FourPHFfit.bulk: Fit four-parameter hill function for multiple samples

In germinationmetrics: Seed Germination Indices and Curve Fitting

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

\insertRef

el-kassaby_seed_2008germinationmetrics

See Also

This function is a wrapper around the FourPHFfit function for fitting four-parameter hill curve.

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 documentation built on Aug. 19, 2023, 1:07 a.m.