GermIndex: Germination Index

Description Usage Arguments Details Value References See Also Examples

View source: R/GermIndex.R

Description

Compute the Germination index according to \insertCitemelvilleSeedGerminationEarly1980;textualgerminationmetrics and its modification by \insertCitede_santana_alise_2004;textualgerminationmetrics \insertCiteranal_how_2006germinationmetrics. \loadmathjax

Usage

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

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 (\mjseqnGI) is computed as follows \insertCitemelvilleSeedGerminationEarly1980germinationmetrics.

\mjsdeqn

GI = \sum_i=1^k\frac\left | \left ( T_k - T_i \right ) N_i\right |N_t

Where, \mjseqnT_i is the time from the start of the experiment to the \mjseqnith interval (day for the example), \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), \mjseqnN_t is the total number of seeds used in the test, and \mjseqnk is the total number of time intervals.

A modified germination index (\mjseqnGI_mod) was proposed by \insertCitede_santana_alise_2004germinationmetrics where total number of seeds tested (\mjseqnNt) is replaced by the total number of germinated seeds (\mjseqnNg) in the expression of \insertCitemelvilleSeedGerminationEarly1980;textualgerminationmetrics to remove the effect of sample size \insertCiteranal_how_2006germinationmetrics.

\mjsdeqn

GI_mod = \sum_i=1^k\frac\left | \left ( T_k - T_i \right ) N_i\right |N_g

The term Germination index (\mjseqnGI) has also been used to describe the mathematical expression for Speed of germination (GermSpeed) by \insertCiteaosa_seed_1983;textualgerminationmetrics.

Value

The value of the Germination index.

References

\insertAllCited

See Also

GermSpeed

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
#----------------------------------------------------------------------------
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")

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