Compute germination indices from a data frame of germination counts recorded at specific time intervals for multiple samples in batch.
germination.indices(data, total.seeds.col, counts.intervals.cols,
intervals, partial = TRUE, FirstGermTime = TRUE,
LastGermTime = TRUE, PeakGermTime = TRUE, TimeSpreadGerm = TRUE,
t50 = TRUE, MeanGermTime = TRUE, VarGermTime = TRUE,
SEGermTime = TRUE, CVGermTime = TRUE, MeanGermRate = TRUE,
CVG = TRUE, VarGermRate = TRUE, SEGermRate = TRUE,
GermRateRecip = TRUE, GermSpeed = TRUE,
GermSpeedAccumulated = TRUE, GermSpeedCorrected = TRUE,
WeightGermPercent = TRUE, MeanGermPercent = TRUE,
MeanGermNumber = TRUE, TimsonsIndex = TRUE, GermRateGeorge = TRUE,
max.int, PeakValue = TRUE, GermValue = TRUE, gv.k = 10,
CUGerm = TRUE, GermSynchrony = TRUE, GermUncertainty = TRUE)A data frame with the germination count data. It should possess columns with
Partial or cumulative germination counts per
time interval (to be indicated by the argument counts.intervals.cols
and
Total number of seeds tested (to be indicated by the argument
total.seeds.col).
The name of the column in data with the total
number of seeds tested.
The names of columns in data with the
germination counts (partial or cumulative, as indicated by the argument
partial) per time interval (indicated by the argument
intervals).
The time intervals at which germination counts (in the
columns specified in argument counts.intervals.cols) were recorded.
logical. If TRUE, germination counts in
counts.intervals.cols is considered as partial and if FALSE,
it is considered as cumulative. Default is TRUE.
logical. If TRUE, the Time of first germination
or Germination time lag
()
edwards_temperature_1932,czabator_germination_1962,goloff_germination_1975,labouriau_germinacao_1983,ranal_effects_1999,quintanilla_effect_2000germinationmetrics
is computed. Default is TRUE.
logical. If TRUE, the Time of last germination
()
edwards_temperature_1932,labouriau_germinacao_1983,ranal_how_2006germinationmetrics.
is computed. Default is TRUE.
logical. If TRUE, the Peak time of germination or
Modal time of germination ranal_how_2006germinationmetrics
is computed. Default is TRUE.
logical. If TRUE, the Time spread of germination
al-mudaris_notes_1998,kader_comparison_2005germinationmetrics
or Germination distribution
schrader_seed_2000germinationmetrics. is computed. Default
is TRUE.
logical. If TRUE, the Median germination time
()
coolbear_effect_1984,farooq_thermal_2005germinationmetrics
is computed. Default is TRUE.
logical. If TRUE, the Mean germination time
() or
Mean length of incubation time
edmond_effects_1958,czabator_germination_1962,ellis_improved_1980,labouriau_germinacao_1983,ranal_how_2006germinationmetrics.
or Sprouting index ()
smith_germinating_1964germinationmetrics or Germination
Resistance ()
gordon_observations_1969,gordon_germination_1971;textualgerminationmetrics
is computed. Default is TRUE.
logical. If TRUE, the Variance of germination time
()
labouriau_germinacao_1983,ranal_how_2006germinationmetrics
is computed. Default is TRUE.
logical. If TRUE, the Standard error of germination
time ()
labouriau_germinacao_1983,ranal_how_2006germinationmetrics.
is computed. Default is TRUE.
logical. If TRUE, the Coefficient of variation of
the germination time
()
ranal_how_2006germinationmetrics is computed. Default is
TRUE.
logical. If TRUE, the Mean germination rate
()
labouriau_germination_1976,labouriau_uma_1983,ranal_how_2006germinationmetrics.
is computed. Default is TRUE.
logical. If TRUE, the Coefficient of velocity/rate of
germination or Kotowski's coefficient of velocity
()
kotowski_temperature_1926,nichols_two_1968,labouriau_uma_1983,scott_review_1984,bewley_seeds:_1994germinationmetrics.
is computed. Default is TRUE.
logical. If TRUE, the Variance of germination rate
()
labouriau_uma_1983,ranal_how_2006germinationmetrics is
computed. Default is TRUE.
logical. If TRUE, the Standard error of germination
rate ()
labouriau_uma_1983,ranal_how_2006germinationmetrics is
computed. Default is TRUE.
logical. If TRUE, the Germination rate as
reciprocal of median time
()
went_experimental_1957,labouriau_uma_1983,ranal_how_2006germinationmetrics
is computed.
logical. If TRUE, the 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
considering both counts and percentages is computed.
logical. If TRUE, the Speed of accumulated
germination
bradbeer_seed_1988,wardle_allelopathic_1991,haugland_experiments_1996,de_santana_alise_2004germinationmetrics
considering both counts and percentages is computed.
logical. If TRUE, the Corrected speed of
germination or Corrected germination rate index and the Corrected speed of
accumulated germination
evetts_germination_1972germinationmetrics is computed.
logical. If TRUE, the Weighted germination
percentage or Weighted
germination index
reddy_effect_1978,reddy_effect_1985germinationmetrics is computed.
logical. If TRUE, the Mean/average germination
percentage per unit time ()
czabator_germination_1962germinationmetrics is computed.
logical. If TRUE, the Number of seeds germinated
per unit time ()
khamassi_optimal_2013germinationmetrics is computed.
logical. If TRUE, the Timson's index or Timson's
germination velocity index
grose_laboratory_1958,timson_new_1965,brown_representing_1988,baskin_seeds:_1998germinationmetrics
and it's modifications by Labouriau
ranal_how_2006germinationmetrics and
khan_effect_1984germinationmetrics is computed.
logical. If TRUE, the George's index
george_influence_1961;textualgerminationmetrics is computed.
The maximum interval value up to which Timson's index/George's germination rate is to be computed.
logical. If TRUE, the Peak value
() or Emergence Energy
()
czabator_germination_1962,bonner_ideal_1967germinationmetrics
is computed.
logical. If TRUE, the Germination value
czabator_germination_1962,djavanshir_germination_1976germinationmetrics
and its modification considering duration from start of test instead of
from onset of germination
brown_representing_1988germinationmetrics is computed.
The k Constant for computation of germination value. Default is 10.
logical. If TRUE, the Coefficient of uniformity of
germination (CUG)
heydecker_seed_1972,bewley_seeds:_1994germinationmetrics is
computed.
logical. If TRUE, the Synchrony of germination
( index)
primack_longevity_1985,ranal_how_2006germinationmetrics is
computed.
logical. If TRUE, the Synchronization index
() or Uncertainty of the
germination process () or
Informational entropy ()
shannon_mathematical_1948,labouriau_germination_1976,labouriau_uma_1983germinationmetrics
is computed.
A data frame with the original data along with the various single-value germination indices specified in the function arguments.
This function is a wrapper around the different functions for
computation of single-value germination indices in
germinationmetrics
(FirstGermTime,
LastGermTime,
PeakGermTime,
TimeSpreadGerm,
t50,
MeanGermTime,
VarGermTime,
SEGermTime,
CVGermTime,
MeanGermRate,
CVG,
VarGermRate,
SEGermRate,
GermRateRecip,
GermSpeed,
GermSpeedAccumulated,
GermSpeedCorrected,
WeightGermPercent,
MeanGermPercent,
MeanGermPercent,
TimsonsIndex,
GermRateGeorge,
GermValue,
PeakValue,
CUGerm,
GermSynchrony,
GermUncertainty)
# NOT RUN {
data(gcdata)
counts.per.intervals <- c("Day01", "Day02", "Day03", "Day04", "Day05",
"Day06", "Day07", "Day08", "Day09", "Day10",
"Day11", "Day12", "Day13", "Day14")
germination.indices(gcdata, total.seeds.col = "Total Seeds",
counts.intervals.cols = counts.per.intervals,
intervals = 1:14, partial = TRUE, max.int = 5)
# }
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