P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-06-24 07:36:21 +02:00
Code Releases Activity

Built site for AMR@3.0.1.9061: 0c1709c

Browse Source
This commit is contained in:
github-actions
2026-06-23 18:00:14 +00:00
parent 9447e0f2c2
commit 2a7bfb9ffb
328 changed files with 5357 additions and 3687 deletions
Download Patch File Download Diff File Expand all files Collapse all files

70
reference/first_isolate.md
View File

@@ -11,34 +11,40 @@ that also supports grouping with the `dplyr` package.
## Usage
``` r
first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, col_testcode = NULL, col_specimen = NULL,
col_icu = NULL, col_keyantimicrobials = NULL, episode_days = 365,
testcodes_exclude = NULL, icu_exclude = FALSE, specimen_group = NULL,
type = "points", method = c("phenotype-based", "episode-based",
"patient-based", "isolate-based"), ignore_I = TRUE, points_threshold = 2,
info = interactive(), include_unknown = FALSE,
include_untested_sir = TRUE, ...)
first_isolate(
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
col_testcode = NULL,
col_specimen = NULL,
col_icu = NULL,
col_keyantimicrobials = NULL,
episode_days = 365,
testcodes_exclude = NULL,
icu_exclude = FALSE,
specimen_group = NULL,
type = "points",
method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
ignore_I = TRUE,
points_threshold = 2,
info = interactive(),
include_unknown = FALSE,
include_untested_sir = TRUE,
...
)
filter_first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, episode_days = 365, method = c("phenotype-based",
"episode-based", "patient-based", "isolate-based"), ...)
filter_first_isolate(
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
episode_days = 365,
method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
...
)
```
## Source
Methodology of these functions is strictly based on:
- **M39 Analysis and Presentation of Cumulative Antimicrobial
Susceptibility Test Data, 5th Edition**, 2022, *Clinical and
Laboratory Standards Institute (CLSI)*.
<https://clsi.org/standards/products/microbiology/documents/m39/>.
- Hindler JF and Stelling J (2007). **Analysis and Presentation of
Cumulative Antibiograms: A New Consensus Guideline from the Clinical
and Laboratory Standards Institute.** Clinical Infectious Diseases,
44(6), 867-873. [doi:10.1086/511864](https://doi.org/10.1086/511864)
## Arguments
- x:
@@ -318,6 +324,20 @@ taking into account all antimicrobial test results. If no antimicrobial
test results are available in the data set, only the episode-based
method is applied at default.
## References
Methodology of these functions is strictly based on:
- **M39 Analysis and Presentation of Cumulative Antimicrobial
Susceptibility Test Data, 5th Edition**, 2022, *Clinical and
Laboratory Standards Institute (CLSI)*.
<https://clsi.org/standards/products/microbiology/documents/m39/>.
- Hindler JF and Stelling J (2007). **Analysis and Presentation of
Cumulative Antibiograms: A New Consensus Guideline from the Clinical
and Laboratory Standards Institute.** Clinical Infectious Diseases,
44(6), 867-873. [doi:10.1086/511864](https://doi.org/10.1086/511864)
## See also
[`key_antimicrobials()`](https://amr-for-r.org/reference/key_antimicrobials.md)