A web app for fitting Tonner et al's Phenom model to Microbial Growth Data, created with RShiny
This app is currently hosted at https://davidabuch.shinyapps.io/phenom_web_app
If you would like to run this Shiny app locally, you can do so using RStudio.
To get started, open RStudio and enter
install.packages("devtools")
in the command console.
You will then use the "devtools" package to install the app's helper package PhenomStanModel.
To install that package, enter
devtools::install_github("davidbuch/PhenomStanModel")
in the command console. In the process, you may be prompted by RStudio or your operating system to install other packages
which support the download and compilation of the PhenomStanModel package. You may see a lot of warning messages depending
on your current version of rstan, but these will not impact your results.
Next, download this repository (using the green "code" button above, if you are using GitHub) and open either ui.R or server.R with RStudio. You may receive a warning about remaining package dependencies in the editor window, but all of these will be available on CRAN so you should be able to click "install" when prompted to download those.
Finally, click "Run App" in the top right corner of the script editor pane, and the Web App interface will open.
To test that the app is running correctly, you can try fitting the datasets in the test_data folder. test_data/simple contains data from a very simple microbial growth experiment with a single treatment variable administered at three levels for a small number of replicates. test_data/pseudomonas contains raw data as well as preprocessed data files; the processed data have beeb modified from the raw data by subsampling the observation timepoints and dropping columns from the metadata file to a few covariates of interest.