Zika revisions release

Merge pull request #73 from mrc-ide/fix-zika-workflow

Fix zika workflow

Zika test release

Merge pull request #69 from mrc-ide/prepare-redcap-id-log-update

Updates pk creation & adds merging to process log

SARS updates

Merge pull request #59 from mrc-ide/db_extraction_prep

Adds functionality to process REDCap extractions

SARS First Release

Merge pull request #44 from mrc-ide/pipeline

Continuous Integration

Ebola review code

Code accompanying the Ebola paper (in press)
To test this code, clone the repo, navigate to the directory and do

Rscript ebola_workflow.R -l "../"

where "../" can be replaced by any temporary location on your machine, outside priority-pathogens root directory.

Note to contributors: any edits to the code should be tested against the outputs produced from this point of the repo.

lassa_branch_release

This release will run for Windows-users only. Functionality for Mac-users to be provided shortly.