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diff for freq, fix for mo_shortname

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dr. M.S. (Matthijs) Berends
2018-09-29 21:54:32 +02:00
parent a6aa9e95fb
commit 92c9cc2608
12 changed files with 79 additions and 26 deletions
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23
NEWS.md
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@@ -7,15 +7,15 @@
* Semantic names: `mo_fullname`, `mo_shortname`
* Microbial properties: `mo_type`, `mo_gramstain`.
They also come with support for German, Dutch, French, Italian, Spanish and Portuguese, and it defaults to the systems locale:
They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:
```r
mo_gramstain("E. coli")
# [1] "Gram negative"
mo_gramstain("E. coli", language = "de") # "de" = Deutsch / German
mo_gramstain("E. coli", language = "de") # "de" = German
# [1] "Gramnegativ"
mo_gramstain("E. coli", language = "es") # "es" = Español / Spanish
mo_gramstain("E. coli", language = "es") # "es" = Spanish
# [1] "Gram negativo"
mo_fullname("S. group A") # when run on a on a Portuguese system
mo_fullname("S. group A", language = "pt") # Portuguese
# [1] "Streptococcus grupo A"
```
@@ -31,11 +31,11 @@
* Functions `as.mo` and `is.mo` as replacements for `as.bactid` and `is.bactid` (since the `microoganisms` data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The `as.mo` function determines microbial IDs using Artificial Intelligence (AI):
```r
as.mo("E. coli")
# [1] ESCCOL
# [1] B_ESCHR_COL
as.mo("MRSA")
# [1] STAAUR
# [1] B_STPHY_AUR
as.mo("S group A")
# [1] STCGRA
# [1] B_STRPTC_GRA
```
And with great speed too - on a quite regular Linux server from 2007 it takes us 0.009 seconds to transform 25,000 items:
```r
@@ -54,7 +54,8 @@
* Function `ab_property` and its aliases: `ab_name`, `ab_tradenames`, `ab_certe`, `ab_umcg` and `ab_trivial_nl`
* Introduction to AMR as a vignette
* Removed clipbaord functions as it violated the CRAN policy
* Removed clipboard functions as it violated the CRAN policy
* Renamed `septic_patients$sex` to `septic_patients$gender`
#### Changed
* Added three antimicrobial agents to the `antibiotics` data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)
@@ -92,14 +93,14 @@
* Added longest en shortest character length in the frequency table (`freq`) header of class `character`
* Support for types (classes) list and matrix for `freq`
```r
my_matrix = with(septic_patients, matrix(c(age, sex), ncol = 2))
my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2))
freq(my_matrix)
```
For lists, subsetting is possible:
```r
my_list = list(age = septic_patients$age, sex = septic_patients$sex)
my_list = list(age = septic_patients$age, gender = septic_patients$gender)
my_list %>% freq(age)
my_list %>% freq(sex)
my_list %>% freq(gender)
```
#### Other