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0.4.0, just published on CRAN

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dr. M.S. (Matthijs) Berends 2018-10-01 19:36:42 +02:00
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2
DESCRIPTION
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Package: AMR Package: AMR
Version: 0.3.0.9011 Version: 0.4.0
Date: 2018-10-01 Date: 2018-10-01
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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# 0.3.0.90xx (latest development version) # 0.4.0
#### New #### New
* The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms. * The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms.
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#### Other #### Other
* More unit tests to ensure better integrity of functions * More unit tests to ensure better integrity of functions
# 0.3.0 (latest stable version) # 0.3.0
**Published on CRAN: 2018-08-14** **Published on CRAN: 2018-08-14**
#### New #### New

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README.md
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@ -472,7 +472,7 @@ microbenchmark(A = as.mo(repetive_results),
unit = "ms") unit = "ms")
# Unit: milliseconds # Unit: milliseconds
# expr min lq mean median uq max neval # expr min lq mean median uq max neval
# A 14.61282 14.6372 14.70817 14.72597 14.76124 14.78498 1 # A 14.61282 14.6372 14.70817 14.72597 14.76124 14.78498 10
``` ```
So transforming 25,000 times (!) `"Staphylococcus aureus"` only takes 4 ms (0.004 seconds) more than transforming it once. You only lose time on your unique input values. So transforming 25,000 times (!) `"Staphylococcus aureus"` only takes 4 ms (0.004 seconds) more than transforming it once. You only lose time on your unique input values.
@ -489,7 +489,7 @@ microbenchmark(A = mo_fullname("B_STPHY_AUR"),
# expr min lq mean median uq max neval # expr min lq mean median uq max neval
# A 13.548652 13.74588 13.8052969 13.813594 13.881165 14.090969 10 # A 13.548652 13.74588 13.8052969 13.813594 13.881165 14.090969 10
# B 15.079781 15.16785 15.3835842 15.374477 15.395115 16.072995 10 # B 15.079781 15.16785 15.3835842 15.374477 15.395115 16.072995 10
# C 0.171182 0.185639 0.2306307 0.2034135 0.224610 0.492312 10 # C 0.171182 0.18563 0.2306307 0.203413 0.224610 0.492312 10
``` ```
So going from `mo_fullname("Staphylococcus aureus")` to `"Staphylococcus aureus"` takes 0.0002 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: So going from `mo_fullname("Staphylococcus aureus")` to `"Staphylococcus aureus"` takes 0.0002 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: