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dr. M.S. (Matthijs) Berends
2018-11-09 13:11:54 +01:00
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README.md
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@@ -81,9 +81,9 @@ The `AMR` package basically does four important things:
### ITIS
<img src="man/figures/itis_logo.jpg" height="100px">
This package contains the **complete microbial taxonomic data** (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov).
This package contains the **complete microbial taxonomic data** (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov).
All (sub)species from the **taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package**, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from **the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package**, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists.
@@ -575,18 +575,20 @@ microbenchmark(A = mo_species("aureus"),
F = mo_class("Bacilli"),
G = mo_phylum("Firmicutes"),
H = mo_subkingdom("Posibacteria"),
I = mo_kingdom("Bacteria"),
times = 10,
unit = "ms")
# Unit: milliseconds
# expr min lq mean median uq max neval
# A 0.096801 0.120966 0.1264836 0.1262045 0.135773 0.158192 10
# B 0.102807 0.123899 0.1258339 0.1286835 0.132420 0.143245 10
# C 0.122503 0.128299 0.1374623 0.1292070 0.139683 0.187315 10
# D 0.087372 0.093239 0.1053774 0.1026330 0.113633 0.128299 10
# E 0.084020 0.098617 0.1124383 0.1094420 0.113423 0.178515 10
# F 0.080667 0.085346 0.1068579 0.1128295 0.115030 0.133537 10
# G 0.087443 0.090026 0.1030171 0.0995250 0.106369 0.152325 10
# H 0.084648 0.103156 0.1058313 0.1095120 0.112864 0.117265 10
# A 0.105181 0.121314 0.1478538 0.1465265 0.166711 0.211409 10
# B 0.132558 0.146388 0.1584278 0.1499835 0.164895 0.208477 10
# C 0.135492 0.160355 0.2341847 0.1884665 0.348857 0.395931 10
# D 0.109650 0.115727 0.1270481 0.1264130 0.128648 0.168317 10
# E 0.081574 0.096940 0.0992582 0.0980915 0.101479 0.120477 10
# F 0.081575 0.088489 0.0988463 0.0989650 0.103365 0.126482 10
# G 0.091981 0.095333 0.1043568 0.1001530 0.111327 0.129625 10
# H 0.092610 0.093169 0.1009135 0.0985455 0.101828 0.120406 10
# I 0.087371 0.091213 0.1069758 0.0941815 0.109302 0.192831 10
```
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.