write_paper: Master function to replicate all analyses in the manuscript
In adsteen/subspec: What the package does (one line)

Description Usage Arguments Details Value

Reproduces data analysis from Steen et al (2015) AME paper about peptidase substrate specificity

1	write_paper(path = "", print_plots = TRUE, save_plots = FALSE)

`path`	Where to save plot files
`print_plots`	Whether to print plots to the default graphics device (usually your screen) Note that this may have no effect in command-line R.
`save_plots`	Whether to save plots.

Running this as write_paper(print_plots=TRUE, save_plots=FALSE) *should* work and be platform-independant. Beyond that I don't really make any guarantees but I'm happy to help via email. Notably, save_plots=TRUE requires the existence of a subdirectory of the working directory named 'plots' and may be platform-dependant (this was built using OSX 10.10.4 and the cairo device). If you wish to take apart my analysis to understand it better or show that it is totally bogus, I recommend copy-pasting the inside of this function from R and running it as a script.

A data frame with everthing calculated in Fig 7

adsteen/subspec documentation built on May 10, 2019, 7:27 a.m.