germinationmetrics (version 0.1.3)

GermSpeed: Speed of germination

Description

Compute the following metrics:

GermSpeed

Speed of germination or Germination rate index or Index of velocity of germination or Germination index or Emergence Rate Index throneberry_relation_1955,maguire_speed_1962,allan_seedling_1962,kendrick_photocontrol_1969,bouton_germination_1976,aosa_seed_1983,khandakar_jute_1983,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics.

GermSpeedAccumulated

Speed of accumulated germination bradbeer_seed_1988,wardle_allelopathic_1991,haugland_experiments_1996,de_santana_alise_2004germinationmetrics.

GermSpeedCorrected

Corrected speed of germination or Corrected germination rate index evetts_germination_1972germinationmetrics.

Usage

GermSpeed(germ.counts, intervals, partial = TRUE, percent = FALSE,
  total.seeds = NULL)
GermSpeedAccumulated(germ.counts, intervals, partial = TRUE,
  percent = FALSE, total.seeds = NULL)
GermSpeedCorrected(germ.counts, intervals, partial = TRUE, total.seeds,
  method = c("normal", "accumulated"))

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.

percent

logical. If TRUE, germination percentage is used instead of counts for computation. Default is FALSE.

total.seeds

Total number of seeds. Mandatory for computation when percent = TRUE.

method

The method for computing germination speed in GermSpeedCorrected. Either "normal" (GermSpeed) or "accumulated" (GermSpeedAccumulated).

Value

For GermSpeed, the value of germination speed as % .

For GermSpeedAccumulated, the value of accumulated germination speed as % .

For GermSpeedCorrected, the corrected speed of germination.

Details

GermSpeed computes the speed of germination according to the following formula throneberry_relation_1955,maguire_speed_1962,allan_seedling_1962,kendrick_photocontrol_1969,bouton_germination_1976,aosa_seed_1983,khandakar_jute_1983,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics.

Where, , , , , are the number of germinated seeds observed at time (days or hours) , , , , after sowing. (Not accumulated/cumulative number, but the number of seeds that germinated at the specific time).

GermSpeedAccumulated computes the speed of accumulated germination as follows bradbeer_seed_1988,wardle_allelopathic_1991,haugland_experiments_1996,de_santana_alise_2004germinationmetrics.

Where, , , , , are the number of germinated seeds observed at time (days or hours) , , , , after sowing. (Not accumulated/cumulative number, but the number of seeds that germinated at the specific time).

Speed of germination expresses the rate of germination in terms of the total number of seeds that germinate in a time interval. Higher values indicate greater and faster germination. This is useful for comparisons only when samples or treatments possess similar germinabilities. This is overcome by either using the corrected speed of germination or by using germination percentages instead of counts for computing speed.

GermSpeedCorrected computes the corrected speed of germination as follows evetts_germination_1972germinationmetrics.

Where, is the final germination percentage or germinability.

With percent = TRUE, germination percentage is used instead of counts for computation in GermSpeed and GermSpeedAccumulated.

References

Examples

# NOT RUN {
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
#----------------------------------------------------------------------------
GermSpeed(germ.counts = x, intervals = int)
GermSpeedAccumulated(germ.counts = x, intervals = int)
GermSpeedCorrected(germ.counts = x, intervals = int, total.seeds = 50,
                   method = "normal")
GermSpeedCorrected(germ.counts = x, intervals = int, total.seeds = 50,
                   method = "accumulated")

# From partial germination counts (with percentages instead of counts)
#----------------------------------------------------------------------------
GermSpeed(germ.counts = x, intervals = int,
          percent = TRUE, total.seeds = 50)
GermSpeedAccumulated(germ.counts = x, intervals = int,
                     percent = TRUE, total.seeds = 50)

# From cumulative germination counts
#----------------------------------------------------------------------------
GermSpeed(germ.counts = y, intervals = int, partial = FALSE)
GermSpeedAccumulated(germ.counts = y, intervals = int, partial = FALSE)
GermSpeedCorrected(germ.counts = y, intervals = int,
                   partial = FALSE, total.seeds = 50, method = "normal")
GermSpeedCorrected(germ.counts = y, intervals = int,
                   partial = FALSE, total.seeds = 50, method = "accumulated")

# From cumulative germination counts (with percentages instead of counts)
#----------------------------------------------------------------------------
GermSpeed(germ.counts = y, intervals = int, partial = FALSE,
          percent = TRUE, total.seeds = 50)
GermSpeedAccumulated(germ.counts = y, intervals = int, partial = FALSE,
                     percent = TRUE, total.seeds = 50)
# }