scale_phgrofit: scale_phgrofit Copyright (c) 2019. Kaleido Biosciences. All...

In Kaleido-Biosciences/phgrofit: Extracting Physiological Data From Kinetic OD600 and pH Curves

Description

This function allows the user to scale the results of phgrofit. This should be used upstream of functions requiring a standardization of data. Note that starting_od600 and starting pH are not scaled because they are not physiologically interesting parameters. Likewise, columns dealing with model error are ignored here. Scaling is done outside of the plotting functions in order to allow more transparancy as to what is acutally being plotted than would be apparent otherwise. Additionally, this will allow the user to choose the appropriate scaling function for their application.

Usage

scale_phgrofit(phgrofit_output, group_by = NULL)

Arguments

phgrofit_output	This is the output from the phgrofit
group_by	This is a character vector of the groups that you would like to scale within

Value

a dataframe containing all of content of phgrofit with each model parameter scaled such that the mean = 0 and values represent Z scores.

Examples

## Not run: phgropro_output = phgrofit::phgropro("rawdata.txt","metadata.csv",384)
phgrofit_output = phgrofit::phgrofit(phgropro_output)
## End(Not run)

#To get the scaled data
## Not run: scaled_phgrofit = phgrofit::scale_phgrofit(phgrofit_output)

#To get data that has been independantly scaled per community
## Not run: scaled_phgrofit = phgrofit::scale_phgrofit(phgrofit_output,group_by = "Community")

Kaleido-Biosciences/phgrofit documentation built on Feb. 8, 2022, 5:16 a.m.