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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# audit
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#experimental)
<!-- badges: end -->
An interactive application that ushers you through the inspection and analysis of your growth curve experiments.
## Example
To start a new AUDIT session:
```{r example2, eval=FALSE}
audit::run()
```
## Installation
Audit is currently only available on github and can be installed like any other
remote r package:
``` r
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.
```r
install.packages(c("devtools", "tidyverse", "remotes"))
```
4. Install AUDIT and its dependencies by entering the line below into the console
``` r
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.
```r
audit::run()
```
## More Info
### What is AUDIT?
AUDIT stands for **A**utomated **U**sher for **D**ata **I**nspection and **T**idying (**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>
[shiny]: http://shiny.rstudio.com
[R]: https://cran.r-project.org
[cran]: https://cran.r-project.org
[Rstudio]: https://www.rstudio.com/products/rstudio
[download page]: https://www.rstudio.com/products/rstudio/download/#download
[readcg12]: https://github.com/npjc/readcg12
[readgp1]: https://github.com/npjc/readgp1
[readyg]: https://github.com/npjc/readyg
[readbioscreen]: https://github.com/npjc/readbioscreen
[growr]: https://github.com/npjc/growr
[mtpview]: https://github.com/npjc/mtpview
[mtpview1]: https://github.com/npjc/mtpview1
[shinyapps.io]: https://shinyapps.io
[cg12report]: https://nicolascoutin.shinyapps.io/cg12report/
[audit-lite]: https://nicolascoutin.shinyapps.io/audit-lite/
[d3]: https://d3js.org
[r2d3]: https://github.com/rstudio/r2d3
[PROPHECY]: http://prophecy.lundberg.gu.se/Main.aspx?Mainmnu=PRECOG
[PRECOG]: http://precog.lundberg.gu.se/Pages/Content/Precog
[ACCESS]: https://doi.org/10.1007/978-1-61779-173-4_15
[bgfit]: http://sels.tecnico.ulisboa.pt/bgfit/
[YODA]: http://kaeberleinlab.org/yoda/
[growthcurver]: https://CRAN.R-project.org/package=growthcurver
[plater]: https://CRAN.R-project.org/package=plater
[Colonyzer]: https://doi.org/10.1186/1471-2105-11-287
[agce]: https://CRAN.R-project.org/package=agce
[drc]: https://CRAN.R-project.org/package=drc
[fitderiv]: http://swainlab.bio.ed.ac.uk/software/fitderiv/
[FitSearch]: http://fitsearch.kaist.ac.kr
[getgrowth]: https://pypi.org/project/getgrowth/
[grofit]: https://CRAN.R-project.org/package=grofit
[growcurves]: https://CRAN.R-project.org/package=growcurves
[growthcurver]: https://CRAN.R-project.org/package=growthcurver
[growthmodels]: https://CRAN.R-project.org/package=growthmodels
[pygrowthmodels]: https://pypi.org/project/pygrowthmodels/