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small as.mo fix

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dr. M.S. (Matthijs) Berends
2019-03-06 14:39:02 +01:00
parent 5c7a061a5d
commit 0c0c6e289b
15 changed files with 212 additions and 150 deletions
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vignettes/benchmarks.Rmd
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@ -23,7 +23,7 @@ knitr::opts_chunk$set(
)
```
One of the most important features of this package is the complete microbial taxonomic database, supplied by the [Catalogue of Life](http://catalogueoflife.org). We created a function `as.mo()` that transforms any user input value to a valid microbial ID by using AI (Artificial Intelligence) combined with the taxonomic tree of Catalogue of Life.
One of the most important features of this package is the complete microbial taxonomic database, supplied by the [Catalogue of Life](http://catalogueoflife.org). We created a function `as.mo()` that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.
Using the `microbenchmark` package, we can review the calculation performance of this function. Its function `microbenchmark()` runs different input expressions independently of each other and measures their time-to-result.
@ -38,7 +38,7 @@ library(AMR)
In the next test, we try to 'coerce' different input values for *Staphylococcus aureus*. The actual result is the same every time: it returns its MO code `B_STPHY_AUR` (*B* stands for *Bacteria*, the taxonomic kingdom).
But the calculation time differs a lot. Here, the AI effect can be reviewed best:
But the calculation time differs a lot:
```{r}
S.aureus <- microbenchmark(as.mo("sau"),