germinationmetrics: FourPHFfit.bulk – R documentation

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FourPHFfit.bulk

Fit four-parameter hill function for multiple samples

Description

Fit four-parameter hill function from a data frame of germination counts recorded at specific time intervals for multiple samples in batch.

Usage

FourPHFfit.bulk(
  data,
  total.seeds.col,
  counts.intervals.cols,
  intervals,
  partial = TRUE,
  fix.y0 = TRUE,
  fix.a = TRUE,
  tmax,
  xp = c(10, 60),
  umin = 10,
  umax = 90,
  tries = 3
)

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.
`partial`	logical. If `TRUE`, `germ.counts` is considered as partial and if `FALSE`, it is considered as cumulative. Default is `TRUE`.
`fix.y0`	Force the intercept of the y axis through 0.
`fix.a`	Fix a as the actual maximum germination percentage at the end of the experiment.
`tmax`	The time up to which AUC is to be computed.
`xp`	Germination percentage value(s) for which the corresponding time is to be computed as a numeric vector. Default is `c(10, 60)`.
`umin`	The minimum germination percentage value for computing uniformity. Default is `10`. Seed `Details`.
`umax`	The maximum germination percentage value for computing uniformity. Default is `90`. Seed `Details`.
`tries`	The number of tries to be attempted to fit the curve. Default is 3.

Value

A data frame with the original data along with the various parameters of the respective fitted four-parameter hill function.

References

El-Kassaby YA, Moss I, Kolotelo D, Stoehr M (2008). “Seed germination: Mathematical representation and parameters extraction.” Forest Science, 54(2), 220–227.

Examples

data(gcdata)

counts.per.intervals <- c("Day01", "Day02", "Day03", "Day04", "Day05",
                          "Day06", "Day07", "Day08", "Day09", "Day10",
                          "Day11", "Day12", "Day13", "Day14")

FourPHFfit.bulk(gcdata, total.seeds.col = "Total Seeds",
                    counts.intervals.cols = counts.per.intervals,
                    intervals = 1:14, partial = TRUE,
                    fix.y0 = TRUE, fix.a = TRUE, xp = c(10, 60),
                    tmax = 20, tries = 3, umax = 90, umin = 10)

germinationmetrics

Seed Germination Indices and Curve Fitting

v0.1.5

GPL-2 | GPL-3

Authors

J. Aravind [aut, cre] (<https://orcid.org/0000-0002-4791-442X>), S. Vimala Devi [aut], J. Radhamani [aut], Sherry Rachel Jacob [aut], Kalyani Srinivasan [aut], ICAR-NBGPR [cph] (www.nbpgr.ernet.in)

Initial release