functions for generating worklists and reading data from reader. It is geared toward the setup we have in the (Theoretical Biology Group)[www.tb.ethz.ch] at ETH Zürich but might be useful, or at least a starting point for others, so here goes.

Obviously, use at your own risk. Make sure you know what the commmands do (they usually correspond to a single Basic or advanced worklist command that you can find in the EvoWare Documentation.)

To install the package directly from git you will need the following things:

• on Mac OS

  • Xcode (to build the packages; from the App Store (for free)).
  • git
  • devtools (from CRAN or and/or github, see below)

• On Windows (i think, not tested)

  • Rtools to build packages
  • git
  • devtools (from CRAN and/or github, see below)

to install directly from git:

    
    ### run once ###
    # macOS / probably other unix systems (not tested):
    # install.packages(c("devtools"))
    # for dev-version run: devtools::install_github("r-lib/devtools")
    
    # Windows:
    # install.packages(c("devtools","stringr"))
    # library(devtools)
    # build_github_devtools()

    # !! Restart R before continuing !!#
    # install.packages("devtools.zip", repos = NULL)
    # Remove the package after installation
    # unlink("devtools.zip")
    ### end run once ###

    devtools::install_github("dcangst/rrobot")

First, load package and initialize defaults and worklist:

    library(rrobot)
    init()
    gwl #displays the initialized worklist & worktable

init has some reasonable (?) defaults, see ?init for more info.

After that you can use the commands provided. Every command adds a row to gwl$worklist. See ?rrobot, or use ? in general, for details about the commands available, or check the source and implement more! Obviously all commands can be looped etc.

all commands have a some helpful information, use e.g. ?adv_aspirate. ?rrobot lists the most useful commands.

When finished with assembling your worklist use write.gwl(gwl) to write the worklist to the current working directory using the filename specified in init.

One can run R code from the command line on Windows: RScript.exe --vanilla --slave Rfile.R --args arg1 arg2 arg3... arguments can then be accessed within the R script like this: args <- commandArgs(TRUE) where args[1] = "arg1" (a character vector).

one can also write a batch script:

    set R_Script="C:\Program Files\R\R-3.1.2\bin\RScript.exe"
    %R_Script% --vanilla --slave Rfile.R --args arg1 arg2 arg3...`

more info: http://cran.r-project.org/doc/manuals/R-intro.pdf , appendix B or ?Rscript

This can then be called from within EvoWare

I started to develop the package using devtools which uses roxygen2 to document packages.

here is how I build the documentation and package:

library(devtools)

dev_mode()

setwd("path to local git")
document()
build()
load_all()

after that you're ready to use the current build and commit! dev_mode() changes into dev_mode: this means that you do not overwrite your (potentially more stable) packages, but work in a safe development environment.