germinationmetrics (version 0.1.8)

GermIndex: Germination Index

Description

Compute the Germination index according to melville_seed_1980;textualgerminationmetrics and its modification by de_santana_alise_2004;textualgerminationmetrics ranal_how_2006germinationmetrics.

Usage

GermIndex(
  germ.counts,
  intervals,
  partial = TRUE,
  total.seeds,
  modification = c("none", "santanaranal")
)

Value

The value of the Germination index in the same unit of time as specified in the argument intervals.

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.

total.seeds

Total number of seeds.

modification

The modification to be applied. Either "none" or "santanaranal". Default is "none" (see Details).

Details

Germination index (GI) is computed as follows melville_seed_1980germinationmetrics.

GI = _i=1^k | ( T_k - T_i ) N_i |N_t

Where, T_i is the time from the start of the experiment to the ith interval (day for the example), 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), N_t is the total number of seeds used in the test, and k is the total number of time intervals.

A modified germination index (GI_mod) was proposed by de_santana_alise_2004germinationmetrics where total number of seeds tested (N_t) is replaced by the total number of germinated seeds (N_g) in the expression of melville_seed_1980;textualgerminationmetrics to remove the effect of sample size ranal_how_2006germinationmetrics. It is computed as follows (Specified by the argument modification = "santanaranal").

GI_mod = _i=1^k | ( T_k - T_i ) N_i |N_g

The term Germination index (GI) has also been used to describe the mathematical expression for Speed of germination (GermSpeed) by aosa_seed_1983;textualgerminationmetrics.

References

See Also

GermSpeed

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
#----------------------------------------------------------------------------
GermIndex(germ.counts = x, intervals = int, total.seeds = 50)
GermIndex(germ.counts = x, intervals = int, total.seeds = 50,
          modification = "none")
GermIndex(germ.counts = x, intervals = int, total.seeds = 50,
          modification = "santanaranal")

# From cumulative germination counts
#----------------------------------------------------------------------------
GermIndex(germ.counts = y, intervals = int, partial = FALSE,
          total.seeds = 50)
GermIndex(germ.counts = y, intervals = int, partial = FALSE,
          total.seeds = 50,
          modification = "none")
GermIndex(germ.counts = y, intervals = int, partial = FALSE,
          total.seeds = 50,
          modification = "santanaranal")