Code `TODO` Tracker

[msberends]

See comment below for the overview

The below overview is automatically updated on each push to main.

[msberends]

TODO Report

Last Updated: 9 July 2026 21:08:36 CEST

This overview is automatically updated on each push to main. It scans for TODO, FIXME, HACK, and XXX markers across the codebase.

Summary

Metric	Value
Total markers	22
TODO	20
XXX	2
Files affected	4
Stale (> 6 months)	17
Oldest marker	1y 7m, R/sir.R L1757
Linked to issues	6
Unlinked (no issue ref)	16

By Referenced Issue

#170 (open): Set attributes for SIR values with their interpretation history — 5 marker(s)

• R/sir.R L412 (1y 3m ago) ⚠️
  # TODO for #170
• R/sir.R L2189 (3m ago)
  # TODO #170 add here in AMR 3.1.0 details about guideline
• R/sir.R L2210 (1y 7m ago) ⚠️
  # TODO for #170
• R/sir.R L2302 (1y 7m ago) ⚠️
  # TODO for #170
• R/sir.R L2312 (1y 7m ago) ⚠️
  # TODO for #170

#187 (open): Prepare comprehensive VetMed implementation — 1 marker(s)

• R/sir.R L156 (1y 2m ago) ⚠️
  ###### TODO #187 When applying veterinary breakpoints (by setting hostor by settingbreakpoint_type = "animal"), the [CLSI VET09 guideline](https://clsi.org/standards/products/veterinary-medicine/documents/vet09/) will be applied to cope with missing animal species-specific breakpoints.

By File

.github/workflows/publish-to-pypi.yml — 1 marker(s)

L81:       # TODO - Support Miniconda and Anaconda too  ◁ 10m ago !!

R/sir.R — 15 marker(s)

L156: ###### TODO #187 When applying veterinary breakpoints (by setting `host` or by setting `breakpoint_type = "animal"`), the [CLSI VET09 guideline](https://clsi.org/standards/products/veterinary-medicine/documents/vet09/) will be applied to cope with missing animal species-specific breakpoints.  ◁ 1y 2m ago !!

L185: ###### TODO  - **CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet09/>.  ◁ 1y 3m ago !!

L412:     # TODO for #170  ◁ 1y 3m ago !!

L1323:   # TODO add a switch to turn this off? In interactive sessions perhaps ask the user. Default should be On.  ◁ 1y 7m ago !!

L1407:   # TODO set uti to specimen column here  ◁ 1y 7m ago !!

L1635:     # TODO in case of VET09, we need to keep E. coli, also when users have Proteus in their data set  ◁ 1y 7m ago !!
L1636:     # TODO look up which species, at least E. coli - also Staph or Strep?  ◁ 1y 7m ago !!

L1674:     # TODO for VET09 do not filter out E. coli and such  ◁ 1y 7m ago !!

L1703:     ## TODO actually implement this well  ◁ 1y 3m ago !!

L1708:         gram_plus_cocci_vet09 <- microorganisms$mo[microorganisms$genus %in% c("Staphylococcus", "Streptococcus", "Peptostreptococcus", "Aerococcus", "Micrococcus") & microorganisms$rank == "genus"] # TODO should probably include genera that were either of these before  ◁ 1y 7m ago !!

L1757:           # TODO do we still have dogs breakpoints at this point???  ◁ 1y 7m ago !!

L2189:   # TODO #170 add here in AMR 3.1.0 details about guideline  ◁ 3m ago

L2210:   # TODO for #170  ◁ 1y 7m ago !!

L2302:   # TODO for #170  ◁ 1y 7m ago !!

L2312:   # TODO for #170  ◁ 1y 7m ago !!

data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R — 2 marker(s)

L164: # no XXX  ◁ 1y 2m ago !!
L165: organisms <- organisms |> filter(code != "XXX")  ◁ 1y 2m ago !!

data-raw/_reproduction_scripts/reproduction_of_microorganisms.R — 4 marker(s)

L31: # TODO Giardia zat in protozoa en animalia, dus sorteren op prioriteit kingdom en dan distinct op fullname  ◁ 16d ago

L1212:   # TODO ONLY IN 2026!  ◁ 16d ago

L1214:   # END OF TODO  ◁ 16d ago

L1439: # TODO perhaps only for 2026: remove old kingdoms  ◁ 16d ago