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saezlab / CARNIVAL

CAusal Reasoning for Network Identification with integer VALue programming in R
https://saezlab.github.io/CARNIVAL/
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Documentation + Prep files for R-package release #3

Closed ptrairatphisan closed 5 years ago

ptrairatphisan commented 5 years ago

::: Summary :::

-> @anikaliu: please try to make a fresh installation of CARNIVAL from this branch (either go through install_github() from devtools [might also need a token to access] or download the source code and install from source). Then please use the vignette file to test if at least Example 1 (Toy model) and Example 2 (EGF-SBVimprover) are working fine on your machine. Please also note that now we require only the path to interactive cplex (to be set in the vignette file) instead of a physical copy in the R folder (which won't exist anymore in the office R-package version).

-> @enio23: please check if the added documentations fit well to each function. I've corrected several typos and missing elements and they should be all consistent now. If you have any remarks, please leave your thoughts as comments on this pull request thread.

enio23 commented 5 years ago

On some functions it is noted the purpose of what it is doing and on some others it doesn't. Should we decide for all how to do it in the same way?

ptrairatphisan commented 5 years ago

Each function should indeed describe briefly what it does. Some are still missing and could be added see the current manual: CARNIVAL-manual.pdf. This is not urgent but please feel free to update and commit to this branch so that they will be merge to the master branch at the same time.

ptrairatphisan commented 5 years ago

The new wrapper/driver function "runCARNIVAL.R" and the new version of CARNIVAL vignette have been introduced (see new commit).

@anikaliu @enio23 could you pull the commit, re-install the package and test if it works on your machines? Note that let's focus only on the usability of the package for now. We'll start cleaning up after merging this branch to the master branch.

ptrairatphisan commented 5 years ago

Delete this dev branch after merged to master