README.md

In dmarginean/aqua: Assay Qualification Tools

aqua - assay qualification and validation tools

The (future, long term, eventual) goal of aqua is to provide tools that help with different assay qualification and validation project analysis and reporting.

Installation

You can install aqua. I hope. You’re on your own.

devtools::install_github("cgtc/aqua")    # fingers crossed

Examples

library(aqua)

sd(c(2,3,2))   # boring
#> [1] 0.5773503
sd.u(c(2,3,2)) # amazing
#> [1] 0.65147

sd.u produces a very unbiased standard deviation estimate. Makes every small sample size data look horrible. The sad but true reality. Uses a chi-distributed correction factor.

library(lme4)
#> Loading required package: Matrix

funky_model <- lmer(total.fruits ~ 1 + (1|amd) + (1|status), data = Arabidopsis)

get_intermed_levels(funky_model) |>
  knitr::kable(escape = F) |>
  kable_style()

Error term CV % status 18.836883 amd 5.834408

Boom. Clearly the contribution of amd and status to variations in fruit.growth (in a vacuum) in this model I just invented that makes no sense is what it says there.

You can get repeatability and overall intermediate precision / reproducibility of an assay if you turned it into an lme4 random model with the only fixed term being an intercept. Just describe your model like 1 + (1|Lab/Operator/Day) + (1|SampleType) or whatever your assay design structure is and fire it up.

You can also do the whole TCID50 assay calculations. There’s a lot of functions for that that tend to even work! Does anyone use TCID50 anymore? Hello?

Version

Currently 0.2 ALPHA

dmarginean/aqua documentation built on March 16, 2024, 1:03 a.m.