Future Actions

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This list of things to do could be also logged using github issues.

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Think about the combination therapy resistance index (or activity index). It is kind of an spectrum of activity that counts the number of species (or genera) that can be treated when a combination therapy is applied.

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Reformat names in all the .csv files. Also create a sample dataset with microbiology data to be loaded automatically using the pyamr module. The file must contain the following columns:

Column Name

Description

date_sample

The date the sample was taken (datetime64[ns])

date_outcome

The date the outcome was available (or last edited)

patient_id

The anonymised patient id

lab_number

The laboratory number associated to the test.

order_name

The order type (e.g. sputum, urine, …)

order_code

The order code

order_description

The order description (at the moment is called specimen type)

microorganism_name

microorganism_code

antimicrobial_name

antimicrobial_code

sensitivity_method

sensitivity

mic

The Minimum Inhibitory Concentration

reported

The result was reported to clinicians (selective reporting)

genus_name

specie_name

gram_type

Microorganism classification based on cell wall.

antimicrobial_class

Also note that it would be very useful to find open source databases with all this information already available. In addition, they might contain other relevant information: (i) organisms grouped by shape, (ii) organisms group by …. (iii) antimicrobials grouped by …

Note

We are ignoring the OrgPieceCounter.

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Computing SART using Robust Regression. [1]

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CSV

Generate big csv files with the main outcomes (freq, sari, sart, asai, …)

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HTML

Create HTML files that based on the information contained in the CSV file, allows to dynamically explore different organism and antimicrobial pairs, different order codes, …

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ANIMATION

Create animations that based on the information contained in the CSV file, displays the evolution of the aforementioned AMR statistics in time. Similar examples seen in…. d3.js?

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LATEX

Generate automatically from the data the latex/html tables and graphs describing the Antimicrobial Spectrum of Activity Index - ASAI - (see example below). For more information check out the PhD thesis (Chapter 4).

ASAI

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LATEX

Generate automatically from the data the latex/html tables and graphs describing the Single Antimicrobial Resistance Trend - SART - (see example below). For more information check out the PhD thesis (Chapter 4).

SART