msberends/AMR

Issues

• Add denominators to each antibiotic in antibiogram

  #153 opened 15 days ago by andrewjmc
  2

• extra factor level in class SIR (as.sir/is.sir)

  #151 opened a month ago by iDudeRPS
  2

• AMR

  #145 opened 23 days ago by Samuel-Vinicius
  1

• `as.mo()`: give preference to species if subspecies is non-existent

  #152 opened 23 days ago by msberends
  0

• Update `microorganisms` data set to latest taxonomy

  #135 opened 3 months ago by msberends
  9

• Group isolates

  #147 opened a month ago by andrewjmc
  7

• as.sir reports invalid results as coming from wrong columns

  #150 opened a month ago by andrewjmc
  2

• Check groups for antibiotics: aminoglycosides all right?

  #149 opened a month ago by msberends
  0

• Not all mo_transforms work with antibiogram

  #148 opened a month ago by andrewjmc
  1

• Incorporate EUCAST 13 and 14

  #137 opened 3 months ago by msberends
  6

• Veterinary breakpoint substitutions incorrect

  #142 opened 2 months ago by samueljpearce
  3

• CLSI 2024 Veterinary Breakpoints

  #140 opened 3 months ago by samueljpearce
  7

• MIssing/extra veterinary breakpoints

  #143 opened 2 months ago by samueljpearce
  1

• To-do list for AMR v3.0.0

  #138 opened 3 months ago by msberends
  0

• AMR for R as a One Health approach

  #132 opened 5 months ago by msberends
  0

• Need Update Some Microorganisms

  #144 opened 2 months ago by chauvinhtth13
  1

• uti argument in as.sir not working as expected

  #141 opened 2 months ago by samueljpearce
  10

• two genera/species that I can't seem to be able to classify using as.mo()

  #131 opened 5 months ago by send2dan
  2

• Add new logo for this AMR package to catch One Health approach

  #136 opened 3 months ago by msberends
  0

• Implement mathematically sound WISCA algorithm

  #133 opened 5 months ago by msberends
  0

• Support for working with multiple patient species for veterinary antibiograms?

  #127 opened 6 months ago by samueljpearce
  1

• MIC decimals on dark RStudio too black

  #128 opened 6 months ago by msberends
  0

• Improvements for `as.mic()` and MIC plotting

  #129 opened 6 months ago by msberends
  0

• Errors in CLSI interpretation

  #123 opened 7 months ago by a-cienfuegos
  3

• Add more LOINC codes for antibiotics

  #126 opened 7 months ago by msberends
  1

• Add `keep_synonyms = TRUE` to internal 1st isolate determination

  #125 opened 7 months ago by msberends
  0

• Phenotype-based first isolate determination selects too many isolates

  #122 opened 7 months ago by msberends
  1

• Decrease time in printing tibbles

  #124 opened 8 months ago by msberends
  1

• EUCAST rules where there shouldn't be interpretations

  #94 opened a year ago by theanita1
  3

• Rework EUCAST Expert Rules

  #116 opened 10 months ago by msberends
  1

• UTI coding not being recognised in SIR interpretation

  #108 opened a year ago by theanita1
  12

• how are IE cut-offs used in MIC graphs

  #119 opened a year ago by theanita1
  7

• Possibility of adding EUCAST ECOFF values

  #102 opened a year ago by hkaspersen
  9

• Update clinical_breakpoints to WHONET 2023

  #115 opened a year ago by erwinhassing
  0

• In `clinical_breakpoints`, some values in `ref_tbl` are missing

  #112 opened a year ago by msberends
  0

• Problem with getting S. coagulans instead of old S. schleiferi coagulans

  #113 opened a year ago by msberends
  0

• `minimum_matching_score` not always considered

  #114 opened a year ago by msberends
  0

• typo in function name in tutorial for "Predicting future antimicrobial resistance using regression models"

  #111 opened a year ago by send2dan
  3

• First isolate: ICU filtering based on wrong ordering

  #110 opened a year ago by msberends
  0

• NA converted to first defined custom micro-organism

  #107 opened a year ago by bennsal
  5

• Breakpoints prefer PK/PD

  #106 opened a year ago by msberends
  0

• Clinical breakpoints for *Burkholderia mallei* and *Burkholderia pseudomallei* for all antibiotic might be wrong

  #105 opened a year ago by msberends
  2

• help with %like%

  #100 opened a year ago by iDudeRPS
  3

• as.sir function not found

  #101 opened a year ago by arsp-dev
  2

• strange results, when using first isolate()

  #99 opened a year ago by jukkiebah
  3

• set body site for SIR intepretation

  #96 opened a year ago by theanita1
  6

• g.test doesn't handle zero counts

  #95 opened a year ago by jtufto
  4

• Add `mo_pathogenicity()`

  #92 opened a year ago by msberends
  1

• Add Bartlett et al. (2022) for human pathogenicity?

  #90 opened a year ago by msberends
  1

• Antibiotic resistance prediction challenge 1

  #85 opened a year ago by sengeruan
  2