jags_data: jags_data
In soniamitchell/SpARKjags:

jags_data

R Documentation

jags_data

Description

Function to generate data input for jags models

Usage

jags_data(classification, categories, pathogen, ...)

Arguments

`classification`	a `string` specifying the antibiotic classification, options are: "all" or any combination of the following, in a `vector`: "Aminoglycoside" "Penicillin Combination" "Penicillin" "Monobactam" "Cephalosporin" "Fluoroquinolone" "Colistin" "Carbapenem" "Fosfomycin" "Penicillin (Penams)" "Quinolone" "Nitrofurantoin" "Tetracycline" "Trimethoprim" "Trimethoprim/Sulfamethoxazole"
`categories`	a `string` specifying data category, options are: "human" c("human", "animal")
`pathogen`	a `string` specifying pathogen name (taken from Kleborate data), options are: "all" or any combination of the following, in a `vector`: "Klebsiella pneumoniae "Klebsiella quasipneumoniae subsp. quasipneumoniae" "Klebsiella michiganensis" "Klebsiella (Raoultella) planticola" "Klebsiella variicola subsp. variicola" "Klebsiella quasipneumoniae subsp. similipneumoniae" "Klebsiella grimontii" "Klebsiella oxytoca" "Klebsiella (Raoultella) ornithinolytica" "Klebsiella aerogenes" "Klebsiella pasteurii" "Klebsiella spallanzanii" "Klebsiella quasivariicola" "Klebsiella (Raoultella) terrigena" "Klebsiella huaxiensis" "unknown" - Removed from possible options "Raoultella quasiterrigena"
`...`	Additional parameters may be included: indeterminate: a `string` specifying how indeterminate samples should be interpreted; options are "R", "S", or "I"; default is "I" removeCarbapenem: a boolean flag to indicate removal of Carbapenem resitant samples (`TRUE`); default is `FALSE` onlyCarbapenem: a boolean flag to indicate removal of everything but Carbapenem resitant samples (`TRUE`); default is `FALSE` removeQuinPen: a boolean flag to indicate removal of Quinolone and Penicillin samples (`TRUE`); default is `TRUE`