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AMR
Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
https://msberends.github.io/AMR/
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as.sir() hangs in latest beta if unknown column present
#166
samueljpearce
opened
3 days ago
0
Extrapolating breakpoints for animals in line with CLSI VET09 document
#165
samueljpearce
opened
1 week ago
1
Some organisms not in database
#164
theanita1
opened
2 weeks ago
1
uti is false bug?
#163
theanita1
opened
2 weeks ago
2
Turn off information as.mo mo_gramstain etc
#162
iDudeRPS
closed
1 month ago
3
suppress information 'warning' with as.mo mo_gramstain etc
#161
iDudeRPS
closed
1 month ago
2
scale_x_mic not working
#160
theanita1
opened
1 month ago
1
AMR 3.0: let reverse dependencies know
#159
msberends
opened
1 month ago
0
scale_y_percent
#158
theanita1
opened
1 month ago
1
Teleomorph vs anamorph ID of yeasts
#157
send2dan
opened
2 months ago
3
Error when antibiogram empty
#156
andrewjmc
closed
2 months ago
4
Acknowledge data availability when using `first_isolate(method = "phenotype)`
#154
msberends
opened
3 months ago
0
Add denominators to each antibiotic in antibiogram
#153
andrewjmc
opened
4 months ago
2
`as.mo()`: give preference to species if subspecies is non-existent
#152
msberends
closed
3 months ago
0
extra factor level in class SIR (as.sir/is.sir)
#151
iDudeRPS
closed
3 months ago
5
as.sir reports invalid results as coming from wrong columns
#150
andrewjmc
closed
4 months ago
2
Check groups for antibiotics: aminoglycosides all right?
#149
msberends
closed
3 months ago
1
Not all mo_transforms work with antibiogram
#148
andrewjmc
closed
4 months ago
1
Group isolates
#147
andrewjmc
opened
4 months ago
7
AMR
#145
Samuel-Vinicius
closed
4 months ago
3
Need Update Some Microorganisms
#144
chauvinhtth13
closed
5 months ago
1
MIssing/extra veterinary breakpoints
#143
samueljpearce
opened
5 months ago
3
Veterinary breakpoint substitutions incorrect
#142
samueljpearce
opened
5 months ago
8
uti argument in as.sir not working as expected
#141
samueljpearce
closed
5 months ago
10
CLSI 2024 Veterinary Breakpoints
#140
samueljpearce
opened
6 months ago
9
To-do list for AMR v3.0.0
#138
msberends
opened
6 months ago
0
Incorporate EUCAST 13 and 14
#137
msberends
closed
3 months ago
7
Add new logo for this AMR package to catch One Health approach
#136
msberends
closed
6 months ago
0
Update `microorganisms` data set to latest taxonomy
#135
msberends
opened
6 months ago
15
Added support for 'html' in italicize_taxonomy()
#134
r0ssing
closed
7 months ago
1
Implement mathematically sound WISCA algorithm
#133
msberends
opened
8 months ago
0
AMR for R as a One Health approach
#132
msberends
closed
2 months ago
0
two genera/species that I can't seem to be able to classify using as.mo()
#131
send2dan
opened
8 months ago
2
Improvements for `as.mic()` and MIC plotting
#129
msberends
closed
9 months ago
0
MIC decimals on dark RStudio too black
#128
msberends
closed
9 months ago
0
Support for working with multiple patient species for veterinary antibiograms?
#127
samueljpearce
closed
9 months ago
1
Add more LOINC codes for antibiotics
#126
msberends
closed
11 months ago
1
Add `keep_synonyms = TRUE` to internal 1st isolate determination
#125
msberends
closed
11 months ago
0
Decrease time in printing tibbles
#124
msberends
closed
11 months ago
1
Errors in CLSI interpretation
#123
a-cienfuegos
closed
11 months ago
3
Phenotype-based first isolate determination selects too many isolates
#122
msberends
closed
11 months ago
1
how are IE cut-offs used in MIC graphs
#119
theanita1
closed
1 year ago
7
Update clinical breakpoints and fix some `as.mo()` bugs
#117
msberends
closed
1 year ago
1
Rework EUCAST Expert Rules
#116
msberends
closed
1 year ago
1
Update clinical_breakpoints to WHONET 2023
#115
erwinhassing
closed
1 year ago
0
`minimum_matching_score` not always considered
#114
msberends
closed
1 year ago
0
Problem with getting S. coagulans instead of old S. schleiferi coagulans
#113
msberends
closed
1 year ago
0
In `clinical_breakpoints`, some values in `ref_tbl` are missing
#112
msberends
closed
1 year ago
0
typo in function name in tutorial for "Predicting future antimicrobial resistance using regression models"
#111
send2dan
closed
1 year ago
3
First isolate: ICU filtering based on wrong ordering
#110
msberends
closed
1 year ago
0
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