ipg_multisample {ipolygrowth}

Growth parameter estimates for multiple samples

Description

This function estimates growth parameters for multiple (biological) samples. Technical replicates (multiple time series) are allowed.

Usage

ipg_multisample(data, id, time.name, y.name, epsilon = 0.2/100)

Arguments

data

Input data frame containing the time and dependent variable (y) of multiple biological samples. Data needs to be in long format (i.e. one row per time point per sample). Remove rows with missing in the dependent variable (y).

id

Unique identifier to indicate each biological sample.

time.name

Name of the time variable. The variable needs to be numeric.

y.name

Name of the dependent variable (y). The variable needs to be numeric.

epsilon

Convergence threshold for max y time calculation. The input represents the fraction of the range of the observed dependent variable (y). It needs to be between 0 and 1, and a small value is recommended. The input can be either a single value or a vector of different values (in the same length and order as id) for multiple samples. Default is 0.2% for all samples.

Details

The function uses the same approach to estimate growth parameters as in ipg_singlesample().

Value

A list that contains a table of estimates, polynomial models, a table of beta coefficients, and a table of fitted values, all by sample ID. Growth parameters include peak growth rate, peak growth time, doubling time (at the peak growth), lag time, max y, and max y time.

Examples

library(dplyr)
data <- growthrates::bactgrowth
data <- data %>% mutate(id = paste(strain, conc, sep = "-"))
out.multisample <- ipg_multisample(data, "id", "time", "value", 0.2/100)