NCBI AST parser

[jhawkey]

make a parser for AST data downloaded from NCBI

[katholt]

created basic function:
https://github.com/interpretAMR/AMRgen/blob/main/R/import_pheno.R

to import NCBI AST files, parse antibiotic/species/mic/disk data into relevant classes, and optionally interpret them with as.sir (on by default)

desirable features to add:

1. if no testing standard is specified, EUCAST will be used but it would be good to allow more options for this interpretation step in future - added parameter 'default_guideline' however currently assumes only 'EUCAST' or 'CLSI' are allowed, and all values are interpreted using the human breakpoint (if interpret=T) and/or ECOFF (if interpret=T), would be good to expand options
2. currently the input is a file path to a NCBI AST file, would be good to allow this to be a dataframe already read in by the user - DONE
3. would be good to support downloading latest NCBI AST file for a given query organism (e.g. from https://www.ncbi.nlm.nih.gov/pathogens/ast#Pseudomonas%20aeruginosa)

[katholt]

forgot to include the measurement sign in the new column 'mic', of class 'mic'
this is now done properly (prior to the optional interpretation step)

[katholt]

added interpretation with ecoff rather than breakpoint, reported in new column 'ecoff' as NWT/WT

[katholt]

remaining to-do list:

1. expand options for interpreting breakpoints (e.g. allow animal breakpoints to be used)
2. add support for downloading latest NCBI AST file for a given query organism (e.g. from https://www.ncbi.nlm.nih.gov/pathogens/ast#Pseudomonas%20aeruginosa)