An interactive workshop to provide an overview of how to use πŸ“¦ [malariasimulation] and the malariaverse to run context-specific simulations for a country or region.

Workshop details

πŸ—“οΈ Thursday 2nd February 2023

⏰ 0930-1700

🏨 Meeting room 1&2, 20 Eastbourne Terrace, Paddington. Please bring ID.

πŸ’» Please bring your laptop!

Before the workshop

Please make sure you have the following installed:

  1. An up-to-date (Version >=4.2.0) installation of R. Please note, for those updating to R version 4.2 and above who have not updated recently you may also require an updated version of Rtools.
  2. An up-to-date (Version >= 2022.12.0) installation of RStudio. See help->check for updates.
  3. πŸ“¦ [malariasimulation]
  4. The workshop πŸ“¦ [mvw]
  5. The malariaverse πŸ“¦ [foresite]

When installing packages please say β€œyes” to any prompts asking you to update or install dependencies.

# For malariasimulation
remotes::install_github("mrc-ide/individual") 
options(repos = c(
    mrcide = "https://mrc-ide.r-universe.dev",
    CRAN = "https://cloud.r-project.org"))
install.packages("malariasimulation") # v1.4.3

# The workshop package (and its dependencies) can be installed directly from github:
remotes::install_github("mrc-ide/mvw")  # v0.1.2

# Private packages require network access to the "malaria drive": \\fi--didef3.dide.ic.ac.uk/malaria. 
# Contact Pete if you don't have access.
drat::addRepo("malariaverse", "file:\\\\projects.dide.ic.ac.uk/malaria/malariaverse/drat")
install.packages("foresite", type = "source") # v0.1.0
# Or, if that doesn't work
drat::addRepo("malariaverse", "file:\\\\fi--didef3.dide.ic.ac.uk/malaria/malariaverse/drat")
install.packages("foresite", type = "source") # v0.1.0

Following installation you should be able to successfully run:

output <- malariasimulation::run_simulation(100)
output

and

mvw::run_tutorial("Test")

If you can’t, please contact Pete before the workshop, by 30/01/2023 latest.

Schedule

Time Activity
09:30 - 11:00 Introduction to context-specific modelling
11:00 - 11:20 Coffee break
11:20 - 12:50 Calibrating a site
12:50 - 13:30 Lunch break (Lunch provided)
13:30 - 15:00 Bed nets
15:00 - 15:30 Coffee break
15:30 - 16:15 Lighting round: umbrella, treasure & om
16:15 - 17:00 Feedback & Discussion
17:30 - 20:00 Optional social (at the Mitre)