jic-csb / babar

Bayesian Bacterial Growth Curve Analysis in R

BaBaR - Bayesian Bacterial growth curve analysis in R

This is the code repository for the babar package. For examples of use, see:

• Fitting a growth curve with babar
• Comparing two growth curves with babar
• Comparing distibutions with nested sampling

Building and installing

This section describes the process for installing the package from source.

Prerequisites

To build the package, make sure that your version of R has the following packages (needed to build the package vignettes):

• knitr
• R.rsp

You can install these from the R command prompt with:

install.packages(c('R.rsp', 'knitr'))

Build and install

To build the package (including vignettes), from the command prompt type:

R CMD build babar

Then to install:

R CMD INSTALL babar_1.0.tar.gz

Viewing the installed documentation

You can browse the package vignettes with:

browseVignettes(package='babar')

from within R.

Generating documentation

Code functions are documented using inlinedocs. To rebuild the documentation:

install.packages('inlinedocs')
library(inlinedocs)
package.skeleton.dx('babar')

Generating the vignettes

Compile in R using:

knit("worksheet1.Rnw")

or from the shell:

R -e 'library(knitr); knit("doc/worksheet1.Rnw");'

then run pdflatex (twice) on the resulting .tex file. Generally you can ignore the warnings if the PDF looks fine.

babar's Issues

Converting Mu max to Log10 scale

Hi,

If I understand correctly, the babar package returns the estimated growth parameters on ln scale. Now I want to convert the obtained growth rate (mu max) to Log10 scale to be able to compare it with other data calculated on the respective scale. Is it possible to convert the growth rate between both scales (ln and log10) and if yes, how?

Rickett's 2015 supplemental material describes the following (p 7): 'We note that although that the bacterial concentration is transformed to the ln x scale for use in the model, all results are transformed back afterwards to the log 10 x scale.'

Thanks in advance for your response!