knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(antibodyKinetics)
This vignette provides a brief bit of documentation regarding how to use the parameter viewer app for the antibodyKinetics
package. The purpose of this app is to allow users generate parameter and exposure input tables with custom specified settings and exposure schedules. Through using the app, there will be options to download 3 .csv files that can be fed directly into the antibodyKinetics
package code.
If you'd like to run this app (eg. see what titre trajectories would be generated given your own model structure and exposure schedule), the shiny
, shinyBS
and rhandsontable
packages are required. The app can then be run with:
paramViewer()
This was not developed as a piece of software to be released. Rather, it was developed for personal use and for a very keen user of the antibodyKinetics
package to generate different models and exposure schedules. There is no guarantee that this app won't crash or generate slightly unexpected results. I recommend that you load it up and play around to get a feel for what it's doing, but don't worry if it crashes. If you run this from the R console, then some information will be printed as you run the app.
The first tab allows the user to specify options for the model. You should see the following window upon starting the app:
{width=500px}
The key for these options is as follows:
gamma
and boost_limit
can be ignored. Parameters correspond to those in the paper.Upload
must be pressed once the correct file is selected.Set the following to get going quickly:
Weak typing (3 types)
Competitive
3
Cross reactivity
Beta=0.6; c=4; gamma=0; boost_limit=0; tau=0
all
, 1
This tab allows the user to input exposure events of the desired type, time and to specify which strains are affected. By adding these exposures to the table, the expected antibody trajectories are constructed.
{width=500px}
Key:
Clear
removes all exposures from the table. Download
downloads the table to the right as a .csv.Model settings
tab. Upload
must be pressed after selecting the fileCopy the exposure schedule in the example table - using "New" for each new exposure ID and matching the times and strains to the table; pressing "Add" for each new exposure. If you make a mistake, change the ID
dropdown to the incorrect exposure and then press Remove
.
Shows the expected titre trajectories given the options and exposure schedule specified on the previous tabs. The user may also change the model parameter values for each exposure using the sliders.
{width=500px}
Key:
log2
scale) and what is the maximum observable titre?Model settings
tab.antibodyKinetics
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