Convert a modelling group's stochastic files into an intermediate format including all the original data, separated by country and scenario, and in PQ format for later processing. As much as possible, we'll try and detect the input formats.
stone_stochastic_standardise(
group,
in_path,
out_path,
scenarios,
files,
index = 1,
rubella_fix = TRUE,
missing_run_id_fix = TRUE
)The modelling group.
The folder or network path where the original files are found.
The folder or network path to write output files to.
A vector of strings giving each scenario name.
This can either be a vector of strings of the same length to
the vector of scenarios, in which case each entry should match the scenario,
providing the filename for the original uploads for that scenario. Most
groups provide files numbered between 1 and 200 for their stochastic runs;
replace that number with :index in the filename to match. Alternatively,
files can be a single entry containing the string :scenario; in this case,
files must exist that match each entry in the scenarios parameter, and
the same file string can be used to match all of them (perhaps additionaly
wiht :index).
This is usually a vector of ints, 1:200 to match the
range of stochastic files uploaded per scenario. A few groups upload one
large file containing everything, in which case :index shouldn't occur
in the files parameter, and should be omitted.
Historically Rubella uploads used the burden outcome
rubella_deaths_congenital and rubella_cases_congenital instead of
the simpler deaths and cases, and additionally provided a
rubella_infections field. rubella_fix needs to be TRUE to standardise
these to the simpler names. Processing Rubella stochastic files without
this set to TRUE will fail - so while we should always do this, keeping
the parameter makes it more clear in the code what we're doing and why.
Some groups in the past have omitted run_id from the files, but included them in the filenames. This fix inserts that into the files if the index parameter indicates we have 200 runs to process.