".

Details

MeanGermRate computes the mean germination rate (\mjseqn\overlineV) according to the following formula \insertCitelabouriau_germination_1976,labouriau_uma_1983,ranal_how_2006germinationmetrics.

\mjsdeqn\overline

V = \frac\sum_i=1^kN_i\sum_i=1^kN_iT_i

Where, \mjseqnT_i is the time from the start of the experiment to the \mjseqnith interval, \mjseqnN_i is the number of seeds germinated in the \mjseqnith time interval (not the accumulated number, but the number corresponding to the \mjseqnith interval), and \mjseqnk is the total number of time intervals.

It is the inverse of mean germination time (\mjseqn\overlineT).

\mjsdeqn\overline

V = \frac1\overlineT

VarGermRate computes the variance of germination rate (\mjseqns_V^2) according to the following formula \insertCitelabouriau_uma_1983,ranal_how_2006germinationmetrics.

\mjsdeqn

s_V^2 = \overlineV^4 \times s_T^2

Where, \mjseqns_T^2 is the variance of germination time.

SEGermRate computes the standard error of germination time (\mjseqns_\overlineV) according to the following formula \insertCitelabouriau_uma_1983,ranal_how_2006germinationmetrics.

\mjsdeqn

s_\overlineV = \sqrt\fracs_V^2\sum_i=1^kN_i

Where, \mjseqnN_i is the number of seeds germinated in the \mjseqnith time interval (not the accumulated number, but the number corresponding to the \mjseqnith interval), and \mjseqnk is the total number of time intervals.

CVG computes the coefficient of velocity/rate of germination or Kotowski's coefficient of velocity (\mjseqnCVG) according to the following formula \insertCitekotowski_temperature_1926,nichols_two_1968,labouriau_uma_1983,scott_review_1984,bewley_seeds_1994germinationmetrics.

\mjsdeqn

CVG = \frac\sum_i=1^kN_i\sum_i=1^kN_iT_i \times 100

\mjsdeqn

CVG = \overlineV \times 100

Where, \mjseqnT_i is the time from the start of the experiment to the \mjseqnith interval, \mjseqnN_i is the number of seeds germinated in the \mjseqnith time interval (not the accumulated number, but the number corresponding to the \mjseqnith interval), and \mjseqnk is the total number of time intervals.

GermRateRecip computes the germination rate \mjseqnv_50) as the reciprocal of the median germination time (\mjseqnt_50) \insertCitewent_experimental_1957,labouriau_uma_1983,ranal_how_2006germinationmetrics computed according to the methods of \insertCitecoolbear_effect_1984;textualgerminationmetrics or \insertCitefarooq_thermal_2005;textualgerminationmetrics as follows.

\mjsdeqn

v_50 = \frac1t_50

Value

For MeanGermRate, the mean germination rate value as \mjseqn\mathrmtime^-1.

For VarGermTime, the variance of germination rate value as \mjseqn\mathrmtime^-2.

For SEGermTime, the standard error of germination rate as \mjseqn\mathrmtime^-1.

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 \mjseqn\mathrmtime^-1.

References

\insertAllCited

See Also

MeanGermTime, t50

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
#----------------------------------------------------------------------------
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)

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