Any Growth Rates/ Growthcurver experts?


First time posting here, so sorry in advanced if I do this wrong.
I am working on my Master thesis right now and for that i am measuring the Bacterial growth of different bacterial strains with a Platereader. I need to calculate the Lag Phase of my Bacterial Strains and I would like to use R for that. But my R knowledge is basic at best. I looked into the two Packages GrowthRates and Growthcurver because they looked promising, but I was not able to calculate the lag phase using those.
If someone already used those Packages and could give some help if it is possible to use these Packages for my goal of calculating the lag phase or maybe has another method for calculating the lag phase of bacterial growth, that would be really appreciated.

If it was me, I'd want to be able to fit a growth model myself without a specific package first to make sure that I understand it completely. Then, if there is something specific that a package can do for me, consider using it in addition to my own solution.

I am not an expert on cell growth, but I have done some work in the area. If there isn't a stationary phase or death phase, you might be able to fit a linear model on the log of cell concentration or OD and use the slope and intercept to measure the lag time and first order growth rate. For example from this page of Bioprocess Engineering (Liu) text.

If there is a stationary phase, then you need a more complex model. There is a "logistic" growth model with some parameters you can fit to data with nonlinear optimization (optim in R). The function is too complex in this case to allow a linear regression solution.

If there is a stationary phase and a death phase you want to model, I believe you have to then solve a set of ODEs.

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.