audit

An interactive application that ushers you through the inspection and analysis of your growth curve experiments.

Example

To start a new AUDIT session:

audit::run()

Installation

Audit is currently only available on github and can be installed like any other remote r package:

remotes::install_github("npjc/audit")

Step-by-step

1. Install R by downloading the appropriate package for your operating system from cran and following the onscreen instructions.
2. Install Rstudio (Optional), a development environment for R by downloading the appropriate image for your operating system from Rstudio’s download page and follow the onscreen instructions.
3. If this is a new R installation you will need to download some packages before being able to install audit. To do this, open R / Rstudio and enter the line below into the console. Follow the onscreen instructions.

install.packages(c("devtools", "tidyverse", "remotes"))

4. Install AUDIT and its dependencies by entering the line below into the console

remotes::install_github("npjc/audit")

5. To run AUDIT enter the line below at the console. This will open a new session in your default web browser.

audit::run()

More Info

What is AUDIT?

AUDIT stands for Automated Usher for Data Inspection and Tidying (AUDIT). As in it helps you audit your growth curves.

AUDIT is really just an interactive interface to multiple modules. These modules are also openly distributed as R packages:

• readcg12
• readgp1
• readyg
• readbioscreen
• growr
• mtpview (and as a current workaround to known issue mtpview1)

If you find a bug

As you use AUDIT, if you find bugs, file an issue (ideally with a reproducible example) at https://github.com/npjc/audit/issues. If you are unsure how to make your example reproducible: provide input data used and a description of the steps used or a link to a video demonstrating it.

Known Issue

The only change from previous communication is that mptview currently exists as 2 separate packages (mptview and mtpivew1). This is a temporary workaround for a bug in the underlying grid graphics system. I will fold the mtpview1 back into the normal mtpview in the next R release (grid is shipped with base R, more info).

Experimental tag

The explore section is tagged as experimental as I will add new views beyond what is already there. Once I have added all the views I will remove the experimental tag.

Additional Functionality Elsewhere

Earlier versions of this tool were used as prototypes and made publically available through the shinyapps.io service. These are still freely accesible via web browser (no installation needed).

• cg12report provides the ability to download a .pdf report of cg12 formatted data

• audit-lite provides interactive plate view where you can add reference line plots onto all wells of the plate (powered by d3 via r2d3).

Absolutely No Guarantees

I have tried my very hardest to ensure that the software performs as intended. I use the same underlying tools for my own work. I however make absolutely no guarantees about the use and or results of AUDIT and its associated software. I therefore encourage you to validate your assumptions and check your work.

Alternatives and Prior Work

There are a number of other tools that may provide similar and/or other useful functionality (in no particular order):

Interactive Applications:

• PROPHECY: Described in https://doi.org/10.1093/nar/gki126
• PRECOG: Described in https://doi.org/10.1186/s12859-016-1134-2
• bgfit: Described in https://doi.org/10.1186/1471-2105-14-283
• ACCESS: Described in https://doi.org/10.1007/978-1-61779-173-4_15
• YODA: Described in https://doi.org/10.1186/1471-2105-11-141
• fitderiv: Described in https://doi.org/10.1038/ncomms13766

Software Packages:

• growthcurver R package
• plater R package
• Colonyzer
• agce R package ARCHIVED
• drc R package described in https://doi.org/10.18637/jss.v012.i05
• FitSearch described in https://doi.org/10.1186/1471-2164-14-S1-S6
• getgrowth Python package
• grofit R package ARCHIVED, described in https://doi.org/10.18637/jss.v033.i07
• growcurves R package, described in https://doi.org/10.18637/jss.v057.i03
• growthcurver R package, described in https://doi.org/10.1186/s12859-016-1016-7
• growthmodels R package
• pygrowthmodels Python package
• odelay described in http://dx.doi.org/10.3791/4018