GermValue {germinationmetrics}

Peak value and germination value

Description

Compute the Peak value (\(PV\)) or Emergence Energy (\(EE\)) (Czabator 1962; Bonner 1967) and Germination value (\(GV\)) (Czabator 1962; Djavanshir and Pourbeik 1976; Brown and Mayer 1988).

Usage

PeakValue(germ.counts, intervals, total.seeds, partial = TRUE)

GermValue(
  germ.counts,
  intervals,
  total.seeds,
  partial = TRUE,
  method = c("czabator", "dp"),
  from.onset = TRUE,
  k = 10
)

Arguments

germ.counts

Germination counts at each time interval. Can be partial or cumulative as specified in the argument partial.

intervals

The time intervals.

total.seeds

Total number of seeds.

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 germination value. Either "czabator" or "dp".

from.onset

logical. If TRUE, duration is considered only from the onset of germination. If FALSE, full duration of germination test is considered. Default is TRUE.

k

Constant (See Details). Default is 10.

Details

Peak value (\(PV\)) is the maximum quotient obtained by dividing successive cumulative germination values by the relevant incubation time (Czabator 1962).

\[PV = \max\left ( \frac{G_{1}}{T_{1}},\frac{G_{2}}{T_{2}},\cdots \frac{G_{k}}{T_{k}} \right )\]

Where, \(T_{i}\) is the time from the start of the experiment to the \(i\)th interval, \(G_{i}\) is the cumulative germination percentage in the \(i\)th time interval, and \(k\) is the total number of time intervals.

It represents the mean daily germination of the most vigorous component of the seed lot, and is a mathematical expression of the break, or shoulder, of a typical sigmoid germination curve (Djavanshir and Pourbeik 1976). It is the accumulated number of seeds germinated at the point on the germination curve at which the rate of germination starts to decrease. It is also described as Emergence energy (Bonner 1967).

For daily germination counts, germination value (\(GV\)) is computed as follows (Czabator 1962) (Specified by the argument method = "czabator").

\[GV = PV \times MDG\]

Where, \(PV\) is the peak value, and \(MDG\) is the mean daily germination percentage from the onset of germination.

Germination value (\(GV\)) can also be computed for other time intervals of successive germination counts, by replacing \(MDG\) with the mean germination percentage per unit time (\(\overline{GP}\)).

A new estimation of germination value was given by Djavanshir and Pourbeik (1976) as follows (Specified by the argument method = "dp").

\[GV = \frac{\sum DGS}{N} \times GP \times c\]

Where, \(DGS\) is the daily germination speed computed by dividing cumulative germination percentage by the number of days since the onset of germination, \(N\) is the frequency or number of DGS calculated during the test, \(GP\) is the germination percentage expressed over 100, and \(c\) is a constant. The value of \(c\) is decided on the basis of average daily speed of germination (\(\frac{\sum DGS}{N}\)). If it is less than 10, then \(c\) value of 10 can be used and if it is more than 10, then value of 7 or 8 can be used for \(c\).

For both methods of computing \(GV\), only the duration from the onset of germination is considered by default. Alternatively, modified \(GV\) (\(GV_{mod}\)), where the entire duration from the beginning of the test is considered can be obtained by using the argument from.onset = FALSE (Brown and Mayer 1988).

Value

A list with the following components:

Germination Value

The germination value.

Calculations

The data frame of calculations.

testend

The end of test value (Only for method dp).

References

Bonner FT (1967). “Ideal sowing depth for sweetgum seed.” Tree Planters' Notes, 18(1), 1–1.

Brown RF, Mayer DG (1988). “Representing cumulative germination. 1. A critical analysis of single-value germination indices.” Annals of Botany, 61(2), 117–125.

Czabator FJ (1962). “Germination value: An index combining speed and completeness of pine seed germination.” Forest Science, 8(4), 386–396.

Djavanshir K, Pourbeik H (1976). “Germination value-A new formula.” Silvae Genetica, 25(2), 79–83.

Examples

x <- c(0, 0, 34, 40, 21, 10, 4, 5, 3, 5, 8, 7, 7, 6, 6, 4, 0, 2, 0, 2)
y <- c(0, 0, 34, 74, 95, 105, 109, 114, 117, 122, 130, 137, 144, 150,
      156, 160, 160, 162, 162, 164)
int <- 1:length(x)
total.seeds = 200

# From partial germination counts
#----------------------------------------------------------------------------
PeakValue(germ.counts = x, intervals = int, total.seeds = 200)
GermValue(germ.counts = x, intervals = int, total.seeds = 200,
          method = "czabator")
GermValue(germ.counts = x, intervals = int, total.seeds = 200,
          method = "dp", k = 10)
GermValue(germ.counts = x, intervals = int, total.seeds = 200,
          method = "czabator", from.onset = FALSE)
GermValue(germ.counts = x, intervals = int, total.seeds = 200,
          method = "dp", k = 10, from.onset = FALSE)

# From cumulative germination counts
#----------------------------------------------------------------------------
PeakValue(germ.counts = y, interval = int, total.seeds = 200,
          partial = FALSE)
GermValue(germ.counts = y, intervals = int, total.seeds = 200,
          partial = FALSE, method = "czabator")
GermValue(germ.counts = y, intervals = int, total.seeds = 200,
          partial = FALSE, method = "dp", k = 10)
GermValue(germ.counts = y, intervals = int, total.seeds = 200,
          partial = FALSE, method = "czabator", from.onset = FALSE)
GermValue(germ.counts = y, intervals = int, total.seeds = 200,
          partial = FALSE, method = "dp", k = 10, from.onset = FALSE)