germinationmetrics (version 0.1.8)

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,erbach_tillage_1982,aosa_seed_1983,khandakar_jute_1983,hsu_planting_1986,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")
)

Value

For GermSpeed, the value of germination speed as

count \, time^-1 or % time^-1.

For GermSpeedAccumulated, the value of accumulated germination speed as count \, time^-1 or % time^-1.

For GermSpeedCorrected, the corrected speed of germination as

time^-1.

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 throneberry_relation_1955,maguire_speed_1962,allan_seedling_1962,kendrick_photocontrol_1969,bouton_germination_1976,erbach_tillage_1982,aosa_seed_1983,khandakar_jute_1983,hsu_planting_1986,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics.

S = N_1T_1 + N_2T_2 + N_3T_3 + + N_kT_k

Where, N_1, N_2, N_3, , N_k are the number of germinated seeds observed at time (days or hours) T_1, T_2, T_3, , T_k after sowing (Not accumulated/cumulative number, but the number of seeds that germinated at the specific time) and k is the total number of time intervals.

It is the same as Emergence Rate Index (ERI) described by allan_seedling_1962;textualgerminationmetrics, erbach_tillage_1982;textualgerminationmetrics and hsu_planting_1986;textualgerminationmetrics as well as Germination Index (GI) according to aosa_seed_1983;textualgerminationmetrics.

The formula can also be described as follows.

S = _i=1^kN_iT_i

Where, T_i is the time from the start of the experiment to the ith interval, 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), and k is the total number of time intervals.

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

S_accumulated = N_1T_1 + N_1 + N_2T_2 + N_1 + N_2 + N_3T_3 + +N_1 + N_2 + + N_kT_k

Where, N_1, N_2, N_3, , N_k are the number of germinated seeds observed at time (days or hours) T_1, T_2, T_3, , T_k after sowing (Not accumulated/cumulative number, but the number of seeds that germinated at the specific time), and k is the total number of time intervals.

The formula can also be described as follows.

S_accumulated = _i=1^k_j=1^iN_jT_i

Where, T_i is the time from the start of the experiment to the ith interval, _j=1^iN_j is the cumuative/accumulated number of seeds germinated in the ith time interval, and k 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 evetts_germination_1972germinationmetrics.

S_corrected = SFGP

Where, S is the germination speed (either standard or accumulated as specified by the argument method = "normal" or method = "accumulated" respectively) computed with germination percentage instead of counts and FGP is the final germination percentage or germinability.

With percent = TRUE, germination percentage is used instead of counts for computation in GermSpeed and GermSpeedAccumulated. In case of GermSpeedCorrected, germination percentage is always used for the numerator.

References

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