enve.growthcurve: Enveomics: Growth Curve

In enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

Enveomics: Growth Curve

Description

Calculates growth curves using the logistic growth function.

Usage

enve.growthcurve(
  x,
  times = 1:nrow(x),
  triplicates = FALSE,
  design,
  new.times = seq(min(times), max(times), length.out = length(times) * 10),
  level = 0.95,
  interval = c("confidence", "prediction"),
  plot = TRUE,
  FUN = function(t, K, r, P0) K * P0 * exp(r * t)/(K + P0 * (exp(r * t) - 1)),
  nls.opt = list(),
  ...
)

Arguments

x	Data frame (or coercible) containing the observed growth data (e.g., O.D. values). Each column is an independent growth curve and each row is a time point. NA's are allowed.
times	Vector with the times at which each row was taken. By default, all rows are assumed to be part of constantly periodic measurements.
triplicates	If TRUE, the columns are assumed to be sorted by sample with three replicates by sample. It requires a number of columns multiple of 3.
design	Experimental design of the data. An array of mode list with sample names as index and the list of column names in each sample as the values. By default, each column is assumed to be an independent sample if triplicates is FALSE, or every three columns are assumed to be a sample if triplicates is TRUE. In the latter case, samples are simply numbered.
new.times	Values of time for the fitted curve.
level	Confidence (or prediction) interval in the fitted curve.
interval	Type of interval to be calculated for the fitted curve.
plot	Should the growth curve be plotted?
FUN	Function to fit. By default: logistic growth with paramenters K: carrying capacity, r: intrinsic growth rate, and P0: Initial population.
nls.opt	Any additional options passed to nls.
...	Any additional parameters to be passed to plot.enve.GrowthCurve.

Value

Returns an enve.GrowthCurve object.

Author(s)

Luis M. Rodriguez-R [aut, cre]

Examples

# Load data
data("growth.curves", package = "enveomics.R", envir = environment())

# Generate growth curves with different colors
g <- enve.growthcurve(growth.curves[, -1], growth.curves[, 1],
                      triplicates = TRUE)

# Generate black-and-white growth curves with different symbols
plot(g, pch=15:17, col="black", band.density=45, band.angle=c(-45,45,0))

enveomics.R documentation built on April 13, 2022, 5:10 p.m.