germination.indices: Germination Indices
In germinationmetrics: Seed Germination Indices and Curve Fitting

germination.indices

R Documentation

Germination Indices

Description

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

Usage

germination.indices(
  data,
  total.seeds.col,
  counts.intervals.cols,
  intervals,
  partial = TRUE,
  PeakGermPercent = 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,
  GermIndex = TRUE,
  EmergenceRateIndex = TRUE,
  PeakValue = TRUE,
  GermValue = TRUE,
  gv.k = 10,
  CUGerm = TRUE,
  GermSynchrony = TRUE,
  GermUncertainty = TRUE
)

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`.
`PeakGermPercent`	logical. If `TRUE`, then the Peak germination percentage \insertCitevallance_studies_1950,roh_maturity_2004germinationmetrics is computed. 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 \insertCitemelville_seed_1980;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 shmueli_emergence_1971;textualgerminationmetrics and it's modification by \insertCitede_santana_alise_2004;textualgerminationmetrics \insertCiteranal_how_2006germinationmetrics; \insertCite bilbro_soil_1982;textualgerminationmetrics; and \insertCite fakorede_relation_1980;textualgerminationmetrics, \insertCitefakorede_variability_1981;textualgerminationmetrics, and \insertCitefakorede_heterotic_1983;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

Examples



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 Aug. 19, 2023, 1:07 a.m.