One of the most important features of this package is the complete microbial taxonomic database, supplied by ITIS (https://www.itis.gov). We created a function as.mo() that transforms any user input value to a valid microbial ID by using AI (Artificial Intelligence) and based on the taxonomic tree of ITIS.

Using the microbenchmark package, we can review the calculation performance of this function.

library(microbenchmark)

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:

In the table above, all measurements are shown in milliseconds (thousands of seconds), tested on a quite regular Linux server from 2007 (Core 2 Duo 2.7 GHz, 2 GB DDR2 RAM). A value of 6.9 milliseconds means it will roughly determine 144 input values per second. It case of 39.2 milliseconds, this is only 26 input values per second. The more an input value resembles a full name (like C, D and F), the faster the result will be found. In case of G, the input is already a valid MO code, so it only almost takes no time at all (0.0001 seconds on our server).

To achieve this speed, the as.mo function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined far less faster. See this example for the ID of Burkholderia nodosa (B_BRKHL_NOD):

That takes up to 11 times as much time! A value of 158.4 milliseconds means it can only determine ~6 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance.

To relieve this pitfall and further improve performance, two important calculations take almost no time at all: repetitive results and already precalculated results.

Repetitive results

Repetitive results mean that unique values are present more than once. Unique values will only be calculated once by as.mo(). We will use mo_fullname() for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) and uses as.mo() internally.

So transforming 500,000 values (!) of 96 unique values only takes 0.12 seconds (120 ms). You only lose time on your unique input values.

Results of a tenfold - 5,000,000 values:

Even the full names of 5 Million values are calculated within a second.

Precalculated results

What about precalculated results? If the input is an already precalculated result of a helper function like mo_fullname(), it almost doesn’t take any time at all (see ‘C’ below):

So going from mo_fullname("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0001 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:

Of course, when running mo_phylum("Firmicutes") the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes" too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known microorganisms (according to ITIS), it can just return the initial value immediately.

Results in other languages

When the system language is non-English and supported by this AMR package, some functions take a little while longer:

Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.