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new unit tests for ggplot, small fixes

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dr. M.S. (Matthijs) Berends
2018-08-12 17:44:06 +02:00
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@ -136,43 +136,61 @@ guess_bactid("VRSA") # Vancomycin Resistant S. aureus
This package contains two new S3 classes: `mic` for MIC values (e.g. from Vitek or Phoenix) and `rsi` for antimicrobial drug interpretations (i.e. S, I and R). Both are actually ordered factors under the hood (an MIC of `2` being higher than `<=1` but lower than `>=32`, and for class `rsi` factors are ordered as `S < I < R`).
Both classes have extensions for existing generic functions like `print`, `summary` and `plot`.
```r
# Transform values to new classes
mic_data <- as.mic(c(">=32", "1.0", "8", "<=0.128", "8", "16", "16"))
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
```
These functions also try to coerce valid values.
Quick overviews with `summary`:
#### RSI
The `septic_patients` data set comes with antimicrobial results of more than 40 different drugs. For example, columns `amox` and `cipr` contain results of amoxicillin and ciprofloxacin, respectively.
```r
summary(rsi_data)
# Mode :rsi
# <NA> :0
# Sum S :474
# Sum IR:406
# -Sum R:370
# -Sum I:36
summary(septic_patients[, c("amox", "cipr")])
# amox cipr
# Mode :rsi Mode :rsi
# <NA> :1002 <NA> :596
# Sum S :336 Sum S :1108
# Sum IR:662 Sum IR:296
# -Sum R:659 -Sum R:227
# -Sum I:3 -Sum I:69
```
You can use the `plot` function from base R:
```r
plot(septic_patients$cipr)
```
![example_1_rsi](man/figures/rsi_example1.png)
Or use the `ggplot2` and `dplyr` packages to create more appealing plots:
```r
septic_patients %>%
select(amox, cipr) %>%
ggplot_rsi()
```
![example_2_rsi](man/figures/rsi_example2.png)
```r
septic_patients %>%
select(amox, cipr) %>%
ggplot_rsi(x = "Interpretation", facet = "Antibiotic")
```
![example_3_rsi](man/figures/rsi_example3.png)
#### MIC
```r
# Transform values to new class
mic_data <- as.mic(c(">=32", "1.0", "8", "<=0.128", "8", "16", "16"))
summary(mic_data)
# Mode:mic
# <NA>:0
# Min.:<=0.128
# Max.:>=32
```
A plot of `rsi_data`:
```r
plot(rsi_data)
```
![example1](man/figures/rsi_example.png)
A plot of `mic_data` (defaults to bar plot):
```r
plot(mic_data)
```
![example2](man/figures/mic_example.png)
![example_mic](man/figures/mic_example.png)
Other epidemiological functions: