GermSpeed: Speed of germination

Description Usage Arguments Details Value References Examples

View source: R/GermSpeed.R

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 \insertCitethroneberry_relation_1955,maguire_speed_1962,allan_seedling_1962,kendrick_photocontrol_1969,bouton_germination_1976,erbachTillageContinuousCorn1982,aosa_seed_1983,khandakar_jute_1983,hsuPlantingDateEffects1986,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics.

GermSpeedAccumulated

Speed of accumulated germination \insertCitebradbeer_seed_1988,wardle_allelopathic_1991,haugland_experiments_1996,de_santana_alise_2004germinationmetrics.

GermSpeedCorrected

Corrected speed of germination or Corrected germination rate index \insertCiteevetts_germination_1972germinationmetrics.

\loadmathjax

Usage

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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).

Details

GermSpeed computes the speed of germination according to the following formula \insertCitethroneberry_relation_1955,maguire_speed_1962,allan_seedling_1962,kendrick_photocontrol_1969,bouton_germination_1976,erbachTillageContinuousCorn1982,aosa_seed_1983,khandakar_jute_1983,hsuPlantingDateEffects1986,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics.

\mjsdeqn

S = \fracN_1T_1 + \fracN_2T_2 + \fracN_3T_3 + \cdots + \fracN_kT_k

Where, \mjseqnN_1, \mjseqnN_2, \mjseqnN_3, \mjseqn\cdots, \mjseqnN_k are the number of germinated seeds observed at time (days or hours) \mjseqnT_1, \mjseqnT_2, \mjseqnT_3, \mjseqn\cdots, \mjseqnT_k after sowing (Not accumulated/cumulative number, but the number of seeds that germinated at the specific time) and \mjseqnk is the total number of time intervals.

It is the same as Emergence Rate Index (\mjseqnERI) described by \insertCiteallan_seedling_1962;textualgerminationmetrics, \insertCiteerbachTillageContinuousCorn1982;textualgerminationmetrics and \insertCitehsuPlantingDateEffects1986;textualgerminationmetrics as well as Germination Index (\mjseqnGI) according to \insertCiteaosa_seed_1983;textualgerminationmetrics.

The formula can also be described as follows.

\mjsdeqn

S = \sum_i=1^k\fracN_iT_i

Where, \mjseqnT_i is the time from the start of the experiment to the \mjseqnith interval, \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), and \mjseqnk is the total number of time intervals.

GermSpeedAccumulated computes the speed of accumulated germination as follows \insertCitebradbeer_seed_1988,wardle_allelopathic_1991,haugland_experiments_1996,de_santana_alise_2004germinationmetrics.

\mjsdeqn

S_accumulated = \fracN_1T_1 + \fracN_1 + N_2T_2 + \fracN_1 + N_2 + N_3T_3 + \cdots +\fracN_1 + N_2 + \cdots + N_kT_k

Where, \mjseqnN_1, \mjseqnN_2, \mjseqnN_3, \mjseqn\cdots, \mjseqnN_k are the number of germinated seeds observed at time (days or hours) \mjseqnT_1, \mjseqnT_2, \mjseqnT_3, \mjseqn\cdots, \mjseqnT_k after sowing (Not accumulated/cumulative number, but the number of seeds that germinated at the specific time), and \mjseqnk is the total number of time intervals.

The formula can also be described as follows.

\mjsdeqn

S_accumulated = \sum_i=1^k\frac\sum_j=1^iN_jT_i

Where, \mjseqnT_i is the time from the start of the experiment to the \mjseqnith interval, \mjseqn\sum_j=1^iN_j is the cumuative/accumulated number of seeds germinated in the \mjseqnith time interval, and \mjseqnk is the total number of time intervals.

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 \insertCiteevetts_germination_1972germinationmetrics.

\mjsdeqn

S_corrected = \fracSFGP

Where, \mjseqnFGP is the final germination percentage or germinability.

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

Value

For GermSpeed, the value of germination speed as % \mjseqn\mathrmtime^-1.

For GermSpeedAccumulated, the value of accumulated germination speed as % \mjseqn\mathrmtime^-1.

For GermSpeedCorrected, the corrected speed of germination.

References

\insertAllCited

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

Example output

--------------------------------------------------------------------------------
Welcome to germinationmetrics version 0.1.4


# To know how to use this package type:
  browseVignettes(package = 'germinationmetrics')
  for the package vignette.

# To know whats new in this version type:
  news(package='germinationmetrics')
  for the NEWS file.

# To cite the methods in the package type:
  citation(package='germinationmetrics')

# To suppress this message use:
  suppressPackageStartupMessages(library(germinationmetrics))
--------------------------------------------------------------------------------

[1] 6.138925
[1] 34.61567
[1] 0.07673656
[1] 0.4326958
[1] 12.27785
[1] 69.23134
[1] 6.138925
[1] 34.61567
[1] 0.07673656
[1] 0.4326958
[1] 12.27785
[1] 69.23134

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