search

mrc-ide / vivax

Individual-based model for P. vivax malaria transmission
MIT License
2 stars 1 forks source link

Initial commit #1

Closed giovannic closed 4 years ago

giovannic commented 4 years ago

This is a very minimal R wrapper for the P. Vivax model. It allows you to parameterise and run the default model and mosquito parameters through run_simulation.

Parameterising interventions and analysing the output is complicated and unspecified at the moment, so I've saved it for later. Michael's original code for parameterising interventions and analysing the output is in the R directory, but it's as yet untested.

Feel free to ignore files from the "man" and "docs" directories. They are autogenerated documentation by roxygen and pkgdown.

Commit messages:

giovannic commented 4 years ago

@richfitz I've addressed the comments and made issues for the rest.

Travis is failing because of those cpp issues you mentioned, but I would really prefer to look at them in a different PR as you mentioned. I've made an issue for that too.

codecov[bot] commented 4 years ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (dev@aed252f). Click here to learn what that means. The diff coverage is 16.34%.

Impacted file tree graph

@@          Coverage Diff          @@
##             dev      #1   +/-   ##
=====================================
  Coverage       ?   1.17%           
=====================================
  Files          ?       7           
  Lines          ?    2886           
  Branches       ?       0           
=====================================
  Hits           ?      34           
  Misses         ?    2852           
  Partials       ?       0
Impacted Files Coverage Δ
src/com.cpp 0% <ø> (ø)
src/randlib.cpp 0% <ø> (ø)
src/linpack.cpp 0% <ø> (ø)
src/model.cpp 0% <0%> (ø)
R/Output_overview.R 0% <0%> (ø)
R/Intervention_file_generator.R 0% <0%> (ø)
R/run.R 97.14% <97.14%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update aed252f...367d279. Read the comment docs.