germination.indices: Germination Indices

Description Usage Arguments Value References See Also Examples

View source: R/germination.indices.R

Description

Compute germination indices from a data frame of germination counts recorded at specific time intervals for multiple samples in batch. \loadmathjax

Usage

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Arguments

data

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).

total.seeds.col

The name of the column in data with the total number of seeds tested.

counts.intervals.cols

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).

intervals

The time intervals at which germination counts (in the columns specified in argument counts.intervals.cols) were recorded.

partial

logical. If TRUE, germination counts in counts.intervals.cols is considered as partial and if FALSE, it is considered as cumulative. Default is TRUE.

FirstGermTime

logical. If TRUE, the Time of first germination or Germination time lag (\mjseqnt_0) \insertCiteedwards_temperature_1932,czabator_germination_1962,goloff_germination_1975,labouriau_germinacao_1983,ranal_effects_1999,quintanilla_effect_2000germinationmetrics is computed. Default is TRUE.

LastGermTime

logical. If TRUE, the Time of last germination (\mjseqnt_g) \insertCiteedwards_temperature_1932,labouriau_germinacao_1983,ranal_how_2006germinationmetrics. is computed. Default is TRUE.

PeakGermTime

logical. If TRUE, the Peak time of germination or Modal time of germination \insertCiteranal_how_2006germinationmetrics is computed. Default is TRUE.

TimeSpreadGerm

logical. If TRUE, the Time spread of germination \insertCiteal-mudaris_notes_1998,kader_comparison_2005germinationmetrics or Germination distribution \insertCiteschrader_seed_2000germinationmetrics. is computed. Default is TRUE.

t50

logical. If TRUE, the Median germination time (\mjseqnt_50) \insertCitecoolbear_effect_1984,farooq_thermal_2005germinationmetrics is computed. Default is TRUE.

MeanGermTime

logical. If TRUE, the Mean germination time (\mjseqn\overlineT) or Mean length of incubation time \insertCiteedmond_effects_1958,czabator_germination_1962,ellis_improved_1980,labouriau_germinacao_1983,ranal_how_2006germinationmetrics. or Sprouting index (\mjseqnSI) \insertCitesmith_germinating_1964germinationmetrics or Germination Resistance (\mjseqnGR) \insertCitegordon_observations_1969,gordon_germination_1971;textualgerminationmetrics is computed. Default is TRUE.

VarGermTime

logical. If TRUE, the Variance of germination time (\mjseqns_T^2) \insertCitelabouriau_germinacao_1983,ranal_how_2006germinationmetrics is computed. Default is TRUE.

SEGermTime

logical. If TRUE, the Standard error of germination time (\mjseqns_\overlineT) \insertCitelabouriau_germinacao_1983,ranal_how_2006germinationmetrics. is computed. Default is TRUE.

CVGermTime

logical. If TRUE, the Coefficient of variation of the germination time (\mjseqnCV_T) \insertCiteranal_how_2006germinationmetrics is computed. Default is TRUE.

MeanGermRate

logical. If TRUE, the Mean germination rate (\mjseqn\overlineV) \insertCitelabouriau_germination_1976,labouriau_uma_1983,ranal_how_2006germinationmetrics. is computed. Default is TRUE.

CVG

logical. If TRUE, the Coefficient of velocity/rate of germination or Kotowski's coefficient of velocity (\mjseqnCVG) \insertCitekotowski_temperature_1926,nichols_two_1968,labouriau_uma_1983,scott_review_1984,bewley_seeds_1994germinationmetrics. is computed. Default is TRUE.

VarGermRate

logical. If TRUE, the Variance of germination rate (\mjseqns_V^2) \insertCitelabouriau_uma_1983,ranal_how_2006germinationmetrics is computed. Default is TRUE.

SEGermRate

logical. If TRUE, the Standard error of germination rate (\mjseqns_\overlineV) \insertCitelabouriau_uma_1983,ranal_how_2006germinationmetrics is computed. Default is TRUE.

GermRateRecip

logical. If TRUE, the Germination rate as reciprocal of median time (\mjseqnv_50) \insertCitewent_experimental_1957,labouriau_uma_1983,ranal_how_2006germinationmetrics is computed.

GermSpeed

logical. If TRUE, the 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,aosa_seed_1983,khandakar_jute_1983,bradbeer_seed_1988,wardle_allelopathic_1991germinationmetrics considering both counts and percentages is computed.

GermSpeedAccumulated

logical. If TRUE, the Speed of accumulated germination \insertCitebradbeer_seed_1988,wardle_allelopathic_1991,haugland_experiments_1996,de_santana_alise_2004germinationmetrics considering both counts and percentages is computed.

GermSpeedCorrected

logical. If TRUE, the Corrected speed of germination or Corrected germination rate index and the Corrected speed of accumulated germination \insertCiteevetts_germination_1972germinationmetrics is computed.

WeightGermPercent

logical. If TRUE, the Weighted germination percentage \mjseqnWGP or Weighted germination index \mjseqnWGI \insertCitereddy_effect_1978,reddy_effect_1985germinationmetrics is computed.

MeanGermPercent

logical. If TRUE, the Mean/average germination percentage per unit time (\mjseqn\overlineGP) \insertCiteczabator_germination_1962germinationmetrics is computed.

MeanGermNumber

logical. If TRUE, the Number of seeds germinated per unit time (\mjseqn\overlineN) \insertCitekhamassi_optimal_2013germinationmetrics is computed.

TimsonsIndex

logical. If TRUE, the Timson's index or Timson's germination velocity index \insertCitegrose_laboratory_1958,timson_new_1965,brown_representing_1988,baskin_seeds_1998germinationmetrics and it's modifications by Labouriau \insertCiteranal_how_2006germinationmetrics and \insertCitekhan_effect_1984germinationmetrics is computed.

GermRateGeorge

logical. If TRUE, the George's index \insertCitegeorge_influence_1961;textualgerminationmetrics is computed.

max.int

The maximum interval value up to which Timson's index/George's germination rate is to be computed.

GermIndex

logical. If TRUE, the Germination index according to \insertCitemelvilleSeedGerminationEarly1980;textualgerminationmetrics and its modification by \insertCitede_santana_alise_2004;textualgerminationmetrics \insertCiteranal_how_2006germinationmetrics are computed.

EmergenceRateIndex

logical. If TRUE, the Emergence rate index or Germination rate index are computed according to

  • \insertCite

    shmueliEmergenceEarlyGrowth1971;textualgerminationmetrics and it's modification by \insertCitede_santana_alise_2004;textualgerminationmetrics \insertCiteranal_how_2006germinationmetrics;

  • \insertCite

    bilbroSoilCrustsCotton1982;textualgerminationmetrics; and

  • \insertCite

    fakoredeRelationSeedlingVigor1980;textualgerminationmetrics, \insertCitefakoredeVariabilitySeedlingVigour1981;textualgerminationmetrics, and \insertCitefakoredeHeteroticEffectsAssociation1983;textualgerminationmetrics.

PeakValue

logical. If TRUE, the Peak value (\mjseqnPV) or Emergence Energy (\mjseqnEE) \insertCiteczabator_germination_1962,bonner_ideal_1967germinationmetrics is computed.

GermValue

logical. If TRUE, the Germination value \insertCiteczabator_germination_1962,djavanshir_germination_1976germinationmetrics and its modification considering duration from start of test instead of from onset of germination \insertCitebrown_representing_1988germinationmetrics is computed.

gv.k

The k Constant for computation of germination value. Default is 10.

CUGerm

logical. If TRUE, the Coefficient of uniformity of germination (CUG) \insertCiteheydecker_seed_1972,bewley_seeds_1994germinationmetrics is computed.

GermSynchrony

logical. If TRUE, the Synchrony of germination (\mjseqnZ index) \insertCiteprimack_longevity_1985,ranal_how_2006germinationmetrics is computed.

GermUncertainty

logical. If TRUE, the Synchronization index (\mjseqn\overlineE) or Uncertainty of the germination process (\mjseqnU) or Informational entropy (\mjseqnH) \insertCiteshannon_mathematical_1948,labouriau_germination_1976,labouriau_uma_1983germinationmetrics is computed.

Value

A data frame with the original data along with the various single-value germination indices specified in the function arguments.

References

\insertAllCited

See Also

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, GermIndex, EmergenceRateIndex, GermValue, PeakValue, CUGerm, GermSynchrony, GermUncertainty)

Examples

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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)

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