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support A. species for as.mo, cleanup

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dr. M.S. (Matthijs) Berends
2018-11-24 20:25:09 +01:00
parent 63ba4b2980
commit 9ddf6dc530
14 changed files with 126 additions and 93 deletions
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14
NEWS.md
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@@ -23,6 +23,13 @@
* Added column `kingdom` to the microorganisms data set, and function `mo_kingdom` to look up values
* Tremendous speed improvement for `as.mo` (and subsequently all `mo_*` functions), as empty values wil be ignored *a priori*
* Fewer than 3 characters as input for `as.mo` will return NA
* Function `as.mo` (and all `mo_*` wrappers) now supports genus abbreviations with "species" attached
```r
as.mo("E. species") # B_ESCHR
mo_fullname("E. spp.") # "Escherichia species"
as.mo("S. spp") # B_STPHY
mo_fullname("S. species") # "Staphylococcus species"
```
* Added parameter `combine_IR` (TRUE/FALSE) to functions `portion_df` and `count_df`, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)
* Fix for `portion_*(..., as_percent = TRUE)` when minimal number of isolates would not be met
* Added parameter `also_single_tested` for `portion_*` and `count_*` functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see `?portion`
@@ -45,9 +52,9 @@
* Now prints in markdown at default in non-interactive sessions
* No longer adds the factor level column and sorts factors on count again
* Support for class `difftime`
* New parameter `na`, to choose with character to print for empty values
* New parameter `header` to turn it off (default when `markdown = TRUE`)
* New parameter `title` to replace the automatically set title
* New parameter `na`, to choose which character to print for empty values
* New parameter `header` to turn the header info off (default when `markdown = TRUE`)
* New parameter `title` to manually setbthe title of the frequency table
* `first_isolate` now tries to find columns to use as input when parameters are left blank
* Improvements for MDRO algorithm (function `mdro`)
* Data set `septic_patients` is now a `data.frame`, not a tibble anymore
@@ -66,6 +73,7 @@
* In `g.test`, when `sum(x)` is below 1000 or any of the expected values is below 5, Fisher's Exact Test will be suggested
* `ab_name` will try to fall back on `as.atc` when no results are found
* Removed the addin to view data sets
* Percentages will now will rounded more logically (e.g. in `freq` function)
#### Other
* New dependency on package `crayon`, to support formatted text in the console