Description Usage Arguments Details Value References Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 
germ.counts 
Germination counts at each time interval. Can be partial
or cumulative as specified in the argument 
intervals 
The time intervals. 
partial 
logical. If 
percent 
logical. If 
total.seeds 
Total number of seeds. Mandatory for computation when

method 
The method for computing germination speed in

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.
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.
\mjsdeqnS = \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.
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.
\mjsdeqnS_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.
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
.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35  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)


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
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