Identify/Upload sources of model data on data repository

[peter-t-fox]

For each data item identified in #437 as being sourced from the SCRC data pipeline, we need the following information:

• The identifier/path of the corresponding data structure within the pipeline
• The type (estimate, table, array, etc.) required for the API call to fetch the data
• Whether or not any transformation is required after the data is fetched from the pipeline (e.g. if the data is part of a larger data structure, it may need to be extracted)

[github-actions[bot]]

Heads up @thibaud-porphyre @peter-t-fox - the "Covid19_EERAModel" label was applied to this issue.

[kzscisoft]

Sourcing

Data sets

Identifier	Description	SCRC Remote Address	Comment
cfr_byage	Case Fatality Ratio by age group
scot_age	Proportion of population in each age group, by health board (Includes HCW implicitly)
scot_data	Timeseries of observed disease cases, by health board Also stores population of health board
scot_data	Timeseries of observed disease deaths, by health board Also stores population of health board
waifw_home	Age mixing matrix (home only)
waifw_norm	Age mixing matrix (All contact included)
waifw_sdist	Age mixing matrix (excludes school and work contact - social distancing)

Parameters.ini: [Priors settings]

Prior identifier	Description	SCRC Remote Address	Comment
pinf	Probability of infection (non-HCW)	DataRepository/SCRC/human/infection/SARS-CoV-2/symptom-probability/0.1.0.toml	Value is a point-estimate as opposed to required Beta distribution. No distinction between HCW/non-HCW.
phcw	Probability of infection (HCW)	DataRepository/SCRC/human/infection/SARS-CoV-2/symptom-probability/0.1.0.toml	Value is a point-estimate as opposed to required Beta distribution. No distinction between HCW/non-HCW.
chcw	Mean number of HCW-patient contacts per day
d	Proportion of population observing social distancing
q	Proportion of contacts made by self-isolaters
ps	Age-dependent probability of developing symptoms
rrd	Risk of death if not hospitalised
lambda	Background transmission rate

Parameters.ini: [Fixed parameters]

Parameter identifier	Description	SCRC Remote Address	Comment
totN_hcw	Total population of HCW
day_shut	Point in observations where lockdown starts
T_lat	Mean latent period	DataRepository/SCRC/human/infection/SARS-CoV-2/latent-period/0.1.0.toml	Value is 123.12 in remote data vs our 4 suggesting different units?
juvp_s	Probability of juvenile developing symptoms
T_inf	Mean asymptomatic period	DataRepository/master/SCRC/human/infection/SARS-CoV-2/asymptomatic-period/0.1.0.toml	Value is 192 in remote data vs our 1.5 suggesting different units?
T_rec	Mean time to recovery if infection is symptomatic
T_sym	Mean symptomatic period prior to hospitalisation
T_hos	Mean hospitalisation duration
K	Bed capacity for Covid19 patients
inf_asym	reduction factor of infectiousness for asymptomatic infectious individuals

[kzscisoft]

UPDATE: Due to there currently being very little overlap between what is available on the registry and what we require, this issue now consists of the following:

• [X] Upload "version 1" of parameters as they currently stand into the new accepted TOML form using the SCRCdataAPI templates. This consists of pushing an update to the registry as well as adding the parameters to the DataRepository GitHub.
• [x] Upload data itself as "version 1" in the form of HDF5 files to the relevant storage space, add again add entries to the data registry. Ultimately the exact structure of this data is likely to change from the current time series form, but such updates will just form a new version.

[peter-t-fox]

Situation has ben clarified: data are now available on the repository.