enve.growthcurve {enveomics.R}

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))