v2.6.5

What's Changed

• fix co-resistance upset plot.
• terminate app when window is closed.

v2.6.2

• Add PH001 site.
• Increase lab data file size upload limit to 50Mb.
• Fix Unicode encoding of mg.
• Handle "dmY HM" format for specimen date.

v2.6.0

• Fix SIR colors
• Use ACORN2_lab_codes_v2.4.3.xlsx
• Check that all 'patient_id' in REDCap match a 'patid' in the lab file.

v2.5.8

There are two key updates in this version:

• Hopefully a “final” fix to the issue of missing specimen numbers in the lab data file – if these are encountered, the app should now correctly define an arbitrary specimen number to each row of data where there is a missing value and then proceed with matching to clinical data. This will remove the situation where, if there were many missing specimen numbers, all of the rows would be assigned the same specimen number value (so it would like you had a single specimen in the lab file with potentially hundreds of isolates attached to it). This was only noticed in two locations, should be a silent update for most sites.
• An improvement to the AMR plots which show co-resistance. These plots are useful but they can only display isolate data where all antibiotics were tested. This is obviously not always the case, such as when second line tests are done only on isolates resistance to key first line drugs. We have added now an option to remove antibiotics from this plot so you can see what you would like in this plot (see the bottom image) – you can select multiple antibiotics to remove if needed / helpful.

v2.5.6

• update AWaRe classification (WHO 2021)
• add "No organism name / culture result" bar
• fix the “NA” issues with Acinetobacter sp / Salmonella sp on the AMR tab
• improve colours of culture per specgroup
• deal with rows with missing specimen IDs

v2.5.5

• fix: patient dead not flagged for D28 date
• option to not check if ACORN and Patient Ids match
• added theme to Highcharts plots
• added site NP003

v2.5.4

• Remove tests on "consistent outcomes" and "age category”
• Fix episode_count variable
• Optimisation by replacing gather/spread functions with pivot_ functions
• Fix number of “Isolates of Target Pathogens”
• Stop generating .acorn_non_anonymised files
• Add monitoring of CPU time of lab processing
• Small internal fixes

v2.5.3

• Allow different number of columns from the REDCap dataset.

v2.5.1

• Fix AST interpretation.
• Proceed with regexp only if data_dictionary$organisms.patterns is not empty.
• Build episode_id on date_episode_enrolment

v2.5.0

• Filter lab data to remove any specimen id not present in acorn
• "Lab File Overview" in Excel format
• lab_dta filtered on specid from acorn_dta
• recode d28_status for extra categories in Malawi
• check CRAN compliant only on released versions of OS
• added instructions for use in R in https://github.com/acornamr/acorn-dashboard#use-case