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Description

Individual Growth Curve Parameter Calculation using Polynomial Functions.

Calculation of key bacterial growth curve parameters using fourth degree polynomial functions. Six growth curve parameters are provided including peak growth rate, doubling time, lag time, maximum growth, and etc. 'ipolygrowth' takes time series data from individual biological samples (with technical replicates) or multiple samples.

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

The example data comes from the growthrates package.
This is a basic example which shows you how to use the single sample function:

library(ipolygrowth)
library(dplyr)

# example data comes from the growthrates package (available on CRAN)
data <- growthrates::bactgrowth

# 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")

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, please refer to the vignette.

Metadata

Version

0.1.2

License

Unknown

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