Individual Growth Curve Parameter Calculation using Polynomial Functions.

ipolygrowth

The goal of ipolygrowth is to calculate bacterial growth curve parameters using fourth degree polynomial functions. Functions are available for a single biological sample or multiple samples.

Installation

The package can be installed from CRAN with:

install.packages("ipolygrowth")

or the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("https://github.com/kivanvan/ipolygrowth", upgrade = F, quiet = T)

Example

Load the packages first.

library(ipolygrowth)
library(dplyr)

The example data comes from the growthrates package.

# example data comes from the growthrates package (available on CRAN)
if (!"growthrates" %in% installed.packages()) {install.packages("growthrates")}
data <- growthrates::bactgrowth

Alternatively, download the bactgrowth.txt from here to the directory of your script. The data can then be read using the following code.

data <- read.table("bactgrowth.txt", header = TRUE) %>%
  mutate(strain = factor(strain, levels = c("D", "R", "T")))

This is a basic example which shows you how to use the single sample function:

# subset data to a single biological sample
df.singlesample <- data %>% dplyr::filter(strain == "D", conc == 0)

# calculate growth curve parameters using ipolygrowth function
out.singlesample <- ipg_singlesample(data = df.singlesample, time.name = "time", y.name = "value")
#> max y time is equal to the largest value of "time"

The output is a list, including a table of growth parameter estimates, the polynomial model, a table of beta coefficients, and a table of fitted values. Growth parameters include peak growth rate, peak growth time, doubling time (at the peak growth), lag time, max y, and max y time. View the results by calling each list element like:

out.singlesample$estimates
#>   peak growth rate peak growth time doubling time  lag time     max y
#> 1      0.005474298         3.636922      126.6185 0.1231345 0.1073791
#>   max y time
#> 1         30

For more instructions and the expected output of vignette, please refer to the vignette on CRAN.