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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.