GermSpeed: Speed of germination
In germinationmetrics: Seed Germination Indices and Curve Fitting
GermSpeed R Documentation
Speed of germination
Description
Compute the following metrics:
GermSpeedSpeed 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,erbach_tillage_1982,aosa_seed_1983,khandakar_jute_1983,hsu_planting_1986,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics.
GermSpeedAccumulatedSpeed of accumulated germination
\insertCitebradbeer_seed_1988,wardle_allelopathic_1991,haugland_experiments_1996,de_santana_alise_2004germinationmetrics.
GermSpeedCorrectedCorrected speed of germination or
Corrected germination rate index
\insertCiteevetts_germination_1972germinationmetrics.
\loadmathjax
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).
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,erbach_tillage_1982,aosa_seed_1983,khandakar_jute_1983,hsu_planting_1986,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics.
\mjsdeqnS = \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,
\insertCiteerbach_tillage_1982;textualgerminationmetrics and
\insertCitehsu_planting_1986;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.
\mjsdeqnS_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.
\mjsdeqnS_corrected = \fracSFGP
Where, \mjseqnS 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 \mjseqnFGP 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.
Value
For GermSpeed, the value of germination speed as
\mjseqn\mathrmcount \, time^-1 or % \mjseqn\mathrmtime^-1.
For GermSpeedAccumulated, the value of accumulated germination speed
as \mjseqn\mathrmcount \, time^-1 or % \mjseqn\mathrmtime^-1.
For GermSpeedCorrected, the corrected speed of germination as
\mjseqn\mathrmtime^-1.
References
\insertAllCited
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)
germinationmetrics documentation built on Aug. 19, 2023, 1:07 a.m.
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| GermSpeed | R Documentation |
Speed of germination
Description
Compute the following metrics:
GermSpeedSpeed 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,erbach_tillage_1982,aosa_seed_1983,khandakar_jute_1983,hsu_planting_1986,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics.
GermSpeedAccumulatedSpeed of accumulated germination \insertCitebradbeer_seed_1988,wardle_allelopathic_1991,haugland_experiments_1996,de_santana_alise_2004germinationmetrics.
GermSpeedCorrectedCorrected speed of germination or Corrected germination rate index \insertCiteevetts_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 |
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
|
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,erbach_tillage_1982,aosa_seed_1983,khandakar_jute_1983,hsu_planting_1986,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, \insertCiteerbach_tillage_1982;textualgerminationmetrics and \insertCitehsu_planting_1986;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, \mjseqnS 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 \mjseqnFGP 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.
Value
For GermSpeed, the value of germination speed as
\mjseqn\mathrmcount \, time^-1 or % \mjseqn\mathrmtime^-1.
For GermSpeedAccumulated, the value of accumulated germination speed
as \mjseqn\mathrmcount \, time^-1 or % \mjseqn\mathrmtime^-1.
For GermSpeedCorrected, the corrected speed of germination as
\mjseqn\mathrmtime^-1.
References
\insertAllCitedExamples
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)
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