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README.md

README.md

"Time-kill curve analysis and pharmacodynamic functions for in vitro evaluation of antimicrobials against Neisseria gonorrhoeae"


Sunniva Förster, Magnus Unemo, Lucy J. Hathaway, Nicola Low, Christian L. Althaus


Contains data and scripts to reproduce the figures of the paper:

Software Versions Used
R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200)
locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] censReg_0.5-20 maxLik_1.2-4 miscTools_0.6-16 magicaxis_1.9.4 sm_2.2-5.4 plotrix_3.5-12 metafor_1.9-7 Matrix_1.2-0 [9] XLConnect_0.2-11 XLConnectJars_0.2-9 drc_2.5-12 MASS_7.3-40
loaded via a namespace (and not attached): [1] Rcpp_0.12.0 nloptr_1.0.4 plyr_1.8.3 tools_3.2.0 lme4_1.1-8 nlme_3.1-120 lattice_0.20-31 mgcv_1.8-6 glmmML_1.0 [10] parallel_3.2.0 mvtnorm_1.0-3 SparseM_1.6 rJava_0.9-7 gtools_3.5.0 grid_3.2.0 nnet_7.3-9 survival_2.38-1 multcomp_1.4-1 [19] TH.data_1.0-6 minqa_1.2.4 car_2.0-25 scales_0.2.5 codetools_0.2-11 splines_3.2.0 pbkrtest_0.4-2 colorspace_1.2-6 quantreg_5.11 [28] sandwich_2.3-3 munsell_0.4.2 zoo_1.7-12

Figure 1
Example to illustrate the parameters of the pharmacodynamic function Example to illustrate the parameters of the pharmacodynamic function
Figure 2
script Figure2.R fits linear regression to data from WHO G, WHO K, WHO L, WHO M, WHO N treated with 11 doubling concentrations of ciprofloxacin and untreated control.
Figure 3
script Figure3.R fits linear regression to one representative experiment of DOGK18 treated with gentamicin, spectinomycin, azithromycin, benzylpenicillin, ceftriaxone, cefixime, chloramphenicole, tetracycline
Figure 4
A: script Figure4A.R fits linear regression to DOGK18 treated with cefixime. Regressions are shown as dotted lines.
B: script Figure4B.R fits pharmacodynamic function to DOGK18 treated with cefixime. Dotted line shows fit without outliers removed.
C: script Figure4C.R takes model parameters of plots from figure 2 from file singleplot_statistics_panel.xls and plots them as solid lines in different colors for comparison.
D: script Figure4D.R takes model parameters of plots from figure 3 from file summary_statistics_9AB (arithmetic mean of parameters from 2 replicates) and plots them as solid lines in different colors for comparison.
ABCD: Latex script to make panel from A,B,C,D
Table 1
script Pharmacodynamics_DOGK18 fits pharmacodynamic function to two independent experiments of DOGK18 treated with gentamicin, spectinomycin, azithromycin, benzylpenicillin, ceftriaxone, cefixime, chloramphenicole, tetracycline. Table 1 shows the arithmetic mean of the parameters and resistance determinants as published elsewhere. script Table1 means calculates the means of the two independent experiments.
Figure S1
script growthcurves_3curves.R fits gompertz model to Growth_GW_short.txt (data from decline phase removed, complete raw data in Growth_GW.txt)
Table S1
Pharmacodynamics_wt.R fits pharmacodynamic function to two independent experiments of DOGK18 treated with gentamicin, spectinomycin, azithromycin, benzylpenicillin, ceftriaxone, cefixime, chloramphenicole, tetracycline and summarizes parameter estimates and standard errors.
Table S2
Pharmacodynamics_panel.R fits pharmacodynamic function to to data from WHO G, WHO K, WHO L, WHO M, WHO N treated with 11 doubling concentrations of ciprofloxacin and untreated control and summarizes parameter estimates and standard errors.