Code implementing the methods to generate the figures and tables of the AMP Neutralization Titer Biomarker manuscript
- System requirements
Unless otherwise specified software was tested on Ubuntu 18.04.5 LTS running R version 3.6.3 (2020-02-29)
Specific R libraries and R files required by each program are listed below.
gen_fig1_extFig2.R: magrittr version 1.5 dplyr version 0.8.5 CCC_time.R
gen_fig2_extFig4.R sievePH version 1.0.1 plot.summary.sievePH.R
gen_fig3.4.5.6_extFig5.6.7.8.9.10.R dplyr version 1.0.4 ggplot2 version 3.3.3 tidyr version 1.1.2 gridExtra version 2.3 triple-bnab-BH-titer.R tested on Windows 10.0.19042 Build 19042 running R version 4.0.2 (2020-06-22)
gen_suppTable1.R survival version 3.1.12 cmprsk version 2.2.9 dplyr version 0.8.5
gen_suppTable2.R dplyr version 0.8.5 haven version 2.2.0
- Installation guide
Install required version of R. Install required R packages. Create a local directory for code and data Unzip Supplemental Software file to a local directory (should take less than 2 minutes). Clone this repository (should take less than 2 minutes).
- Demo
Each code file should run in under 2 minutes with the exception of gen_fig3.4.5.6_extFig5.6.7.8.9.10.R which takes approximately 2 days to run. Output corresponds to figure(s) (as pdf(s) file in the figures directory) or table (as output in gen_suppTable1.Rout).
From the command line starting in the code directory run the following commands:
R CMD BATCH gen_fig1_extFig2.R &
R CMD BATCH gen_fig2_extFig4.R &
R CMD BATCH gen_fig3.4.5.6_extFig5.6.7.8.9.10.R &
R CMD BATCH gen_suppTable1.R &
- Instructions for use
Same as demo instructions above.