Code for "Quantifying antibiotic susceptibility and inoculum effects using transient dynamics of Pseudomonas aeruginosa" (SA Sundius, J Farrell, KL Eick, R Kuske, SP Brown)
MScode_PaMer_Final.m: Main code file for analysis of Pseudomonas aeruginosa + meropenem data set
PA mer varied inoc varied mer conc org by mer.xlsx is the data file organized to be read into the main code (corresp. to S1 Data)
Includes code to fit all models included in the main text (Eq 2&3, 5, 7) and S1 Text (Eq S.3-S.6), and produce figures: Fig 1-6, S1-8 Fig
MScode_PaTob_Final.m: Main code file for analysis of Pseudomonas aeruginosa + tobramycin data set
PA tob varied inoc varied tob conc org by tob 3 - tet0.xlsx is the data file organized to be read into the main code (corresp. to S2 Data)
Includes code to fit the main text models (Eq 2&3, 5, 7), and produce figures: Fig 7A, 8A&C
MScode_PaTet_Final.m: Main code file for analysis of Pseudomonas aeruginosa + tetracycline data set
PA tet varied inoc varied tet conc org by tet 3.xlsx is the data file organized to be read into the main code (corresp. to S3 Data)
Includes code to fit the main text models (Eq 2&3, 5, 7), and produce figures: Fig 7B, 8B&D
For fitting via Algorithms 1 or 3: SingleSp_PtoODEfcn.m, odesolver.m, modelfit.m, makecoeffmatrix.m
For fitting via Algorithm 2: SingleSp_PtoODEfcn2.m, odesolver2.m
For computing error metrics (RMSE and R^2): RMSE.m, Rsquare.m