germinationmetrics (version 0.1.8)

MeanGermRate: Germination rate

Description

Compute the following metrics:

MeanGermRate

Mean germination rate (V) labouriau_germination_1976,labouriau_uma_1983,ranal_how_2006germinationmetrics.

VarGermRate

Variance of germination rate (s_V^2) labouriau_uma_1983,ranal_how_2006germinationmetrics.

SEGermRate

Standard error of germination rate (s_V) labouriau_uma_1983,ranal_how_2006germinationmetrics.

CVG

Coefficient of velocity/rate of germination or Kotowski's coefficient of velocity (CVG) kotowski_temperature_1926,nichols_two_1968,labouriau_uma_1983,scott_review_1984,bewley_seeds_1994germinationmetrics.

GermRateRecip

Germination rate as reciprocal of median time (v_50) 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")
)

Value

For MeanGermRate, the mean germination rate value as

time^-1.

For VarGermTime, the variance of germination rate value as

time^-2.

For SEGermTime, the standard error of germination rate as

time^-1.

For CVG, the value of Coefficient of of velocity/rate of germination or Kotowski's coefficient of velocity as % time^-1.

For GermRateRecip, the value of germination rate as

time^-1.

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 (V) according to the following formula labouriau_germination_1976,labouriau_uma_1983,ranal_how_2006germinationmetrics.

V = _i=1^kN_i_i=1^kN_iT_i

Where, T_i is the time from the start of the experiment to the ith interval, N_i is the number of seeds germinated in the ith time interval (not the accumulated number, but the number corresponding to the ith interval), and k is the total number of time intervals.

It is the inverse of mean germination time (T).

V = 1T

VarGermRate computes the variance of germination rate (s_V^2) according to the following formula labouriau_uma_1983,ranal_how_2006germinationmetrics.

s_V^2 = V^4 s_T^2

Where, s_T^2 is the variance of germination time.

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

s_V = s_V^2_i=1^kN_i

Where, N_i is the number of seeds germinated in the ith time interval (not the accumulated number, but the number corresponding to the ith interval), and k is the total number of time intervals.

CVG computes the coefficient of velocity/rate of germination or Kotowski's coefficient of velocity (CVG) according to the following formula kotowski_temperature_1926,nichols_two_1968,labouriau_uma_1983,scott_review_1984,bewley_seeds_1994germinationmetrics.

CVG = _i=1^kN_i_i=1^kN_iT_i 100

CVG = V 100

Where, T_i is the time from the start of the experiment to the ith interval, N_i is the number of seeds germinated in the ith time interval (not the accumulated number, but the number corresponding to the ith interval), and k is the total number of time intervals.

GermRateRecip computes the germination rate (v_50) as the reciprocal of the median germination time (t_50) went_experimental_1957,labouriau_uma_1983,ranal_how_2006germinationmetrics according to the methods of coolbear_effect_1984;textualgerminationmetrics (Specified by the argument method = "coolbear") or farooq_thermal_2005;textualgerminationmetrics (Specified by the argument method = "farooq") as follows.

v_50 = 1t_50

References

See Also

MeanGermTime, t50

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