1
0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 02:32:07 +02:00

styled, unit test fix

This commit is contained in:
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions

View File

@ -43,14 +43,18 @@ It is basically as easy as:
resistance_predict(tbl = example_isolates, col_date = "date", col_ab = "TZP", model = "binomial")
# or:
example_isolates %>%
resistance_predict(col_ab = "TZP",
model "binomial")
example_isolates %>%
resistance_predict(
col_ab = "TZP",
model = "binomial"
)
# to bind it to object 'predict_TZP' for example:
predict_TZP <- example_isolates %>%
resistance_predict(col_ab = "TZP",
model = "binomial")
predict_TZP <- example_isolates %>%
resistance_predict(
col_ab = "TZP",
model = "binomial"
)
```
The function will look for a date column itself if `col_date` is not set.
@ -58,7 +62,7 @@ The function will look for a date column itself if `col_date` is not set.
When running any of these commands, a summary of the regression model will be printed unless using `resistance_predict(..., info = FALSE)`.
```{r, echo = FALSE, message = FALSE}
predict_TZP <- example_isolates %>%
predict_TZP <- example_isolates %>%
resistance_predict(col_ab = "TZP", model = "binomial")
```
@ -92,7 +96,7 @@ Resistance is not easily predicted; if we look at vancomycin resistance in Gram-
```{r}
example_isolates %>%
filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE, model = "binomial") %>%
resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE, model = "binomial") %>%
ggplot_rsi_predict()
```
@ -113,7 +117,7 @@ For the vancomycin resistance in Gram-positive bacteria, a linear model might be
```{r}
example_isolates %>%
filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE, model = "linear") %>%
resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE, model = "linear") %>%
ggplot_rsi_predict()
```