This runs on Datalabs.

1. Open the SOCCATOA project.
2. Open the Notebook currently called "madda's notebook" (should be renamed 'SOCCATOA WP5 app'?.
3. Open app.R and click on the "Run app" button or just enter golem::run_dev() at the terminal. The app will open in a new tab.
4. Click on login and enter user:test pass:test or make an account.
5. Currently we need to upload data each time, but this is work in progress. Test data is available here. Select file and click on Submit.
6. After uploading, click on Run.

Connecting to GitHub needs to use the http url, as ssh is not available on Datalabs. This requires using a personal token in place of a password - see Generate a personal access token. Each user's live here. Thereafter, this can be used in http authentication in place of a password, from the command line or via the Rstudio dialogues.

To convert a project

# to get the dev version of usethis
pak::pak("r-lib/usethis")
library(usethis)
usethis::use_air()

# create a github action to check every pull request
usethis::use_github_action(url = "https://github.com/posit-dev/setup-air/blob/main/examples/format-suggest.yaml")

Thereafter in VS code use Ctrl+Shift+P: Air: Format Workspace Folder For Rstudio, see here.

I suggest using a consistent naming convention throughout the code as far as possible, where names are constructed as noun_modifier1_modifier2.

• "_" means subscript i.e modifier
• following the tidyverse style guide which is the default for 'lintr' and 'styler'
• i.e. snake_case not camelCase, so no capital letters except where these are need for disambiguation in maths ('F' for "flux not 'f(x)') Where possible, define the maths in LaTeX/markdown and use the same in the R code
• e.g. $\theta_{obs}$, is written as 'theta_obs' in both LaTeX/markdown and R
• Use "Hungarian notation" to make the object type explicit - many/most coding errors arise through confusion over the object type
  • add a systematic prefix / suffix denoting type / class
  • df_ for data frames, r_ for rasters ...

Suggested prefixes for common R data structures

df_ for data frame (or tibble) dt_ for data table spdf_ for spatial point data frame v_ for vector m_ for matrix (note potential confusion with model fit object) a_ for array l_ for list t_ for table r_ for raster layer s_ for raster stack b_ for raster brick