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(v0.7.0.9010) mo_synonyms, plot/barplot fixes

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dr. M.S. (Matthijs) Berends
2019-06-16 21:42:40 +02:00
parent 980be2b22d
commit 9c39c35f86
72 changed files with 595 additions and 802 deletions
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NEWS.md
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@@ -1,7 +1,7 @@
# AMR 0.7.0.9009
# AMR 0.7.0.9010
#### New
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combinations of existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
```r
septic_patients %>%
select(AMX, CIP) %>%
@@ -12,14 +12,31 @@
# 3 Ciprofloxacin SI 0.8381831 1181
# 4 Ciprofloxacin R 0.1618169 228
```
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are:
* AIEC (Adherent-Invasive *E. coli*)
* ATEC (Atypical Entero-pathogenic *E. coli*)
* DAEC (Diffusely Adhering *E. coli*)
* EAEC (Entero-Aggresive *E. coli*)
* EHEC (Entero-Haemorrhagic *E. coli*)
* EIEC (Entero-Invasive *E. coli*)
* EPEC (Entero-Pathogenic *E. coli*)
* ETEC (Entero-Toxigenic *E. coli*)
* NMEC (Neonatal Meningitis‐causing *E. coli*)
* STEC (Shiga-toxin producing *E. coli*)
* UPEC (Uropathogenic *E. coli*)
All these lead to the microbial ID of *E. coli*:
```r
as.mo("UPEC")
# B_ESCHR_COL
mo_fullname("UPEC")
mo_name("UPEC")
# "Escherichia coli"
mo_gramstain("EHEC")
# "Gram-negative"
```
* Function `mo_info()` as an analogy to `ab_info()`. The `mo_info()` prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism
* Function `mo_synonyms()` to get all previously accepted taxonomic names of a microorganism
#### Changed
* Column names of output `count_df()` and `portion_df()` are now lowercase
@@ -36,6 +53,7 @@
* Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
* Fixed bug where not all old taxonomic named would not be printed when using a vector as input for `as.mo()`
* Manually added *Trichomonas vaginalis* from the kingdom of Protozoa, which is missing from the Catalogue of Life
* Small improvements to `plot()` and `barplot()` for MIC and RSI classes
#### Other
* Fixed a note thrown by CRAN tests